diff --git a/README.md b/README.md index c52df170123afd51da6cbae5babb5929b99e571c..ecc5e59ac0f248d116bb0212f510ebdac641ca31 100644 --- a/README.md +++ b/README.md @@ -20,328 +20,92 @@ configs: # ClinSeek-Bench -The exact evaluation set used for the ClinSeek hierarchical benchmark -(`UCSC-VLAA/ClinSeek-Evaluation-Results`, under `hierarchical/`). This -repository ships **everything** needed to reproduce a run end to end: +ClinSeek-Bench provides the evaluation manifests used by ClinSeekAgent. The +multimodal split is released as a source-only manifest because MIMIC-derived +patient databases, chest X-ray JPG files, radiology reports, and rendered EHR +contexts are protected assets and must be rebuilt locally under each user's own +credentialed access and data-use agreements. -- the original benchmark inputs (questions, gold labels, patient pointers); -- per-patient SQLite databases for every `subject_id` referenced; -- the linked chest X-ray images and radiology reports for the multimodal - split; -- table-description metadata used by the EHR MCP server. +| Split | # data points | Modality | Released here | +| --- | ---: | --- | --- | +| `ehr_bench` | 1,800 | text-only EHR | evaluation manifest | +| `mm_bench` | 989 | EHR + chest X-ray | source manifest only | -| Split | # data points | Modality | Total assets | -|--------------|--------------:|--------------------------------|---------------------| -| `ehr_bench` | **1,800** | text-only | 1,563 patient DBs | -| `mm_bench` | **989** | text + chest X-ray (image) | 560 patient DBs · 827 CXR JPGs · 356 radiology reports | -| **Total** | **2,789** | | | +`mm_bench` is restricted to image-grounded multimodal examples. It contains 497 +EHRXQA-derived CXR question-answering rows and 492 MedMod-derived ICU/CXR +prediction rows. -`mm_bench` here is restricted to **image-grounded** questions only — text-only EHR-query questions from the upstream -multimodal test set are excluded because they are not part of the multimodal evaluation track. +## Files -## Two evaluation modes, one question set - -Each data point is evaluated under **two** modes that share an identical question set: - -| Mode | Driver | Patient EHR delivered as | Notes | -|-----------|---------------------------------|--------------------------------|-----------------------------------------------------------------------| -| `agentic` | `deploy_agent.py` / `deploy_agent_mm.py` | **fetched at runtime** via an EHR MCP server (`ehr.load_ehr` + SQL/lookup tools) | Multi-turn tool use; agent decides what to look up. | -| `oneshot` | `deploy_reasoning_model.py` / `deploy_reasoning_model_mm.py` | **inlined** in the prompt (pre-rendered EHR slice) | Single LLM call; everything the model needs is in the prompt. | - -The same `qid` produces one row in -`UCSC-VLAA/ClinSeek-Evaluation-Results/hierarchical/agentic///.../rows.jsonl` -**and** one row in -`UCSC-VLAA/ClinSeek-Evaluation-Results/hierarchical/oneshot///.../rows.jsonl`, -so the two scores are directly comparable. - -## How each mode reads the inputs - -### `ehr_bench` - -Both modes consume the same file: **`inputs/ehr_bench.json`** — a JSON list of 1,800 records. Each record carries fields -for both modes: - -| Mode | Fields the driver actually reads | Prompt the model sees | -|-----------|----------------------------------|-----------------------| -| `agentic` | `instruction`, `prediction_time`, `subject_id`, `candidates` | A small instruction wrapper that names the patient and lists candidate answers. **No patient EHR is inlined.** The agent must call `ehr.load_ehr(subject_id, prediction_time)` against the MCP server (which opens `data/ehr_bench/database/patient_.db`) and then issue further `ehr.*` tool calls. | -| `oneshot` | `question` | A fully self-contained prompt (instruction + entire patient timeline rendered as Markdown) plus `` block. **No external lookup needed.** | - -Why two prompt forms? `question` is a long pre-rendered timeline (avg ≈10 KB, max ≈90 KB) — appropriate for one-shot -inference but redundant in agentic mode where the agent should retrieve only what it needs. - -```python -import json - -# Load the shared input file. -rows = json.load(open("inputs/ehr_bench.json")) -row = next(r for r in rows if r["qid"] == "ehr_bench_decision_making_0") - -# --- agentic input (build the agent prompt + open the patient DB) ----------- -agentic_prompt_template = """The current time is {prediction_time}. -The patient subject_id is {subject_id}. -{instruction} - -{candidates} -""" -agentic_prompt = agentic_prompt_template.format( - prediction_time=row["prediction_time"], - subject_id=row["subject_id"], - instruction=row["instruction"], - candidates=json.dumps(row["candidates"]), -) -patient_db = f"data/ehr_bench/database/patient_{row['subject_id']}.db" # the agent's MCP server opens this - -# --- oneshot input (single LLM call, prompt is fully self-contained) -------- -oneshot_prompt = row["question"] # 1 kB → 90 kB, depending on the patient -``` - -The exact agentic prompt template is `EHR_Bench_Prompt` in -[`openresearcher_ehr/data_utils.py:135`](https://github.com/Letian2003/DeepMed/blob/deepresearch/openresearcher_ehr/data_utils.py) -(function `generate_ehr_bench_prompt`). The exact oneshot wrapper is -[`build_user_content` in `deploy_reasoning_model.py:70`](https://github.com/Letian2003/DeepMed/blob/deepresearch/openresearcher_ehr/deploy_reasoning_model.py) -(it appends a short `...` extraction trailer to `row["question"]`). - -### `mm_bench` - -Both modes consume the same file: **`inputs/mm_bench.jsonl`** — a JSONL of 989 records. Each record carries fields for -both modes: - -| Mode | Fields the driver actually reads | Prompt the model sees | -|-----------|----------------------------------|-----------------------| -| `agentic` | `question`, `image_paths`, `report_paths`, `subject_id`, `source_benchmark` | The bare task instruction (`question`, ≈540 chars). Patient EHR is fetched at runtime via EHR MCP (`ehr.load_ehr(subject_id, prediction_time)` against `data/mm_bench//database/patient_.db`); CXR images are attached to the user turn as image blocks; radiology reports may be inlined via tool calls. | -| `oneshot` | `input_text` (preferred) or `question` (fallback), `image_paths` | A pre-rendered prompt (`input_text`, avg ≈24 KB, max ≈64 KB) that already contains `` + `` + sliced `` (top-N rows from each table) + `` listing. CXR images are inlined into the user turn as base64 image blocks. **No DB lookup needed.** | - -```python -import json - -# Load the shared input file. -mm = [json.loads(l) for l in open("inputs/mm_bench.jsonl")] -row = next(r for r in mm if r["qid"] == "medmod_radiology_test_56445431") - -# Pick the right bench root for assets and the per-patient DB. -bench_root = f"data/mm_bench/{ 'ehrxqa' if row['source_benchmark']=='ehrxqa' else 'medmod' }" -patient_db = f"{bench_root}/database/patient_{row['subject_id']}.db" - -# Resolve image_paths against bench_root (paths keep an upstream prefix that -# we strip — see openresearcher_ehr/deploy_reasoning_model_mm.py:78). -def resolve(p): - first, sep, rest = p.partition("/") - if sep and (first.endswith("OriginalLinked_v1") or first.endswith("AgentBench_v3")): - p = rest - return f"{bench_root}/{p}" - -image_files = [resolve(p) for p in (row.get("image_paths") or [])] - -# --- agentic input ---------------------------------------------------------- -agentic_prompt = row["question"] # ≈ 540 chars -agentic_assets = {"images": image_files, "patient_db": patient_db} - -# --- oneshot input (preferred form) ----------------------------------------- -oneshot_prompt = row.get("input_text") or row["question"] # ≈ 24 kB -oneshot_assets = {"images": image_files} # no DB needed -``` - -`row["input_text"]` is the model-ready oneshot rendering; if it is missing or empty, fall back to `row["question"]`. -The actual logic is `build_text_payload` in -[`deploy_reasoning_model_mm.py:150`](https://github.com/Letian2003/DeepMed/blob/deepresearch/openresearcher_ehr/deploy_reasoning_model_mm.py). - -## Directory layout - -``` +```text ClinSeek-Bench/ -├── README.md # this file ├── inputs/ -│ ├── ehr_bench.json # 1,800 records (text-only EHR-Bench) -│ └── mm_bench.jsonl # 989 records (multimodal MM-Bench, image-grounded) -└── data/ - ├── ehr_bench/ - │ ├── database/ - │ │ ├── candidate_table.db # vocabulary / candidate-answer table - │ │ └── patient_.db # 1,563 per-patient SQLite DBs (≈2.0 GB) - │ └── table_description/ # JSON metadata used by the EHR MCP server - │ ├── link_information.json - │ ├── shorten_description.json - │ └── table_description.json - └── mm_bench/ - ├── ehrxqa/ # rows where source_benchmark == "ehrxqa" (497 rows) - │ ├── database/ # 165 per-patient SQLite DBs - │ ├── mimic-cxr/2.0.0/files/... # linked CXR JPGs + report .txt - │ └── table_description/ - └── medmod/ # rows where source_benchmark == "medmod" (492 rows) - ├── database/ # 395 per-patient SQLite DBs - ├── mimic-cxr/2.0.0/files/... # linked CXR JPGs - └── table_description/ +│ ├── ehr_bench.json +│ └── mm_bench.jsonl +└── rebuild/ + └── text_bench/ + └── ClinSeek-Bench_text.json ``` -## Running an evaluation against this repo +The multimodal manifest `inputs/mm_bench.jsonl` stores released `qid`s, +questions, normalized labels, patient identifiers, prediction-time cutoffs, and +relative CXR/report references. It intentionally does not store `input_text`, +patient SQLite databases, CXR JPG files, or report text. -After cloning, point each driver at the matching `--data` and `--bench-root` (or `--ehr_path`) inside this folder. +## Reconstructing Multimodal Assets -### EHR-Bench +Multimodal reconstruction scripts are maintained in the ClinSeekAgent GitHub +repository, matching the text benchmark data-preparation workflow: -```bash -# 0. Start the EHR MCP server on the ehr_bench root (agentic mode only) -python src/run_mcp_server.py \ - --mode http --host 127.0.0.1 --port 5103 \ - --data_path /path/to/ClinSeek-Bench/data/ehr_bench -# This server exposes ehr.load_ehr / ehr.run_sql_query / ehr.* tools backed -# by the patient_*.db files in data/ehr_bench/database/. - -# 1a. Agentic — multi-turn tool use; reads instruction/subject_id/candidates, -# fetches EHR via the MCP server above. -python openresearcher_ehr/deploy_agent.py \ - --data_path /path/to/ClinSeek-Bench/inputs/ehr_bench.json \ - --output_dir ./out_agentic_ehr \ - --mcp_url http://127.0.0.1:5103/mcp \ - --model +- documentation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_multimodal_data_prepare.md +- scripts: https://github.com/UCSC-VLAA/ClinSeekAgent/tree/main/scripts/data_build -# 1b. One-shot — single LLM call; reads `question` (which already inlines the -# patient timeline). No MCP server needed. -python openresearcher_ehr/deploy_reasoning_model.py \ - --data /path/to/ClinSeek-Bench/inputs/ehr_bench.json \ - --output-dir ./out_oneshot_ehr \ - --model -``` - -### MM-Bench +At a high level: ```bash -# 0. Start the MM EHR MCP server on each multimodal sub-root (agentic only). -# The driver accepts multiple --bench-root paths so a single server isn't -# required, but the simplest setup is one MCP server per source split. -python src/run_mcp_server.py --port 5113 --data_path /path/to/ClinSeek-Bench/data/mm_bench/ehrxqa & -python src/run_mcp_server.py --port 5114 --data_path /path/to/ClinSeek-Bench/data/mm_bench/medmod & - -# 1a. Agentic — reads `question` + image_paths + subject_id; image MCP + -# EHR MCP servers handle assets and DB. -python openresearcher_ehr/deploy_agent_mm.py \ - --data /path/to/ClinSeek-Bench/inputs/mm_bench.jsonl \ - --output_dir ./out_agentic_mm \ - --bench_root /path/to/ClinSeek-Bench/data/mm_bench/ehrxqa \ - /path/to/ClinSeek-Bench/data/mm_bench/medmod \ - --image_mcp_url http://127.0.0.1:5203/mcp \ - --enable_ehr --ehrxqa_mcp_url http://127.0.0.1:5113/mcp \ - --medmod_mcp_url http://127.0.0.1:5114/mcp \ - --model - -# 1b. One-shot — reads `input_text` (already has EHR inlined) + image_paths. -# No MCP server needed; just resolve the images. -python openresearcher_ehr/deploy_reasoning_model_mm.py \ - --data /path/to/ClinSeek-Bench/inputs/mm_bench.jsonl \ - --output-dir ./out_oneshot_mm \ - --bench-root /path/to/ClinSeek-Bench/data/mm_bench/ehrxqa \ - /path/to/ClinSeek-Bench/data/mm_bench/medmod \ - --model +git clone https://huggingface.co/datasets/UCSC-VLAA/ClinSeek-Bench +git clone https://github.com/UCSC-VLAA/ClinSeekAgent.git ``` -The drivers above live in this repo: -- -- -- -- - -## Schema reference - -### `inputs/ehr_bench.json` +Then run the scripts under `ClinSeekAgent/scripts/data_build/` with local paths +to the official source datasets. -```jsonc -[ - { - "qid": "ehr_bench_risk_prediction_329", // stable id; matches results rows.jsonl - "subject_id": 12345678, // → patient DB lookup key - "hadm_id": 23456789, - "prediction_time": "2183-08-13 01:15:18", // cutoff time the patient EHR is sliced at - "latest_event_time": "2183-08-13 01:15:17", - "task": "ED_Critical_Outcomes", // L4-style task tag - "task_type": "decision_making" | "risk_prediction", - "label": "yes" | ["..."], // gold answer - "question": "...full timeline...", // ONESHOT prompt - "instruction": "Given the sequence of events ...", // AGENTIC prompt - "input": "## Patient Demographics ...", // structured EHR (also fed into `question`) - "output": "OBSERVATION ADMIT", // gold (string form) - "candidates": ["...", "..."], // discrete answer options - "task_info": { "...": "..." }, // metric / target / split info - "source_idx": 0, - "source_file": "ehr_bench_risk_prediction.jsonl" - } -] -``` - -### `inputs/mm_bench.jsonl` +Required multimodal source data: -```jsonc -{ - "qid": "medmod_radiology_test_56445431", // stable id - "subject_id": 17795062, // → patient DB lookup key - "hadm_id": 22792685, - "stay_id": 39825171, - "prediction_time": "2177-07-25 22:04:23", - "task": "medmod_radiology", // task tag - "answer_type": "list" | "label", - "modalities": ["cxr_image", "cxr_table"], // which assets are referenced - "ground_truth": [{"name": "Cardiomegaly"}, ...], // gold answer - "question": "...question only, no EHR...", // AGENTIC prompt - "input_text": "......inlined CSV slices...", // ONESHOT prompt - "image_paths": ["MedModOriginalLinked_v1/mimic-cxr/2.0.0/files/p17/p17795062/s56445431/.jpg"], - "report_paths": [], // optional radiology report .txt - "source_benchmark": "medmod" | "ehrxqa", // → which bench root to resolve assets against - "source_split": "test", - "source_index": 0 -} -``` +| Dataset | Source | +| --- | --- | +| MIMIC-IV | https://physionet.org/content/mimiciv/ | +| MIMIC-CXR | https://physionet.org/content/mimic-cxr/ | +| MIMIC-CXR-JPG | https://physionet.org/content/mimic-cxr-jpg/ | +| MIMIC-IV-Note | https://physionet.org/content/mimic-iv-note/ | +| EHRXQA | https://physionet.org/content/ehrxqa/ | +| MedMod code | https://github.com/nyuad-cai/MedMod | -> **Path note.** `image_paths` and `report_paths` keep an upstream layout prefix (`MedModOriginalLinked_v1/...` or -> `EHRXQAOriginalLinked_v1/...`). The drivers strip the first segment and re-resolve under each bench root, so the -> physical files in this repo live at `data/mm_bench//mimic-cxr/2.0.0/...`. If you write your own loader, -> mirror that strip-prefix-then-join logic. +The final local reconstruction materializes `ClinSeek-MM-Bench/inputs/mm_bench.jsonl` +with rendered `input_text`, plus `data/mm_bench/ehrxqa/` and +`data/mm_bench/medmod/` containing patient SQLite databases, linked CXR JPGs, +radiology reports when available, and table-description metadata. -## Pairing with the result repository +## Validation -Per-row scored predictions live in **`UCSC-VLAA/ClinSeek-Evaluation-Results`** under -`hierarchical/{agentic,oneshot}/{bench}/{model}/L1./L2./L3./L4./rows.jsonl`. To pull both -modes for the same data point under one model: +After cloning ClinSeekAgent, validate the released multimodal source manifest: -```python -import json, os - -INPUTS = "inputs/ehr_bench.json" # or inputs/mm_bench.jsonl (read line-by-line) -RESULTS_REPO = "/path/to/ClinSeek-Evaluation-Results" - -with open(INPUTS) as f: - rows = json.load(f) -row = rows[0] # any data point -qid = row["qid"] - -def load_score(model, mode, bench): - base = f"{RESULTS_REPO}/hierarchical/{mode}/{bench}/{model}" - for dirpath, _, files in os.walk(base): - if "rows.jsonl" in files: - with open(os.path.join(dirpath, "rows.jsonl")) as f: - for line in f: - r = json.loads(line) - if r["qid"] == qid: - return r - return None - -agentic = load_score("claude_opus_4_6", "agentic", "ehr_bench") -oneshot = load_score("claude_opus_4_6", "oneshot", "ehr_bench") -print("agentic F1:", agentic["f1"], "| oneshot F1:", oneshot["f1"]) +```bash +python ClinSeekAgent/scripts/data_build/validate_multimodal_release.py \ + --bench-root ClinSeek-Bench \ + --manifest-only ``` -## Provenance +Expected source-manifest counts: -- **`ehr_bench`** is the 40-rows-per-task balanced subset of EHR-Bench. The full upstream files are - `data/EHR-Bench/ehr_bench_decision_making.jsonl` (13,500 rows) + - `data/EHR-Bench/ehr_bench_risk_prediction.jsonl` (7,721 rows) → - `ehr_bench_sampled_40_per_task.json` (1,800 rows = 27 decision_making leaves × 40 + 18 risk_prediction leaves × 40). -- **`mm_bench`** is the image-grounded subset of the combined multimodal test set - (`combined_test_set.jsonl` / `model_ready_combined_test_set.jsonl`, 2,703 rows total). The 1,704 text-only - EHR-query rows are excluded; the 989 rows kept here are the rows scored under `mm_bench` in the result repository. -- **EHR-Bench DBs** are sourced from the upstream EHR-Bench release (MIMIC-IV-derived per-patient snapshots). -- **MM-Bench DBs / images / reports** are sourced from `EHRXQAAgentBench_v3` (EHR-XQA test rows) and - `MedModAgentBench_v3` (MedMod test rows) — both are MIMIC-IV / MIMIC-CXR-JPG derivatives. +- 989 total multimodal rows. +- 497 EHRXQA-derived rows. +- 492 MedMod-derived rows. +- 350 unique EHRXQA linked CXR JPG paths. +- 477 unique MedMod linked CXR JPG paths. +- 356 unique EHRXQA linked CXR report paths. -## License & access +## Citation -Private. Inherits the access constraints of MIMIC-IV (PhysioNet credentialed) and MIMIC-CXR-JPG (PhysioNet credentialed) -for the underlying patient data. Use only in accordance with those data-use agreements. +Please cite the ClinSeek paper and the upstream source benchmarks used for any +reconstructed multimodal assets. diff --git a/data/mm_bench/ehrxqa/database/patient_10020740.db b/data/mm_bench/ehrxqa/database/patient_10020740.db deleted file mode 100644 index be1005aedb9ada19e3a231e0ab53deb851fe3a3d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/database/patient_10020740.db +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:e40190e2121733dce90354fc65b7e62b42f7d328fb2496b70260ff971df2765d -size 110592 diff --git a/data/mm_bench/ehrxqa/database/patient_10037020.db b/data/mm_bench/ehrxqa/database/patient_10037020.db deleted file mode 100644 index 5fba86772732e472f006ca7601b75202ef5b4a24..0000000000000000000000000000000000000000 Binary files a/data/mm_bench/ehrxqa/database/patient_10037020.db and /dev/null differ diff --git a/data/mm_bench/ehrxqa/database/patient_10110584.db 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b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/files/p19/p19969031/s50515411/9aaba37f-76c7ea79-5b725634-d63275b5-018254ab.jpg deleted file mode 100644 index 040de298518bd7037ab2a4cc12106ee6de946157..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/files/p19/p19969031/s50515411/9aaba37f-76c7ea79-5b725634-d63275b5-018254ab.jpg +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:2289f7e495ce55c0c758e3693b53f8531efaefc3d55a2bb3c495a1104783b336 -size 6814 diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/files/p19/p19969031/s54877992/4e78a467-5eede0ee-476cb29e-af0db15d-69c4465c.jpg b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/files/p19/p19969031/s54877992/4e78a467-5eede0ee-476cb29e-af0db15d-69c4465c.jpg deleted file mode 100644 index b43e21a7972dbbc14096b720763a072ab6ac45ff..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/files/p19/p19969031/s54877992/4e78a467-5eede0ee-476cb29e-af0db15d-69c4465c.jpg +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d2b3b4464eca5ccea1cb08d84d69424c16b81676dfa8a0667c9cfecdb9efba19 -size 7898 diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s51970847.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s51970847.txt deleted file mode 100644 index e0690a6ad3ed38fd45136d389a38a21afe460183..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s51970847.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with necrotizing pancreatitis, catatonia, and - history of respiratory failure now with tachycardia and diaphoresis // - Evidence of pulmonary infiltrate, pulm edema Evidence of pulmonary - infiltrate, pulm edema - - IMPRESSION: - - In comparison with the study of ___, there addendum are low lung - volumes that accentuate the transverse diameter of the heart. Small right - pleural effusion extending along the lower chest wall is again seen. Mild - atelectatic changes are seen at the bases. The right PICC line is not - optimally seen, though it appears to be within the brachiocephalic system. - The right ribs are not optimally seen, so that the possible fracture of the - lateral aspect of the sixth rib cannot be assessed. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s53160696.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s53160696.txt deleted file mode 100644 index 4e5ffdf9af8373ff8534f6eac52e4b4c9de1fdc7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s53160696.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___ year old man with schizoaffective disorder intubated for - hypoxemic respiratory distress // ET tube and NG tube position - - COMPARISON: Chest radiographs ___ through ___ at 04:54. - - IMPRESSION: - - New endotracheal tube in standard position. Nasogastric tube passes into the - upper stomach and would need to be advanced 5 cm to move all the side ports - beyond the gastroesophageal junction. Lung volumes have improved generally, - particularly in the right lower lobe below the right hemidiaphragm is still - elevated. Residual consolidation in the lower lobe could be atelectasis or - pneumonia. Heart size normal has decreased substantially since earlier in the - day. Left PIC line ends at the origin of the SVC diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s55522869.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s55522869.txt deleted file mode 100644 index 7622781150339a875f8943d3a4cbb42b623cc23d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s55522869.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with h/o acute pancreatitis // ET tube - placement, PNA? ARDS? ET tube placement, PNA? ARDS? - - IMPRESSION: - - No previous images. There is an endotracheal tube in place with its tip - approximately 3 cm above the carina. Nasogastric tube extends well into the - stomach. Right subclavian catheter extends to the level of the carina. Mild - basilar atelectatic changes without evidence of acute pneumonia or vascular - congestion. There may well be a small right pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s56201490.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s56201490.txt deleted file mode 100644 index e91eac16d31c970e5185b758e9c4fce3e5010f05..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s56201490.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___ year old man with cataonia // n/g evaluation - - COMPARISON: Chest radiographs ___ - - IMPRESSION: - - As before the left PIC line ends in the upper right atrium and would need to - be withdrawn 2 cm to reposition it low in the SVC if desired. Nasogastric - tube ends in the upper stomach. Lung zone volume, but aside from a band of - linear atelectasis or scarring on the left, there are clear. Heart size is - normal. No pneumothorax. Thickening of the right lower costal pleural margin - could be scarring or a small effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s57037479.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s57037479.txt deleted file mode 100644 index ac68bddeb6b343eae68a869103de0ccaca5a3776..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s57037479.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with malignant catonia, and recurernt aspiration, - spike to 101 // eval for e/o of pna or aspiration - - COMPARISON: Compare prior study from ___. - - IMPRESSION: - - Endotracheal tube has been removed. The feeding tube and left-sided PICC line - are unchanged in position. There are mildly low lung volumes. There is no - focal consolidation. There is mild atelectasis at the lung bases. There are no - pneumothoraces. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s58116104.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s58116104.txt deleted file mode 100644 index 8254e19d892a5d7dc6706e0ccfea19560bf6ed8a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s58116104.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man w pancreatitis who was intub for airway - protection // f/u on lung - - COMPARISON: ___. - - IMPRESSION: - - - As compared to the previous radiograph, the lung volumes remain extremely low. - The position of the endotracheal tube, the nasogastric tube and the right PICC - line are constant and normal. Mild atelectasis at both lung bases. Minimal - fluid overload but no overt pulmonary edema. No larger pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s59638055.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s59638055.txt deleted file mode 100644 index dc92a318c7ce7aedf3826a4deea3704e75fd0c56..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10020740/s59638055.txt +++ /dev/null @@ -1,26 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man being intubated for ECT // Evaluate ET tube - placement - - TECHNIQUE: Frontal chest radiograph - - COMPARISON: ___ - - FINDINGS: - - There has been interval placement of the ET tube which terminates 5.5 cm above - the carina. Left PICC line terminates in the mid SVC. NG tube terminates in - the stomach however its side-port appears to be at the GE junction. Left lower - lobe atelectasis has improved. There is new right middle lung atelectasis. A - small right pleural effusion is seen. - - IMPRESSION: - - NG tube's side port is at the GE junction. The ET tube is as a satisfactory - location. - - NOTIFICATION: The findings were discussed by Dr. ___ with RN taking care - of the patient on the telephone on ___ at 1:21 PM, 1 minutes after - discovery of the findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10037020/s58400371.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10037020/s58400371.txt deleted file mode 100644 index 51b859d230ca3a9011e704159b1d209432efe9a4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10037020/s58400371.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - PORTABLE AP CHEST X-RAY - - INDICATION: Patient with ILD and VATS wedge resection. Chest tube position. - - COMPARISON: Preop chest x-ray of ___. - - FINDINGS: - - New right-sided chest tube ends at the apex. There is no visible - pneumothorax. Subcutaneous air adjacent to the chest tube is moderate. The - lung volumes are low which explains increased interstitial markings in this - patient with known interstitial lung disease. There is no pleural effusion or - pneumothorax. Mediastinal and cardiac contours are normal. - - CONCLUSION: - - Right chest tube projects at the apex, and there is no pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10110584/s52265451.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10110584/s52265451.txt deleted file mode 100644 index 451c0c404bbf3ceb4f426a4411d4c3804dfa6504..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10110584/s52265451.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with copd and now ams pod 3 spine surgery // - eval for pna - - TECHNIQUE: CHEST (PORTABLE AP) - - COMPARISON: None - - IMPRESSION: - - Heart size is enlarged. Mild vascular congestion in the mediastinum is noted - but there is no overt pulmonary edema. Right upper lobe opacity is unclear if - represent a chronic finding or new infection as well as right basal opacity - that might represent atelectasis but infectious process is a possibility. - Left basal atelectasis is minimal. Rib fractures are multiple on the left, - old. Close attention to the right lung findings is recommended to exclude the - possibility of developing infectious process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s51763901.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s51763901.txt deleted file mode 100644 index 3e01dd44702dbd3f8b3ea2f3056e71afd4301562..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s51763901.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with cirhosis, UGIB, SBP, possible PNA // eval - ET/OGT placement eval ET/OGT placement - - COMPARISON: Prior chest radiographs ___ through ___. - - IMPRESSION: - - Relatively uniform widespread pulmonary opacification developed between ___ - and ___ accompanied by increasing mediastinal and pulmonary vascular - caliber, improved slightly on ___, subsequently unchanged though looking - worse because of lower lung volumes. Left lower lobe opacification is - probably atelectasis though pneumonia is not excluded and small to moderate - bilateral pleural effusions are present and probably increased since ___. - Heart size is mildly enlarged. Overall findings point to volume dependent - pulmonary edema. - - Small nodular opacity projecting over the right costo sternal junction could - be superimposition of normal structures. It should be re-evaluated when edema - has improved. - - ET tube and nasogastric drainage tube in standard placements respectively. No - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s53976240.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s53976240.txt deleted file mode 100644 index 2479d729faf74105a56fa90b2ca7ebdfe7a83a53..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s53976240.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old man with cirrhosis // eval for intrathoracic process - eval for intrathoracic process - - COMPARISON: There are no prior chest radiographs available. - - IMPRESSION: - - Anterior costal calcifications project over a region of possible peribronchial - infiltration in the right lower lobe centrally, projecting lateral to the - heart, is of uncertain chronicity. It could be an early infection. Any prior - chest radiograph should be evaluated to see if this is a new finding - warranting further investigation. If there is none, I would recommend routine - oblique views to confirm its appearance. - - Lungs are otherwise clear. Heart size normal. Normal mediastinal and hilar - silhouettes and pleural contours. - - RECOMMENDATION(S): Prior radiograph should be obtained to evaluate possible - right lower lobe lesion. Oblique views would be useful if there is any - question about its chronicity or its presence. CT scanning may ultimately be - necessary if oblique views are equivocal. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s57525853.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s57525853.txt deleted file mode 100644 index a6a142da96372d2972915dd83ed9bea59ca6f33a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10117273/s57525853.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with hypoxic respiratory failure and PNA // - Please eval for interval change - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the pre-existing parenchymal opacities - have substantially improved. However, there still is evidence of perihilar - haziness as well as of minimal fluid overload. Lung volumes remain low. - Monitoring and support devices are constant. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10127462/s56032421.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10127462/s56032421.txt deleted file mode 100644 index 2900a44449430b775c2935a48379401b9cc538bd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10127462/s56032421.txt +++ /dev/null @@ -1,17 +0,0 @@ - WET READ: ___ ___ ___ 9:03 PM - No radiographic evidence for acute process. - ______________________________________________________________________________ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Status post fusion, elevated temperature, assessment for lung - pathology. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, the lung volumes have - increased. The size of the cardiac silhouette is still at the upper range of - normal. The radiographic evidence of mild pulmonary edema is still present - but less severe than on the previous image. Minimal right pleural effusion, - causing blunting of the right costophrenic angle. Minimal areas of - atelectasis at the right and left lung bases. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10130585/s50087560.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10130585/s50087560.txt deleted file mode 100644 index 5ac08e8bae4ad0722114f5955faba9a7b5b1c755..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10130585/s50087560.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - HISTORY: Shortness of breath, dyspnea. - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: None. - - FINDINGS: - - There is a mild elevation of the right hemidiaphragm. No focal consolidation - is seen. There is slight blunting of the bilateral costophrenic angles on the - frontal view of the no large pleural effusion is seen on the lateral view. - There is no pneumothorax. The cardiac and mediastinal silhouettes are - unremarkable. No pulmonary edema is seen. - - IMPRESSION: - - Mild elevation of the right hemidiaphragm without focal consolidation or large - pleural effusion seen. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10156395/s56372742.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10156395/s56372742.txt deleted file mode 100644 index 845701d8b56ad377161f40a07e065617ddae6835..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10156395/s56372742.txt +++ /dev/null @@ -1,43 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman s/p intubation // pls eval ET tube placement - - COMPARISON: Chest x-ray from ___ - - FINDINGS: - - An ET tube is present. The tip lies at the level of mid clavicular heads are - of the carina. An NG tube is present. The tip extends beneath the diaphragm, - off the film. - - An apparent intra-aortic balloon pump is present. The radiopaque tip overlies - the upper edge of the aortic arch -- clinical correlation regarding retraction - by approximately 3 cm to lie in the proximal descending aorta is requested. - - Faint cylindrical density overlying the thoracic spine at the level of the - aortic arch likely represents material outside the patient. - - Heart size is at the upper limits of normal or minimally enlarged. - - Vascular plethora and diffusely increased interstitial markings is present. - This could represent CHF with interstitial edema, though a diffuse - interstitial process could have a similar appearance. There is subsegmental - atelectasis at both lung bases. No gross effusion. - - IMPRESSION: - - ET tube 6.1 cm above the carina. - - Radiopaque tip of an intra-articular balloon pump overlies the upper edge of - the aortic arch. Clinical correlation regarding retraction into the proximal - descending aorta by approximately 3 cm is requested. - - Diffusely increased interstitial markings and bibasilar atelectasis. The - appearance is compatible with CHF, though a diffuse interstitial process could - have a similar appearance. No gross effusions. - - NOTIFICATION: Position of aortic balloon pump tip and recommendation for - slight retraction was discussed by Dr. ___ with covering physician Dr ___ - ___, by telephone, at 9:14 am on ___, approximately ___ min after - discovery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10163947/s59905689.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10163947/s59905689.txt deleted file mode 100644 index c44ea9b32e9b4ea41698d6ce9289d5dfab6ba177..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10163947/s59905689.txt +++ /dev/null @@ -1,18 +0,0 @@ - WET READ: ___ ___ ___ 9:26 PM - Increased left pleural effusion since ___ with adjacent atelectasis. - Pulmonary vasculature is less engorged. Interval removal of R IJ catheter. No - pneumothorax. - ______________________________________________________________________________ - FINAL REPORT - PA AND LATERAL CHEST, ___ - - HISTORY: Recent CABG, assess pleural effusions. - - IMPRESSION: - PA and lateral chest compared to preoperative chest radiograph, ___ and - postoperative on ___: - - Moderate left and small right pleural effusions, both increased minimally - since ___. Stable mild enlargement of postoperative cardiac silhouette. - Tiny left apical pneumothorax unchanged. Moderately severe left lower lobe - atelectasis has improved. There is no pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s56890461.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s56890461.txt deleted file mode 100644 index 084adcd0148b5dcda2d9f42ec1ef4ed70fa0d7aa..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s56890461.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Sepsis, evaluation for pulmonary edema. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, the signs of intrapulmonary - fluid overload have decreased but small to moderate bilateral pleural - effusions have newly occurred. The monitoring and support devices are - unchanged. Unchanged size of the cardiac silhouette. Moderate retrocardiac - atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s59201217.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s59201217.txt deleted file mode 100644 index 3b4c784c723d754ac6925e925ea1292ae1887dc1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10176458/s59201217.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: Patient status post AAA repair, now with increased work of - breathing. Assess for effusion. - - COMPARISONS: Chest radiographs from ___ to ___. - - FINDINGS: - Semi-upright portable view of the chest demonstrates right internal jugular - central venous catheter projecting over mid SVC. Nasogastric tube is seen - coursing through the esophagus, its tip out of view. Costophrenic angles are - obscured, suggestive of small pleural effusions. Bibasilar opacities may - represent atelectasis. There is no pulmonary edema. Hilar and mediastinal - silhouettes are unremarkable. Heart size is normal. There is no - pneumothorax. - - IMPRESSION: - - Bibasilar opacities with small pleural effusions, may represent atelectasis or - infection in the appropriate clinical setting. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s53560067.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s53560067.txt deleted file mode 100644 index 5bdbf1dd59be26947f78e31df5f3233e8847e159..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s53560067.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with endocarditis and respiratory failure, // - Interval change - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ 16:59 - - FINDINGS: - - The patient is rotated to the right. Lung volumes are low. There is mild to - moderate pulmonary edema, worse on the left than right, and improved from - ___. Pleural effusions are presumed. Left descending pulmonary vein is - engorged with severe cardiomegaly which is unchanged from ___. - - Right jugular catheter ends in the mid SVC. Tip of ET tube is in appropriate - position but appears low likely due to patient positioning.. Esophageal - drainage tube/NG tube extends into stomach and out of view. - - IMPRESSION: - - Mild to moderate pulmonary edema, more pronounced on the left than right, - which is improved from ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s54676500.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s54676500.txt deleted file mode 100644 index 5ae144ceeadff4b4e2d1c8eccb0db31f4fc43d68..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s54676500.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with ESRD on HD, Afib, CHF, admitted for MRSA - endocarditis and bacteremia // assess for OG tube placement assess for OG - tube placement - - COMPARISON: Chest radiographs ___ through ___ at 14:39. - - IMPRESSION: - - Nasogastric drainage tube ends in the stomach. ET tube in standard placement. - Right jugular line ends in the region of the superior cavoatrial - junction.Borderline pulmonary edema and moderate to severe cardiomegaly - persist. There is no focal abnormality to suggest pneumonia but the lung - bases are poorly demonstrated by this study. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s55470773.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s55470773.txt deleted file mode 100644 index 05778466febef377d313193e8e9c5513c4ecaafc..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s55470773.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with acute resp failure requiring intubation - // ETT position s/p intubation - - TECHNIQUE: Chest PA and lateral - - FINDINGS: - - In comparison with the study from earlier that day, there is mild improvement - of the interstitial pulmonary edema. Again there are low lung volumes with - enlargement of the cardiac silhouette and. The tip of the endotracheal tube - is 2 cm from the carina. No pneumothorax. Monitoring and support devices are - unchanged. - - IMPRESSION: - - The tip of the endotracheal tube is 2 cm from the carina. Mild interval - improvement in the interstitial pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58232655.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58232655.txt deleted file mode 100644 index 17184c0a9a466e8f45a84f7e79936c6728fded80..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58232655.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with bacteremia // Post intubation- check ETT - placement Post intubation- check ETT placement - - IMPRESSION: - - In comparison with the earlier study of this date, there has been placement of - an endotracheal tube with its tip approximately 2.5 cm above the carina. Low - lung volumes with little definite change given the degree of obliquity of the - patient. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58277096.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58277096.txt deleted file mode 100644 index 4171e1bc791cb2355eec6e904b67146f8784842c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s58277096.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with CHF and now w/SOB. // Is there a new - pulmonary process? Is there a new pulmonary process? - - IMPRESSION: - - In comparison with the study of ___, there is little change. Again the - patient is rotated to the right. There are slightly improved lung volumes - with more engorgement of pulmonary vessels suggesting some increasing - pulmonary venous pressure. Chronic moderate enlargement the cardiac - silhouette is again seen. - Monitoring and support devices are unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s59817909.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s59817909.txt deleted file mode 100644 index 55727135de3e9839e265f6b5b144fdc23f07c07c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10304606/s59817909.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with endocarditis and respiratory failure // - interval change interval change - - COMPARISON: Chest radiographs ___ through ___. - - IMPRESSION: - - Patient is persistently rotated to the right obscuring some of the right lower - lobe, but the imaged lungs are relatively clear. There is vascular - engorgement on the left but no appreciable atelectasis or edema. Pleural - effusion is minimal on the right if any. It is moderate to severe - cardiomegaly is chronic. No pneumothorax. - - ET tube, nasogastric tube, and left internal jugular line are in standard - placements respectively. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10397160/s50496560.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10397160/s50496560.txt deleted file mode 100644 index f05083e4a841221a4e26858bf284a19e6dc66d4d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10397160/s50496560.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiograph - - INDICATION: Hypoglycemia - - TECHNIQUE: AP and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - Moderate to severe cardiomegaly is similar to the prior examination. Hilar - contours are unremarkable with mild prominence of the central pulmonary - vasculature though there is no frank interstitial edema. Lungs are clear. The - pleural surfaces are clear without effusion or pneumothorax. Median - sternotomy wires are intact. Surgical clips are noted along the upper left - mediastinum from prior left hemithyroidectomy. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s50423170.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s50423170.txt deleted file mode 100644 index 559ed7fc1a4800758f1e4b7abba522899c0eabb7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s50423170.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with h/o stab wound to chest, bilateral chest - tubes in place // please evaluate positioning of chest tubes; interval change - please evaluate positioning of chest tubes; interval change - - IMPRESSION: - - In comparison with the study of ___, there is little overall change. - Monitoring and support devices are stable with a continued low position of the - right chest tube. No evidence of pneumothorax. Minimal residual subcutaneous - gas along the right lateral chest wall. - Otherwise little change in the appearance of the heart and lungs. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s54645315.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s54645315.txt deleted file mode 100644 index 50e8c30ebaa7f41a9b9293e6c6285ce044a0f7bf..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s54645315.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with chest tube post stab wounds. // r/o - pneumonia post CT water seal - - TECHNIQUE: Portable AP chest radiograph. - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Lung volumes remain low, particularly on the right where there is blunting of - the costophrenic angle consistent with a small pleural effusion. The - right-sided chest tube is unchanged in position, post lateral chest wall. No - pneumothorax seen. The cardiomediastinal contour is unchanged. No - consolidation seen. - - IMPRESSION: - - No significant interval change when compared to the prior study. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s57115390.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s57115390.txt deleted file mode 100644 index 30558d20d1ecf614c8cbcc97d1ab56f10a5859b3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10405915/s57115390.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p thoracotomy // Right CT removed, assess for - pneumo Right CT removed, assess for pneumo - - IMPRESSION: - - In comparison with the study of ___, following right chest tube - removal there is no definite pneumothorax. Postsurgical changes are again - seen in the right hemithorax. The left lung is clear. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10410672/s59859275.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10410672/s59859275.txt deleted file mode 100644 index 39cfe1abb0fee1cd314c594f4f1c6f35945eb500..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10410672/s59859275.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - HISTORY: Worsening right sided weakness with facial numbness. - - COMPARISON: Chest radiograph from ___. - - FINDINGS: - - Chest, PA and lateral. The lungs are clear. Moderate cardiomegaly is - unchanged. There is no pneumothorax or pleural effusion. Pulmonary - vascularity is normal. - - IMPRESSION: - - 1. No acute cardiopulmonary process. - - 2. Unchanged chronic moderate cardiomegaly. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10441850/s51766785.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10441850/s51766785.txt deleted file mode 100644 index 5807c1e9cabec4d9e9ef205e2ebaa05b1460fab9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10441850/s51766785.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___F with syncope // ?infection - - COMPARISON: ___. - - FINDINGS: - - PA and lateral views of the chest provided. - There is no focal consolidation, effusion or pneumothorax. Subtle ground-glass - opacities seen within the lungs on the frontal projection raising potential - concern for mild edema. Thoracic aorta is moderately calcified. Heart size is - within normal limits. Mediastinal contours unremarkable. Bony structures are - intact. No free air below the right hemidiaphragm. - - IMPRESSION: - - Possible mild edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s50494231.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s50494231.txt deleted file mode 100644 index 77bfc47f6983646a6463b4522686fc338c901e29..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s50494231.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: History: ___M with shortness of breath, edema - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ - - FINDINGS: - - Lung volumes are low with bibasilar linear opacities compatible with - atelectasis. Small bilateral pleural effusions are also demonstrated. Heart - size appears unchanged and within normal limits. Mediastinal and hilar - contours are unremarkable. Pulmonary vasculature is not engorged. The right - hemidiaphragm remains elevated. Azygos fissure is again noted. No acute - osseous abnormality. - - IMPRESSION: - - Low lung volumes with bibasilar atelectasis and small bilateral pleural - effusions. Persistent elevation of the right hemidiaphragm. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s52176984.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s52176984.txt deleted file mode 100644 index 8028f08382897f9a89b9f21581ea8bfdba527fb2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s52176984.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - EXAMINATION: PA and lateral chest radiograph. - - INDICATION: ___ year old man with hepatic decompensation, and recent CXR - ___ ___ showed bibasal opacities and left pleural effusion. // Please - evaluate for interval change. Please have patient take full inspiration, as - previous CXR did not show good inspiration. - - COMPARISON: Chest radiograph dated ___. - - FINDINGS: - - Lung volumes remain low. An azygos fissure, normal variant, is re- - demonstrated in the right upper hemithorax. Small left pleural effusion is - overall unchanged. Blunting of the right costophrenic angle with silhouetting - of the lateral aspect of the right hemidiaphragm may reflect a combination of - moderate atelectasis and elevated right hemidiaphragm. No definite right - pleural effusion, and if present, is minimal/trace. Appearance of the heart - and mediastinum are unchanged. No frank pulmonary edema or pneumothorax. - - IMPRESSION: - - 1. Unchanged small left pleural effusion. - 2. Moderate right lung atelectasis. - 3. No pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s55509622.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s55509622.txt deleted file mode 100644 index f024fdc7c753723b3f86a9e68f06f5bd6ccc4d4c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10501557/s55509622.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male with a PMHx of MI s/p PCI in ___ and recent - hospitalization here at ___ for decompensated cirrhosis secondary to - biopsy-proven NASH and autoimmune hepatitis who was admitted with ascites, - hepatic encephalopathy, and now developed a cough and tachycardia. // - evaluate for interval change, infiltrate - - TECHNIQUE: Chest PA and lateral - - FINDINGS: - - Lung volumes are low with bibasilar linear opacities compatible with - atelectasis. Small bilateral pleural effusions are also demonstrated. Heart - size appears unchanged and within normal limits. Mediastinal and hilar - contours are unremarkable. Pulmonary vasculature is not engorged. The right - hemidiaphragm remains elevated. Azygos fissure is again noted. No acute - osseous abnormality. - - IMPRESSION: - - No significant interval change, low lung volumes with small effusions diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s52018897.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s52018897.txt deleted file mode 100644 index 82d849eec7add1f103c2b294bbca326472355f81..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s52018897.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - HISTORY: Altered mental status and likely opiate overdose. - - TECHNIQUE: Portable AP view of the chest. - - COMPARISON: Chest radiograph ___. CT torso ___. - - FINDINGS: - - There are low lung volumes. The heart size appears top normal, and likely - accentuated by the low lung volumes. Mediastinal and hilar contours are - relatively unchanged with apparent widening of the superior mediastinum likely - attributable to mediastinal fat as seen on the prior CT. There is crowding of - the bronchovascular structures. Patchy airspace opacities in the lung bases - may reflect atelectasis. Ill-defined 1 cm nodular opacity projecting over the - right upper lung field appears new compared to the prior study, an and area of - infection cannot be completely excluded. There is no large pleural effusion - or pneumothorax. Loss of the right acromial humeral interval is compatible - with underlying rotator cuff disease. Moderate to severe degenerative changes - of both glenohumeral acromioclavicular joints are re-demonstrated. - - IMPRESSION: - - Low lung volumes. Patchy bibasilar airspace opacities could reflect - atelectasis but infection is not excluded. Ill-defined nodular opacity in the - right upper lung field may also represent a site of infection but is - nonspecific. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s57980419.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s57980419.txt deleted file mode 100644 index 0b3480b3050bb5de139bed7731169afeaa393a74..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10518993/s57980419.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: ___-year-old male with history of fever. - - COMPARISON: ___. - - FINDINGS: Frontal and lateral views of the chest were obtained. Slight left - base retrocardiac opacity most likely relates to atelectasis, less likely - early infectious process. Right lung is clear. There are low lung volumes. - No pleural effusion or pneumothorax is seen. The cardiac silhouette is not - enlarged. The aorta is calcified and tortuous. - - Degenerative changes are seen along the spine, although not well evaluated. - - IMPRESSION: Mild left base opacity most likely represents atelectasis, - although an early consolidation is not entirely excluded, but felt less - likely. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10646008/s53041609.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10646008/s53041609.txt deleted file mode 100644 index 41435bce355c8555d7cc75a3d66da393a6c73909..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10646008/s53041609.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - PA AND LATERAL CHEST, ___ - - HISTORY: ___-year-old man with right chest pain. - - IMPRESSION: PA and lateral chest reviewed in the absence of prior chest - radiographs: - - Lung volumes are low. Bulging mediastinum projecting over the left main - bronchus and aortopulmonic window could be due to fat deposition exaggerated - by low lung volumes. I would recommend a repeat frontal chest radiograph at - full inspiration to see if this is a real finding. Lower lungs are grossly - clear, though there is vascular crowding. In the upper lobes, there is the - suggestion of emphysema. Lateral view shows tiny right pleural effusion. - Heart size is normal. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10667992/s53900228.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10667992/s53900228.txt deleted file mode 100644 index a226230ee5571f6859e29dc11d33972fdab12772..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10667992/s53900228.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - HISTORY: Motor vehicle collision, unrestrained, struck chest on steering - wheel with chest wall pain. - - TECHNIQUE: PA and lateral views of the chest. - - COMPARISON: None. - - FINDINGS: - - Lung volumes are low. Heart size is normal. Rightward deviation of the - cervical trachea may be due to a left sided thyroid nodule or goiter. - Mediastinal and hilar contours are otherwise unremarkable. Linear opacities - in the lung bases are compatible with subsegmental atelectasis. No pleural - effusion or pneumothorax is seen. No displaced fractures are identified. - - IMPRESSION: - - Subsegmental atelectasis within the lung bases. No displaced fractures - identified. Rightward deviation of the cervical trachea may be due to a left - thyroid nodule or goiter and clinical correlation is recommended. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10680329/s54197100.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10680329/s54197100.txt deleted file mode 100644 index 07b565ea7f37a40a3e61f5d759477032d053951b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p10/p10680329/s54197100.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old male with chest pain, past medical history of congenital - heart disease including ASD and small VSD. - - COMPARISON: None. - - FINDINGS: - - Frontal and lateral views of the chest. The lungs are clear of consolidation, - effusion, pneumothorax, or pulmonary vascular congestion. There is moderate - cardiomegaly with left ventricular and left atrial enlargement likely related - to patient's congenital heart disease. The main pulmonary artery is not - enlarged. Lower thoracic vertebral bodies superiorly is partially fused with - no clear intervertebral disc space and probable single pedicle on the right. - Additional narrowed intervertebral disc more superiorly may also be - congenital. There is evidence of prior left midclavicular fracture.Osseous - structures are otherwise unremarkable. - - IMPRESSION: - - Cardiomegaly compatible with patient's history without definite acute - cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11049760/s57777582.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11049760/s57777582.txt deleted file mode 100644 index 254c9aa6adc234c4b021c0e4c17911f3a857d644..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11049760/s57777582.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - PORTABLE CHEST: ___. - - HISTORY: ___-year-old female with altered mental status. Low-grade fevers. - - FINDINGS: Single portable view of the chest compared to previous exam from - ___. There is engorgement of the central pulmonary vasculature - with indistinctness of the vascular markings. There is no confluent - consolidation. Blunting of the left costophrenic angle could be due to - technique and overlying soft tissues; however, small effusion is not excluded. - Cardiomediastinal silhouette is not significantly changed given differences in - positioning and technique. Osseous and soft tissue structures are - unremarkable. - - IMPRESSION: - Findings suggestive of pulmonary vascular congestion without frank edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11053589/s56374336.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11053589/s56374336.txt deleted file mode 100644 index 8fe5bbecad75f555d99f8f11a94a3e6bda0ce66f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11053589/s56374336.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: ___M w/ severe biscuspid AV, CM EF ___%, Afib RVR, T2DM, htn/hl, - newly diagnosed cirrhosis, deemed not to be a candidate for surgical valve - repair, now s/p TAVR // eval for interval changes - - TECHNIQUE: AP chest x-ray - - COMPARISON: ___ - - FINDINGS: - - Since the prior study, the patient has had a TAVR, which has the expected - appearance. There is mildly increased opacity in the left midlung with - peribronchial opacity that likely reflects a small amount of pulmonary edema. - The right lung remains clear. Cardiomegaly persists. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s56476070.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s56476070.txt deleted file mode 100644 index 2ccb1501c15270ed68e8b96c1544272ef4aea3ef..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s56476070.txt +++ /dev/null @@ -1,28 +0,0 @@ - WET READ: ___ ___ 8:02 AM - - - - Slight improvement in right lung base opacity. Otherwise stable exam from - prior.--___ - WET READ VERSION #___ ___ ___ ___ 9:10 PM - Slight improvement in right lung base opacity. Otherwise stable exam from - prior.--___ - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with aspiration event leading to out of hospital - cardiac arrest, now with some hypoxia // Pulmonary edema? Pulmonary - edema? - - COMPARISON: Comparison to prior study dated ___ at 07:49 - - IMPRESSION: - - Interval removal of the right internal jugular central line. Nasogastric tube - seen coursing below the diaphragm. Endotracheal tube and esophageal probe are - stable in position. Stable small bilateral effusions. Overall cardiac and - mediastinal contours are stable. Given differences in technique, no - significant interval change in the right lower lobe airspace opacity and the - other scattered patchy opacities in the left mid and lower lung. No - pneumothorax or pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s58471346.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s58471346.txt deleted file mode 100644 index 384aef2f9697d1189c6b45548d7201d75bbf9f27..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s58471346.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with respiratory failure. // Comparison to - previous. Comparison to previous. - - IMPRESSION: - - In comparison with the study of ___, of the monitoring and support devices - remain in place. There is again evidence of increased pulmonary venous - pressure without definite cardiomegaly. Retrocardiac opacification is - consistent with volume loss in the left lower lobe and there is blunting of - the costophrenic angle consistent with small pleural effusion. - On the right, there are areas of increased opacification in the mid and lower - lungs with poor definition of the lateral aspect of the hemidiaphragm. - Although this could merely represent atelectasis and a small pleural effusion. - The extent of this process is strongly suggestive of aspiration or infectious - pneumonia if this is consistent with the clinical history. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s59749649.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s59749649.txt deleted file mode 100644 index 99311a185df3fd908bad694cf092e0279b22f437..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11111102/s59749649.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with sudden cardiac arrest, intubated, on - cooling-rewarming protocol // Tube placement? Cause of increased resistance? - Tube placement? Cause of increased resistance? - - IMPRESSION: - - In comparison with the study of ___, there is little change in the - appearance of the monitoring and support devices. Little change in the - appearance of the heart and lungs. Continued elevation of the right - hemidiaphragm with a configuration that could reflect subpulmonic effusion. - Blunting of the left costophrenic angle is again seen. Retrocardiac - opacification obscuring the hemidiaphragm is consistent with volume loss in - the left lower lobe. Mild atelectatic changes are seen at the right base. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11198939/s54787712.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11198939/s54787712.txt deleted file mode 100644 index 444ee7acc737f260e9eb769bbd4a2350fddb7b88..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11198939/s54787712.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: History of respiratory arrest, now intubated. Please evaluate - for intrapulmonary process or ET tube placement. - - COMPARISONS: Chest radiograph from ___. - - TECHNIQUE: Portable supine AP radiograph of the chest. - - FINDINGS: The ET tube terminates approximately 5.6 cm above the carina. - There is mild thickening of the right minor fissure which may be secondary to - a tiny right-sided effusion. Left-sided rib deformities may be secondary to - prior surgery. There is no evidence of a pneumothorax or large pleural - effusion. There is no evidence of significant pulmonary edema. - - IMPRESSION: ET tube terminates approximately 5.6 cm above the carina. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s51598070.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s51598070.txt deleted file mode 100644 index 98192542458be9ecef28e779131fdca78f5aa173..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s51598070.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with cardiac arrest intubated // interval change - - COMPARISON: Chest x-ray from ___ at 13:20 - - FINDINGS: - - An ET tube is present. The carina is not well delineated, but the ET tube - probably lies approximately 2.2 cm above the carina. An NG tube is present, - tip beneath diaphragm, overlying gastric fundus. - - There are low inspiratory volumes. Heart size is borderline enlarged. There is - upper zone redistribution, but doubt overt CHF. Compared with the prior film, - however, there is new increased retrocardiac density and new blunting of the - left costophrenic angle, consistent with left lower lobe collapse and/or - consolidation. Some patchy opacity in the right infrahilar region is similar - to the prior film. - - - IMPRESSION: - - New left lower lobe collapse and/or consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s54936962.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s54936962.txt deleted file mode 100644 index 324ca35f2106641c1adefc553d2ad94ca49c9f30..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s54936962.txt +++ /dev/null @@ -1,21 +0,0 @@ - WET READ: ___ ___ ___ 5:32 PM - Marked worsening of bibasilar opacities, now with moderate bilateral pleural - effusions. Tiny left apical pneumothorax is no longer appreciated. D/w Dr. - ___ at 5:30 p.m.. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with hypoxia on ventilator // eval for PNA vs. - collapse vs. edema eval for PNA vs. collapse vs. edema - - COMPARISON: Have chest radiographs ___ through ___. - - IMPRESSION: - - New severe heterogeneous consolidation right lower lobe, progressive - consolidation left lower lobe, both accompanied by small to moderate pleural - effusion, greater on the left. Findings are most consistent with severe - pneumonia. Pneumo mediastinum ___ pneumopericardium persist. No pneumothorax. - ET tube in standard placement. Nasogastric tube ends at the level of the left - hemidiaphragm. Its precise location is unclear. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s55999850.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s55999850.txt deleted file mode 100644 index ea85d7a4c1f3baea947c2eab17b0b8327455b398..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11320106/s55999850.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___M with intubated // eval for ETT - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: None. - - FINDINGS: - - Endotracheal tube tip is approximately 3.2 cm from the carina. Enteric tube - seen within the stomach with tip pointed towards the fundus. Lung volumes are - low. Cardiac silhouette is mildly enlarged even giving technique. Opacity at - the right lung base may be due to atelectasis although aspiration or infection - are also possible. No acute osseous abnormalities identified. - - IMPRESSION: - - Support lines and tubes as above. - Enlarged cardiac silhouette. - Right basilar opacity, potentially any combination of atelectasis, infection - or aspiration. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s52065761.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s52065761.txt deleted file mode 100644 index 8ad6edd3d5022c8964f6d5fab168285643e36351..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s52065761.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - AP CHEST, 9:57 A.M. ON ___ - - HISTORY: ___-year-old man with diabetes and end-stage renal disease, on - hemodialysis. Osteomyelitis with fever. Suspect pneumonia. - - IMPRESSION: PA and lateral chest compared to ___: - - Mild interstitial edema and possible bibasilar pneumonia have both cleared - since ___. Heart remains mildly enlarged. There is no pleural - effusion. Right supraclavicular dual-channel dialysis catheter set ends in - the low SVC and mid right atrium. No pneumothorax or pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s53817559.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s53817559.txt deleted file mode 100644 index bc1ab316ebe2682ca245d4a674f22af2c61db87d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11350319/s53817559.txt +++ /dev/null @@ -1,10 +0,0 @@ - FINAL REPORT - SINGLE FRONTAL VIEW OF THE CHEST - - REASON FOR EXAM: Followup pulmonary edema. - - Comparison is made with prior study, ___. - - Moderate pulmonary edema has markedly improved. Cardiomegaly is stable. - Widened mediastinum has improved. There is no pneumothorax. Sternal wires - are aligned. Right central catheter is in standard position. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s51929606.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s51929606.txt deleted file mode 100644 index b8e64cb46994a535876a63b1b59b797c1f73b1bd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s51929606.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old with history of CHF, please assess for pulmonary - edema. - - TECHNIQUE: Frontal and lateral radiographs of the chest were obtained. - - COMPARISON: Chest radiograph from ___. - - The patient is status post coronary bypass graft surgery. A right ventricular - pacemaker is unchanged. There is similar moderate cardiomegaly. A diffuse - interstitial abnormality is similar to perhaps slightly increased from - baseline without focal opacities. There is no pleural effusion or - pneumothorax. - - IMPRESSION: Similar to perhaps slightly increased interstitial abnormality - which may reflect acute on chronic vascular congestion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s57060345.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s57060345.txt deleted file mode 100644 index c19cdb1bbc9def2aa3aec090cd753f6d397fe10e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11422357/s57060345.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old man with systolic heart failure, ejection fraction of - 15%, and history of coronary artery disease. Presents with shortness of - breath. - - COMPARISON: PA and lateral chest radiograph ___, - - TECHNIQUE: PA and lateral chest radiograph. - - FINDINGS: There are bilateral low lung volumes with prominent pulmonary - vasculature and interstitial markings most likely representing worsening - pulmonary edema; however, atypical pneumonia cannot be excluded but is much - less likely. No areas of focal consolidation concerning for infection. There - is a small right pleural effusion. No pneumothorax is identified. Pleural - surfaces are unremarkable. The heart is stably enlarged with the proximal - electrode of a left-sided pacer device extending from the SVC into the low - right atrium, unchanged in longstanding position. The lead terminates at the - apex of the right ventricle. Median sternotomy wires are again noted in - alignment and with no evidence of failure. - - IMPRESSION: Low lung volumes with increased vascular prominence suggestive of - worsening pulmonary edema. Though much less likely, an atypical pneumonia - cannot be excluded, diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11461300/s59948950.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11461300/s59948950.txt deleted file mode 100644 index 03cf5bd5c38e0f96962eeff162b9ddf4a66220e4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11461300/s59948950.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old female with shortness of breath. - - COMPARISON: Prior study dated ___. - - FINDINGS: - - PA and lateral views of the chest were provided. Lung volumes are low with - chronic interstitial opacity likely reflective of chronic interstitial lung - disease with evidence of mild interval progression. Correlation with - high-resolution chest CT may be helpful to further assess. The possibility of - a superimposed atypical pneumonia is impossible to exclude given the - underlying interstitial opacities. No large effusion or pneumothorax is seen. - The heart and mediastinal contour appear overall stable. The bony structures - are intact. No free air is seen below the right hemidiaphragm. - - IMPRESSION: - - Progression of interstitial opacities compatible with chronic fibrosis. - Consider high-resolution chest CT to further assess. Please note, due to the - presence of interstitial opacity the possibility of an atypical superimposed - pneumonia is impossible to exclude. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11572460/s51849973.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11572460/s51849973.txt deleted file mode 100644 index a9d7a9039687e85a3e97ae2116de645a04231cad..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11572460/s51849973.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with stroke. Intubated and sedated // Confirm ETT - and OG tube - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: None. - - FINDINGS: - - Endotracheal tube terminates 4.7 cm above the carina. Enteric tube courses - below the diaphragm, out of the field of view. There is a small to moderate - right and trace left pleural effusion, with overlying atelectasis. The - cardiac silhouette is mild to moderately enlarged. Mediastinal contours - unremarkable. No pneumothorax is seen. No overt pulmonary edema. - - IMPRESSION: - - Small moderate right and trace left pleural effusions with overlying - atelectasis. Underlying aspiration not excluded. - - Mild to moderate enlargement of the cardiac silhouette. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11632359/s59940756.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11632359/s59940756.txt deleted file mode 100644 index c3a3a11d06e1624b2f65d677eaf6d7db956b0348..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11632359/s59940756.txt +++ /dev/null @@ -1,31 +0,0 @@ - WET READ: ___ ___ ___ 4:47 PM - No definite acute cardiopulmonary process. Possible hilar enlargement, - particularly on the left. This appearance could partially be accounted for by - a tortuous descending thoracic aorta. Dedicated chest x-ray with 2 views is - suggested to further characterize this finding and apparent increased opacity - projecting over the anterior right 2nd rib as well. - - ______________________________________________________________________________ - FINAL REPORT - HISTORY: ___-year-old female with shortness of breath and elevated white blood - cell count. Cough. Question pneumonia. - - COMPARISON: None. - - FINDINGS: - - Single portable view of the chest. Left PICC is seen with tip in the mid SVC. - There is an opacity projecting over the anterior right 2nd rib, potentially - related to osseous structures however underlying parenchymal changes are also - possible. The lungs are otherwise grossly clear. The descending thoracic - aorta is tortuous and may account for apparent left hilar enlargement. There - is however possible right hilar enlargement as well. Cardiac silhouette is - enlarged even given technique. No acute osseous abnormality detected. - - IMPRESSION: - - No definite acute cardiopulmonary process. Possible hilar enlargement, - particularly on the left. This appearance could partially be accounted for by - a tortuous descending thoracic aorta. Dedicated chest x-ray with 2 views is - suggested to further characterize this finding and apparent increased opacity - projecting over the anterior right 2nd rib as well. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s50819334.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s50819334.txt deleted file mode 100644 index 701c385c25b20221136ebd539edb54db42383161..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s50819334.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: Cardiac arrest. Evaluation for tube position. - - TECHNIQUE: Supine radiographs of the chest. - - COMPARISON: None available. - - FINDINGS: Evaluation is limited by underlying board and supine positioning. - The second radiograph demonstrates ET tube within the right main stem - bronchus. Lung volumes are low with mild pulmonary edema. No large - pneumothorax is identified on this supine radiograph. There is severe - cardiomegaly. The patient is status post median sternotomy with fracture of - the second and fourth median sternotomy wires. Epicardial pacing wires are - noted. There is gaseous distention of the stomach, partially imaged. - - IMPRESSION: Endotracheal tube within the right main stem bronchus. Pulmonary - edema with severe cardiomegaly. - - Findings regarding ETT discussed with Dr. ___ at 4:20 p.m., ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s53083434.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s53083434.txt deleted file mode 100644 index a84ee4c9b84c0504c4d8d2ed73cf9a49b6139893..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s53083434.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - AP CHEST, 7:56 A.M., ___ - - HISTORY: Persistent oxygen requirement after extubation. - - IMPRESSION: AP chest compared to ___ through ___: - - Severe right lower lobe atelectasis continues to worsen since ___, now - following tracheal extubation. Pulmonary vasculature is engorged but there is - no edema and pleural effusions are small if any. Moderate cardiomegaly is - longstanding. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s55949143.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s55949143.txt deleted file mode 100644 index 2aedde1792e5f391fb7184848dd1ccecd5b2d7dc..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s55949143.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - AP CHEST, 12:13 A.M. ON ___ - - HISTORY: Cardiac arrest. - IMPRESSION: AP chest compared to ___: - - Mild cardiomegaly has improved since ___, but there is new - opacification at the base of the left lung which could be asymmetric edema, - since there are clear septal lines, but the marked asymmetry raises concern - for pneumonia particularly aspiration. Lesser degree of atelectasis is new at - the right lung base. There is no pneumothorax. Pleural effusions are small - if any. Upper mediastinum is not widened. ET tube is in standard placement. - Left subclavian line ends in the left brachiocephalic vein, and a nasogastric - tube passes into the stomach and out of view. The fracture of the second from - uppermost sternal wire dates from at least ___, 3:55 p.m., the - earliest examination available. There has been no subsequent derangement of - wires. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s57610437.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s57610437.txt deleted file mode 100644 index 65d87c098e66a25664119ec6707261f9e52d6db8..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11636169/s57610437.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Endotracheal tube placement. - - COMPARISON: ___, 4:38 p.m. - - FINDINGS: As compared to the previous radiograph, lung volumes have - increased, reflecting improved ventilation. Unchanged position of the - endotracheal tube and the nasogastric tube. Unchanged position of the left - central venous access line. There is currently no evidence of pneumothorax, - pulmonary edema, or pneumonia. Unchanged borderline size of the cardiac - silhouette. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s52097122.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s52097122.txt deleted file mode 100644 index c6de298d59db518241c1d45e38b6a216ef6ddf09..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s52097122.txt +++ /dev/null @@ -1,31 +0,0 @@ - WET READ: ___ ___ ___ 5:40 PM - In comparison to the examination from 3 hours prior there has been interval - placement of a tracheal tube which ends in the mid thoracic trachea. Mild - cardiomegaly is stable. There has been rapid opacification of the inferior - right lower lobe, which may be due to rapidly accumulating pleural effusion or - aspiration, as there is no sign of volume loss. A left IJ line ends at the - mid SVC. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with new ETT // ETT position? ETT - position? - - IMPRESSION: - - Prior chest radiograph, 14:15 earlier on ___. - - With the chin down, tip of the ET tube, at the upper margin of the clavicles - and more than 5 cm from the carina should be advanced at least 2 cm for more - secure positioning. Left internal jugular line ends in the lower SVC. - Transesophageal drainage tube ends in the upper portion of a nondistended - stomach. - - New abnormality in the right lower chest could be either consolidation in the - lower lobe due to rapid pneumonia or collapse, and/or moderate right pleural - effusion, more likely abnormality in the lung because of absent contralateral - mediastinal shift. - - Heart is moderately enlarged. Left lung is clear and there is no left pleural - abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s59208327.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s59208327.txt deleted file mode 100644 index be3647d8488c1c5ba6fc88387dc0f8aba5af7393..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11801290/s59208327.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman s/p exlap and SBR, NGT self-d/c'd and replaced - overnight. // pls eval NGT placement - - COMPARISON: The comparison is made with prior studies including ___. - - IMPRESSION: - - The left IJ is unchanged. Nasogastric tube is in the stomach. The - endotracheal tube is no longer visualized and presumably has been removed. - There is persistent consolidation or atelectasis in the right lower lobe. - There is cardiomegaly but no CHF. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s50078800.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s50078800.txt deleted file mode 100644 index c054ff2024fdac1473d169134dbfa32d980d6b39..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s50078800.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with new ureteral stents // Stent placement - - TECHNIQUE: Chest single view - - COMPARISON: ___ - - FINDINGS: - - Endotracheal tube tip in stable position. Enteric tube tip at - gastroesophageal junction, should be advanced. Small right pleural effusion. - Mild right basilar opacity, likely atelectasis. Postoperative change left - breast. Normal heart size, pulmonary vascularity. No pneumothorax. - - IMPRESSION: - - Enteric tube tip at gastroesophageal junction, should be advanced. Small - right pleural effusion, mild right basilar opacity, likely atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s57860317.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s57860317.txt deleted file mode 100644 index d3baf25fa6a892d5eb7fce6b9257620ba2449eeb..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11929103/s57860317.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman POD ___ s/p radical cystectomy and POD ___ s/p - repair of fascial dehiscence // etiology for AMS, ?PNA - - TECHNIQUE: AP portable chest radiograph - - COMPARISON: ___ - - FINDINGS: - - Interval removal of the endotracheal and enteric feeding tubes. - - Interval increase in right basilar opacities which may reflect atelectasis - and/or consolidation. Minimal left basilar atelectasis is noted. No large - pleural effusion or pneumothorax identified. The size of the cardiac - silhouette is within normal limits. - - Surgical clips project over the left lower hemithorax. - - IMPRESSION: - - Increased opacities at the right lung base may reflect atelectasis or - pneumonia in the proper clinical context. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s55750370.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s55750370.txt deleted file mode 100644 index 039bde9d8093df5a3fc664ff24d3eff9ccd689d3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s55750370.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman intubated, awaiting organ donation // further - eval of pulm edema status - - COMPARISON: The comparison is made with prior studies including ___ 00:31. - - IMPRESSION: - - Endotracheal tube tip is 6 cm above the carina. Nasogastric tube is beyond - the GE junction and off the edge of the film. There is a esophageal probe in - the cervical esophagus at the cervical thoracic junction. There is - cardiomegaly and stable pulmonary edema. There is no dense consolidation or - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s56993572.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s56993572.txt deleted file mode 100644 index ca564b566dbe3de178cbaf60e4f1f5443b4d35f0..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11950244/s56993572.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman s/p cardiac arrest, intubated and sedation // - ? effusion, consolidation - - COMPARISON: The comparison is made with prior studies including ___. - - IMPRESSION: - - Endotracheal tube tip is 3 cm above the carina. Nasogastric tube to is beyond - the GE junction and beyond the edge of the film. - There are findings consistent with CHF. There is stable cardiomegaly. There - is probable atelectasis in both lung bases. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s50631849.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s50631849.txt deleted file mode 100644 index 54cf8ff4f719db1295fd83f83d68b2df1837b150..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s50631849.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___ - - COMPARISON: ___. - - CLINICAL HISTORY: Feeling unwell, assess pneumonia. - - FINDINGS: PA and lateral views of the chest provided. An AICD is unchanged - in position with lead tips extending to the right atrium and right ventricle. - Midline sternotomy wires and mediastinal clips are again noted. External - pacing wires are seen positioned over the low chest. There is no focal - consolidation suggestive of pneumonia. There is no overt edema or effusion. - No pneumothorax. The heart is mildly enlarged and the aorta is unfolded, - though this is stable. Bony structures are intact. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s52066024.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s52066024.txt deleted file mode 100644 index 35d3bc3f3f8a4ef65b2e98dcee9b66b1792bc821..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s52066024.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old male with chest pain. - - STUDY: AP and lateral chest radiograph. - - COMPARISON: ___, ___ and ___. - - FINDINGS: Sternotomy wires are unchanged as are mediastinal clips. A pacer - defibrillator unit projects over the left chest with leads in the right atrium - and right ventricle as well as a set of abandoned leads, all similar to prior - exam. The heart continues to be enlarged but not changed from prior exam. - The mediastinal contours are not widened. The lungs demonstrate prominent - pulmonary vasculature and mild edema. There is no large pleural effusion or - pneumothorax. - - IMPRESSION: Stable cardiomegaly with mild edema - may represent early heart - failure. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s56139465.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s56139465.txt deleted file mode 100644 index 92f1928d205274dd739a7a3ccbeef85213f5dac3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11966699/s56139465.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAM: CHEST, FRONTAL AND LATERAL VIEWS. - - CLINICAL INFORMATION: Confusion. - - COMPARISON: ___. - - FINDINGS: Frontal and lateral views of the chest were obtained. Left-sided - AICD is stable in position. The cardiac silhouette remains mild to moderately - enlarged. The aorta and mediastinal contours are unremarkable. The patient - is status post median sternotomy and CABG. Subtle linear left basilar - opacities are improved since the prior study and likely represent chronic - changes. No new focal consolidation is seen. There is no pleural effusion or - pneumothorax. The lungs are relatively hyperinflated with flattening of the - diaphragms, suggesting chronic obstructive pulmonary disease. - - IMPRESSION: Cardiomegaly. No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s52406507.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s52406507.txt deleted file mode 100644 index d0ba90e80d4234cb75c03c71250d2df211f06561..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s52406507.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with Hemothorax, now s/p Left chest tube - placement // Progression of hemothorax Progression of hemothorax - - IMPRESSION: - - In comparison with the study of ___, the left chest tube remains in - place and there is no pneumothorax. The opacification at the left base has - decreased. Atelectatic changes are seen at the right base. - Continued enlargement of the cardiac silhouette with pulmonary vascular - congestion that appears less prominent than on the prior study. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56610858.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56610858.txt deleted file mode 100644 index 5ce0760a11aa4eb0e689d61a12dd19ce7cc6c17e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56610858.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with increasing pain, hypoxia // eval for - pneumothorax - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: Earlier today, ___ at 16:48 - - FINDINGS: - - Right costophrenic angle not fully included on the image. Left-sided chest - tube terminates at the left lung apex, slightly more superior as compared to - the prior study. There are low lung volumes. Enlargement of the - cardiomediastinal silhouette is stable with the mediastinum slightly less - prominent as compared to the prior study. Perihilar opacities, left greater - than the right, are re- demonstrated. No evidence of enlarging pneumothorax. - Multiple left-sided rib fractures again seen. Evidence of some left - subcutaneous emphysema along the left chest wall at the level of the chest - tube insertion site. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56890888.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56890888.txt deleted file mode 100644 index ad2375bbb04ff2c46614568ffbc5d99d11d1b016..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s56890888.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: - Portable chest x-ray - - INDICATION: ___ year old man with Hemothorax, now s/p Left chest tube - placement // Progression of hemothorax - - TECHNIQUE: Frontal portable radiograph of the chest - - COMPARISON: Compared to prior dated ___ at 11:15. - - FINDINGS: - - Position of the left chest tube is stable. Stable amount of mild left - pulmonary edema and left pleural effusion. Moderate cardiomegaly. No new - focal consolidation. - - This preliminary report was reviewed with Dr. ___, ___ - radiologist. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s57535354.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s57535354.txt deleted file mode 100644 index 1184bfd82928a814956cf1a5f3d8930697261306..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11982468/s57535354.txt +++ /dev/null @@ -1,39 +0,0 @@ - WET READ: ___ ___ ___ 8:28 PM - Mediastinum remains widened. - - Left lung appears somewhat re- expanded, likely due to interval drain is of - some left pleural effusion. Scattered patchy bilateral pulmonary opacities, - possibly due to underlying pulmonary contusions. - - Several left-sided rib fractures, better depicted on CT. - - Repeat chest CT pending. - - - - - - *** ED URGENT ATTENTION *** - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with Placement of chest tub // Placement of chest - tub - - TECHNIQUE: Supine AP portable views of the chest - - COMPARISON: Earlier today, ___ at 15:35 - - FINDINGS: - - Interval placement of left-sided chest tube, the initial image shows a the - tube coursing inferior, out of the field of view. Subsequent image shows the - left chest tube readjusted and terminating at the left lung apex. - - The mediastinum remains widened. The cardiac silhouette remains moderately to - markedly enlarged. Left lung appears somewhat re-expanded, likely due to - interval drainage of some of left pleural effusion. The right hemidiaphragm - is mildly elevated. Scattered patchy pulmonary opacities are seen, underlying - pulmonary contusions not excluded. Several left-sided rib fractures seen, - better depicted on CT. Repeat chest CT is pending. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11999272/s56039952.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11999272/s56039952.txt deleted file mode 100644 index f5e9bef4bf2973268f4e822906fab02b437f781b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p11/p11999272/s56039952.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - HISTORY: Hypotension, chest pain, question pneumonia. - - CHEST, TWO VIEWS. - - Inspiratory volumes are slightly low. Allowing for this, heart size is at the - upper limits of normal. The patient is status post sternotomy. There is a - left-sided dual-lead pacemaker with lead tips over the right atrium and right - ventricle. There is some patchy opacity at both lung bases, with some - crowding of vessels in the right middle and question left lower zones. There - is blunting of the left costophrenic angle posteriorly where some patchy - opacity is also likely present. No gross effusion. - - IMPRESSION: Patchy opacity at both lung bases, question right middle and left - lower lobe. Although nonspecific, the differential diagnosis includes - infectious infiltrates. Inflammatory infiltrates and aspiration could have a - similar appearance. No gross effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56469261.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56469261.txt deleted file mode 100644 index 5b1bb5bc0f03755edf0c5a8a4de75161b986dc20..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56469261.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with severe AS, urosepsis // worsening SOB, - concern for volume overload - - TECHNIQUE: Portable chest radiograph. - - COMPARISON: Chest radiograph dated ___ - - FINDINGS: - - There is enlargement of the bronchovascular markings with increased - interstitial opacity consistent with pulmonary edema. The bilateral hazy - opacities are likely due to atelectasis. There is increased pleural effusion - bilaterally. The cardiac silhouette is mildly enlarged compared to prior. No - pneumothorax No fractures. - - IMPRESSION: - - The findings are consistent with fluid overload. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56655821.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56655821.txt deleted file mode 100644 index d5422ee62da317583a43d28de649f5bf0d318540..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12106566/s56655821.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with sepsis - - TECHNIQUE: Upright AP view of the chest - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Heart size is normal. The aorta remains tortuous. The mediastinal and hilar - contours are similar. The pulmonary vasculature is not engorged. Patchy - opacities in the lung bases likely reflect areas of atelectasis. No focal - consolidation, pleural effusion or pneumothorax is present. Multilevel mild - to moderate degenerative changes are seen in the thoracic spine. - - IMPRESSION: - - Mild bibasilar atelectasis without focal consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12108393/s50581026.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12108393/s50581026.txt deleted file mode 100644 index b46c79d59a8757b703d3b87f740218734eaceb07..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12108393/s50581026.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest PA and lateral. - - INDICATION: ___-year-old man with a heroin overdose. - - TECHNIQUE: Chest PA and lateral. - - COMPARISON: Prior chest radiograph from ___. - - FINDINGS: - - Normal cardiomediastinal contours. Interval improvement in bilateral - perihilar airspace opacities with air bronchograms, particularly on the left, - suggests improving noncardiogenic pulmonary edema. Peripheral, right upper - lobe consolidation appears slightly worse, concerning for superimposed - aspiration. There is no pneumothorax or pleural effusion. - - IMPRESSION: - - Improving bilateral perihilar opacities suggest improving noncardiogenic - edema. Worsening right upper lobe consolidation suggests possible - superimposed aspiration or evolving aspiration pneumonia, although - asymmetrical edema is also possible. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s55608075.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s55608075.txt deleted file mode 100644 index 64fb6877f780b27fbcfc7b68eb32fb56ef7685a8..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s55608075.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with repositioning of right IJ // right IJ - repositioning, will be repositing with assistance of xray ___, ___ require - multiple images right IJ repositioning, will be repositing with assistance - o - - COMPARISON: Conventional chest radiographs ___ through ___. - - IMPRESSION: - - Lung volumes are lower today than any time since ___. This could be - due to severe distention of the stomach. Left lung is virtually collapsed and - small to moderate left pleural effusion is larger today than on ___. - - In the Right lung is a combination of mild edema and severe pulmonary vascular - congestion. Moderate right pleural effusion has probably increased. Moderate - cardiomegaly has not changed appreciably. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s56249693.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s56249693.txt deleted file mode 100644 index 5aec69e7be58e99c4c287b5ef45a60e34f7735a2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s56249693.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___M with a h/o DM2 on orals, obesity and nephroplithasis with - associated heavy use of NSAIDs p/w melena and hematemesis with necrotic - gastric fundus ulcer and multiple ulcers seen on EGD. // PNA PNA - - COMPARISON: Chest radiographs ___ through ___. - - IMPRESSION: - - No interval radiographic change in persisting consolidation in the left lower - lobe, not clearly atelectasis or pneumonia. Left pleural effusion is small. - Heart size top-normal. Right lung clear aside from mild subsegmental - atelectasis. No pneumothorax. - - Right PIC line has been partially withdrawn to the origin of the right - brachiocephalic vein. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s59403367.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s59403367.txt deleted file mode 100644 index 463025c4c53a1883e84d583dca12c8e7111a6184..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12215941/s59403367.txt +++ /dev/null @@ -1,36 +0,0 @@ - WET READ: ___ ___ ___ 8:23 AM - - - - 1. Hypoinflated lungs with crowding of vasculature. - 2. New left pleural effusion. - 3. No free air under the diaphragm on this semi upright film. If persistent - concern consider left lateral decubitus abdominal radiograph for further - evaluation. - - The findings were discussed by Dr. ___ with Dr. ___ on the telephone on - ___ at 5:26 PM, 5 minutes after discovery of the findings. - WET READ VERSION #1 ___ ___ ___ 5:34 PM - 1. Hypoinflated lungs with crowding of vasculature. - 2. New left pleural effusion. - 3. No free air under the diaphragm on this semi upright film. If persistent - concern consider left lateral decubitus abdominal radiograph for further - evaluation. - - The findings were discussed by Dr. ___ with Dr. ___ on the telephone on - ___ at 5:26 PM, 5 minutes after discovery of the findings. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with new abd pain, tachycardia, hx of gastric - ulcers // UPRIGHT PLEASE for eval of free air - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the elevation of the left - hemidiaphragm has increased. New left pleural effusion. Atelectasis at the - left lung bases. Moderate cardiomegaly. Unchanged appearance of the right - lung. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s55945774.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s55945774.txt deleted file mode 100644 index ad3b00f83de3d78bb69e170469ded406bf8c5944..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s55945774.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old woman with severe pancreatitis, intra-abdominal - cystic mass now spiking temps to 102. // Please evaluate for infection. - - COMPARISON: ___ - - IMPRESSION: - - No change as compared to the previous image. Mild cardiomegaly. Platelike - atelectasis at the right lung bases. Small left pleural effusion. No - pulmonary edema. No pneumonia, no pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s57553376.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s57553376.txt deleted file mode 100644 index 85731623aafa361ed458c2405a501bd3e2de4fb4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s57553376.txt +++ /dev/null @@ -1,30 +0,0 @@ - FINAL REPORT - HISTORY: Dobbhoff tube placed that appears to be freely moving. - - CHEST, SINGLE AP PORTABLE VIEW CENTERED LOW. - - COMPARISON: Abdominal film dated ___. - - The distal tip of the Dobbhoff tube is not included on these views. The - pattern of the Dobbhoff tube suggests reduction in the degree of redundancy - seen on the prior film, with the gastric fundus loop no longer visualized. - The mid abdomen loop appears slightly narrowed, but appears similar in - appearance, possibly with narrowing accentuated by differences in x-ray beam - angulation. - - New on the current film, there is considerable overlying coiled tubing over - the left mid abdomen. This tubing appears separate from the Dobhoff and - could lie outside the patient. Additional redundant tubing overlying the - chest, presumably overlies outside the patient. Multiple EKG leads are - present. - - Increased retrocardiac density, consistent with left lower lobe collapse - and/or consolidation is noted, similar to a chest x-ray from ___. - - IMPRESSION: - 1. Dobbhoff tube present, with tip extending beneath the inferior edge of the - film (just below the level of the iliac crest). If clinically indicated, a - full abdominal film could help for more complete assessment. - - 2. Tubing overlying the mid abdomen, which appears separate from Dobbhoff - tube, ? outside of patient. Clinical correlation requested. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s59155718.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s59155718.txt deleted file mode 100644 index 9f7e60ee08809a992928386a208447e2a152abdd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12250782/s59155718.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with pnacreatitis, rising WBC // ?pna or large - effusion - - COMPARISON: ___ radiographs. - - IMPRESSION: - - The feeding tube and right-sided PICC line are unchanged in position and - appropriately sited. There is a persistent left retrocardiac opacity and - left-sided pleural effusion. Atelectasis at the right lung base is also - present. There are no pneumothoraces or overt pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12262788/s52574159.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12262788/s52574159.txt deleted file mode 100644 index e951fa1e91f5306ca47c9a6db0df53a3beb697f1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12262788/s52574159.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: Dyspnea on exertion while walking. - - COMPARISON: ___. - - FINDINGS: Frontal and lateral views of the chest were obtained. No focal - consolidation is seen. There is no pleural effusion or pneumothorax. The - cardiac and mediastinal silhouettes are stable with the cardiac silhouette top - normal to mildly enlarged. The previously seen PICC is no longer seen. There - is partially imaged hardware in the right humerus, not well evaluated; - however, there may be lucency around the proximal portion. Findings could be - due to hardware loosening, infection not excluded. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s56369541.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s56369541.txt deleted file mode 100644 index e5464520db4568b506ebd0f89abd956a3b63cf7f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s56369541.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - EXAMINATION: Portable AP chest radiograph. - - INDICATION: ___ year old woman with acute onset respiratory distress, - intubated for CT scan // ET tube placement, NG tube placement - - COMPARISON: Chest radiograph dated ___. - - FINDINGS: - - The patient is rotated. The newly placed endotracheal tube ends approximately - 3 cm from the carina, and the neck appears to be flexed. Newly placed enteric - tube traverses the diaphragm and the tip and side-port project over the left - upper quadrant in a nondistended stomach. The right-sided Port-A-Cath tip is - intact and unchanged in position, ending in the approximate region of the - right upper atrium. - Lung volumes remain low with bilateral atelectasis, improved on the right. - Interval improvement in right pleural effusion. Heart size is difficult to - assess given technique and lower lung volumes, but grossly appears similar the - prior exam. No pneumothorax or pneumomediastinum. - - IMPRESSION: - - ETT in standard position. Interval improvement in right atelectasis and - pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s59975175.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s59975175.txt deleted file mode 100644 index a18ebec538e353527ec9653a8319348544478838..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12360014/s59975175.txt +++ /dev/null @@ -1,37 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ y/o female w/ rectosigmoid adenocarcinoma s/p robotic assisted - LAR w/ diverting loop ileostomy (___) s/p ileostomy takedown on ___. - Transferred to the ICU for respiratory distress. // interval change - - COMPARISON: Chest x-ray from ___ at 539 - - FINDINGS: - - Again seen is an right sided indwelling catheter with tip at SVC/RA junction - an NG tube, with tip and side-port curled in the expected location of the - gastric fundus. - - There are low inspiratory volumes, similar to 1 day earlier. Triangular - opacity at the left base medially, with new obscuration of the medial left - hemidiaphragm, could reflect some superimposed atelectasis. Otherwise, I - doubt significant interval change. - - Again seen is vascular plethora, likely accentuated by low lung volumes and - patchy atelectasis at the right lung base. The cardiomediastinal silhouette - is not well delineated due to low inspiratory volumes. Prominence of the - right hilar region probably reflects part of the cardiomediastinal - silhouette, accentuated by low lung volumes and differences in rotation. No - pneumothorax detected. - - IMPRESSION: - - - 1. Persistent low lung volumes with bibasilar atelectasis. New triangular - opacity at the left base medially may reflect some superimposed segmental - atelectasis. If clinically indicated, a lateral view may help for further - assessment. - 2. No pneumothorax detected. - 3. Mild vascular plethora is similar to the prior film and likely accentuated - by low lung volumes. No gross effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12405140/s55220622.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12405140/s55220622.txt deleted file mode 100644 index f1afb7f7813f0b8b2f05b975c08ce7801e780543..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12405140/s55220622.txt +++ /dev/null @@ -1,23 +0,0 @@ - WET READ: ___ ___ 3:38 AM - Portable frontal supine radiograph of the chest demonstrates the ET tube - ending 1.7 cm above the carina. An NG tube extends below the diaphragm and - into the stomach. Compared to the prior chest radiograph, there has been - interval increase in widespread bilateral patchy opacities greater on the left - than the right likely representing aspiration given the clinical situation. No - pleural effusion or pneumothorax. Stable cardiomediastinal contours. - ______________________________________________________________________________ - FINAL REPORT - INDICATION: History: ___F with drowning, ett // ? ett placement - - COMPARISON: Outside hospital chest radiograph dated ___ at 12:55 and - outside hospital CT torso dated ___ at 1:15. - - FINDINGS: - - Portable frontal supine radiograph of the chest demonstrates the ET tube - ending 1.7 cm above the carina and could be pulled back slightly. An NG tube - extends below the diaphragm and into the stomach. Compared to the prior chest - radiograph, there has been interval increase in widespread bilateral patchy - opacities greater on the left than the right likely representing aspiration - given the clinical situation. No pleural effusion or pneumothorax. Stable - cardiomediastinal contours. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s54904043.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s54904043.txt deleted file mode 100644 index 80be2a2abf5f4a14362493d3393bf1812a3dcd5f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s54904043.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: Evaluate for infiltrate in a patient with RCC metastatic to the - lungs, presenting with hemoptysis. - - TECHNIQUE: Chest PA and lateral - - COMPARISON: CT chest from ___. Chest radiographs from ___. - - FINDINGS: - - Frontal and lateral chest radiographs demonstrate bulky mediastinal and hilar - lymph node enlargement, consistent with known metastatic lesions. A poorly - defined mass in the left lower lung is also compatible with known metastatic - lesion. No new focal consolidation to suggest pneumonia is identified. There - is no appreciable flow pleural effusion or pneumothorax. The visualized upper - abdomen is unremarkable. - - IMPRESSION: - - - 1. No new focal lesion to suggest bacterial pneumonia. - 2. Bulky intrathoracic lymphadenopathy and left lower lobe mass are compatible - with known metastatic disease as seen on CT from ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s57593512.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s57593512.txt deleted file mode 100644 index 39310dba6ebfec31f876db34e87d2beecc7c68a2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12429112/s57593512.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with renal cell carcinoma s/p electrocautery to - LUL for endobronchial lesion // ?PTX ?PTX - - COMPARISON: Chest radiographs since ___, most recently ___, - read in conjunction with chest CT and CTA ___. . - - IMPRESSION: - - Even though the triangular opacity in the left lower lobe looks less - radiodense today than it did on ___, it is not an infarct or - pneumonia. It is a mass, as documented by serial chest CT scans. Central - adenopathy is bulky in the hila and mediastinum. Heart size is normal. Right - lung is clear. - - RECOMMENDATION(S): ___ diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12604446/s54249072.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12604446/s54249072.txt deleted file mode 100644 index 3392a67643349c0ac44f4dd156cc3c1d9e0a0280..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12604446/s54249072.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - INDICATION: Hypertension and acute mitral regurgitation, status post - intra-aortic balloon pump. - - TECHNIQUE: Portable frontal chest radiograph. - - COMPARISON: ___. - - FINDINGS: Cardiomediastinal silhouette and hilar contours are stable. - Intra-aortic balloon pump is in appropriate position 2.5 cm caudal to the - aortic knob. A right femoral approach Swan-Ganz catheter is in place with tip - pointing slightly cranially, in a right upper lobar pulmonary artery. There - is continued improvement of pulmonary edema. There is no large effusion or - pneumothorax. - - IMPRESSION: - 1. Swan-Ganz catheter in a right upper lobar pulmonary artery and withdrawal - of the catheter by 3 cm is recommended. IABP in appropriate position. - 2. Continued improvement of edema. - - Results were discussed over the telephone with Deb, CCU nurse, by ___ - at 9:42 a.m. on ___ at the time of discovery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12648153/s54124690.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12648153/s54124690.txt deleted file mode 100644 index e26033a7ac16e1e594ba18fa0fac1c697c0b5eff..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12648153/s54124690.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - HISTORY: Right hip fracture, requires preoperative x-ray. - - TECHNIQUE: PA and lateral views of the chest. - - COMPARISON: Reference chest radiograph ___ and ___. - - FINDINGS: - - Multiple mediastinal clips are again seen along with a manubrial cerclage - wire. The heart size remains mildly enlarged. Aortic knob is calcified. The - mediastinal and hilar contours are unchanged. There is no pulmonary vascular - congestion. No focal consolidation, pleural effusion or pneumothorax is - present. Minimal atelectasis is noted in the lung bases. Degenerative - changes of the right AC joint are noted. No acute osseous abnormality seen. - - IMPRESSION: - - Lung volumes with minimal bibasilar atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s51429527.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s51429527.txt deleted file mode 100644 index ca39e3927f36dee57eb774f686b7354636861da5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s51429527.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - PORTABLE AP CHEST X-RAY - - INDICATION: Patient with flash pulmonary edema, interval change. - - COMPARISON: ___. - - FINDINGS: - - This patient presented with asymmetric right more than left opacities on ___ that rapidly deteriorated over a course of two hours. A bronchoscopy - was done and found no blood and no mucus plugging. The patient is now treated - with pneumonia. On today's exam ET tube ends 3.6 cm above the carina. NG - tube is in the stomach. The severe widespread opacities have worsened at the - lung bases and left upper lobe, but improved in right upper lobe. There is - possibly adjacent pleural effusions, hard to assess. Mediastinal and cardiac - contours are top normal. There is no pneumothorax. - - CONCLUSION: - - 1. Tube and lines are in adequate position. - 2. Widespread severe lung opacities have worsened in the lower lungs and left - upper lobe but improved in right upper lobe. The evolution and lack of - vascular engorgement go against pulmonary edema. Considering that the - bronchoscopy was negative for pulmonary hemorrhage, severe pneumonia is the - most likely diagnosis. - - This was discussed with the medical team. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52588947.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52588947.txt deleted file mode 100644 index d98d6e8b79b933b274feba9094513d57a3513ffd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52588947.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: Cirrhosis, prolonged intubation for respiratory failure, - evaluation for pathology. - - COMPARISON: No comparison available at the time of dictation. - - FINDINGS: The lung volumes are low. The patient is intubated. The patient - has a nasogastric tube, the tip of the tube is not visualized on the image. - The lung volumes are low. There is moderate cardiomegaly with enlargement of - the left ventricle but no evidence of fluid overload or pulmonary edema. No - pleural effusions. No evidence of pneumonia. No pneumothorax. Minimal - decrease in transparency in the retrocardiac lung areas reflect local - atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52868811.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52868811.txt deleted file mode 100644 index 2384ae8df909d7042bcb7a0c553e4aae6211265d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s52868811.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - PORTABLE AP CHEST FILM ___ AT 402 - - CLINICAL INDICATION: ___-year-old status post liver transplant, fluid - overloaded, assess for change in pulmonary edema. - - Comparison is made to the patient's prior study of ___ at ___. - - A semi-supine chest film ___ at 402 is submitted. - - IMPRESSION: - - 1. A dual lumen left internal jugular central line and right internal jugular - Swan-___ catheter are unchanged in position. Overall, cardiac and - mediastinal contours are stable. There is an improving aeration in both lung - bases suggestive of resolving edema. Haziness at the right lung base may - reflect an element of a layering pleural effusion. No pneumothorax. Overall, - cardiac and mediastinal contours are unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53821710.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53821710.txt deleted file mode 100644 index 752cc18331cc9182575650449f1fada91676fad1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53821710.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: Post-Dobbhoff placement. - - COMPARISON: Radiograph available from ___. - - FRONTAL CHEST RADIOGRAPH: A left IJ terminates at the upper SVC. A Dobbhoff - tube terminates at the GE junction. The heart size is top normal. The hilar - and mediastinal contours are within normal limits. Mild pulmonary vascular - congestion is unchanged since the ___ examination. There is no - interstitial edema, focal consolidation, pneumothorax, or pleural effusion. - - IMPRESSION: Dobbhoff tube terminating at the GE junction. - - The initial findings were discussed by Dr. ___ with Dr. ___ by telephone at - the time of interpretation, 9:13 a.m. ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53897905.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53897905.txt deleted file mode 100644 index cefbe4dcaf592aa340c7ca2f9aa35f14ee340c4a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s53897905.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male patient with HCV and replaced feeding tube. - Study requested for assessment of location. - - COMPARISON: Prior chest radiographs from ___. - - TECHNIQUE: Portable AP chest radiograph. - - FINDINGS: The tip of the nasogastric tube is seen within the stomach and is - pointing towards the fundus. A left IJ terminates at the upper SVC. The - heart size is unchanged. The hilar - and mediastinal contours are within normal limits. There is no focal - consolidation, pneumothorax or pleural effusion. - - IMPRESSION: Feeding tube within the stomach, pointing towards the fundus. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55058373.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55058373.txt deleted file mode 100644 index 5128fde22b70bc03d2ed3c926d1551f5db6aca7a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55058373.txt +++ /dev/null @@ -1,7 +0,0 @@ - FINAL REPORT - HISTORY: Nasogastric tube placement. - - FINDINGS: In comparison with the earlier study of this date, nasogastric tube - extends at least to the lower body of the stomach where it crosses the lower - margin of the image. The endotracheal tube has been removed. Otherwise, - little change. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55937122.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55937122.txt deleted file mode 100644 index 9e1ef1a0c7480bb9e2b843ce3d12d66170283de8..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s55937122.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male patient with HCV, cirrhosis with placement of - feeding tube, advanced 5 cm. Study requested for assessment of location. - - COMPARISON: Prior chest radiograph from ___. - - TECHNIQUE: Portable AP chest radiograph. - - FINDINGS: The NG tube tip is seen outside the limits of the image field. A - left IJ terminates at the upper SVC. The heart size is unchanged. The hilar - and mediastinal contours are within normal limits. There is no focal - consolidation, pneumothorax or pleural effusion. - - IMPRESSION: NG tube tip outside limits of the image field. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s57790744.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s57790744.txt deleted file mode 100644 index 4b92a5895d97194d2dc83c5f35d7d54db9aba1d5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s57790744.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male with cirrhosis and altered mental status, who - presents for evaluation of NG tube location. - - COMPARISONS: Chest radiographs from ___, ___. - - TECHNIQUE: Single AP portable exam of the chest. - - FINDINGS: There is stable cardiomegaly, unchanged since at least ___. The NG tube courses below the diaphragm with the tip likely in the - pylorus. The lung volumes are low. There is no focal consolidation, pleural - effusion, or pneumothorax. There is mild bilateral pulmonary edema. - - IMPRESSION: NG tube courses below the diaphragm with the tip in the pylorus - of the stomach. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s58578695.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s58578695.txt deleted file mode 100644 index c2c2b865fb87ddf3ec1e3bcdee8593c3e5139218..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12716528/s58578695.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - INDICATION: History of a prior liver transplant with cough, malaise, and - hemoptysis. - - COMPARISONS: Chest radiograph from ___. - - TECHNIQUE: PA and lateral views of the chest were obtained with a total of - three exposures. - - FINDINGS: Since the prior exam, there is a new opacity involving the central - portions of the right lung. Other than mild left basilar atelectasis, the - left lung is clear. There is no pleural effusion or pneumothorax. The heart - is mildly enlarged, and appears slightly bigger than in the prior exam. The - mediastinal contours are normal. The known left lower lobe granuloma is not - well evaluated on this exam. - - IMPRESSION: - 1. New central right lung opacity. This likely represents diffuse pulmonary - hemorrhage; alternatively, an atypical pneumonia or new asymmetric edema are - considerations. - 2. Mild cardiomegaly, slightly increased from the prior exam. - - Results were discussed with Dr. ___ at 5:50 a.m. on ___ via telephone by - Dr. ___ at the time the findings were discovered. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56104878.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56104878.txt deleted file mode 100644 index 2c586366bfe4605f3a48707934b8d548698e45a7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56104878.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with ARDS, fluid overload s/p polytrauma // - interval change interval change - - IMPRESSION: - - Compared to chest radiographs ___ through ___. - - Mild pulmonary edema has worsened, moderate cardiac enlargement is worse and - mediastinal veins are more distended. Findings point to biventricular heart - failure with or without volume overload. - - Moderate right pleural effusion is new. No pneumothorax. - - An esophageal drainage tube can be traced only as far as the mid esophagus. - ET tube is in standard placement. Upper esophageal probe ends the level of - the carina. Right subclavian line diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56929352.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56929352.txt deleted file mode 100644 index f6a19ce7ccdef8739cfe4dd7fc43d0376f0fb4e1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12724975/s56929352.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: s/p L chest tube removal // pneumothorax - - COMPARISON: The comparison is made with prior studies including earlier the - same day 12:24. - - IMPRESSION: - - The right PICC line tip is in the SVC right atrial junction. There is no - pneumothorax. There is been improvement of the previously noted congestive - heart failure. Cardiac silhouette remains enlarged. There is patchy density - the right and possibly left lower lobes. Postoperative fusion hardware is - seen in the lower cervical spine. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57113568.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57113568.txt deleted file mode 100644 index 5051afd14724d554daf07790071c0623e6c0c16d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57113568.txt +++ /dev/null @@ -1,30 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPHS - - HISTORY: Status post fall, on Coumadin. Question injury. - - COMPARISONS: ___. - - TECHNIQUE: Chest, PA and lateral. - - FINDINGS: Coronary arteries are heavily calcified. There is a - moderate-to-large pleural effusion on the left, new since the prior study. - Associated left basilar atelectasis is likely. Patchy right basilar opacity - is not specific, but could be explained by atelectasis. There is no - pneumothorax. - - A moderate-to-severe upper thoracic wedge compression deformity appears - unchanged. Mild degenerative changes are similar along the lower thoracic - spine. A new contour deformity of the left sixth rib is incompletely - characterized, but apparently new; however the single image of it is more - suggestive of prior than recent injury. - - IMPRESSION: - - 1. New moderate-to-large left-sided pleural effusion; differential - considerations include hemothorax. - - 2. Contour abnormality of the left sixth rib fracture, not completely - characterized but apparently new. Dedicated left rib films may be helpful if - acute injury is suspected to refer to this area, although the contour - abnormality may be more chronic. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57737821.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57737821.txt deleted file mode 100644 index 1910e9878711c9718d8639cb36e0d811b1385111..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12727273/s57737821.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___ - - COMPARISON: Chest radiograph dated ___ as well as a CT of the chest dated - ___. - - CLINICAL HISTORY: Dyspnea on exertion, congestive heart failure, question - acute intrathoracic process. - - FINDINGS: PA and lateral views of the chest provided demonstrate bilateral - pleural effusions, left greater than right, with associated compressive lower - lobe atelectasis. There is no frank pulmonary edema. Heart size cannot be - assessed. No pneumothorax. Patient rotated to the left, which limits - evaluation of the mediastinum. - - IMPRESSION: Bilateral pleural effusions, left greater than right without - frank signs of pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12791659/s51894136.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12791659/s51894136.txt deleted file mode 100644 index 06ee49bba98641ba8f4cc9b74207516882051f8f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12791659/s51894136.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - AP CHEST, 10:14 P.M., ___. - - HISTORY: ___-year-old female with COPD and lung cancer treated with - radiotherapy. - - IMPRESSION: AP chest compared to ___, at 10:59 a.m., read in conjunction - with a chest CTA, 6:48 p.m. on ___. The upper lobe component of severe - mass-like consolidation is unchanged, lower lung component has improved over - 36 hours. Findings are consistent with at least some of the abnormality in - the right lung, being due to pneumonia. Since we do not have chest - radiographs following an even more serious doubt of right lung consolidation - in ___, I cannot tell how much of the current findings are residual, - how much is new, nor can we determine the time course. That would be - necessary to determine if there is any residual or recurrent tumor in the - right lung. Moderate cardiomegaly is chronic. Left lung is clear. There is - no appreciable pleural effusion and no pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55344983.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55344983.txt deleted file mode 100644 index 4efca088d19d0cb507cb76abf4c8457dd4e9385b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55344983.txt +++ /dev/null @@ -1,29 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M intubated - - TECHNIQUE: Portable semi-upright AP view of the chest - - COMPARISON: None. Patient is currently listed as EU critical. - - FINDINGS: - - Endotracheal tube is in standard position, terminating approximately 5.6 cm - from the carina. An enteric tube tip and side port are within the stomach. - Left internal jugular central venous catheter tip terminates at the confluence - of the brachiocephalic veins. Heart size is mildly enlarged. Mediastinal and - hilar contours are unremarkable. No pulmonary edema is demonstrated. No large - pleural effusion or pneumothorax is seen. Retrocardiac opacity may reflect - atelectasis but infection or aspiration cannot be excluded. No acutely - displaced fractures are seen. - - IMPRESSION: - - - - 1. Standard positioning of the endotracheal and enteric tubes. - 2. Left internal jugular central venous catheter tip at the confluence of the - brachiocephalic veins. - 3. Retrocardiac opacity may reflect atelectasis but infection or aspiration - cannot be excluded. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55946215.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55946215.txt deleted file mode 100644 index 5be3e828bd5d142ed1daa22533f395ff456ab46d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s55946215.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___ year old man with cardiogenic shock // Eval ETT, pulmonary - edema - - COMPARISON: Chest radiographs ___. - - IMPRESSION: - - Mild interstitial edema continues to improve. The previously airless left - lower lobe has partially cleared. Whether this is pneumonia or resolving - atelectasis is radiographically indeterminate. No appreciable pleural - effusion. - - Tip of the endotracheal tube at the thoracic inlet, 7 cm from the carina could - be advanced 2 cm for more secure seating. Left internal jugular line ends in - the upper SVC. Nasogastric tube passes into the stomach and out of view. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s59443693.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s59443693.txt deleted file mode 100644 index 5aef2ced4f3386b35c4d272c27a501531ae5e170..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12822417/s59443693.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with subq ICD // lead placement lead - placement - - COMPARISON: Conventional chest radiographs ___, most recently ___. - - IMPRESSION: - - New subcutaneous defibrillator projects over the heart to the right of midline - as high as the aortic knob. There is no pneumothorax mediastinal widening or - pleural effusion. Heart size is normal. Pulmonary vasculature is top-normal - size but there is no edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12839549/s53494661.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12839549/s53494661.txt deleted file mode 100644 index 9dd2f6a191ea9cdcd3dbb154bc0058b480679de6..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12839549/s53494661.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - CHEST, TWO VIEWS: ___. - - HISTORY: ___-year-old man with fevers, rigors and cough. Question pneumonia. - - FINDINGS: PA and lateral views of the chest. Comparison is made to previous - exam from earlier the same day and from ___. The lungs are clear of - focal consolidation, effusion or pulmonary vascular congestion. - Cardiomediastinal silhouette is within normal limits. Osseous and soft tissue - structures are unremarkable. - - IMPRESSION: No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12844682/s58386843.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12844682/s58386843.txt deleted file mode 100644 index 4e2722cd0ec0671a0c4a82eeadc2b65bd36371c1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12844682/s58386843.txt +++ /dev/null @@ -1,35 +0,0 @@ - WET READ: ___ ___ ___ 4:43 AM - 1. No pneumothorax. - - 2. Endotracheal tube ends 7.2 cm from the carina, and should be advanced for - more secure seating. - - 3. Bibasilar opacities consistent with aspiration in the setting of - intubation. - ______________________________________________________________________________ - FINAL REPORT - INDICATION: History: ___M with ICH and femur fracture after fall // trauma - film for pneumothorax - - TECHNIQUE: Portable supine chest x-ray. - - COMPARISON: CT torso dated ___. - - FINDINGS: - - There is asymmetrical elevation of the right hemidiaphragm. Bibasilar - opacities, more prominent on the right are consistent with - aspiration/atelectasis in the setting of intubation. The heart is enlarged. - No acute displaced rib fracture identified. Endotracheal tube ends 7.2 cm - from the carina. Nasogastric tube courses into the stomach in of the field of - view. No pneumothorax. - - IMPRESSION: - - 1. No pneumothorax. - - 2. Endotracheal tube ends 7.2 cm from the carina, and should be advanced for - more secure seating. - - 3. Bibasilar opacities consistent with aspiration in the setting of - intubation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s54036536.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s54036536.txt deleted file mode 100644 index 23b1cdd8fa91e1f84b803e663d7e743e4367aec9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s54036536.txt +++ /dev/null @@ -1,31 +0,0 @@ - WET READ: ___ ___ 8:15 AM - Unchanged areas of subsegmental atelectasis with mild vascular congestion but - no frank pulmonary edema. - WET READ VERSION #1 ___ ___ ___ 7:21 AM - Unchanged areas of subsegmental atelectasis without significant vascular - congestion or pulmonary edema. - ______________________________________________________________________________ - FINAL REPORT - INDICATION: ___F with progressive dyspnea, POD#___ s/p CABG w aortic valve - replacement, evaluate for pulmonary mid. - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Multiple prior chest radiographs dating back to ___. - - FINDINGS: - - A nodular opacity in the right mid lung is unchanged from prior studies, - likely representing stable atelectasis. Subsegmental atelectasis in the - peripheral left lung is also unchanged. There are small pleural effusions - bilaterally. Mild pulmonary vascular congestion is present without frank - pulmonary edema. There is no pneumothorax or focal consolidation. The - cardiomediastinal silhouette, including moderate cardiomegaly, is unchanged. - Median sternotomy wires, multiple mediastinal clips, and a prosthetic aortic - valve are noted. Chronic appearing left-sided rib fractures and severe - osteoarthritic changes of the right shoulder are stable. - - IMPRESSION: - - Unchanged areas of subsegmental atelectasis with mild vascular congestion but - no frank pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s59654172.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s59654172.txt deleted file mode 100644 index b1ec5dace78da2b46cac7db7ef88d98c73ab6fe3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12904315/s59654172.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with effusions // interval change in effusions - - COMPARISON: The comparison is made with prior studies including ___. - - IMPRESSION: - - There small bilateral pleural effusions present which are unchanged or - slightly larger than on the earlier study. There are stable compression - fractures in a mid and a lower thoracic vertebrae. Extensive degenerative - changes are present. There is probable osteopenia in the spine. There is no - pneumothorax or CHF. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s56523555.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s56523555.txt deleted file mode 100644 index ca7959e52e08729415c46a8080fbc0f3d1e5ad44..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s56523555.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male post intubation. - - COMPARISON: ___ at 5:36. - - CHEST, AP: Endotracheal tube has been placed, with tip 3.8 cm from the - carina. There is no significant pleural effusion or pneumothorax. Lung - volumes remain low, with mild right lower lobe atelectasis. The - cardiomediastinal and hilar contours are normal. Prominent air-filled stomach - is noted. - - IMPRESSION: Endotracheal tube in standard position. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s58473174.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s58473174.txt deleted file mode 100644 index 34934ef95c9e81c24fce86d979ecd76eca30205f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12930426/s58473174.txt +++ /dev/null @@ -1,7 +0,0 @@ - FINAL REPORT - CHEST ON ___. - - HISTORY: Dobbhoff tube placement. - - FINDINGS: NG tube tip is in the stomach. ET tube tip is 6.7 cm above the - carina. The lungs are clear without infiltrate or effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12957707/s59788377.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12957707/s59788377.txt deleted file mode 100644 index bcece3d2cfb942a8a609e5f8cccf0c11452e2a90..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p12/p12957707/s59788377.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: Dizziness. - - COMPARISON: ___. - - FINDINGS: - - Frontal and lateral views of the chest were obtained. The lungs are clear - without focal consolidation. No pleural effusion or pneumothorax is seen. - The cardiac silhouette is top normal. The aorta is calcified. Degenerative - changes are again seen along the spine, similar to prior. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13066324/s57263945.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13066324/s57263945.txt deleted file mode 100644 index 1e75bac2c24a68ebcbccd29560d5c5f3ba18705d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13066324/s57263945.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - HISTORY: Status post DHT placement. Evaluate position. - - CHEST, SINGLE AP PORTABLE VIEW. - - There is an apparent ___- or oro-gastric tube with radiopaque tip present. - The tube forms a haripin loop over the upper mediastinum and the tip overlies - the lower neck. - - There is mild cardiomegaly. There are bibasilar opacities with a small left - and possible small right effusion. Upper zone redistribution, without overt - CHF. Probable diffuse osteopenia. - - IMPRESSION: Tube with hairpin curve in upper mediastinum and with tip - overlying lower neck. Repositioning required. Please see report of - already-obtained subsequent film from 10:22 a.m. on the same day, - demonstrating that this has been addressed. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13122104/s59579116.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13122104/s59579116.txt deleted file mode 100644 index 913d9dbff81341c234f9ae0ee754b8a226fafb92..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13122104/s59579116.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with AICD firing for fib, elevated lactate, wet - // pulmonary edema, masses, infiltrates - - TECHNIQUE: Portable - - COMPARISON: ___ - - FINDINGS: - - Dual lead defibrillator with the tips in the right atrium and right ventricle - have not changed, given for differences in patient positioning. Low lung - volumes with minimal atelectasis, most pronounced in the right middle lobe. - Pulmonary vascular congestion has improved. No pulmonary edema. No pleural - effusions. Moderate cardiomegaly. - - IMPRESSION: - - Improved pulmonary vascular congestion. No acute consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s56952163.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s56952163.txt deleted file mode 100644 index 3ef33b9a0dd45e5c7d3288e448d0f8e8f102da07..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s56952163.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with immunosuppression, fever, hypoTN, - tachycardia*** WARNING *** Multiple patients with same last name! // ? PNA - - COMPARISON: Multiple prior radiographs most recent on ___ - - FINDINGS: - - A right-sided Port-A-Cath terminates in the mid SVC. Heart size is normal. - The mediastinal and hilar contours are normal. The pulmonary vasculature is - normal. Lungs are clear. No pleural effusion or pneumothorax is seen. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s57440490.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s57440490.txt deleted file mode 100644 index 4bdf280e6136f1589ea08d244817799e2f57ad78..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s57440490.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: PA and lateral views of the chest - - INDICATION: ___ year old man with burkitt's lymphoma, fever last night, r/o - infiltrates // r/o infiltrates - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ - - FINDINGS: - - Right-sided Port-A-Cath in the mid SVC. The nodular opacities throughout the - lungs have resolved. No new acute focal consolidation. The cardiomediastinal - silhouette is unremarkable. No pleural effusions or pneumothorax. - - IMPRESSION: - - No acute cardiopulmonary abnormality diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s59138461.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s59138461.txt deleted file mode 100644 index e5f8851c2b818ccfb1e11e413fc716885398ce02..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13336663/s59138461.txt +++ /dev/null @@ -1,28 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with respiratory failure // please assess for - interval change, pneumonia please assess for interval change, pneumonia - - COMPARISON: Prior chest radiographs since ___ most recently ___ - through ___. - - IMPRESSION: - - Scores of pulmonary nodules developed between ___ and ___, progressed, - accompanied by probable pulmonary edema on ___. Today both the nodules - and the edema are substantially improved. Differential diagnosis of the - nodular abnormality is unclear. It is decided early on characteristic for - edema alone, and in the absence of effective antibiotic treatment is unlikely - to be fungal infection or even bacterial septicemia. Widespread viral - infection is only slightly more likely to recede so quickly. Pulmonary - hemorrhage and transfusion related lung injury should be considered. - - Normal heart size has decreased from ___. There is no appreciable pleural - effusion. - - Right jugular infusion port ends in the upper SVC, left PIC line in the mid - SVC. - - NOTIFICATION: Dr. ___ reported the findings to Dr ___ by telephone on - ___ at 12:59 PM, 1 minutes after discovery of the findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13428588/s52911993.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13428588/s52911993.txt deleted file mode 100644 index b9fd9cd0fb9e17358952956b516e52400dc417ee..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13428588/s52911993.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___. - - COMPARISON: None. - - CLINICAL HISTORY: ___-year-old female with tachycardia and URI symptoms, - question pneumonia. - - FINDINGS: AP upright portable chest radiograph is obtained. The lung volumes - are low. There is perihilar mid and lower lung streaky opacity which could - represent atelectasis and/or atypical pneumonia. No effusion or pneumothorax. - Cardiomediastinal silhouette is normal. Bony structures are intact. - - IMPRESSION: Streaky lower lung opacities could represent an atypical - pneumonia or atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51019884.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51019884.txt deleted file mode 100644 index fe0f5cca604356c8f33afa2b34f4c1fb4df24deb..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51019884.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: ___F on levoquin for PNA now likely septic*** WARNING *** Multiple - patients with same last name! // ? worsening pneumonia - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: ___. - - FINDINGS: - - Low lung volumes seen particularly on the right which is likely in part - positional and due to scoliosis. There secondary crowding of the - bronchovascular markings without confluent consolidation worrisome for - pneumonia. Left lung is clear. The cardiomediastinal silhouette is stable. - No acute osseous abnormalities. PEG tube projects over the left upper - quadrant. - - IMPRESSION: - - No definite acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51260577.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51260577.txt deleted file mode 100644 index 1d7665a09257d7224e87dafa5817190eb8835b2f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s51260577.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___F with cough and low temp // eval for PNA - - TECHNIQUE: AP and lateral views the chest. - - COMPARISON: ___. - - FINDINGS: - - The lungs are clear without focal consolidation. Nodular opacities projecting - over the lungs bilaterally are compatible with nipple shadows. The - cardiomediastinal silhouette is within normal limits. There is marked - thoracolumbar scoliosis as on prior. G-tube projecting over the upper abdomen - on the lateral view. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s57246651.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s57246651.txt deleted file mode 100644 index fa45810a546d1c332b72d1be76ad5e205f363c37..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13551252/s57246651.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with CP, aspiration, with new hypoxia // - interval change - - TECHNIQUE: Portable - - FINDINGS: - - As compared to chest radiograph from the same day, low lung volumes. Central - opacities, slightly asymmetrically worse on the right, can be asymmetric edema - or pneumonia given the history of aspiration. Mild cardiomegaly. No pleural - effusions or pneumothorax. Severe S shaped scoliosis. - - IMPRESSION: - - Central asymmetric opacities can be asymmetric edema or right-sided aspiration - pneumonia with superimposed edema. This has slightly progressed. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50268332.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50268332.txt deleted file mode 100644 index 60a8576907d716ee8590b276c30defb4c511de8a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50268332.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - PORTABLE AP X-RAY - - INDICATION: Patient with SAH, rhonchorous on exam, evaluation for edema or - effusion. - - COMPARISON: ___. - - FINDINGS: - - Moderate pulmonary edema has worsened since prior exam with increased small - bilateral pleural effusions. Mediastinal and cardiac contours are unchanged. - NG tube is in the stomach. Bibasilar increased opacities i mostly compatible - with dependent edema, superimposed infection or aspiration cannot be excluded - in appropriate clinical settings. There is no pneumothorax. - - CONCLUSION: - - 1. Moderate pulmonary edema has worsened. Small bilateral pleural effusion - has also increased. - 2. Bibasilar opacities are probably compatible with dependent edema. - Superimposed infection or aspiration cannot be excluded in appropriate - clinical settings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50713027.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50713027.txt deleted file mode 100644 index 217dad272e3f0bc1932fb61adec896e18e48e613..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s50713027.txt +++ /dev/null @@ -1,17 +0,0 @@ - WET READ: ___ ___ 11:13 PM - Further improvement in pulmonary hemorrhage from ___. Minimal bibasilar - atelectasis. NG tube tip and side-hole project over the expected location of - the stomach. Extubated. - ______________________________________________________________________________ - FINAL REPORT - REASON FOR EXAMINATION: Subarachnoid hemorrhage, NG tube placement - assessment. - - AP radiograph of the chest was reviewed in comparison to ___. - - Heart size and mediastinum are stable in appearance. The NG tube tip is in - the stomach. Widespread parenchymal opacities are noted in the lung bases - that are in some areas improved and some progressed since the prior study and - there is interval resolution of right mid lung opacity. Overall, dynamic in - appearance are concerning for aspiration. No pneumothorax or pleural effusion - seen. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57081799.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57081799.txt deleted file mode 100644 index 416510c544c6c50abbad5b367238b2be455538d2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57081799.txt +++ /dev/null @@ -1,8 +0,0 @@ - FINAL REPORT - CHEST ON ___ - - HISTORY: Subarachnoid hemorrhage, question interval change. - - FINDINGS: The ET tube is 2.4 cm above the carina, slightly low. The - appearance of the lungs is unchanged. NG tube tip is in the stomach. Left - subclavian line tip is in the superior vena cava. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57222450.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57222450.txt deleted file mode 100644 index a3ee610cc2fa0e3253dcf92643d70e48a1b04132..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s57222450.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - PORTABLE CHEST RADIOGRAPH OF ___ - - COMPARISON: Study of one day earlier. - - FINDINGS: Indwelling support and monitoring devices are unchanged in - position, with endotracheal tube terminating about 2.3 cm above the carina - with the neck in a flexed position. Heterogeneous opacities persist in both - lungs with relative sparing of the left upper lobe. As compared to the recent - exam of one day earlier, there are worsening opacities in both lung bases as - well as the development of a small left pleural effusion. The etiology of - these findings is uncertain, but they are concerning for multifocal infection - in the appropriate clinical setting. Outside of the chest, note is made of - dense calcifications in the expected location of the right carotid artery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s58639715.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s58639715.txt deleted file mode 100644 index e7444389334fadc4d9bd1bc9bcb67efa251ba50a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s58639715.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old female with subarachnoid hemorrhage and respiratory - failure status post reintubation. - - COMPARISONS: Multiple prior chest radiographs, most recently of ___. - - FINDINGS: Single frontal view of the chest was obtained. A new endotracheal - tube terminates 3.5 cm above the carina. NG tube terminates below the - diaphragm. Cardiomediastinal contours are stable. Pulmonary edema has - improved since the prior exam. Residual left base opacity may represent - resolving edema or potentially infection. No pneumothorax. - - IMPRESSION: Status post reintubation with ETT in proper position. Pulmonary - edema has overall improved, but residual left base opacity may represent - resolving edema or potentially infection. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59650682.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59650682.txt deleted file mode 100644 index f396c1692113ab71986af3017cab4c877de8e1fe..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59650682.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___ - - COMPARISON: CTA chest from ___, also a chest radiograph from that same - date. - - CLINICAL HISTORY: Ruptured aneurysm, ET tube, assess position. - - FINDINGS: Supine portable AP view of the chest provided. 3 images provided - during serial retraction of the endotracheal tube. On the final image of the - series, endotracheal tube tip is well positioned 3.8 cm above the carina. An - orogastric tube extends into the left upper abdomen in the expected location - of the stomach. There is a 4.2 x 5.5 cm rounded opacity in the right upper - lung, new from prior exam, concerning for mass lesion though given that this - finding is new from prior exam, the possibility of infection or aspiration - cannot be excluded. Followup to resolution advised. Left basilar atelectasis - noted. No pneumothorax or pleural effusion. Cardiomediastinal silhouette is - normal. Bony structures are intact. - - IMPRESSION: Adequate position of the ET tube on the third image of the - series. NG tube positioned appropriately. Rounded opacity in the right upper - lung which is concerning for mass lesion versus infection/aspiration. - Followup to resolution is advised. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59691135.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59691135.txt deleted file mode 100644 index 2b7427b9e226d1941e2c1f43321a3451815d48ff..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13655979/s59691135.txt +++ /dev/null @@ -1,7 +0,0 @@ - FINAL REPORT - CHEST ON ___ - - HISTORY: Dobbhoff placement. - - FINDINGS: The Dobbhoff tube tip is in the stomach. ET tube, left subclavian - line are unchanged. The appearance of the lung is unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s50757865.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s50757865.txt deleted file mode 100644 index 394c14e3f566eebc9e667f5617e6c40bed06d778..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s50757865.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man s/p Whipple GJ tube ___ now w/ failure to thrive - // ? pulmonary edema - - TECHNIQUE: Portable AP semi-upright view of the chest - - COMPARISON: ___ - - FINDINGS: - - Port-A-Cath terminates in the lower SVC, unchanged. A single chamber - pacemaker is appropriately positioned. In comparison to the prior study, there - is increased diffuse bilateral hazy opacification with perihilar and lower - lung predominance, consistent with moderate asymmetric pulmonary edema. - Cardiomediastinal silhouette is stable. No large effusion or pneumothorax. - - IMPRESSION: - - Increased moderate diffuse pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54597893.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54597893.txt deleted file mode 100644 index ca914d8afbbcc2f747ee70c746a2ef54bb25d041..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54597893.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___ - - COMPARISON: ___ and chest CT from ___. - - CLINICAL HISTORY: Pancreatic cancer with liver metastasis, presenting with - fever and fatigue, question pneumonia. - - FINDINGS: Portable AP upright chest radiograph was provided. A Port-A-Cath - resides over the right chest wall with catheter tip extending to the region of - the mid SVC. An AICD is again seen over the left chest wall with lead - extending into the region of the right ventricle. Subtle opacity in the - medial right lung base likely reflects bronchovascular markings, though the - possibility of a subtle pneumonia is difficult to exclude without a lateral - view. Otherwise, the lungs are clear. No definite pleural effusion or - pneumothorax is seen. The cardiomediastinal silhouette appears normal. No - acute osseous abnormalities are seen. No free air below the right - hemidiaphragm. Calcification adjacent to the left humeral head is unchanged - from prior studies, likely reflective of chronic tendinopathy. - - IMPRESSION: Subtle opacity in the medial right lung base which could - represent pneumonia. Consider lateral view to confirm. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54711520.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54711520.txt deleted file mode 100644 index 1f5e9eac2c1760f1b9a9cfb5efc35de4a4572c1b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s54711520.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - STUDY: AP chest, ___. - - CLINICAL HISTORY: Patient with aspiration pneumonia. - - FINDINGS: Comparison is made to prior study from ___. - - There is a single-lead left AICD which is intact and unchanged. There are two - central venous catheters in the right, a PICC line and a Port-A-Cath. Distal - lead tips are projected over the distal SVC. Heart size is within normal - limits. There are again seen areas of consolidation within the lungs - bilaterally but more confluent at the bases. Findings can be seen with - pulmonary edema, although a superimposed infection is also possible. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s57179088.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s57179088.txt deleted file mode 100644 index b5dd87ba0f8c1a573d3c2707262bd461b1b99395..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s57179088.txt +++ /dev/null @@ -1,19 +0,0 @@ - WET READ: ___ ___ 10:18 PM - ET Tube in appropriate postion, terminating 6cm above carina. Pulmonary edema, - mildly increased in the bilateral lung bases since the prior study from 3 - hours earlier. - - WET READ VERSION #1 - ______________________________________________________________________________ - FINAL REPORT - STUDY: AP chest, ___ - - CLINICAL HISTORY: ___-year-old man post-op day 1 for Whipple's procedure. - Acute respiratory distress. - - FINDINGS: Comparison is made to previous study performed three hours earlier. - Endotracheal tube is in appropriate positioning terminating 6 cm above the - carina. There remains pulmonary edema and mild increase in the densities at - the bases. There is a left retrocardiac opacity. Heart size is within normal - limits. There is a left-sided Port-A-Cath with the distal lead tip in the - cavoatrial junction. There is a single-lead left pacemaker. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58461308.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58461308.txt deleted file mode 100644 index ed50b436f772428cb3280a808dcb14761eed262d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58461308.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___ year old man with respiratory failure // progression of - infiltrate - - COMPARISON: Chest radiographs ___ through ___ - - IMPRESSION: - - Endotracheal tube is been removed. Dense consolidation in the left lower lobe - unless severe right lower lobe consolidation or still present, as well as - likely small bilateral pleural effusion. Upper lungs are grossly clear. There - is no pneumothorax. Heart size top- normal. Nasogastric tube passes into the - stomach and out of view. Left trans subclavian pacer defibrillator lead - follows the expected course to the rib right ventricle. Right subclavian - infusion port ends in the right atrium. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58563171.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58563171.txt deleted file mode 100644 index 66fc023b7577847f843e98a7db4c49906ea52cff..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s58563171.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - AP CHEST, 9:49 A.M. - - HISTORY: ___-year-old man with shortness of breath. Possible pneumonia. - - IMPRESSION: AP chest compared to ___: - - Heart size is top normal, unchanged, and pulmonary vascular congestion - persists. New opacification at both lung bases could be a combination of - edema and atelectasis, though pneumonia is not excluded, particularly on the - left side. Subclavian line ends in the mid SVC, transvenous right ventricular - pacer defibrillator lead runs along the floor of the right ventricle. There - is no pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s59643339.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s59643339.txt deleted file mode 100644 index 38f9b0dd30ad0aca1c916a9d3799d2fde1707ba3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13724767/s59643339.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with respiratory failure. Evaluate interval - change - - TECHNIQUE: Portable semi-upright chest radiograph - - COMPARISON: In ___ and CT of the chest ___. - - FINDINGS: - - As seen on the prior chest CT and prior radiograph, there are layering - bilateral pleural effusions, moderate in size, with continued collapse of the - left and right lower lobe. The right chest wall port catheter, right internal - jugular central venous line, and endotracheal tubes are standard in position. - No new parenchymal opacity or pneumothorax. Stable cardiomegaly. - - IMPRESSION: - - Appropriate positioning of support lines and tubes. Moderate bilateral - pleural effusions with continued left lower lobe atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13748634/s51949631.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13748634/s51949631.txt deleted file mode 100644 index bbf6ebec967c3e51b642b5505d3439c0a6601567..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13748634/s51949631.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with chest pain, hemoptysis - - TECHNIQUE: Portable upright AP view of the chest - - COMPARISON: CT chest ___ at 14:26 - - FINDINGS: - - Study is slightly limited by patient rotation. Cardiac silhouette size is - mildly enlarged. While the mediastinal and hilar contours appear grossly - unremarkable, the previous chest CT did demonstrate prevascular - lymphadenopathy. Pulmonary vasculature is not engorged. Patchy opacity is - seen within the right lung base corresponding to the area of infarction seen - on the prior CT. Linear atelectasis seen within the left lung base. No - pleural effusion or pneumothorax is identified. No acute osseous abnormality - is visualized. - - IMPRESSION: - - Right basilar patchy opacity corresponding to an area of infarction seen on - recent CT. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13792998/s51298827.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13792998/s51298827.txt deleted file mode 100644 index 685eba1bd6e7cbb6b883d0c8ec4b5049782f5dee..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13792998/s51298827.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: COPD exacerbation, evaluation for endotracheal tube placement. - - COMPARISON: Outside hospital film from ___. - - FINDINGS: As compared to the previous radiograph, there is evidence of an - unchanged endotracheal tube, with the tip positioned 2.7 cm above the carina. - The course of the nasogastric tube is also unchanged. The tip is not clearly - visualized on the image but appears to project over the distal parts of the - stomach. There is unchanged moderate cardiomegaly with bilateral parenchymal - changes suggesting moderate pulmonary edema. Minimal blunting of the - costophrenic sinus could indicate a small left pleural effusion. Unchanged - mild left retrocardiac atelectasis. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s50941142.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s50941142.txt deleted file mode 100644 index 293a759d6bb9310c93f7e5cb56356917e6b5bce3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s50941142.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with AKA, now elevated white count // ? PNA - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the signs of right predominant - pulmonary edema and retrocardiac atelectasis as well as moderate cardiomegaly - are constant. No new parenchymal opacities. No pneumothorax. The monitoring - and support devices are in unchanged position. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s51892967.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s51892967.txt deleted file mode 100644 index 226f65fea6936b9e48111cc48cca34aa84d13b1d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s51892967.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with PVD with RLE ischemia // eval for - interval change - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: ___ - - IMPRESSION: - - Pulmonary edema has markedly improved. Cardiomegaly is a stable. Lines and - tubes are in standard position. Bibasilar atelectasis are larger on the left. - There is no pneumothorax or enlarging pleural effusions. There are no new - lung abnormalities. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s52578813.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s52578813.txt deleted file mode 100644 index 86756b23433e584a27bbfd3ff7d257c88f15ffec..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s52578813.txt +++ /dev/null @@ -1,20 +0,0 @@ - WET READ: ___ ___ ___ 8:04 AM - - - - No focal consolidations concerning for pneumonia identified. - WET READ VERSION #1 ___ ___ ___ 9:53 PM - No focal consolidations concerning for pneumonia identified. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman s/p AKA with sepsis // eval for infiltrate - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the left central access line was - removed. Normal appearance of the cardiac silhouette. No pulmonary edema. - No pneumonia, no pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s54719086.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s54719086.txt deleted file mode 100644 index 7260e560a6b04864e7878dd90a318189b8885e38..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s54719086.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - STUDY: AP chest ___. - - CLINICAL HISTORY: ___-year-old woman status post vascular surgery and - thrombectomy. Evaluate position of the endotracheal tube. - - FINDINGS: Comparison is made to prior radiographs from ___ and of - the CT scan performed on ___ at 11:35 a.m. - - There is an endotracheal tube whose tip is 5 cm above the carina. This could - be advanced 1 cm for more optimal placement. There is a left-sided IJ central - line whose distal tip is not well seen but appears to be within the - brachiocephalic vein. The heart size is within normal limits. There are very - low lung volumes causing crowding of the pulmonary vascular markings and - atelectasis at the lung bases. No overt pulmonary edema or pneumothoraces are - present. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s56089857.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s56089857.txt deleted file mode 100644 index 23fcf497f9a50c8533c761acad4cf76401e93649..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s56089857.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with poorly controlled PVD, obesity, +smoking, - s/p fail RLE thrombectomy with hypoxia // interval change - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ - - FINDINGS: - - The endotracheal tube remains in good position. The left internal jugular - line is also in good position. Perihilar opacities and indistinctness of the - pulmonary vasculature is mild interstitial edema. The left basal opacity and - pleural effusion are stable. Mild interval increase in the opacity in the - right lower lobe, can be worsening atelectasis/consolidation. No - pneumothorax. The cardio pericardial silhouette is stable. - - IMPRESSION: - - Mild interval increase in the opacity in the right lower lobe, can be - worsening atelectasis/consolidation. Stable left basal opacity small pleural - effusion. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59658712.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59658712.txt deleted file mode 100644 index d0b9fe8c1930208518233585815bdc150110587e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59658712.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ yo with aka and ett // Pleural effusion vs Pna? Pleural - effusion vs Pna? - - IMPRESSION: - - In comparison with the study of ___, there again are low lung volumes, - which accentuate the enlargement of the cardiac silhouette. Indistinctness of - pulmonary vessels is consistent with elevated pulmonary venous pressure. At - the left base, there is opacification silhouetting the hemidiaphragm, - consistent with volume loss in the left lower lobe and probable small - effusion. - - Monitoring and support devices are essentially unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59810560.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59810560.txt deleted file mode 100644 index 8fb0a11ea3fd45a9548135dd19217fd4cc121bdf..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13833101/s59810560.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___F s/p intubation after AKA // eval for interval change - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous image, no relevant change is seen. The perihilar - right-sided opacity and the left lower lobe atelectasis are constant. - Moderate cardiomegaly. Unchanged monitoring and support devices. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s53598009.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s53598009.txt deleted file mode 100644 index 1f5ce6ddf7d7b2ca1e0e50bb99dafeb845c79ff4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s53598009.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with plasma cell leukemia // Interval change - - TECHNIQUE: Portable AP chest radiograph. - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Lung volumes are unchanged compared to the prior study. The cardiomediastinal - contour is within normal limits. Visualization of the lung bases is - suboptimal due to overlapping soft tissue structures, however there appears to - be increased opacity with partial silhouetting of the left heart border - suspicious for lingular consolidation. A right-sided PICC terminates in the - mid SVC. - - IMPRESSION: - - Assessment of lung bases is somewhat limited due to the overlapping soft - tissues, nonetheless increased opacity at the left lung base is suspicious for - lingular consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s57035688.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s57035688.txt deleted file mode 100644 index fe0e9d5b0ec3549ef4fafa88ac5dc0614c6aa3b1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s57035688.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiograph - - INDICATION: ___ year old man with tachycardia, fever, concern for PE, refusing - CT r/o PE // Eval for pneumonia. - - TECHNIQUE: Portable AP upright chest radiograph. - - COMPARISON: Chest radiograph dated ___. - - FINDINGS: - - The right Port-A-Cath tip projects over the expected region of the mid to - upper SVC, unchanged. No significant interval change from the prior exam. - Cardiomediastinal silhouette is unchanged. There is central pulmonary - vascular prominence, unchanged. No pneumothorax, effusion, or edema. - - IMPRESSION: - - No significant interval change. This exam is not diagnostic for pulmonary - embolus and does not exclude the presence of pulmonary embolus. If there is - high concern, a Chest CTA or nuclear imaging study is recommended. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s59154544.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s59154544.txt deleted file mode 100644 index bc63121ca244a6dac0140e8936b5c8ff32ba13ef..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13880645/s59154544.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with multiple myeloma and new onset pain, - tachycardia, increasing temp // ? PNA ? PNA - - COMPARISON: Chest radiographs since ___ most recently ___. - - Or - - IMPRESSION: - - Lungs are fully expanded and essentially clear. Heart size is top-normal. - There is no obvious pleural abnormality. Pulmonary vasculature is minimally - engorged but there is no edema. Right PIC line ends in the upper SVC. - - RECOMMENDATION(S): Conventional chest radiographs if diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s50671771.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s50671771.txt deleted file mode 100644 index ca2fceedd998c2a23e6bf522631559c8fdfafe9e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s50671771.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with cord compression and desat while intubated - // Assess for new pathology given desating while intubated - - TECHNIQUE: CHEST (PORTABLE AP) - - COMPARISON: ___ obtained at 08:51 - - IMPRESSION: - - ET tube tip is 6.5 cm above the carinal. Left internal jugular line tip is at - the level of left subclavian ___ brachycephalic vein. The mediastinal - lymphadenopathy, right hilar mass and consolidation are better appreciated on - the CT torso obtained the same day later. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s54765161.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s54765161.txt deleted file mode 100644 index 161e6d92cf644e93ab74f12ec09fc36fcd301829..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s54765161.txt +++ /dev/null @@ -1,40 +0,0 @@ - WET READ: ___ ___ 9:28 AM - 1. Left internal jugular central venous line ends at the confluence of the - left brachiocephalic vein and SVC. - - 2. Stable right infrahilar opacity which remains concerning for malignancy - and/or pneumonia. - - 3. Mild pulmonary interstitial edema. - - ______________________________________________________________________________ - FINAL REPORT - INDICATION: History: ___F with hypotension s/p CVL // Eval LIJ line placement - - TECHNIQUE: Portable chest x-ray. - - COMPARISON: Chest radiographs dated ___ and ___, and CT - of the torso dated ___, performed after this study. - - FINDINGS: - - Portable semi-upright radiograph of the chest demonstrates persistent opacity - in the right infrahilar region silhouetting the right hilus and right heart - border, unchanged from the prior study. This is better assessed on CT of the - torso performed after the study, and is consistent with a large right hilar - mass. Streaky opacities at the right lung base appears slightly improved on - this study, and again may represent atelectasis. There is mild pulmonary - vascular congestion and interstitial edema. Mediastinal contours remain - prominent. The cardiac silhouette is incompletely evaluated. No pneumothorax - or pleural effusion. Left internal jugular central venous line ends at the - confluence of the left brachiocephalic vein and SVC. Endotracheal tube ends - 4.3 cm from the carina. - - IMPRESSION: - - 1. Left internal jugular central venous line ends at the confluence of the - left brachiocephalic vein and SVC. - - 2. Stable right infrahilar opacity consistent with infiltrative mass. - - 3. Mild pulmonary interstitial edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s57314708.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s57314708.txt deleted file mode 100644 index b5e56b1b2569d8a2a2a7712a72180abc5f880587..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13925079/s57314708.txt +++ /dev/null @@ -1,36 +0,0 @@ - WET READ: ___ ___ ___ 3:52 AM - - 1. ETT terminating 6 cm above the carina. - 2. Right infrahilar opacity for malignancy and/or pneumonia. - 3. Mild pulmonary interstitial edema. - - - - - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with intubation // eval tube placement eval - tube placement - - TECHNIQUE: Frontal view of the chest was obtained. - - COMPARISON: Outside chest radiograph dated ___. - - FINDINGS: - - The endotracheal tube terminates at the level of the thoracic inlet - approximately 6 cm above the carina. There is a U rounded opacity in the right - infrahilar region silhouetting the right hilus and right heart border. There - is mild pulmonary vascular congestion and interstitial edema. Streaky - opacities at the right lung base may reflect atelectasis. No large pleural - effusion or pneumothorax is seen. The mediastinal contours are prominent, - likely due in part to unfolding of the thoracic aorta. The cardiac silhouette - is incompletely evaluated. - - IMPRESSION: - - 1. ETT terminating 6 cm above the carina. - 2. Right infrahilar opacity for malignancy and/or pneumonia. - 3. Mild pulmonary interstitial edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s50746229.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s50746229.txt deleted file mode 100644 index e7e3ed8ee7e6e53dddfb1837f74fd1400467c361..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s50746229.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old man s/p CABG // eval for effusion eval for - effusion - - IMPRESSION: - - In comparison with the study ___ ___, the right IJ catheter is been - removed. The hemidiaphragms are more sharply seen and the hazy opacification - at the bases is no longer present. Although this may reflect some improvement - in pleural effusions and atelectatic changes, much of the difference in - appearance may be a manifestation of the erect position of the patient. Mild - elevation of the left hemidiaphragm is seen with atelectatic changes at the - base. - No evidence of acute pneumonia or vascular congestion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s52103524.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s52103524.txt deleted file mode 100644 index 3249403bdfb970c06604356b53f41cef1e78a598..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s52103524.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with cabg // r/o ptx, s/p ct d/c - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: ___. - - IMPRESSION: - - Large right and moderate left pleural effusions with adjacent atelectasis are - grossly unchanged. Mediastinal widening has improved. Cardiac size cannot be - evaluated. Right IJ catheter tip is in the lower SVC. Radiolucencies - projecting in the left base suggests the presence of pneumothorax. The - sternal wires are aligned. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s59820109.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s59820109.txt deleted file mode 100644 index 789e126841ef2496f9cf35b051cb8b3a77b9d27e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p13/p13976104/s59820109.txt +++ /dev/null @@ -1,33 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiograph - - INDICATION: ___ year old man s/p cabg w/post-op bleeding // assess for - hemothorax - - TECHNIQUE: Portable chest radiograph - - COMPARISON: Prior chest radiograph from ___, ___, ___. - - FINDINGS: - - Patient is status post CABG. Low lung volumes persist. An ETT is seen 3.3 cm - above the carina. An NG tube is seen coiling in the fundus. A right IJ - catheter seen with the tip in unchanged position. A left pleural drain is - stable. - - There is mildly increased appearance of a widened mediastinum, which may all - be postsurgical, but an enlarging hematoma cannot be excluded. Moderate - bilateral atelectasis and small to moderate bilateral pleural effusions are - stable. - - IMPRESSION: - - There is interval increased appearance of mediastinal widening, which may all - be postsurgical but enlarging hematoma cannot be excluded. - - RECOMMENDATION(S): If clinical concern, a CT Chest can be obtained for - further evaluation. - - NOTIFICATION: The findings were discussed with ___, M.D. by ___ - ___, M.D. on the telephone on ___ at 5:20 PM, 30 minutes after discovery - of the findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s51871687.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s51871687.txt deleted file mode 100644 index 244541cca6582d822e1f9b1ed76c6c8e5f9054f7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s51871687.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - HISTORY: Fever, cough, chest pain, question pneumonia, intrapulmonary - process. - - CHEST, SINGLE AP PORTABLE VIEW. - - COMPARISON: Chest x-ray from ___ at 11:14 a.m. - - Heart size is at the upper limits of normal. The azygos vein appears - prominent, measuring ___.5 mm. This could reflect magnification on this - portable view; however, the azygous vein does appear more prominent than on - the ___ CXR. There is borderline upper zone redistribution, but no overt - CHF. Minimal bibasilar atelectasis. No effusion. There is some increased - retrocardiac density, consistent with left lower lobe collapse and/or - consolidation. Incidental note is made of a subchondral cyst in the right - humeral head. - - IMPRESSION: - 1. Increased retrocardiac density, consistent with left lower lobe collapse - and/or consolidation, which appears more pronounced than on the prior film. - If clinically indicated, lateral view could help to assess for a pneumonic - infiltrate in this location. - 2. Mild prominence of the azygos vein, though this is likely accentuated by - magnification. - 3. Bibasilar linear atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s56370927.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s56370927.txt deleted file mode 100644 index 1cca955c0871636d02ce279ffc31639127eb5816..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14047359/s56370927.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___ year old man with hep C, left leg myositis, new crackles. // - volume status? - - COMPARISON: Chest radiographs ___ - - IMPRESSION: - - Mild interstitial pulmonary edema has worsened since ___. . Top- normal - heart size has not changed. Engorgement of pulmonary upper lobe and - mediastinal vessels is unchanged. Small right pleural effusion has increased. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14112540/s52450944.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14112540/s52450944.txt deleted file mode 100644 index 9e41f694a88b59851ea8745706ea0959e92bd7e8..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14112540/s52450944.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with respiratory insufficiency // interval - change interval change - - IMPRESSION: - - Comparison to ___. Low lung volumes. Borderline size of the cardiac - silhouette. Atelectasis at the left lung bases. No pulmonary edema. No - larger pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s52424260.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s52424260.txt deleted file mode 100644 index 56f48bf9497179e580233a6a205d37e0ec634104..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s52424260.txt +++ /dev/null @@ -1,8 +0,0 @@ - FINAL REPORT - REASON FOR EXAMINATION: Evaluation of the patient after intubation. - - Portable AP radiograph of the chest was reviewed in comparison to ___ obtained at 11:48 p.m. - - The ET tube tip is 6 cm above the carina. Heart size and mediastinum are - unremarkable. Lungs are essentially clear. The NG tube has been pulled out. - No pleural effusion or pneumothorax is seen. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s57935589.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s57935589.txt deleted file mode 100644 index ce67d22a845ce7b8ee5d5258aac60ab19e3e26be..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14148161/s57935589.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male with respiratory compromise. - - COMPARISON: Chest radiograph from ___. - - ONE VIEW OF THE CHEST: - - The lungs are low in volume but clear. The cardiomediastinal silhouette, - hilar contours and pleural surfaces are normal. No pleural effusion or - pneumothorax is present. An ET tube is positioned 6 cm above the carina and - by 2-3 cm for optimal position. An NG tube is located within the esophagus - and should be pushed in by at least ___-20 cm for optimal position. - - IMPRESSION: - - ET tube is 6 cm above the carina and should be pushed in by 2-3 cm for optimal - position. The NG tube is within the esophagus and should be pushed in about - ___-20 cm for optimal position. - - These findings were communicated via telephone to ___, M.D. via - telephone at 12:50 a.m. on ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14256117/s56473110.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14256117/s56473110.txt deleted file mode 100644 index 4c8e4e551098349e17e56ce5c7b5f03e6fa97bac..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14256117/s56473110.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with MM on chemo, p/w fevers, chills // eval - for pneumonia - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: None. - - FINDINGS: - - Relatively low lung volumes are noted accentuating the interstitial markings. - The lungs are clear of confluent consolidation or large effusion. The - cardiomediastinal silhouette is within normal limits. No acute osseous - abnormalities identified. - - IMPRESSION: - - No definite acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s50192862.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s50192862.txt deleted file mode 100644 index 571744d3ce352e0155ba9ac7e26737716595adce..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s50192862.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: Ms. ___ is a ___ year-old female with a history of roux-en-y - gastric bypass ___ c/b marginal ulcerations, ETOH abuse, new cirrhosis, and - bulimia who initially presented to with bulimia and depression admitted to - inpatient psychiatry. Transferred to ICU for septic shock and acute onset - abdominal pain // evaluate for interval change of pleural effusions - evaluate for interval change of pleural effusions - - IMPRESSION: - - Compared to chest radiographs ___ through ___. - - Large right pleural effusion and secondary atelectasis right lower lobe, - unchanged. Mediastinal venous distension and pulmonary vascular engorgement - have worsened, moderate cardiomegaly probably unchanged. No pneumothorax. - - Right jugular line ends in the low SVC. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s51976124.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s51976124.txt deleted file mode 100644 index 8babd7932b73cd67bdadabb908371c930523a11a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s51976124.txt +++ /dev/null @@ -1,48 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old woman with R pleural effusion, suspected alcoholic - hepatitis // evaluate for presence of pneumonia - - COMPARISON: Chest x-ray from ___ at 05:01 - - FINDINGS: - - Compared to earlier the same day, I doubt significant interval change. - - Again seen is a moderate to moderately large right pleural effusion. There is - likely underlying collapse and/or consolidation, although the level of the - diaphragm is obscured. A small amount of fluid is again seen extending into - the minor fissure. - - Heart size is at the upper limits of normal. The cardiomediastinal silhouette - remains midline. The left lung and the upper right lung remain grossly clear. - No CHF or left-sided effusion. - - A small, somewhat rounded density is noted along the lower edge of the left - anterior fourth rib adjacent to the chest wall, not fully characterized --? - question due to something outside the patient. - - Minimal wedging of the presumptive T10 and ___ vertebral bodies, slight - accentuation of kyphosis at T10-___ is again noted, unchanged. - - IMPRESSION: - - Moderate to moderately large right base effusion, unchanged , with underlying - right base collapse and/or consolidation. The right hemidiaphragm itself is - obscured. - - Heart size at the upper limits of normal. - - No CHF, left effusion, or other focal opacity. The left lung remains well - expanded. - - Small (approximately 8.6 mm), rounded density adjacent to the left chest wall - in the mid zone -- question something outside the patient. Attention to this - area on followup films is requested. If clinically indicated, oblique views - of the chest may help for further characterization. - - - RECOMMENDATION(S): Oblique views of the chest may help for further - characterization of the small rounded opacity adjacent to the mid left chest - wall. Please see comment above. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s56086035.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s56086035.txt deleted file mode 100644 index 2fd45544a239d7a1e9675ca6c78c89952b69799a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14410216/s56086035.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: History: ___F with RUQ abd pain, cirrhosis // pleural effusion? - - TECHNIQUE: Chest PA and lateral - - COMPARISON: CT abdomen pelvis dated ___ - - FINDINGS: - - There is a large right pleural effusion with associated underlying collapse - and/or consolidation. Heart size at the upper limits of normal. The left - lung is clear. The upper portion of the right lung is clear. No left pleural - effusion. No pneumothorax - - IMPRESSION: - - Moderate to moderately large right pleural effusion, with underlying collapse - and/or consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14463777/s53255233.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14463777/s53255233.txt deleted file mode 100644 index 7841d4e3cb28af2754dd460191d99e8183f6d77a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14463777/s53255233.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - HISTORY: Weakness and fatigue. - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - There is mild left base atelectasis. No focal consolidation or large pleural - effusion is seen. There is no pneumothorax. The cardiac and mediastinal - silhouettes are stable and unremarkable. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14537002/s52415121.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14537002/s52415121.txt deleted file mode 100644 index e78bd189a5106805e231c89e868af1203b6d6932..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14537002/s52415121.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH PERFORMED ON ___ - - Comparison with an outside hospital chest radiograph from same date earlier - today. - - CLINICAL HISTORY: GI bleed, assess for position of the NG tube. - - FINDINGS: Single portable AP view of the chest was provided. The tip of the - NG tube resides in the left upper quadrant. The lungs are clear. - Cardiomediastinal silhouette is normal with atherosclerotic calcifications - again noted at the aortic knob. Bony structures are intact. The lungs are - hyperinflated with upper lobe lucency and splaying of bronchovasculature - suggesting underlying emphysema. - - IMPRESSION: NG tube positioned appropriately. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s50261148.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s50261148.txt deleted file mode 100644 index c47057e631ffa432ee8ba6891fcebcafc3df9dd9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s50261148.txt +++ /dev/null @@ -1,8 +0,0 @@ - FINAL REPORT - HISTORY: Effusions. - - FINDINGS: In comparison with the study of ___, there are slightly improved - lung volumes. Elevation of the left hemidiaphragm is again seen with - atelectatic changes at the base. No definite vascular congestion at this - time. The tip of the PICC line is difficult to see, though it appears to - extend to the cavoatrial junction or slightly below it. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s53070729.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s53070729.txt deleted file mode 100644 index 4b093fbbf4fd4d8d17925c0473890608e442a833..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s53070729.txt +++ /dev/null @@ -1,12 +0,0 @@ - WET READ: ___ ___ ___ 11:42 PM - no evidence of acute cardiopulmonary process. elevated left hemidiaphragm. - status/post median sternotomy. - ______________________________________________________________________________ - FINAL REPORT - HISTORY: Preoperative. - - FINDINGS: No previous images. Intact midline sternal wires in a patient with - low lung volumes and elevation of the left hemidiaphragm. The lordotic - position may account for the mild prominence of the cardiac silhouette. No - evidence of acute focal pneumonia or vascular congestion. Blunted left - costophrenic angle is seen. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s54611215.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s54611215.txt deleted file mode 100644 index 40b2409fe00ea1f33aee97920f7aad33eccedfb9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s54611215.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - PA AND LATERAL CHEST, ___ - - HISTORY: ___-year-old man readmitted after AVR with shortness of breath. - - IMPRESSION: PA and lateral chest compared to ___. Elevation - of the left hemidiaphragm is less pronounced, but there is still combination - of small left pleural effusion and mild left basal atelectasis. Also - unchanged is small right pleural effusion. Cardiomediastinal silhouette has a - normal postoperative appearance. Drainage catheter projecting over the mid - chest on the frontal view, on the lateral is localized to the chest wall. - Left PIC line, as before ends close to or just beyond the superior cavoatrial - junction. There is no pneumothorax or pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s57142064.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s57142064.txt deleted file mode 100644 index 6e02c7f8a6631d687a98899bb6fe03f9dd68fbc2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14610274/s57142064.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - PA AND LATERAL CHEST X-RAY - - INDICATION: Patient with right-sided chest pain, evaluation for effusion and - infection. - - COMPARISON: Multiple chest x-rays from ___ to ___. - - FINDINGS: The patient had recent redo of sternotomy for aortic valve repair. - - Right lower lung atelectasis has completely resolved. Left residual basal - atelectatic bands are unchanged. There are no new lung consolidations. - Moderate mediastinal and cardiac contours widening is unchanged. The sternal - wires are also in the same position. Left elevation of hemidiaphragm is - chronic and was already present prior to the redo. There is no pneumothorax - and no pleural effusion. - - CONCLUSION: There are no acute cardiopulmonary findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s50697654.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s50697654.txt deleted file mode 100644 index d3bc7111317e85f71cf92108a62377bbb6c10312..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s50697654.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: History: ___M with -free air ___ dudodenal ulcer // To confirm NG - tube - - COMPARISON: ___ at 10:59. - - FINDINGS: - - Portable frontal semi supine radiograph of the chest and upper abdomen - demonstrates an NG tube ending within the stomach. There is otherwise no - significant change from 1 hour prior with stable appearance of the - cardiomediastinal silhouette. The left costophrenic angle is excluded from - this image. No large pleural effusion or pneumothorax. - - IMPRESSION: - - NG tube ending in the stomach. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s58514117.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s58514117.txt deleted file mode 100644 index df3961c10640dc4d28ed9f2091b6d7f15af72236..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14661031/s58514117.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - HISTORY: Right-sided chest pain and vomiting. - - COMPARISONS: None. - - TECHNIQUE: Chest, portable AP upright. - - FINDINGS: The heart appears mildly enlarged. The mediastinal and hilar - contours appear within normal limits. There is no pleural effusion or - pneumothorax. The lungs appear clear. - - IMPRESSION: No evidence of acute cardiopulmonary disease. Borderline - cardiomegaly. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14771014/s55718349.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14771014/s55718349.txt deleted file mode 100644 index 88899c062305f0b2c9c123090be3b8aeffd61614..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14771014/s55718349.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p primary repair of marginal ulcer perforation - with pleural effusions on CT ___, SOB // monitor pleural effusions, r/o - pulmonary edema monitor pleural effusions, r/o pulmonary edema - - IMPRESSION: - - Compared to chest radiographs ___ through ___. - - Previous small pleural effusions are demonstrated by chest CTA on ___, - but difficult to appreciate on chest radiographs. They may still be present, - but there has been improvement on the right, along with in decreasing right - basal atelectasis. Lungs are otherwise clear. Normal cardiomediastinal and - hilar silhouettes. No pneumothorax. - - Right PIC line ends in the low SVC. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14862629/s58745940.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14862629/s58745940.txt deleted file mode 100644 index 212788efb39e758514cdd9dabe65509a909531ff..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14862629/s58745940.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old female with cough and fever, here to evaluate for - pneumonia. - - COMPARISON: No prior studies available. - - FINDINGS: Frontal and lateral radiographs of the chest show small bilateral - pleural effusions. The lungs are otherwise clear without focal consolidation - or pneumothorax. The pulmonary vasculature is not engorged. The cardiac - silhouette is normal in size. The mediastinal and hilar contours are within - normal limits. Mild bilateral apical pleural thickening is incidentally - noted. - - IMPRESSION: Small bilateral pleural effusions. No evidence of pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14881769/s50046286.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14881769/s50046286.txt deleted file mode 100644 index 825a8e9d569fc641716bbedecdf2a9df996ea809..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14881769/s50046286.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p ex-lap with perforated jejunum, intubated for - AMS and hypoxic respiratory failure // please assess for interval change - please assess for interval change - - IMPRESSION: - - In comparison with the study of ___, the monitoring and support devices - are unchanged. Cardiac silhouette remains within normal limits and there is - minimal elevation of pulmonary venous pressure. - The medial portion of the right hemidiaphragm is now silhouetted with - retrocardiac opacification consistent with increasing volume loss in the left - lower lobe. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14932781/s52910153.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14932781/s52910153.txt deleted file mode 100644 index 1c192da06a89e14c195279a51c2f58a947bd55ad..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14932781/s52910153.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - HISTORY: Shortness of breath and cough. - - TECHNIQUE: PA and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - The patient is status post median sternotomy and CABG. The cardiac silhouette - size is top normal, unchanged. The mediastinal and hilar contours are stable. - Lung volumes are slightly decreased compared to the prior exam, causing mild - crowding of the bronchovascular structures. No pulmonary edema is present. - Minimal streaky opacities are seen within both lung bases, likely atelectasis. - There is no focal consolidation, pleural effusion or pneumothorax. Old - right-sided rib fracture is again noted. There are mild degenerative changes - in the thoracic spine. - - IMPRESSION: - - Mild bibasilar atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s51075332.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s51075332.txt deleted file mode 100644 index a0c724cc928a86d797ebdbfbbeec2fb27a583c5b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s51075332.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - HISTORY: Acute shortness of breath and desaturation. - - COMPARISON: None. - - FINDINGS: - - AP portable upright chest radiograph was obtained. The left lung is - relatively well expanded. Increased opacity of the right lower lung is likely - a combination of small to moderate size pleural effusion and consolidation. - Minimal retrocardiac opacity may also be present. There is no pneumothorax or - left pleural effusion. The cardiomediastinal contours and heart size are - unremarkable. - - IMPRESSION: - - Small to moderate right pleural effusion with accompanying consolidative - opacity. Given the respiratory therapy note in the ED dashboard describing - copious secretions, aspiration could be considered; however a right lower lobe - pneumonia is an alternate consideration. Minimal left basilar opacity could - reflect multifocality of disease. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s54786700.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s54786700.txt deleted file mode 100644 index d7362d8d2df652109a5db133b93027848496782e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s54786700.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - AP CHEST, 8:08 A.M., ___ - - HISTORY: A ___-year-old woman with fever, rule out an acute process. - - IMPRESSION: AP chest compared to ___, 4:53 a.m.: - - Over the course of less than four hours, the pulmonary circulation has grown - somewhat more engorged in the left lung, with the major changes in the right - lung where there is new heterogeneous opacification in the mid and lower lung - zones. Appearance is similar to ___ in the right lung, when the left - lung showed mild edema. I suspect most of the abnormality in the right - hemithorax is due to atelectasis and unilateral edema in a patient who - probably lies in a right decubitus position. This would of course make her - prone to aspirate to the right lung as well. - - Left internal jugular line ends in the mid SVC. Heart size is top normal. - Pleural effusion if any is small on the right. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s57331710.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s57331710.txt deleted file mode 100644 index d1cc947d0b1e1c22a46bb1c76b14ad54edb8eb09..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p14/p14972735/s57331710.txt +++ /dev/null @@ -1,19 +0,0 @@ - WET READ: ___ ___ ___ 7:40 PM - worsening bilateral opacities, particulrally in the right upper lobe, - concerning for multifocal pnuemonia that is worsning. -___ d/w dr ___ - - ______________________________________________________________________________ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: No pneumonia and chronic heart failure, evaluation for interval - change. - - COMPARISON: ___. - - FINDINGS: As compared to the previous examination, there is mild progression - with regard to extent and severity of the pre-existing multifocal parenchymal - opacities. In addition, increasing blunting of the right costophrenic sinus - is noted, potentially indicative of a small right pleural effusion. Unchanged - retrocardiac atelectasis and borderline size of the cardiac silhouette. No - pneumothorax. Unchanged position of the left internal jugular vein catheter. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15179275/s53961145.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15179275/s53961145.txt deleted file mode 100644 index 51750387241547d7e957e594303dc26fec1aad7f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15179275/s53961145.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: ___-year-old male with history of fall, back pain. - - COMPARISON: ___. - - FINDINGS: Frontal and lateral views of the chest were obtained. There is - mild lingular and left base linear atelectasis. No focal consolidation, - pleural effusion, or evidence of pneumothorax is seen. Again seen is diffuse - right posterior ribs and the right coracoid process deformity chronic, grossly - stable. The cardiac and mediastinal silhouettes are stable with top normal to - mildly enlarged. Mediastinal and hilar contours are stable. There is no - displaced fracture seen. - - IMPRESSION: No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50162073.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50162073.txt deleted file mode 100644 index 05d6eb9b2870bdda4754761f33797eb6a2c9ae94..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50162073.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with HCV cirrhosis on harvoni p/w hypotension and - anasarca found to have LLE cellulitis. Currently tachypneic to ___ after nebs, - ___% on 3L. // pulm edema? - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the diffuse bilateral parenchymal - opacities have minimally decreased in extent and severity. The lung volumes - remain low. The right PICC line is in unchanged position. Mild cardiomegaly. - No larger pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50523471.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50523471.txt deleted file mode 100644 index 4821ac0ed3c2344af10f4ded3ca4e79ebba44694..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50523471.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___M with hypotension, please r/o infection // Eval for PNA - - TECHNIQUE: PA and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - There are new small bilateral pleural effusions and findings suggesting - pulmonary vascular congestion. There is no confluent consolidation. Linear - opacity in the right midlung is most suggestive of atelectasis. The - cardiomediastinal silhouette is within normal limits. No acute osseous - abnormalities. - - IMPRESSION: - - New small bilateral pleural effusions. No focal consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50615824.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50615824.txt deleted file mode 100644 index 71245072959c989e9f58d4b3280d281287e41dcb..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50615824.txt +++ /dev/null @@ -1,33 +0,0 @@ - WET READ: ___ ___ ___ 8:50 AM - - - - Mild pulmonary edema is unchanged since prior radiograph from earlier this - morning. Monitoring and support devices are unchanged in position. - WET READ VERSION #1 ___ ___ ___ 10:24 PM - Mild pulmonary edema is unchanged since prior radiograph from earlier this - morning. Monitoring and support devices are unchanged in position. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with hx of SBO s/p repair, hx of pulmonary edema, - would like reassessment for possible extubation // assess for evidence of - volume overload or consolidation; pre extubation film assess for evidence - of volume overload or consolidation; pre - - COMPARISON: Comparison to ___ at 05:06 - - FINDINGS: - - Portable semi-erect chest film ___ at 17 41 is submitted. - - IMPRESSION: - - Endotracheal tube has its tip 4 cm above the carina. A feeding tube is seen - coursing below the diaphragm with the tip not identified. Right internal - jugular central line unchanged with its tip in the distal SVC near the - cavoatrial junction. Cardiac and mediastinal contours are unchanged. Lung - volumes are slightly lower resulting in crowding of the vasculature. Overall, - the mild edema is improving. Probable layering right effusion. No - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50778344.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50778344.txt deleted file mode 100644 index 9a1e6d49d8bc5c23d44ed69ed7e4b64479969b1f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s50778344.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with hep c cirrhosis // prior cxr concerning for - fluid overload, guidance on diuresis - - TECHNIQUE: Portable semi-upright chest radiograph. - - COMPARISON: Chest radiograph dated ___. - - FINDINGS: - - There is an NG tube which courses below the diaphragm, however the tip is not - visualized on this image. There is a right IJ with the tip in the cavoatrial - junction. - - The bilateral perihilar airspace opacities appear unchanged. Heart size is - stable. The mediastinal and hilar contours are stable. No pleural effusion - or pneumothorax is seen. There are no acute osseous abnormalities. - - IMPRESSION: - - 1. Appropriate positioning of NG tube and right IJ. - 2. Unchanged bilateral perihilar airspace opacities, likely reflecting - pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s56762387.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s56762387.txt deleted file mode 100644 index 1d1022b2090688c876a1922c97e2fc944e5f4516..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s56762387.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with encephalopathy and DOE // cardiopulmonary - process - - TECHNIQUE: Chest AP - - FINDINGS: - - The tip of the NG tube is in the body of the stomach and the first port in the - fundus, this could be advanced 4 cm. There is a right IJ with the tip in the - cavoatrial junction. - - The mild interstitial edema, slightly more asymmetric on the right, has not - significantly changed. Heart size is stable. The mediastinal and hilar - contours are stable. No pleural effusion - or pneumothorax is seen. There are no acute osseous abnormalities. - - IMPRESSION: - - The mild interstitial edema, slightly more asymmetric on the right, has not - significantly changed. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57049661.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57049661.txt deleted file mode 100644 index 5efeccca01ca32f1b53e73d8b1fc5c3622c646b1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57049661.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p ngt placement // eval positioning - - TECHNIQUE: Portable AP chest radiograph. - - COMPARISON: Multiple prior chest radiographs most recent dated ___ - - FINDINGS: - - A nasogastric tube is in-situ, the tip is in the left upper quadrant. A right - internal jugular catheter is in-situ, the tip is in the distal SVC. Lung - volumes remain low, unchanged compared to the prior study. Left basilar - atelectasis versus consolidation is also unchanged. Between the projection - and the low lung volumes, it is difficult to evaluate the heart size however - it is grossly unchanged compared to the prior study. Probable small left - pleural effusion. - - IMPRESSION: - - No significant interval change when compared to the prior study. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57803724.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57803724.txt deleted file mode 100644 index 8cc99c643ab9632d1ff30ac12df77d6aa54684ac..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s57803724.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man, intubated // cardiopulmomary process - cardiopulmomary process - - COMPARISON: Comparison to ___ 01:11 - - FINDINGS: - - Portable semi-erect chest film ___ 05:07 is submitted. - - IMPRESSION: - - Endotracheal tube, feeding tube, nasogastric tube and right internal jugular - central line are unchanged in position. A catheter is also seen overlying the - right upper quadrant. There is residual mild perihilar edema with a layering - right effusion. No pneumothorax is appreciated. Overall cardiac and - mediastinal contours are stably enlarged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s58357962.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s58357962.txt deleted file mode 100644 index 7a9404adc72aeb4b10cdfe76e275d5637e4f6778..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15353817/s58357962.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - INDICATION: Mr. ___ is a ___ y/o male with a history of HCV genotype 1a - cirrhosis being treated with Harvoni (started ___), who was referred in - from___ clinic for hypotension and anasarca found to have LLE - cellulitis. // improvement of pulmonary edema? infection? - - COMPARISON: Compared to radiographs from ___ - - IMPRESSION: - - The right-sided central line is unchanged in position. There is improved - aeration since the prior study. The multifocal opacities have decreased. - There remains areas of increased density at the lung bases. There is no overt - pulmonary edema or large pleural effusions. There are no pneumothoraces. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15427942/s57578130.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15427942/s57578130.txt deleted file mode 100644 index 71afae3533eb4dc223cbdc395a010f9498e4f106..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15427942/s57578130.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - HISTORY: 2 weeks of worsening chest pain. - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - 6 mm rounded calcified right upper lobe granuloma is stable. No focal - consolidation, large pleural effusion, or evidence of pneumothorax is seen. - The cardiac silhouette is top-normal. Mediastinal contours are stable and - unremarkable. Is no pulmonary edema. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15486932/s52967497.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15486932/s52967497.txt deleted file mode 100644 index 0d49149cd9de8ed003c21e9fd128941d54b7cb44..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15486932/s52967497.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with s/p MVA injury, s/p Humerus fx repair // - elevated hemidiaphragm? any lung pathology from MVA? elevated - hemidiaphragm? any lung pathology from MVA? - - IMPRESSION: - - No previous images. The tip of the endotracheal tube measures approximately 5 - cm above the carina. Low lung volumes accentuate the transverse diameter of - the heart as well as the mediastinum. Some of the mediastinal widening may - reflect the size of the patient. There is increased opacification on the - right marginated by the minor fissure. This could represent posttraumatic - pulmonary hemorrhage or aspiration or infectious process. There is some - engorgement of pulmonary vessels that could reflect over-hydration. - Retrocardiac opacification most likely is an indication of volume loss in left - lower lobe. No evidence of pneumothorax. - Although the widening of the mediastinum to be normal in this patient, if - there is any clinical sign of mediastinal hemorrhage, CT would be mandatory. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51412263.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51412263.txt deleted file mode 100644 index 833b2ebd586b9aba4a48715c00f3a847a4c8d085..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51412263.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___M with AMS // evaluate for acute process - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: ___. - - FINDINGS: - - Exam is limited secondary to portable technique and overlying soft tissues. - Hazy bibasilar opacities may be in part to projectional and in part due to - overlying soft tissues although superimposed effusions are entirely possible. - Bilateral parenchymal opacities have likely progressed and are suggestive of - edema. Right PICC is identified however tip cannot be clearly delineated. - - IMPRESSION: - - Limited exam with progression of pulmonary edema and possible bilateral - effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51688181.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51688181.txt deleted file mode 100644 index 391b4e6af8e43613d9f91650fd3ad086fd43800b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s51688181.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man s/p MVC w/ multiple rib fxs bilterally, pulmonary - contusion // interval change - - TECHNIQUE: Portable - - COMPARISON: ___ - - FINDINGS: - - Interval worsening of the mild interstitial edema and pulmonary vascular - engorgement. Multiple deformed rib fractures are seen on the right. The - cardiopericardial silhouette is compare above. No pneumothorax. - - IMPRESSION: - - Interval worsening of the interstitial pulmonary edema and pulmonary vascular - congestion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s52067228.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s52067228.txt deleted file mode 100644 index 47fe3500f9aa8578c17885d5a27973b67880f2b9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s52067228.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man intubated with resp failure, new o2 sat drop // - eval for interval changes eval for interval changes - - IMPRESSION: - - In comparison with the study of ___, the monitoring and support - devices are unchanged. Continued enlargement of the cardiac silhouette with - pulmonary vascular congestion and bilateral layering effusions with - compressive basilar atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s53339269.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s53339269.txt deleted file mode 100644 index 1a161e7606b924c7bfdafe5831d3810743258c9b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s53339269.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with acute renal failure, now more tachpneic. // - Tachypnea, concern for volume overload - - IMPRESSION: - - Since a recent radiograph of 3 days earlier, cardiomediastinal contours are - stable, with persistent pulmonary vascular congestion accompanied by - interstitial edema and right pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s54360181.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s54360181.txt deleted file mode 100644 index 7956bfe0473dcb13a4fe98225616a14d5558995c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s54360181.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man s/p MVC w/ polytrauma, rib fractures with - increasing oxygen requirement // interval change from admission - - EXAMINATION: CHEST (PORTABLE AP) - - TECHNIQUE: Portable Chest radiograph, chest radiograph - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Lung volume is low. Moderate pulmonary edema is increased. Mediastinum - appears wider compared to 1 day prior, probably due to technical reasons. - Right mid lung pulmonary contusion and adjacent right rib fractures are - similar to prior. No new focal opacity is identified in the lungs. - - IMPRESSION: - - 1. Moderate pulmonary edema is worse compared to 1 day prior. - 2. Right mid lung pulmonary contusion and adjacent right rib fractures are - similar to prior. - 3. Widened mediastinum is probably due to patient's rotated position. - - NOTIFICATION: The findings regarding the widened mediastinum discussed by Dr. - ___ with RN for the patient on the telephone on ___ at 10:50 AM, 10 - minutes after discovery of the findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s55550913.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s55550913.txt deleted file mode 100644 index fd39c3d3276fa790dcca7cef0e246a570d3858bf..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s55550913.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with attempted left subclavian central line - placement // eval for interval development pneumothorax eval for - interval development pneumothorax - - IMPRESSION: - - In comparison with the study of earlier in this date, there is no evidence of - pneumothorax following the attempted placement of a left subclavian central - line. - Little change in the appearance of the heart and lungs. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s58494927.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s58494927.txt deleted file mode 100644 index 0b86d1fcfe141dfbf1d1e4ecd7bc867131dc313b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s58494927.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with multipel rib fractures and pulm contusion - // please eval - - EXAMINATION: CHEST (PORTABLE AP) - - TECHNIQUE: Portable Chest radiograph, frontal view - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Again seen is a right mid lung pulmonary contusion and multiple right rib - fractures. Mildly enlarged cardiac silhouette is unchanged. There is no - pneumothorax or large pleural effusion. - - IMPRESSION: - - No notable interval change. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s59204544.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s59204544.txt deleted file mode 100644 index 826a52d0e686fae300eb6180c9f5497404752ef1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15526304/s59204544.txt +++ /dev/null @@ -1,23 +0,0 @@ - WET READ: ___ ___ ___ 6:12 PM - The endotracheal tube terminates in the mid to upper thoracic trachea. A - right PICC is unchanged in position. A nasoenteric tube extends below the - diaphragm and off the inferior edge of the image. The remainder of the exam - appears similar to prior exam, with severe cardiomegaly, large bilateral - pleural effusions, and right greater than left bilateral opacities. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with respiratory failure // ET tube placement - - TECHNIQUE: CHEST (PORTABLE AP) - - COMPARISON: ___ obtained at 11:01 - - IMPRESSION: - - The endotracheal tube terminates in the mid to upper thoracic trachea. A right - PICC is unchanged in position. A nasoenteric tube extends below the diaphragm - and off the inferior edge of the image. The remainder of the exam appears - similar to prior exam, with severe cardiomegaly, large bilateral pleural - effusions, and right greater than left bilateral opacities. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s50373892.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s50373892.txt deleted file mode 100644 index 06b0579d9817b14c97fa3f1a464c96444591371d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s50373892.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: History: ___M with abdominal pain, difficulty breathing, history - of pancreatitis - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ - - FINDINGS: - - Heart size is normal. Mediastinal and hilar contours are unchanged with - unfolding of the thoracic aorta again demonstrated. Lungs are clear and the - pulmonary vasculature is normal. No pleural effusion or pneumothorax is - present. No acute osseous abnormalities seen. Several clips are noted within - the anterior left upper quadrant of the abdomen. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s52336362.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s52336362.txt deleted file mode 100644 index 13fb76fc3e3aa3277b385f088dbcb9f2f58a247f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s52336362.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - HISTORY: A ___-year-old man with fever. - - COMPARISON: Exam is compared to ___. - - FINDINGS: - - Lung fields are wall inflated and clear. - - There is no pleural fluid or pneumothorax. - - The heart size is top normal and enlarged since last CXR. - - There are aorta profile is slightly elongated, but normal. - - IMPRESSION: - - Slight enlargement of cardiac silhouette, if clinically correlated, cardiology - consultation is recommended. Dr ___, ___ ___ been paged by Dr ___. - to report chest findings at 4.___ pm. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s56507718.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s56507718.txt deleted file mode 100644 index ebadb8fdeadb5912ef7d1bb222fa58720df91b64..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s56507718.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - HISTORY: Chest pain. Question acute process. - - COMPARISON: Prior chest radiograph from ___. - - TECHNIQUE: PA and lateral chest radiographs. - - FINDINGS: - - There is tortuosity of the ascending aorta. The cardiomediastinal and hilar - contours are otherwise within normal limits. Lungs are hyperexpanded. There is - no focal consolidation, pleural effusion or pneumothorax. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57183880.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57183880.txt deleted file mode 100644 index 535af3f9b64f0399e16326474dd24c89bd6e5f67..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57183880.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: - Chest: Frontal and lateral views - - INDICATION: History: ___M with failure to thrive and weight loss, history of - smoking // Evaluate for mass - - TECHNIQUE: Chest: Frontal and Lateral - - COMPARISON: None. - - FINDINGS: - - The lungs are clear without focal consolidation. The lungs are relatively - hyperinflated, suggesting underlying chronic obstructive pulmonary disease. - No pleural effusion or pneumothorax is seen. The cardiac and mediastinal - silhouettes are unremarkable. - - IMPRESSION: - - No acute cardiopulmonary process. If high clinical concern for pulmonary - lesion, chest CT is more sensitive in detecting subtle lesions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57285784.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57285784.txt deleted file mode 100644 index 589558396a566cb000e5ad622450ab89a7446b5e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57285784.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (AP AND LAT) - - INDICATION: History: ___M with brown sputum and dyspnea on exertion - - TECHNIQUE: Upright AP and lateral views of the chest - - COMPARISON: ___ chest radiograph and CT torso - - FINDINGS: - - Heart size is normal. The aorta is mildly unfolded. Lungs are clear and - pulmonary vasculature is normal. Hilar contours are normal. No pleural - effusion or pneumothorax is visualized. No acute osseous abnormalities - detected. Clips are seen projecting over the gastroesophageal junction. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57506301.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57506301.txt deleted file mode 100644 index 2db071a1ef311eea70b84a202436076d490191ee..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s57506301.txt +++ /dev/null @@ -1,18 +0,0 @@ - WET READ: ___ ___ ___ 5:20 PM - New left mid and lower lung opacities consistent with aspiration pneumonia - given history. - - WET READ VERSION #1 - ______________________________________________________________________________ - FINAL REPORT - AP CHEST, P.M., ___ - - HISTORY: ___-year-old man with acute-on-chronic pancreatitis and likely - aspiration. Is there pneumonia? - - IMPRESSION: AP chest compared to ___: - - Extensive consolidation in the left lower lung, involving both upper and lower - lobes is new, consistent with aspiration pneumonia. Right lung clear. Heart - size normal. No appreciable pleural effusion. Right PIC line ends in the mid - SVC. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s58843035.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s58843035.txt deleted file mode 100644 index 782b81e52f314ba6158ac9ca0cc3db7d917bd710..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15528228/s58843035.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - PORTABLE CHEST FILM ON ___ AT 3:05 - - CLINICAL INDICATION: ___-year-old with a feeding tube placement, check - position. - - Comparison is made to the patient's prior study of ___. - - An AP portable upright image of the chest and upper abdomen is submitted dated - ___ at 3:05 a.m. - - IMPRESSION: - - There has been interval placement of a feeding tube, which descends beneath - the diaphragm and appears to have its tip in the proximal jejunum. There - continues to be an area of consolidation in the left mid to lower lung which - has somewhat improved in aeration suggestive of resolving pneumonia. Right - lung remains clear. No pulmonary edema or pneumothorax. No layering - effusions. There has been interval removal of the right PICC line. Overall - cardiac and mediastinal contours are stable. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15570850/s58490514.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15570850/s58490514.txt deleted file mode 100644 index 73440a9c1b757beae2b1cd6b46c72a72d2d29802..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15570850/s58490514.txt +++ /dev/null @@ -1,24 +0,0 @@ - WET READ: ___ ___ ___ 12:40 PM - Endotracheal tube tip 1.0 cm from the carina. - ______________________________________________________________________________ - FINAL REPORT - INDICATION: ___F with intubation // ?tube placement - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: None. - - FINDINGS: - - Endotracheal tube tip is 1 cm from the carina. Enteric tube seen with tip at - the gastric fundus. - - Streaky bibasilar opacities are noted, right greater than left. Superiorly, - lungs are clear. Cardiomediastinal silhouette is within normal limits. No - acute osseous abnormalities. - - IMPRESSION: - - Endotracheal tube tip 1.0 cm from the carina. - Bibasilar opacities, potentially atelectasis noting that infection or - aspiration are possible. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15611926/s58783952.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15611926/s58783952.txt deleted file mode 100644 index b3318e8b24e924cf907a281c226d4477b47b3c1a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15611926/s58783952.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man I D, vac change for R hip. preop CXR // preop - CXR Surg: ___ (vac change, I D) - - FINDINGS: - - Right-sided PICC line with the tip in the low SVC. Previously seen left - retrocardiac opacity has improved. The lungs are mildly hyperinflated with - emphysema. No pulmonary edema. No pleural effusions or pneumothorax. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15621159/s59292546.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15621159/s59292546.txt deleted file mode 100644 index d906cc3fec4a2df9969a333c1a92b24864c26854..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15621159/s59292546.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - INDICATION: ___M with malaise // eval infiltrate - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - The lungs are otherwise . Cardiomediastinal silhouette is stable, tortuosity - of the descending thoracic aorta again noted. No acute osseous abnormalities - are seen. Surgical clips are seen in the upper abdomen. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s53268948.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s53268948.txt deleted file mode 100644 index 91548fc2e5cb2b49b1c07721ffe69d297563ea90..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s53268948.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiographs. - - INDICATION: Shortness of breath and chest pain. - - COMPARISON: ___. - - TECHNIQUE: Chest, PA and lateral. - - FINDINGS: - - The heart is normal in size. The mediastinal and hilar contours appear within - normal limits. The lungs appear clear. There no pleural effusions or - pneumothorax. - - IMPRESSION: - - No evidence of acute disease. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s54366556.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s54366556.txt deleted file mode 100644 index 4d696030ac7d8a6b1c4df5a8a482c46fb1ee1255..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15649581/s54366556.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST RADIOGRAPHS - - INDICATION: Chest pain. - - TECHNIQUE: Chest, PA and lateral. - - COMPARISON: ___. - - FINDINGS: - - The heart is normal in size. The mediastinal and hilar contours appear - stable. There is no pleural effusion or pneumothorax. The lungs appear - clear. There has been no definite change. - - IMPRESSION: - - No evidence of acute cardiopulmonary disease. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s56149313.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s56149313.txt deleted file mode 100644 index 00ad9aa8016db34928ce47fb6b2eb08cdfe60ef1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s56149313.txt +++ /dev/null @@ -1,26 +0,0 @@ - WET READ: ___ ___ ___ 6:51 AM - No acute cardiopulmonary process. No pneumonia or pleural effusion. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: Chest radiograph - - INDICATION: ___-year-old female with upper abdominal and lower thoracic pain. - Assess for possible pleural effusion or left lower lobe pneumonia. - - COMPARISON: Chest radiograph ___, ___, ___. - - FINDINGS: - - Frontal lateral chest radiographdemonstrates a left-sided pacemaker with - intact single lead terminating in the right ventricle. - - The lungs are well expanded. Linear scarring in the right upper lobe with - apparent associated bronchiectasis appears unchanged Mild right upper lobe - atelectasis is noted. No pleural effusion or pneumothorax. Heart size, - mediastinal contour, and hila are unremarkable. - - Limited assessment of the upper abdomen is within normal limits. - - IMPRESSION: - - No acute cardiopulmonary process. No pneumonia or pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s58313672.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s58313672.txt deleted file mode 100644 index 27800c68924d3762238613d155e9cf3dded2ef0c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s58313672.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with cough, sputum production, and - leukocytosis. // Eval for pneumonia. - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: ___ - - IMPRESSION: - - Increasing opacities in the right base could represent atelectasis but - superimposed infection cannot be excluded. There are low lung volumes. Cardiac - size is normal. There is no pneumothorax or effusion. Right IJ catheter tip is - in the cavoatrial junction diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59238409.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59238409.txt deleted file mode 100644 index ea04d02d52ef0c0e13522eaf1b30d8dd8318e321..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59238409.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: - Chest: Frontal and lateral views - - INDICATION: History: ___F with +reproducible cp. +abd pain with n/v. +cough. - Low grade fevers. // ? PNA - - TECHNIQUE: Chest: Frontal and Lateral - - COMPARISON: ___ - - FINDINGS: - - The lungs are clear without focal consolidation. No pleural effusion or - pneumothorax is seen. The cardiac and mediastinal silhouettes are - unremarkable. Single lead left-sided AICD is stable in position. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59583630.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59583630.txt deleted file mode 100644 index 586588896fac42b2ebca06d3eda2b966fc98e196..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15650925/s59583630.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old woman with recent pancreatitis, decreased breath - sounds R base // eval for effusion eval for effusion - - IMPRESSION: - - In comparison with the study of ___, the patient has taken a much - better inspiration and there is no evidence of acute cardiopulmonary disease. - No pneumonia, vascular congestion, or pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15655083/s59443706.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15655083/s59443706.txt deleted file mode 100644 index 211cda251c10db4add7d84cd5862dcffe167e16e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15655083/s59443706.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___M with intubated xfer // eval ETT placement - - TECHNIQUE: Single portable view of the chest. - - COMPARISON: None. - - FINDINGS: - - Endotracheal tube tip is 4.0 cm from the carina. Enteric tube passes below - the field of view and tip projects over the gastric fundus. There may be - small left pleural effusion. There is no confluent consolidation. - Cardiomediastinal silhouette is within normal limits. Atherosclerotic - calcifications seen at the aortic arch. No acute osseous abnormalities. - - IMPRESSION: - - Support lines and tubes in appropriate position. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s51285311.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s51285311.txt deleted file mode 100644 index e3ea1cbc6ca03b93551a252d5844b6d82f66c653..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s51285311.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with chest tube in place // Evolution of - pneumothorax Evolution of pneumothorax - - COMPARISON: Prior chest radiographs ___ through ___ at 04:48. - - IMPRESSION: - - No detectable left pneumothorax, pigtail pleural drainage catheter unchanged - in position. Consolidation at the base of the left lung has worsened since - ___, conceivably atelectasis, but now raising some concern for - pneumonia. Right lung is grossly clear. Heart size is normal. Left pleural - thickening persists,, at the site of several left lateral and anterolateral - rib fractures, perhaps loculated hemothorax, but there is no appreciable - pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s55470878.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s55470878.txt deleted file mode 100644 index 253c279fe3cd2614bbcf211350a694044b0e0a79..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s55470878.txt +++ /dev/null @@ -1,26 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___M s/p single vehicle MCC, helmeted; no LOC; +scalp lac s/p - staple closure, L post rib fx, small PTX // Interval assesment - - TECHNIQUE: Chest PA and lateral - - COMPARISON: CT chest dated ___. - - FINDINGS: - - There is a moderate-sized left pneumothorax with an overlying mid clavicular - fracture and a fracture of the posterior third rib, visualized on the prior - CT. There is a localized hematoma of the left lateral chest wall. There are - linear opacities at the right lung base. There is a more confluent - opacification at the left lung base. Small left pleural effusion. Heart size - is normal. The mediastinal and hilar contours are normal. The pulmonary - vasculature is normal. - - IMPRESSION: - - 1. Moderate left apical pneumothorax, lateral left extrapleural hematoma, and - small dependent left pleural effusion. - 2. Confluent opacity at left lung base, which could represent pulmonary - contusion or aspiration in the appropriate clinical setting. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s56774317.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s56774317.txt deleted file mode 100644 index 1a87e7601faf0532b1e41ebb333e48de24261703..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15662081/s56774317.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with L pneumothorax, now s/p chest tube placement - // chest tube placement chest tube placement - - IMPRESSION: - - In comparison with the earlier study of this date, there has been placement of - a pigtail catheter on the left with resolution of the pneumothorax. Left - basilar opacification again is consistent with atelectasis and possible small - he fusion. The right lung is essentially - In the left clavicular fracture is again seen, though the localized hematoma - of the left lateral chest wall it is less prominent given the change in - patient obliquity. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15696371/s51136547.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15696371/s51136547.txt deleted file mode 100644 index 59e2284f52360c9a9c32b5736c02bf7ba32ef88d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15696371/s51136547.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with shortness of breath// eval for pulmonary edema - - TECHNIQUE: Upright AP view of the chest - - COMPARISON: None. - - FINDINGS: - - Cardiac silhouette size is mildly enlarged. The mediastinal and hilar - contours are unremarkable. Mild pulmonary vascular congestion is demonstrated - with patchy atelectasis in the lung bases. No pleural effusion or - pneumothorax is noted. There are no acute osseous abnormalities. - - IMPRESSION: - - Mild pulmonary vascular congestion and bibasilar atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15717895/s59085602.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15717895/s59085602.txt deleted file mode 100644 index 3dbb7613e202fdecaa00b0a6ce106578e7974646..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15717895/s59085602.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: History: ___M with cough, fever - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Cardiac silhouette size appears mildly enlarged but unchanged. - Atherosclerotic calcifications are noted at the aortic knob. Mediastinal and - hilar contours are similar. Pulmonary vasculature is not engorged. - Interstitial opacities are noted within the lung bases, more so on the right, - which could reflect atelectasis and scarring. No focal consolidation, pleural - effusion or pneumothorax is present. Chronic left-sided rib deformities are - re- demonstrated. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s54104047.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s54104047.txt deleted file mode 100644 index 63d3ae3d54601fb19bc3d6b6836e1607a25e2110..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s54104047.txt +++ /dev/null @@ -1,26 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with neutropenia and laryngitis. Evaluate for - pneumonia. - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiographs from ___ and ___. - - FINDINGS: - - There is no significant change in previously seen left lower lobe atelectasis. - Otherwise, the lungs are clear. Heart size is mildly enlarged.Mediastinal and - hilar contours are unchanged from ___, though significantly decreased - since ___. There is no evidence for pulmonary edema, pleural - effusion, or pneumothorax. There is persistent elevation of the left - diaphragm with left lung volume loss. There has been interval removal of the - right-sided PICC. - - IMPRESSION: - - No pulmonary consolidation concerning for pneumonia. Persistent left lower - lobe atelectasis. - - NOTIFICATION: The findings were discussed by Dr. ___ with Dr. - ___ on the ___ ___ at 1:15 PM, 5 minutes after discovery - of the findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s56330437.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s56330437.txt deleted file mode 100644 index f8f9f71366dab3315216d1c6341e2094f45fbd94..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15790605/s56330437.txt +++ /dev/null @@ -1,23 +0,0 @@ - WET READ: ___ ___ ___ 6:56 PM - - -Stable cardiomediastinal silhouettes, reflective of known mediastinal mass. - Stable elevation of left hemidiaphragm with a gastric air bubble. - -Left basilar atelectasis is similar in appearance. - -Right-sided PICC line is in unchanged position, with tip projecting over the - cavoatrial junction. - -No focal lung consolidation. No pneumothorax or pleural effusion. No - evidence of pulmonary vascular congestion or pulmonary edema. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with mediastinal mass, initiated EPOCH - chemotherapy, new hypoxia. // eval for interval change, ? volume overload - eval for interval change, ? volume overload - - IMPRESSION: - - Comparison to ___. No relevant change. Right PICC line is in - correct position. Moderate cardiomegaly. Substantial elevation of the left - hemidiaphragm with reduction of left hemithoracic volume. The appearance of - the left mediastinal mass is constant. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57385530.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57385530.txt deleted file mode 100644 index 4c19b2c179a2cfe7b65bc8c6a88e2c07cbba743f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57385530.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - HISTORY: Hypotension. - - COMPARISONS: ___. - - TECHNIQUE: Chest, AP upright portable. - - FINDINGS: The cardiac, mediastinal and hilar contours appear unchanged. The - lungs appear clear. There are no pleural effusions or pneumothorax. - - IMPRESSION: No evidence of acute disease. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57730086.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57730086.txt deleted file mode 100644 index d566e7c3beb4527de6b14e8b3e3cc065c52115fa..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s57730086.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male with syncope. - - COMPARISON: ___, ___. - - TECHNIQUE: Frontal and lateral chest radiographs were obtained. - - FINDINGS: No focal consolidation, pleural effusion, pneumothorax, or - pulmonary edema is detected. Nodule over the left lower lung most compatible - with nipple shadow also seen in ___. Heart and mediastinal contours are - within normal limits. The aorta is tortuous. Multilevel loss of disc space - height is seen in the lower thoracic and upper lumbar spine, incompletely - imaged. - - IMPRESSION: No radiographic evidence for acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s58774518.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s58774518.txt deleted file mode 100644 index dfabc1f80794598e315bd97c29b9170e8a818754..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15808118/s58774518.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - HISTORY: Syncope, question pneumonia. - - COMPARISON: ___. - - FINDINGS: - - Normal heart, lungs, mediastinum, hila and pleural surfaces. - - IMPRESSION: - - Normal chest radiograph. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15833469/s57883509.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15833469/s57883509.txt deleted file mode 100644 index beab43f8d7d71b1bd3d541da4825d53176ba407c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15833469/s57883509.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (AP AND LAT) - - INDICATION: History: ___F with spastic MS with cough and weakness - - TECHNIQUE: Upright AP and lateral views of the chest - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Heart size is mildly enlarged. The mediastinal and hilar contours are - unremarkable. The pulmonary vasculature is not engorged. Lung volumes are - slightly low. Patchy atelectasis is demonstrated in the right lung base. No - focal consolidation, pleural effusion or pneumothorax is present. No acute - osseous abnormalities seen. Mildly distended loops of colon are noted in the - left upper abdomen. - - IMPRESSION: - - Slightly low lung volumes with mild right basilar atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15845271/s52861334.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15845271/s52861334.txt deleted file mode 100644 index 4a8fb31d132c647f4e209cec29973413d16ed7d6..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p15/p15845271/s52861334.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: Left anterior chest pain. - - COMPARISON: ___. - - FINDINGS: Lungs are clear without focal consolidation. No pleural effusion - or pneumothorax is seen. The cardiac and mediastinal silhouettes are stable - and unremarkable. No displaced fracture is identified. - - IMPRESSION: No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16015533/s59937280.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16015533/s59937280.txt deleted file mode 100644 index 30f9743d86ab6ae8c781ce862b01c1827083fcef..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16015533/s59937280.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old man with cough // evaluate for pneumonia, effusion, - or pulmonary edema evaluate for pneumonia, effusion, or pulmonary edema - - COMPARISON: The only prior chest radiograph available was performed on - ___. Study is read in conjunction with an abdomen CT showing the - lower chest, performed on ___. . - - IMPRESSION: - - Small right pleural effusion is stable. There may be a small region of new - right infrahilar consolidation either atelectasis or aspiration. Heart size is - normal. There is no pulmonary edema and no pneumothorax. The abdomen CT - scans shows a hiatus hernia with large mediastinal varices. Clinical - correlation advised. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s50993229.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s50993229.txt deleted file mode 100644 index 9ca9ad5db55cba9056f9889305058c9420effb33..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s50993229.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with recent transport, cuff leak of ET tube // - placement of ET tube - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: - Study performed 9 hours earlier - - IMPRESSION: - - ET tube tip is 1.5 cm below the Carina, unchanged from prior study. There are - no other interval changes - - FINDINGS: - - IMPRESSION: diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s58616577.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s58616577.txt deleted file mode 100644 index fb218395c23e3b8fd0806325a44b81c61309be5f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16097925/s58616577.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - STUDY: AP chest, ___. - - CLINICAL HISTORY: ___-year-old woman with alcoholic hepatitis. - - FINDINGS: Comparison is made to prior study from ___. - - Endotracheal tube, feeding tube and PICC line are unchanged in position. The - tip of the PICC line is in the right atrium. This could be pulled back at - least 5 cm for more optimal placement. The heart size is enlarged but stable. - There is atelectasis at the right base. There are very low lung volumes with - elevation of the right hemidiaphragm. There is a left retrocardiac opacity - and small bilateral pleural effusions. No pneumothoraces are seen on either - side. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16132343/s55231622.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16132343/s55231622.txt deleted file mode 100644 index d564a131d25ebe1a1ed19dfe7b74c30f55a3c37b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16132343/s55231622.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - INDICATION: Dobbhoff tube placement. - - COMPARISON: Chest radiograph from ___. - - TECHNIQUE: Frontal chest radiograph. - - FINDINGS: - - A Dobbhoff tube terminates within the gastric antrum or pylorus. A left-sided - PICC terminates at the cavoatrial junction. There is no pneumothorax or focal - consolidation. The heart size is exaggerated by low lung volumes. - - IMPRESSION: - - Dobbhoff terminating within the stomach antrum or pylorus. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16178416/s57134082.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16178416/s57134082.txt deleted file mode 100644 index 4ea3a559631e7f5800c8fdfdf59df431c7f925ad..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16178416/s57134082.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (AP AND LATERAL) - - INDICATION: History: ___F with COPD, CHF presents with atrial fibrillation - with rapid ventricular rate in PCP ___ // ?volume overload - - TECHNIQUE: Upright AP and lateral views of the chest - - COMPARISON: None. - - FINDINGS: - - Tracheostomy tube is in standard position, terminating approximately 5.4 cm - from the carina. Lung volumes are low. Moderate to severe enlargement of the - cardiac silhouette is demonstrated. The mediastinal contours are unremarkable. - Mild pulmonary vascular congestion is demonstrated with vascular - indistinctness and cephalization of vasculature. Retrocardiac opacity may - reflect atelectasis. No large pleural effusion or pneumothorax is present - however the left costophrenic angle is excluded from the field of view. - Multilevel moderate degenerative changes are seen in the thoracic spine. There - are no acute osseous abnormalities. - - IMPRESSION: - - Moderate to severe cardiomegaly with mild pulmonary vascular congestion. - Retrocardiac opacity may reflect atelectasis, but infection is not excluded. - Followup radiographs after diuresis are recommended. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s50591205.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s50591205.txt deleted file mode 100644 index c3fbb7421b0a399d3cb540c297c58acf1c76e633..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s50591205.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with EtOH cirrhosis, now with secondary - peritonitis from recent colectomy, now with tachypnea // Evidence of - pulmonary edema or pleural effusions Evidence of pulmonary edema or - pleural effusions - - IMPRESSION: - - No previous images. Relatively low lung volumes accentuate the transverse - diameter of the heart. Mild elevation of pulmonary venous pressure with - atelectatic changes at both bases. Blunting of the left costophrenic angle - suggests small pleural effusion. - No evidence of acute focal pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s51967138.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s51967138.txt deleted file mode 100644 index a8cb6bfafad6f4fda3be585a12cf2b08bfa56404..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s51967138.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with history of cirrhosis and loculated ascites - with peritonitis, now w worsening dyspnea and new O2 requirement // etiology - of dyspnea, hypoxia? - - COMPARISON: The comparison is made with prior studies including ___. - - IMPRESSION: - - There is cardiomegaly, upper zone redistribution and blurring of vascular - detail suggesting CHF. There is linear atelectasis in the left lung base. - There is no pneumothorax. These findings have increased as compared to the - ___ film. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s53377126.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s53377126.txt deleted file mode 100644 index cc201fa5813c7f27d3fc62c2b7302a3a15d44d89..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s53377126.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman intubated // lines, interval eval lines, - interval eval - - IMPRESSION: - - Comparison to ___. Unchanged bilateral pleural effusions of - moderate extent. Subsequent bilateral areas of atelectasis. The monitoring - and support devices are in constant position. Mild cardiomegaly. No - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s56542038.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s56542038.txt deleted file mode 100644 index da3d098c7781e7567d7697a4c02580d5ab96e6a3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s56542038.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with s/p intubation // tube placement - tube placement - - COMPARISON: Prior chest radiographs ___ and ___. - - IMPRESSION: - - Severe pulmonary edema was new on ___ and has worsened accompanied by - increasing large right and moderate left pleural effusions. Heart is only - mildly enlarged. Mediastinal veins are now severely distended. - - ET tube in standard placement. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s57225514.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s57225514.txt deleted file mode 100644 index d9efeb3933e4de047d1b242c01e9710ca9203f81..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16202057/s57225514.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with cirrhosis, dCHF with pulmonary edema, - ongoing intraabdominal infection. // evaluate for interval change. - evaluate for interval change. - - IMPRESSION: - - Comparison to ___. In the interval, the patient has been - extubated. The nasogastric tube was removed. The right internal jugular vein - catheter remains in situ. Decrease in extent and severity of the pre-existing - left lower lobe atelectasis. A platelike atelectasis at the left lung bases - persists. Borderline size of the cardiac silhouette. No pulmonary edema. No - pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s50339419.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s50339419.txt deleted file mode 100644 index 04954bcd26440352dddec64bf7d6b783d5cf69dd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s50339419.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - SINGLE FRONTAL VIEW OF THE CHEST - - REASON FOR EXAM: Question aspiration. Intubated patient. History of - ___-___ - - Mild pulmonary edema has improved. Bibasilar opacity larger on the left side - are a combination of pleural effusions and adjacent atelectasis, likely - unchanged allowing the difference in positioning of the patient. Right - perihilar opacities have improved. Cardiac size cannot be evaluated. ET tube - is in standard position. NG tube tip is out of view below the diaphragm. - Port-A-Cath tip is at the cavoatrial junction. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s51220275.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s51220275.txt deleted file mode 100644 index 087f6db03841faaaef0eace3d14304d5d87dbfc2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s51220275.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Laparoscopic converted open gastrectomy, evaluation. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is increasing - bilateral pleural effusions at simultaneously/decreasing lung volumes. Areas - of atelectasis are seen at both lung bases. Moderate cardiomegaly with - minimal fluid overload persists. The monitoring and support devices are - constant. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s52513445.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s52513445.txt deleted file mode 100644 index 7c4a838e774bc308a0bf47e50514f2b89c7a0c22..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s52513445.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - HISTORY: Status post esophagojejunostomy. - - COMPARISON: Multiple prior chest radiographs, most recently ___. - - - FINDINGS: - - Single frontal view of the chest. Endotracheal tube, NG tube, left pleural - tube, and right chest wall port are in stable position. Slight displacement - of the trachea is similar to prior and likely due to low lung volumes. The - tip of the ETT may abut the tracheal wall. Stable cardiomegaly and unchanged - configuration of aortic knob calcification. Left pleural effusion is - redistributed or slightly smaller as compared to the prior exam. The right - pleural effusion has slightly increased. Elevation of the left hemidiaphragm - and bibasilar atelectasis are stable. - - IMPRESSION: - - 1. Slight interval increase of right pleural effusion with similar left - pleural effusion. - 2. The trachea is slightly displaced due to low lung volumes and the ET tube - may abut the tracheal wall. Please correlate with ETT function. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s53250124.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s53250124.txt deleted file mode 100644 index e14ce65570a516538c0d0570362c89da9432a557..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s53250124.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Left subclavian central venous line. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, the patient has received a - new left subclavian line. The course of the line is unremarkable, the tip of - the line projects over the upper-to-mid SVC. There is no evidence of - complication, notably no pneumothorax. The other monitoring and support - devices, including the nasogastric tube, a post-surgical tube at the bases of - the left hemithorax, an endotracheal tube, and the right Port-A-Cath are - constant in appearance. As compared to the prior image, the right lung is - better ventilated. The pre-described opacities at the left lung base persist. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55534272.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55534272.txt deleted file mode 100644 index c969291c3c34f43c28689bfb6ae878052ff2934a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55534272.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - INDICATION: Status post total gastrectomy with increased oxygen requirement. - - COMPARISON: ___ through ___. - - FRONTAL PORTABLE CHEST: The nasogastric tube tip is not seen beyond the - gastroesophageal junction. A right Port-A-Cath ends in the right atrium, - unchanged in position. - - Lung volumes remain very low, similar to ___ with severe left lower lobe - atelectasis or consolidation. Mild pulmonary edema is improving, probably - with a small left pleural effusion. Evaluation of the cardiac silhouette is - difficult due to persistent elevation of the left hemidiaphragm. No - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55778051.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55778051.txt deleted file mode 100644 index 3af6a1ba718b951ab25b01d2185d0ffd8fb566c4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s55778051.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Respiratory failure, evaluation for pneumonia. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, the monitoring and support - devices are unchanged. There is unchanged evidence of low lung volumes, - moderate cardiomegaly, and mild fluid overload. In the interval, small - bilateral pleural effusions have developed on the right. Small left pleural - effusion is constant in appearance. Small areas of atelectasis are seen at - both lung bases, but there is currently no evidence of pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56081688.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56081688.txt deleted file mode 100644 index 86d4f2cc90b576eee3422e5ca9ad4bef1de176dd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56081688.txt +++ /dev/null @@ -1,9 +0,0 @@ - FINAL REPORT - HISTORY: Extubation with pulmonary edema. - - FINDINGS: In comparison with the study of ___, the endotracheal tube has - been removed. Nasogastric tube remains in place. - - Continued low lung volumes that accentuate the transverse diameter of the - heart. Bibasilar opacifications persist consistent with pleural effusions and - compressive atelectasis, more prominent on the left. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56846469.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56846469.txt deleted file mode 100644 index 53ba75c2b790321ca1fe2ce8cec0a1cb78307095..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s56846469.txt +++ /dev/null @@ -1,9 +0,0 @@ - FINAL REPORT - HISTORY: Gastric resection, to assess for change. - - FINDINGS: In comparison with the study of ___, there again are low lung - volumes that accentuate the transverse diameter of the heart. Bibasilar - opacifications are consistent with pleural effusions and compressive - atelectasis, more prominent on the left. Continued enlargement of the cardiac - silhouette without definite vascular congestion. Central catheter is - essentially unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58158025.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58158025.txt deleted file mode 100644 index f5c22b469b48afd60b1b9d2067929afa2ff09f36..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58158025.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Intubation, evaluation for endotracheal tube position. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, the patient has been - intubated. Tip is located at the level of the carina, the tube must be pulled - back by approximately 2 to 3 cm. The other monitoring and support devices are - in correct position. - - At the time of dictation and observation, 10:46 a.m., on ___, the - referring physician, ___. ___, was paged for notification. - - The left chest tube is in correct position. Low lung volumes. Unchanged - tortuosity of the thoracic aorta, with unchanged mild borderline diameter of - the aortic arch. Areas of atelectasis at both lung bases persist. No new - parenchymal opacities. No overt pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58291164.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58291164.txt deleted file mode 100644 index 5afc783b995af4f6e466404760414d029ab8346b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16345504/s58291164.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: Guillain-___. The patient was emergently reintubated with - suspected aspiration. - - COMPARISON: ___ through ___, CT ___. - - FRONTAL SEMI-UPRIGHT PORTABLE CHEST: Low lung volumes result in brochovasular - crowding. Endotracheal tube ends 2.9 cm above the carina. Port-A-Cath ends - in the right atrium. Left subclavian line ends in the mid SVC. Nasogastric - tube extends to the stomach. Two surgical drains projects over the left - hemithorax and upper abdomen. There is no change from ___ with - persistent left basilar opacity and small left pleural effusion. No - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16356013/s58352595.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16356013/s58352595.txt deleted file mode 100644 index 18b672f577195314e3c9ebaafbab2249a2a910f4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16356013/s58352595.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP)CHEST (PORTABLE AP)i - - INDICATION: ___M s/p excision of infected aortobifem 5 days ago, now w fevers - // ?PNA - - COMPARISON: Chest radiographs ___. - - IMPRESSION: - - Increasing consolidation in the left lower lobe could be worsening pneumonia. - New consolidative abnormality the base of the right lung is either atelectasis - or second focus of edema. Normal cardiomediastinal and hilar silhouettes. No - pneumothorax. Pleural effusion minimal if any. Epidural infusion catheter - projects over the midline, but the tip is not localized. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16476036/s57688964.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16476036/s57688964.txt deleted file mode 100644 index e0bd1641ceb1302e80e0e8b456060ce81e1a2f32..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16476036/s57688964.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___M with RCC FFT increase more delirious/falls, unclear if LOC - // cxr rule out pna vs pleural effusionct head rule on intracranial - hemorrhagec spine rule out fracture - - TECHNIQUE: AP and lateral views of the chest. - - COMPARISON: ___ and ___ chest x-rays and chest CT - from ___. . - - FINDINGS: - - Bilateral pulmonary nodules are extensive and better seen on prior CT scan. - There are low lung volumes with secondary crowding of the bronchovascular - markings and likely bibasilar atelectasis. Cardiomediastinal silhouette is - within normal limits. No acute osseous abnormalities identified. - - IMPRESSION: - - Low lung volumes with secondary bronchovascular crowding. Bilateral pulmonary - nodules as seen on prior exams including CT. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16484980/s56599514.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16484980/s56599514.txt deleted file mode 100644 index e7dd4f7c723c0960c617018a350d846fd5cfd023..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16484980/s56599514.txt +++ /dev/null @@ -1,19 +0,0 @@ - WET READ: ___ ___ 5:43 PM - Increased atelectasis of the left lung base. No pneumothorax or large pleural - effusion. No new focal consolidation. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old woman POD1 desaturating, new O2 requirement // eval - for atelectasis, effusion, consolidation eval for atelectasis, effusion, - consolidation - - COMPARISON: Chest radiographs since ___ most recently ___. - - IMPRESSION: - - Aside from mild platelike atelectasis and lower lung volumes compared to ___, - lungs are clear. Heart is top-normal size. A very small right pleural - effusion is appreciated only on the lateral view. There is no pulmonary - edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s51750681.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s51750681.txt deleted file mode 100644 index 51ea823ca2fb809b389a7b0e7e97f7c430933b61..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s51750681.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with GPC bacteremia who presents with chest pain, - fever, LUE cellulitis, c/f endocarditis. Unrelated - history of spontaneous - PTX // pneumonia? PTX? etiology of chest pain? - - TECHNIQUE: Portable AP radiograph of the chest. - - COMPARISON: ___ and dating back to ___. - - FINDINGS: - - Right apical chain sutures indicate prior wedge resection. A bandlike opacity - at the left base is most likely due to atelectasis. Calcified granulomas in - the right upper lobe are stable dating back to the ___. There is no - pneumothorax. Heart size is top-normal. - - IMPRESSION: - - Bandlike opacity in the left lower lobe is most likely due to atelectasis, but - infection would be difficult to exclude in the appropriate clinical setting. - No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s56534681.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s56534681.txt deleted file mode 100644 index 8c4c0d779b53b5db8cd50e7eea80d535b8b8cdf3..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16503587/s56534681.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: Portable chest radiograph. - - INDICATION: ___-year-old man with a history of pneumonia who complains of - chest pain; evaluate for pneumothorax. - - TECHNIQUE: Portable AP chest radiograph view was obtained. - - COMPARISON: Chest radiograph dated ___ and ___. - - FINDINGS: - - No pneumothorax. The cardiomediastinal silhouette is overall stable in - appearance. There is mild lower lung atelectasis bilaterally. No pleural - effusion. Right upper lobe and left lower lobe calcified granulomas are stable - since at least ___. Chain sutures in the right upper lung suggest prior - resection. - - IMPRESSION: - - 1. No pneumothorax. - 2. No acute intrathoracic process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16526693/s55446851.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16526693/s55446851.txt deleted file mode 100644 index a78189623be7d37ca8f48e833cf115bd37de283a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16526693/s55446851.txt +++ /dev/null @@ -1,26 +0,0 @@ - WET READ: ___ ___ ___ 5:39 PM - Small left pleural effusion. Nodular opacity projecting over the left lung - base, likely nipple shadow however repeat with nipple markers suggested to - confirm. - ______________________________________________________________________________ - FINAL REPORT - INDICATION: ___ year old man with cirrhosis, low back pain, fever // evaluate - for pneumonia, has known L rib fx - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: None. - - FINDINGS: - - Hazy opacities over the lung bases are likely due to gynecomastia. For focal - nodular density of the left lung base may be a nipple shadow however repeat - with nipple markers suggested to confirm. Small left pleural effusion is - noted. The lungs are otherwise clear. Cardiomediastinal silhouette is within - normal limits. No acute osseous abnormalities. - - IMPRESSION: - - Small left pleural effusion. Nodular opacity projecting over the left lung - base, likely nipple shadow however repeat with nipple markers suggested to - confirm. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16660935/s54829079.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16660935/s54829079.txt deleted file mode 100644 index 79b7c7479d110092a3768ee10aff8b93c87d9f6f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16660935/s54829079.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male status post cardiac arrest. Please evaluate for - acute process, endotracheal tube. - - TECHNIQUE: Portable AP frontal chest radiograph was obtained. - - COMPARISON: Chest CT from ___. - - FINDINGS: - - There are bilateral consolidations, right greater the left, reflective of - aspiration as noted on the same date chest CT. Right pleural fluid is also - noted. Thickening of the right paratracheal stripe is noted, reflective of - examination of volume loss, pleural fluid and mediastinal adenopathy as seen - on the same day chest CT. The cardiac silhouette is enlarged. There is an - endotracheal tube terminating in appropriate position, and an enteric tube - terminates below the view of this radiograph. Cervical and thoracic spinal - hardware is noted, and surgical clips project over the right axilla. - - IMPRESSION: - - 1. Bilateral consolidations compatible with aspiration, better delineated on - the same day chest CT. - 2. Right pleural effusion. - 3. Upper positioning of support lines and devices. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s51673079.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s51673079.txt deleted file mode 100644 index 62f26414dadc3d5f34bb03bb1d649da95ab33865..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s51673079.txt +++ /dev/null @@ -1,38 +0,0 @@ - WET READ: ___ ___:___ AM - Swan-Ganz catheter terminates in the main pulmonary artery, and likely not - advanced enough to get a proper wedge pressure. ___ were d/w Dr. ___ - by Dr. ___ by phone at ___:___p on the day of the exam by phone. - Interval development of left mid lung opacity since the prior study from ___, concerning for infection or aspiration in the appropriate clinical - setting. Low lung volumes persist, as does pulmonary venous congestion. - Right lung base opacity is similar in appearance. - - The findings were discussed with ___, M.D. by ___, M.D. on - the telephone on ___ at 6:___ PM, 2 minutes after discovery of the - findings. - WET READ VERSION #1 ___ ___:___ PM - Interval development of left mid lung opacity since the prior study from ___, concerning for infection or aspiration in the appropriate clinical - setting. Low lung volumes persist, as does pulmonary venous congestion. - Right lung base opacity is similar in appearance. - - The findings were discussed with ___, M.D. by ___, M.D. on - the telephone on ___ at 6:___ PM, 2 minutes after discovery of the - findings. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with acute hypoxia after colonoscopy/EGD // - evaluate for pulm edema vs aspiration evaluate for pulm edema vs - aspiration - - IMPRESSION: - - Compared to prior chest radiographs ___. - - Lung volumes remain low. Heterogeneous areas of peribronchial opacification - have all coalesced in the left upper and right lower lung zones. This could - be atelectasis in the areas of previous pulmonary edema or local infection, - perhaps due to aspiration. Heart is normal size but larger today than it was - on ___. Pleural effusion is small if any. No evidence of pneumothorax. - - Feeding tube is been removed. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s54291275.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s54291275.txt deleted file mode 100644 index b06d4b2e2bffdaba15c5ba146238f31d44b05150..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16684213/s54291275.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___M with weakness, liver mass cough - - COMPARISON: Prior CT chest from ___. - - FINDINGS: - - PA and lateral views of the chest provided. Multiple small pulmonary nodules - are better assessed on prior CT chest. There is no evidence of pneumonia, - edema, effusion, or pneumothorax. Cardio mediastinal silhouette notable for - enlargement of the main pulmonary artery mobile which is confirmed on chest CT - which may indicate underlying pulmonary arterial hypertension. The imaged - bony structures are intact. No free air below the right hemidiaphragm is - seen. - - IMPRESSION: - - - 1. No evidence of pneumonia or edema. - 2. Small pulmonary nodules better assessed on prior CT. - 3. Enlarged main pulmonary artery which likely reflect pulmonary arterial - hypertension. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16690146/s54863731.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16690146/s54863731.txt deleted file mode 100644 index f2cfd011d6b6e493c69db959a0111187fcc8476e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16690146/s54863731.txt +++ /dev/null @@ -1,19 +0,0 @@ - WET READ: ___ ___ ___ 7:50 AM - There is a right infrahilar and a right lung apex opacity, possibly - representing multifocal PNA. - - ______________________________________________________________________________ - FINAL REPORT - INDICATION: ___-year-old with mental status change. - - TECHNIQUE: Frontal and lateral radiographs of the chest were obtained. - - COMPARISON: CT of the abdomen and pelvis from ___. - - FINDINGS: - There is a right infrahilar and a right lung apex opacity, possibly - representing multifocal PNA. - The cardiomediastinal silhouette and hila are normal. There is no pleural - effusion and no pneumothorax. - - dw Dr. ___ at 7.___ am by Dr. ___ ___ the phone. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57092670.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57092670.txt deleted file mode 100644 index 037bcfb4505a565ce094504cdd03e8625d1b3ae5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57092670.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: - ___F with cough, evaluate for pneumonia. - - COMPARISON: None Available. - TECHNIQUE - Frontal and lateral view of the chest and CT chest ___. - - FINDINGS: - - Mild to moderate interstitial abnormality has improved compared to ___, - probably due to resolution of a component of acute pulmonary edema. Heart size - is normal. The mediastinal contour is unremarkable. There is no pleural - effusion or pneumothorax. There is no evidence of a focal consolidation. - - IMPRESSION: - - Overall improved interstitial abnormality compared to ___. No focal - consolidation. No acute pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57165147.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57165147.txt deleted file mode 100644 index 838cc022f5d1b253a151ba8bb329e157be61eb43..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s57165147.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with L ij cvl // eval L ij - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: ___ at 17:41 - - FINDINGS: - - There has been interval placement of a left internal jugular central venous - catheter terminating in the mid to low SVC without evidence of pneumothorax. - Endotracheal tube terminates approximately 3.3 cm above the level of the - carina. A right-sided PICC is grossly stable in position. Diffuse bilateral - opacities again seen worrisome for pulmonary edema, underlying infection not - excluded, appears slightly worsened as compared to the prior study, including - a more confluent area of opacity in the right upper to mid lung. Probable - left pleural effusion persists. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59505045.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59505045.txt deleted file mode 100644 index 8b956f8ad15ac2fc0b2bbae52137864f5ddcb3e9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59505045.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old woman with sepsis-like picture without an identified - source. // Is there any evidence of pneumonia or interstitial disease? - - COMPARISON: Chest radiographs since ___ most recently one ___. - - IMPRESSION: - - Mild to moderate interstitial pulmonary abnormality with a basal predominance - has worsened since ___. Although heart is not large there is mild - engorgement of upper lobe pulmonary vessels and mediastinal veins to this - might all be due to pulmonary edema. Underlying interstitial lung disease may - be present a some extent. There are no finding strongly suggestive of - bacterial pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59834116.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59834116.txt deleted file mode 100644 index 20d12d3a69ccbcdc47d4669cd06d93fa712887c4..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59834116.txt +++ /dev/null @@ -1,26 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with bacteremia, O2 requirement // eval - evolution of infiltrates - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Single AP view of the chest provided. - - Lung volumes are lower. Dilatation and indistinctness of the pulmonary - vasculature have worsened from ___. Diffuse, predominantly - interstitial abnormality looked more nodular on the prior examination. - - No pneumothorax. Probable, bilateral small pleural effusions. - - Cardiomediastinal contours are normal. - - IMPRESSION: - - 1. Moderate pulmonary edema worsened from ___. - - 2. Diffuse, predominately interstitial abnormality appeared more nodular on ___. Because edema may be masking infectious lung nodules, if the - lungs do not clear with therapy, CT is recommended for further evaluation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59920856.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59920856.txt deleted file mode 100644 index 7bf07ddb9094f402b059c14dcab270e64ee9551f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16766035/s59920856.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with sob // chf - - TECHNIQUE: Single frontal view of the chest - - COMPARISON: ___ - - FINDINGS: - - Right-sided PICC is again seen terminating in the low SVC. Since the prior - study, there has been increase in interstitial and airspace opacities - bilaterally suggesting moderate pulmonary edema, possibly of a background of - chronic lung disease. Lateral left lung scarring is again seen. Small pleural - effusions may be present. No pneumothorax is seen. Cardiac and mediastinal - silhouettes are stable. . - - IMPRESSION: - - Moderate pulmonary edema. Small pleural effusions not excluded. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s55365674.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s55365674.txt deleted file mode 100644 index 83ad75b766796a9c3278daa0a46f0ac8256c6d43..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s55365674.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH. - - INDICATION: Evaluation for interval change in pulmonary edema. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is no relevant - change. The pleural effusions have slightly increased. The signs indicative - of pulmonary edema are stable. Stable is the moderate cardiomegaly. Areas of - atelectasis are unchanged. No evidence of new parenchymal opacity suggesting - pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s56277775.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s56277775.txt deleted file mode 100644 index b1a5abfbcdfbd04829ad1e63fe19616eab1c8a40..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s56277775.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - PORTABLE CHEST FILM ___ AT 712 - - CLINICAL INDICATION: ___-year-old with a new diagnosis of acute delayed - cardiomyopathy, question pulmonary edema. - - Comparison is made to the patient's previous study dated ___ at 807. - - AP chest film ___ at 7:12 a.m. is submitted. - - IMPRESSION: - - 1. The heart remains enlarged with a globular configuration which is - consistent with the patient's known cardiomyopathy, although pericardial - effusion cannot be entirely excluded. There is decrease in the bilateral - pleural effusions with a small residual effusion seen only on the right side - at this time. The pulmonary edema has resolved. There continues to be some - cephalization of the vasculature suggestive of pulmonary venous hypertension. - No pneumothorax is seen. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s58806478.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s58806478.txt deleted file mode 100644 index e8688b465582cacedf88d67a458128f60c31e061..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16799095/s58806478.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: Shortness of breath. Evaluation for pulmonary edema. - - COMPARISON: ___. - - FINDINGS: Portable AP chest radiograph. Pulmonary opacification has - progressed in the right lower lobe, but improved in the left lung compared to - three hours prior. The heart size is stable. Small pleural effusion is now - present on the right. There is no pneumothorax. - - IMPRESSION: Worsening right lower opacity in the setting of improving - interstitial edema raises concern for concurrent pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16905933/s53951212.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16905933/s53951212.txt deleted file mode 100644 index 473201b4893510e072946fc954328a8a3b74eebe..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16905933/s53951212.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with intubation // ET tube placement - - TECHNIQUE: Portable semi-upright AP view of the chest - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Endotracheal tube tip terminates approximately 7.7 cm from the carina. An - enteric tube tip terminates within the stomach. Heart size is normal. The - mediastinal and hilar contours are normal. Pulmonary vasculature is not - engorged. Lungs are hyperinflated with moderate emphysematous changes noted - in the upper lobes. Within the left mid lung field is a 7.6 x 9.6 cm mass, - new from the previous study. Remainder of the lungs are clear. No pleural - effusion or pneumothorax is present. No acute osseous abnormality is - detected. - - IMPRESSION: - - - 1. Standard positioning of the endotracheal and enteric tubes. - 2. 9.6 cm left mid lung field mass concerning for malignancy. CT of the chest - with contrast is recommended for further assessment. - 3. Upper lobe predominant moderate emphysema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16919585/s56024483.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16919585/s56024483.txt deleted file mode 100644 index 37041e8ef725d20a5236654e4fc0eb82ed368395..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p16/p16919585/s56024483.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p CT removal // r/o ptx - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, all monitoring and support devices, - with the exception of the right internal jugular vein catheter, have been - removed. No evidence of pneumothorax or larger pleural effusions. Low lung - volumes. Unchanged appearance of the sternal wires and the postoperative - cardiac silhouette. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17029405/s55670644.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17029405/s55670644.txt deleted file mode 100644 index 6de161f802ec6c87aef60a66e1f8626503ad68df..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17029405/s55670644.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: - Chest: Frontal and lateral views - - INDICATION: History: ___F with URI symtpoms, pleuritic chest pain. // rule - out PNA - - TECHNIQUE: Chest Frontal and Lateral - - COMPARISON: None. - - FINDINGS: - - There may be mild left base atelectasis without definite focal consolidation. - There may be minimal scarring along the lateral right upper hemi thorax. No - pleural effusion or pneumothorax is seen. The cardiac and mediastinal - silhouettes are unremarkable. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17033197/s55486789.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17033197/s55486789.txt deleted file mode 100644 index c4ccd50368bc6369f5b4a268ba602f007a7ea19c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17033197/s55486789.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: History: ___F with shortness of breath - - TECHNIQUE: Chest PA and lateral - - COMPARISON: None. - - FINDINGS: - - Extensive lobulated widening of the anterior superior mediastinum is highly - concerning for a mass. Heart size is normal. The aorta is tortuous. The - pulmonary vasculature is normal. Lungs are clear. No pleural effusion or - pneumothorax is seen. S-shaped scoliosis of the thoracolumbar spine is - present. No acute osseous abnormalities demonstrated. - - IMPRESSION: - - Large anterior mediastinal mass. Further assessment with contrast-enhanced CT - is recommended. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17049363/s52056015.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17049363/s52056015.txt deleted file mode 100644 index 69b0ec7c583890cd76a11acadd9d1324f3bff3d8..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17049363/s52056015.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old man with fevers and cough, evaluate for pneumonia. - - COMPARISON: ___. - - TECHNIQUE: PA and lateral views of the chest. - - FINDINGS: Cardiomediastinal silhouettes and hilar contours are stable. - Linear opacities at the left lower lung base, consistent with atelectasis or - pleural scaring, are unchanged. Lung volumes again are very low. No evidence - of failure or focal consolidations worrisome for pneumonia. - - IMPRESSION: No change from the ___ radiograph with no evidence - of pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s51998337.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s51998337.txt deleted file mode 100644 index c56456cf3723d2d581e2d4888a6a919fbcc87c45..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s51998337.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - PORTABLE AP CHEST FILM, ___ at 12:21. - - CLINICAL INDICATION: ___-year-old status post retraction of PICC line, check - tip. - - Comparison is made to the patient's previous study dated ___ at 8:51. - - The left lateral chest and costophrenic angle are not included on the study. - - Portable AP supine chest film ___ at 12:21 is submitted. - - IMPRESSION: - - 1. The right subclavian PICC line now has its tip in the mid SVC in - satisfactory position. The right internal jugular central line continues to - have its tip in the right atrium. A nasogastric tube is seen coursing below - the diaphragm with the tip not identified. Endotracheal tube continues to - have its tip approximately 4 cm above the carina. - - 2. Relatively low lung volumes with crowding of the vasculature and likely - residual perihilar edema. Left basilar airspace process appears slightly - worsened and may reflect worsening lower lobe atelectasis. Pneumonia should - also be considered. No large right effusion. No large pneumothorax on the - supine film. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s53122076.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s53122076.txt deleted file mode 100644 index bcfea80560315a7c3e0d2a2be10688ec313565f2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s53122076.txt +++ /dev/null @@ -1,27 +0,0 @@ - FINAL REPORT - PORTABLE AP CHEST - - CLINICAL INDICATION: ___-year-old with multifocal pneumonia, evaluate for - evolution and check line placement. - - Comparison is made to the patient's previous study of ___ at ___. - - Single portable AP semi-erect chest film ___ at 4:00 a.m. is submitted. - - IMPRESSION: - - 1. Endotracheal tube now has its tip approximately 1.5-2 cm above the carina. - Nasogastric tube is seen coursing below the diaphragm with the tip not - identified. Right internal jugular central line continues to have its tip in - the right atrium and a pullback of 6-7 cm would be recommended at this time. - - 2. Marked interval improvement in aeration at both lung bases with residual - linear opacity in the left mid lung reflecting persistence of segmental - atelectasis. There is also persistent patchy opacity at the left base which - also likely reflects resolving lower lobe atelectasis. The left hilar contour - also appears to be somewhat improved on the current study. The right lung has - reinflated, and there is a slight elevation of the right hemidiaphragm, but no - focal airspace consolidation noted at the right base at this time. No - pneumothorax is seen. No evidence of pulmonary edema. Cardiac and - mediastinal contours are stable. The patient's nurse ___ was notified of the - need to reposition the right IJ line on ___ at 10:11 a.m. by phone. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s57160577.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s57160577.txt deleted file mode 100644 index b96235a48c27a48d563ec199bbe5e058e6eeb979..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17112656/s57160577.txt +++ /dev/null @@ -1,8 +0,0 @@ - FINAL REPORT - HISTORY: Multilobar pneumonia and respiratory failure. - - FINDINGS: In comparison with the study of ___, there are lower lung volumes - that may be accentuating the transverse diameter of the heart. The tip of the - endotracheal tube lies approximately 2.5 cm above the carina. Nasogastric - tube tip, the dense streak of atelectasis at the left base is much less - prominent. No definite vascular congestion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s55820009.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s55820009.txt deleted file mode 100644 index f7a758a819fd243b07f4ce1ea9f542e84d7c58ec..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s55820009.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old man status post right thoracentesis, to rule out - pneumothorax. - - COMPARISON: Chest radiograph, ___. - - FINDINGS: There is complete resolution of a previously seen right pleural - effusion with re-expansion of the right lower lobe. No pneumothorax is seen. - Small left pleural effusion and left basal atelectasis is unchanged. Moderate - cardiomegaly are unchanged. The hilar and mediastinal contours are stable. A - right internal jugular approach dialysis catheter terminates in the lower SVC. - - IMPRESSION: Resolved right pleural effusion. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s56920919.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s56920919.txt deleted file mode 100644 index 2c151be5fdb6fa08e7e5092b4a530113225e05ca..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s56920919.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Chronic heart failure, evaluation for interval change. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is improvement, - determined by a reduction in extent of the right pleural effusion. Moderate - right effusion, however, persists. Unchanged minimal left effusion with - retrocardiac atelectasis. No new parenchymal opacity. No pneumothorax. - Unchanged mild cardiomegaly. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s59659310.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s59659310.txt deleted file mode 100644 index 0968463a4539e2c295ced40440d8f924616ecd49..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17169478/s59659310.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAM: Chest supine AP portable views. - - CLINICAL INFORMATION: Acute CHF from outside hospital. - - COMPARISON: ___. - - FINDINGS: Supine AP portable views of the chest are obtained. There has been - interval removal of the right-sided PICC. Opacity projecting over the right - lung may be due to a layering pleural effusion, although underlying - consolidation is difficult to exclude. The left lung is grossly clear with - possible mild pulmonary vascular engorgement centrally. The cardiac - silhouette is top normal. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17201840/s55277734.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17201840/s55277734.txt deleted file mode 100644 index 4142611c25db273dd7d79a96be570f9b3b992c0f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17201840/s55277734.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: History of neutropenia. Please evaluate for acute process. - - COMPARISONS: Chest radiographs dated back to ___. - - TECHNIQUE: PA and lateral radiographs of the chest. - - FINDINGS: Moderate cardiomegaly has increased in size compared to prior exam - from ___. There is mild-to-moderate pulmonary edema. There is subtle - increase in opacity overlying the left lower lobe concerning for an infectious - process. There is no evidence of a pneumothorax. The visualized osseous - structures are unremarkable. - - IMPRESSION: - - 1. Mild cardiomegaly with worsening mild-to-moderate pulmonary edema is - concerning for heart failure. - - 2. Increase in opacity overlying the left lower lobe is concerning for an - infectious process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s57122941.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s57122941.txt deleted file mode 100644 index ac6e50cfe5efee0171a2108cd57eaa1f878e7095..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s57122941.txt +++ /dev/null @@ -1,10 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with hypoxia // edema vs atelectasis - - IMPRESSION: - - In comparison to ___ chest radiograph, a small to moderate right - pleural effusion has increased in size with adjacent worsening right lower - lobe atelectasis. No other relevant change. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s58854224.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s58854224.txt deleted file mode 100644 index e98a46e1645cfbbe0ee65af4dc7ddd43b5ba06e6..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17230481/s58854224.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman s/p LV mass removal // trend RLL opacity - trend RLL opacity - - IMPRESSION: - - Compared to chest radiographs since ___, most recently ___ through - ___. - - Heterogeneous opacification in the right upper lobe has worsened, more - confluent consolidation right middle lobe and lower lobe unchanged consistent - with extensive pneumonia. Left lung grossly clear. Heart top normal size. - Small right pleural effusion is likely. No appreciable left pleural effusion. - No pneumothorax. - - Right jugular line ends at the origin of the right brachiocephalic vein. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s50138649.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s50138649.txt deleted file mode 100644 index a763d7247fbfd4853d948f5f1c1ab374bd7f47ae..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s50138649.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with ngt placement // tip of ngt? - - COMPARISON: Compared to radiographs from ___ and radiographs from ___. - - IMPRESSION: - - The nasogastric tube is unchanged position. The side port is again at the GE - junction and could be advanced several cm for more optimal placement. There - is unchanged cardiomegaly. There remains minimal right basilar subsegmental - atelectasis. The left lung base and retrocardiac opacity seen on the - radiographs from ___ has resolved. There are no pneumothoraces or - signs for overt pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s52095305.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s52095305.txt deleted file mode 100644 index de06ee4a5b4ac1a662d49bc7d123e323519de8af..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s52095305.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: History: ___M with fatigue status post renal transplant. - - TECHNIQUE: Chest PA and lateral - - COMPARISON: ___ - - FINDINGS: - - Heart size is moderately enlarged but unchanged. The aorta is diffusely - calcified. The mediastinal and hilar contours are unremarkable. Pulmonary - vasculature is not engorged. Minimal streaky opacities in the lung bases - likely reflect areas of atelectasis. Scarring is re- demonstrated in the - right apex. No pleural effusion or pneumothorax is present. There are - moderate multilevel degenerative changes throughout the thoracic spine. - - IMPRESSION: - - Mild bibasilar atelectasis without focal consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s53096835.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s53096835.txt deleted file mode 100644 index 42dece688b1b4c58130795573f2fb9d9a2ebcb01..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s53096835.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (AP AND LAT) - - INDICATION: History: ___M with shaking, confusion, infection and neuro workup - - TECHNIQUE: Upright AP and lateral views of the chest - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Lung volumes are lower compared to the previous examination. Moderate to - severe cardiomegaly is re- demonstrated. The mediastinal and hilar contours - are unchanged. Pulmonary vasculature is not engorged. No focal - consolidation, pleural effusion or pneumothorax is present. Moderate - degenerative changes are noted in the thoracic spine. - - IMPRESSION: - - Moderate to severe cardiomegaly. No focal consolidation to suggest pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s54952488.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s54952488.txt deleted file mode 100644 index 8f3946f20b97544e69b1caf850b688011e82ac54..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s54952488.txt +++ /dev/null @@ -1,24 +0,0 @@ - WET READ: ___ ___ ___ 11:53 PM - 1. Enteric feeding tube in stomach. - - 2. Right PICC tip in mid SVC. - - 3. Persistent severe cardiomegaly. - - 4. Mild vascular congestion - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with NG feeding tube // NG tube placement - NG tube placement - - COMPARISON: Chest radiographs ___ through ___. - - IMPRESSION: - - Severe cardiomegaly is stable. Mild pulmonary edema has improved. Small - pleural effusions unchanged. No pneumothorax. - - Feeding tube with the wire stylet in place ends in the low stomach. Right PIC - line ends in the upper SVC. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s55411906.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s55411906.txt deleted file mode 100644 index 38623657ac70972ac8b175989004bac58430acc2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s55411906.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man for kidney transplant // pre-op Surg: ___ - (transplant) pre-op - - IMPRESSION: - - In comparison with the study of ___, there is again substantial - enlargement of the cardiac silhouette. Relatively mild elevation of pulmonary - venous pressure raises the possibility of underlying cardiomyopathy or - pericardial effusion. - No evidence of acute focal pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s57338935.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s57338935.txt deleted file mode 100644 index e1c0bdb2d01838496508dfc0c7cb2ec838c185df..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s57338935.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiographs. - - INDICATION: ___M with fever // PNA - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiographs dated ___. - - FINDINGS: - - Feeding tube and right upper extremity PICC line are unchanged. Cardiomegaly - is moderate and unchanged. There is pulmonary vascular congestion and - possible mild pulmonary edema. Dense consolidation within the right upper - lobe is concerning for pneumonia. Left lower lobe opacity may also represent - another site of pneumonia. No large effusion or pneumothorax. Bony - structures intact. - - IMPRESSION: - - Cardiomegaly, mild pulmonary edema, multifocal pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s59867439.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s59867439.txt deleted file mode 100644 index 1828ee9a3468fd7611801966db946bd1b9b7d778..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17281190/s59867439.txt +++ /dev/null @@ -1,29 +0,0 @@ - WET READ: ___ ___ ___ 1:41 PM - Right apical 1.5 cm density, potentially within the first rib, however apical - lordotic view recommended to exclude lung nodule. Mild vascular congestion. - No pleural effusion. Free intraperitoneal air, consistent with peritoneal - dialysis. - ______________________________________________________________________________ - FINAL REPORT - HISTORY: Advanced CKD, now with pain and swelling of extremities after - missing 4 days of Lasix with some subjective shortness of breath. - - COMPARISON: Comparison is made with chest radiographs from ___ and - ___. - - FINDINGS: The lungs are well expanded. There are prominent interstitial - markings, increased from prior exam, consistent with mild pulmonary edema. - There is a right apical 1.5 cm density, potentially within the first rib, but - could represent a lung nodule. There is free intraperitoneal air, consistent - with peritoneal dialysis. Cardiomegaly is seen. There is no pneumothorax or - pleural effusion. Visualized osseous structures are unremarkable. - - IMPRESSION: - - 1. Right apical 1.5 cm density, potentially within the first rib, however - apical lordotic view recommended to exclude lung nodule. - - 2. Mild pulmonary edema. - - 3. Small amount of free intraperitoneal air, consistent with peritoneal - dialysis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s51155515.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s51155515.txt deleted file mode 100644 index 3096e0ffb4d44ef5c253987d424e5a189093dbe5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s51155515.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with hypercarbic resp failure s/p extubation - and multifocal pneumonia // interval changes interval changes - - COMPARISON: ___. - - IMPRESSION: - - Heart size and mediastinum are stable. Port-A-Cath catheter tip terminates at - the level of lower SVC. Left pleural effusion on left basal atelectasis are - unchanged as well as small right pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s55292707.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s55292707.txt deleted file mode 100644 index 1d3605bd642af1ecfacb8c2f2ff0bdfc7352f089..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s55292707.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with hypercarbic resp failure s/p extubation - and multifocal pneumonia // interval changes interval changes - - IMPRESSION: - - In comparison with the study of ___, there is little overall change. - Continued enlargement of the cardiac silhouette with opacification in the left - base consistent with a combination of layering effusion and volume loss in the - left lower lobe. No change in the appearance of the Port-A-Cath. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s58895944.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s58895944.txt deleted file mode 100644 index caaf735079a3060ecb467cdc34822b9c684c5f75..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17460568/s58895944.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with MDS with recent respiratory failure and - known LLL PNA // interval change - - TECHNIQUE: Chest PA and lateral - - FINDINGS: - - As compared to ___, moderate right-sided effusion has not - substantially changed into the adjacent opacity, given for differences in - technique. No pulmonary edema. The right lung is clear. No pneumothorax. - Right-sided Port-A-Cath with the tip in the low SVC. - - IMPRESSION: - - Given for differences in technique, no significant change in moderate left - effusion and atelectasis/consolidation. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17729489/s55691624.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17729489/s55691624.txt deleted file mode 100644 index ab8d7e7d48fc55ed33540604d6f670051dc5e484..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17729489/s55691624.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAM: Chest frontal and lateral views. - - CLINICAL INFORMATION: Dyspnea. - - COMPARISON: ___. - - FINDINGS: Frontal and lateral views of the chest were obtained. There is - moderate pulmonary edema. Superimposed infectious process is not entirely - excluded. Trace blunting of the costophrenic angle suggests trace bilateral - pleural effusions. The cardiac and mediastinal silhouettes are grossly - stable. There is no pneumothorax. - - IMPRESSION: Pulmonary edema and small bilateral pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s55106255.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s55106255.txt deleted file mode 100644 index f2e9c13d7e124bee9609fd610e01542469e87994..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s55106255.txt +++ /dev/null @@ -1,35 +0,0 @@ - WET READ: ___ ___ ___ 8:17 AM - - - - Lung volumes are very low with new atelectasis at the lung bases, left greater - than right. There may be a tiny right pleural effusion blunting the - costophrenic sulcus. There is no evidence of pneumomediastinum. There is no - subdiaphragmatic free air. The stomach is notably distended with gas. - - The findings were telephoned to ___ ___ by ___ at 22:05, - ___, ___ min after discovery. - WET READ VERSION #___ ___ ___ 10:10 PM - Lung volumes are very low with new atelectasis at the lung bases, left greater - than right. There may be a tiny right pleural effusion blunting the - costophrenic sulcus. There is no evidence of pneumomediastinum. There is no - subdiaphragmatic free air. The stomach is notably distended with gas. - - The findings were telephoned to ___ by ___ at 22:05, - ___, ___ min after discovery. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man S/P difficult foreign body removal // - ?pneumoperitoneum or pneumomediastinum - - COMPARISON: ___, 15:52 - - IMPRESSION: - - As compared to the previous radiograph, the metallic foreign bodies, visible - on the previous image, are no longer displayed. The stomach is overinflated. - The lung volumes are low and show atelectasis at the left lung bases and in - the right mid lung zones. No evidence of free air under at or over the - diaphragm. Borderline size of the cardiac silhouette without pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s57457715.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s57457715.txt deleted file mode 100644 index a8fee19eb26cd412bca8c3baec090510f906ca0d..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p17/p17938416/s57457715.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: - CHEST (PA AND LAT) - - INDICATION: - ___ year old man with h/o frequent foreign object ingestion now s/p extraction - of ingested battery. // evaluation of esophageal injury - - TECHNIQUE: Chest two-view. - - COMPARISON: ___ - - IMPRESSION: - - There continue to be patchy areas of atelectasis in both lower lungs. There is - a small left effusion has increased compared to the prior study. There is no - mediastinal air to suggest esophageal perforation. The PICC line is - unchanged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18002691/s59240203.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18002691/s59240203.txt deleted file mode 100644 index 7325b4b7d070ef200dbd04ae7852213fea41c79e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18002691/s59240203.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - PORTABLE CHEST, ___ - - No prior studies for comparison. - - FINDINGS: The right cardiomediastinal contour has a pronounced convexity, and - extends farther lateral than expected, particularly considering the normal - appearance of the left cardiac contour. There is an additional rightward - convexity to the left of the spine. It is uncertain whether this represents a - markedly enlarged cardiac chamber or a paracardiac mass such as a hiatal - hernia. Pulmonary vascularity is normal centrally, but paucity of vessels in - upper lobes suggests the possibility of emphysema. With the exception of - atelectasis adjacent to the right cardiac border, lungs are otherwise grossly - clear. - - IMPRESSION: Unusual configuration of right cardiomediastinal contour, which - could be due to an enlarged cardiac chamber or paracardiac mass such as a - large hiatal hernia. - - In the absence of older radiographs for comparison, this could initially be - further evaluated with dedicated PA and lateral chest radiographs when the - patient's condition permits, as communicated by phone to Dr. ___ on - ___ at 8:45 a.m. at the time of discovery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50167331.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50167331.txt deleted file mode 100644 index 1ba872145d71fd8e27d77b4cb84ed6ff4e53302a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50167331.txt +++ /dev/null @@ -1,22 +0,0 @@ - WET READ: ___ ___ ___ 5:38 PM - No acute cardiopulmonary abnormality. Right-sided PICC in the distal SVC. - Numerous stable calcified granulomas. - - ______________________________________________________________________________ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Failure to thrive, treatment for aspiration pneumonia, evaluation - for pneumonia. - - COMPARISON: ___. - - FINDINGS: The radiograph is compared to ___. - - The right PICC line is unchanged. The lung parenchyma shows signs of - overinflation and calcified granulomas in both the left and the right lung. - However, there is no focal increase in lung density that would suggest - pneumonia. The structure of the bones is minimally inhomogeneous, likely - related to the underlying disease. Scoliosis with asymmetry of the rib cage. - Normal size of the cardiac silhouette. Tortuosity of the thoracic aorta. No - pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50903426.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50903426.txt deleted file mode 100644 index dc00c03ed3e76ce89236846cd3a93c8e2820bb16..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s50903426.txt +++ /dev/null @@ -1,20 +0,0 @@ - WET READ: ___ ___ ___ 7:26 PM - No acute cardiopulmonary process. - - WET READ VERSION #1 - ______________________________________________________________________________ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: CLL, evaluation for pneumonia or aspiration. - - COMPARISON: No comparison available at the time of dictation, the exam is - compared to the CT chest from ___. - - FINDINGS: As compared to the CT examination, there is no relevant change. No - evidence of rib lesions. Normal appearance of the lung parenchyma with some - hyperlucencies in the lung apices, consistent with mild pulmonary emphysema. - - No acute changes such as pneumonia or pulmonary edema. Normal size of the - cardiac silhouette. Moderate tortuosity of the thoracic aorta. The nodules - described on the CT examination are not visible on the current radiograph. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s57967524.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s57967524.txt deleted file mode 100644 index a71dc8e2a1f64bc45ddddba87072be347ef47827..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18011403/s57967524.txt +++ /dev/null @@ -1,7 +0,0 @@ - FINAL REPORT - HISTORY: Aspiration and cough. - - FINDINGS: In comparison with study of ___, there has been placement of a - Dobbhoff tube that extends at least to the upper body of the stomach where it - crosses the lower margin of the image. No evidence of acute cardiopulmonary - disease. Central catheter remains in place. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18060672/s58828901.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18060672/s58828901.txt deleted file mode 100644 index 17541edd3931581e7df5e0c32a15ef92208fb890..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18060672/s58828901.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___M with sob and back pain // eval pneumonia - - TECHNIQUE: Frontal and lateral views of the chest. - - COMPARISON: ___ - - FINDINGS: - - Rounded right upper lobe pulmonary mass is again seen which measures - approximately 8.6 cm. The lungs are otherwise clear. The cardiomediastinal - silhouette is within normal limits. No acute osseous abnormalities. - - IMPRESSION: - - 8 cm right upper lobe mass as seen on recent imaging. No superimposed acute - cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18061894/s55209280.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18061894/s55209280.txt deleted file mode 100644 index c352637c512bb2f5570c4f2e0d92ddda23fbd932..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18061894/s55209280.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___F with CP and bibasilar rales - - COMPARISON: None - - FINDINGS: - - AP portable upright view of the chest. Overlying EKG leads are present - somewhat limiting assessment. Evaluation is limited due to underpenetrated - technique especially at the level of the lung bases. Allowing for technical - limitations, the lungs appear clear though hyperinflated with upper lung - lucency suggestive of underlying emphysema. The cardio mediastinal silhouette - is notable for mild prominence of the main pulmonary artery likely reflective - of pulmonary hypertension. No definite signs of pneumonia or edema. No large - effusion or pneumothorax. Imaged bony structures are intact. No free air - below the right hemidiaphragm. - - IMPRESSION: - - COPD with probable pulmonary arterial hypertension. No definite signs of - pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s56469884.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s56469884.txt deleted file mode 100644 index 5813ee6c5c928d97c6c1a7bc425abe4553c99a29..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s56469884.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old man with post-thoracentesis. - - COMPARISON: PA and lateral chest radiograph ___. - - TECHNIQUE: PA and lateral radiographs of the chest. - - FINDINGS: There is a left apical pneumothorax which is 3.8 cm in maximal - span. There has been marked reduction in the amount of pleural effusion seen - in left hemithorax with residual opacity seen in the lingula. Lung is - unremarkable. Cardiomediastinal silhouette is stable and within normal limits. - The pleural surfaces are unremarkable. - - IMPRESSION: Left-sided pneumothorax 3.8 cm in maximal dimension. - - These findings were reported to Dr. ___ via phone at 4:35 p.m. by - ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s59118250.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s59118250.txt deleted file mode 100644 index d32800759b93b7da316412c728863b57bc6ae54e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18092532/s59118250.txt +++ /dev/null @@ -1,24 +0,0 @@ - WET READ: ___ ___ ___ 8:51 PM - Moderate left apical pneumothorax, stable since 2:30 p.m today. Re-expanding - LLL with minimal edema. Right lung is clear. ___ d/w Dr.___ on ___ - at 8:45 p.m who was aware of the findings. - ______________________________________________________________________________ - FINAL REPORT - STUDY: AP portable chest radiograph. - - INDICATION: Assess for possible pneumothorax . - - TECHNIQUE: Portable AP chest radiograph was obtained at 18:25. - - COMPARISON: Same day radiograph obtained at 14:33. - - REPORT: - - There is a left-sided pneumothorax present. This is not changed significantly - in size from prior study. The left-sided pleural effusion is again - identified, with an air-fluid level, although this is not as well appreciated - on current study. - - CONCLUSION: - - Essentially unchanged left-sided pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18150052/s57453418.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18150052/s57453418.txt deleted file mode 100644 index a498f187700d28c0e6318909e2d416f7922f27ab..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18150052/s57453418.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man s/p aortibifem bypass // eval for edema/effusion - eval for edema/effusion - - IMPRESSION: - - Compared to chest radiographs ___ and ___. - - Previous pulmonary edema has largely cleared, persisting only in the lung - bases, and left upper lobe atelectasis has resolved. Heart size is now - normal, there is no appreciable pleural effusion or mediastinal vascular - engorgement. - - Right jugular sheath ends at the origin of the SVC. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18182458/s58849680.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18182458/s58849680.txt deleted file mode 100644 index 81a31f27e1b05311e9bc361440cf3d0367f05aa5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18182458/s58849680.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - PORTABLE CHEST ___ WITH COMPARISON ___ RADIOGRAPH - - FINDINGS: Cardiac silhouette is upper limits of normal in size. Mild - pulmonary vascular congestion is present with minimal interstitial edema. - Patchy opacity at right lung base is probably due to patchy atelectasis, but - followup chest radiograph may be helpful to exclude an early focus of - pneumonia. At that time, the trachea may be reassessed to evaluate whether - apparent rightward deviation is due to the effects of slight rightward - rotation or due to displacement from enlargement of the left lobe of thyroid - gland. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s50195350.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s50195350.txt deleted file mode 100644 index 1a8b03481fe295685268c89b4e5f26652c33f4ed..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s50195350.txt +++ /dev/null @@ -1,19 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man w/ IPH now s/p L crani hematoma evacuation. - Unable to extubate in OR ___ desats. // ?tube placement ?aspiration - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest xray ___ - - FINDINGS: - - The tip of the ET tube is approximately 4 cm from the carina, in appropriate - location. The lung volumes are decreased. There is mild pulmonary edema. - There is mild cardiomegaly. Normal hilar and mediastinal structures. No - pneumonia and no pleural effusions. - - IMPRESSION: - - ET tube tip is approximately 4 cm from carina. Decreased lung volumes. Mild - pulmonary edema with mild cardiomegaly. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53481616.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53481616.txt deleted file mode 100644 index f7c759d3bed311eb07b13ae899b55176dc0718e7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53481616.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with respiratory failure, intubated, being - diuresed // ?interval change - - TECHNIQUE: Portable chest - - COMPARISON: ___. - - FINDINGS: - - The endotracheal tube continues to be slightly low, 1.5 cm above the carina. - Lung volumes are low and there is crowding at the bases. There has been some - interval partial clearing of the left lower lobe volume loss/infiltrate. - There continue to be small bilateral pleural effusions - - IMPRESSION: - - Slight improvement compared to prior diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53510305.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53510305.txt deleted file mode 100644 index 783fda53c227f5f3d5c2ed753880ddf916693c39..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s53510305.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with new OGT // ?OGT placement ?OGT - placement - - IMPRESSION: - - In comparison with the study of ___, there has been placement of a - nasogastric tube that extends to the body of the stomach before curving back - upward with the tip below the esophagogastric junction but pointing toward the - esophagus. - Otherwise, little overall change except for some improved pulmonary - vascularity that could represent better inspiration. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s54764940.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s54764940.txt deleted file mode 100644 index 7160811f426944827e38ccf97680993930ea8a55..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s54764940.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with L frontal IPH and SAH s/p L craniotomy w/ - clot evacuation on ___, still intubated. // interval change - - TECHNIQUE: Portable chest - - COMPARISON: ___. - - FINDINGS: - - There is increased volume loss in the right lower lung with hazy alveolar - infiltrate on the right. There is also increased volume loss in the left - lower lung which could obscure an underlying infiltrate there is mild - pulmonary vascular redistribution. There probable small bilateral effusions. - The ET tube is 2 cm above the carina. NG tube tip is off the film, at least - in the stomach - - IMPRESSION: - - Increased volume loss/ infiltrate in both lower lungs diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s55412390.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s55412390.txt deleted file mode 100644 index bf2fbc3f6aa08e9b8d78573116830560d2832260..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s55412390.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with IPH s/p clot evacuation. Diuresing. // - Interval change. - - TECHNIQUE: CHEST (PORTABLE AP) - - COMPARISON: ___ - - IMPRESSION: - - ET tube tip is 3.5 cm above the carinal. NG tube tip is in the stomach. - Heart size and mediastinum are stable. There is evidence of bibasal - atelectasis as well as unchanged appearance of the right hilar enlargement. - Upper lungs are essentially clear. Assessment of the patient with chest CT is - recommended for precise characterization of the right hilus PE diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s57154737.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s57154737.txt deleted file mode 100644 index f558842aa1800e5fe23c8feb168891ea68ef7e0c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s57154737.txt +++ /dev/null @@ -1,21 +0,0 @@ - WET READ: ___ ___ ___ 8:02 AM - - - - New tracheostomy tube appears to be in appropriate position. - WET READ VERSION #1 ___ ___ ___ 9:56 PM - New tracheostomy tube appears to be in appropriate position. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with new tracheostomy // ?tracheostomy placement - - COMPARISON: ___. - - IMPRESSION: - - As compared to the previous radiograph, the nasogastric tube and the - endotracheal tube was removed, the newly placed tracheostomy tube is in - correct position. No pneumothorax or pneumomediastinum. Moderate - cardiomegaly. Unremarkable appearance of the lung parenchyma. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s58360065.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s58360065.txt deleted file mode 100644 index 11807e53162f9cd14a2935bb43d573d4a670ab82..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s58360065.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with desaturation // R/o pulmonary edema - - TECHNIQUE: Portable chest - - COMPARISON: ___ at 456 - - FINDINGS: - - Lung volumes are low and there is crowding at the bases. Even allowing for - this there is increased opacity at the left base that likely represents a - developing infiltrate there is pulmonary vascular redistribution and mild - cardiomegaly the ET tube tip is 1.5 cm above the carina. NG tube tip is off - the film, at least in the stomach - - IMPRESSION: - - - - 1. CHF, slightly improved compared to prior - 2. Focal area of concern of the left lower lobe could represent a developing - infiltrate diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s59080057.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s59080057.txt deleted file mode 100644 index b7441e6318ac066d77a9bbfc5f13c1ea9d6a95b7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18448597/s59080057.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - INDICATION: ___M with cough // acute process? - - TECHNIQUE: AP and lateral views of the chest. - - COMPARISON: ___. - - FINDINGS: - - Tracheostomy tube with overlying oxygen mass is noted. Right sided PICC tip - seen within the lower SVC. Low lung volumes are seen with right basilar - atelectasis. The lungs are clear of consolidation or effusion. The - cardiomediastinal silhouette is within normal limits. No acute osseous - abnormalities. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18539377/s56971103.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18539377/s56971103.txt deleted file mode 100644 index 5c68442f975ffb18da21b676c1d79c598d8b253e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18539377/s56971103.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___F with confusion - - TECHNIQUE: Semi-upright AP view of the chest - - COMPARISON: None. Patient is currently listed as EU critical. - - FINDINGS: - - Left-sided dual-chamber pacemaker device is noted with leads terminating in - the right atrium and right ventricle. Mild enlargement of the cardiac - silhouette is noted. Mediastinal and hilar contours are grossly unremarkable. - Pulmonary vasculature is not engorged. There may be minimal atelectasis in - the left lung base without focal consolidation. No pleural effusion or - pneumothorax is identified. No acute osseous abnormality is detected. - Degenerative changes of the left glenohumeral joint are incompletely assessed. - - IMPRESSION: - - No acute cardiopulmonary abnormality. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18551168/s58952496.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18551168/s58952496.txt deleted file mode 100644 index 9f843527d7076ddf59f1eb286dadb1c2d21f3538..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18551168/s58952496.txt +++ /dev/null @@ -1,20 +0,0 @@ - WET READ: ___ ___ ___ 8:52 PM - Endotracheal tube terminates 5.3 cm above the carina. An enteric tube - terminates within the stomach. There is persistent, partial collapse of the - right lower lobe however there is improved ventilation of the right lower lobe - compared to 14:43 today. No pneumothorax. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___M brought in by ambulance after being found unresponsive in - community. // ? placement of ETT, improvement in RLL collapse on prior ? - placement of ETT, improvement in RLL collapse on prior - - IMPRESSION: - - ___. Endotracheal tube has been slightly advanced. The tip now - projects approximately 5 cm above the carinal. Improvement of the - pre-existing right atelectasis, with improved. Ventilation of the right lung - base. Moderate cardiomegaly persists. No pleural effusions. No pulmonary - edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18728663/s52124340.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18728663/s52124340.txt deleted file mode 100644 index 29e7301b46df612eff752ab3ed715ab80def67e5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18728663/s52124340.txt +++ /dev/null @@ -1,31 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old male with multi trauma. - - COMPARISON: Outside hospital chest radiograph dated ___. - - TECHNIQUE: Single frontal chest radiograph was obtained portably with the - patient in an upright position. - - FINDINGS: - - New hazy opacification of the right hemithorax likely represents a combination - of new parenchymal opacity and layering fluid. New small left pleural - effusion is seen. No pneumothorax is evident on this view. There is possibly - new pneumomediastinum. Heart size is within normal limits. The stomach is - distended with air. Metallic densities projecting over the left upper - quadrant likely reflect recent splenic embolization. - - Right rib fractures are better seen on recent prior CT. - - IMPRESSION: - - 1. New right parenchymal opacity and pleural effusion, possibly secondary to - aspiration and/or edema. - - 2. Possible new pneumomediastinum. CT could be performed for more definitive - evaluation. - - 3. Distended stomach. - - Findings discussed with ___ by ___ by phone at 4:01 - p.m. on ___ after attending radiologist review. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18771968/s53209617.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18771968/s53209617.txt deleted file mode 100644 index 99a55e8048edc37c77cd022c37690d12d570898a..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18771968/s53209617.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with IPH // intubated, assess for infiltrates - intubated, assess for infiltrates - - IMPRESSION: - - Compared to chest radiograph ___:38. - - Even though Mediastinal veins are more distended, previous pulmonary vascular - congestion has improved slightly, but there is more peribronchial - opacification and consolidation in both lower lobes which could be atelectasis - or alternatively results of recent aspiration, possibly progressing to - pneumonia. Borderline cardiac enlargement is stable. Small left pleural - effusion is likely. - - Cardiopulmonary support devices in standard placements. No pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s53933848.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s53933848.txt deleted file mode 100644 index afd04187955d63d834a1b59a24683bc365a1ad9e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s53933848.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with hypoxia // eval for acute process eval - for acute process - - IMPRESSION: - - In comparison with the study of ___, there is continued enlargement of - the cardiac silhouette with prominence of the aorta. There is now - indistinctness of engorged pulmonary vessels, consistent with developing - pulmonary vascular congestion. This vascular congestion is asymmetric, more - prominent on the left. In the appropriate clinical setting, superimposed - pneumonia would have to be considered. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s58169828.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s58169828.txt deleted file mode 100644 index aa755dedb58d0decf5e67620a30cb9accdd36540..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18773874/s58169828.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: History of recent operation. Please evaluate for fever. - - COMPARISONS: Radiograph from ___. - - TECHNIQUE: AP and lateral radiographs of the chest. - - FINDINGS: Moderate cardiomegaly has been stable compared to exams dated back - to at least ___. There is pulmonary vascular congestion. There - has been an interval increase in left basilar opacification. There is also an - increase in small right pleural effusion. There is no evidence of a - pneumothorax. Nodule previously identified near the left hilus is not well - visualized on this study, possibly obscured by vascular congenstion and - infiltrate/atelectasis. - - IMPRESSION: - - 1. Interval increase in opacity at the left lung base is concerning for - pneumonia. - - 2. Mild pulmonary edema. - - 3. Interval increase in small right pleural effusion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18780188/s51426244.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18780188/s51426244.txt deleted file mode 100644 index cfaa14cc885515f0d94af4ce9921b29da877715c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18780188/s51426244.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: ___M with cough, r sided rib pain // R rib fractures? pna? - - TECHNIQUE: AP and lateral views of the chest. - - COMPARISON: None. - - FINDINGS: - - The lungs are clear. There is no effusion, consolidation, or edema. Mild - cardiomegaly is noted. Atherosclerotic calcifications are seen at the aortic - arch. There is no visualized acute displaced fracture. Deformity of the left - anterior ribs appears chronic. No definite acute displaced fracture - identified. - - IMPRESSION: - - No acute cardiopulmonary process. - No acute displaced rib fractures identified, consider dedicated rib series for - increased sensitivity if desired. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18787238/s57000594.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18787238/s57000594.txt deleted file mode 100644 index f81c2808d6217f6e32d1728d43b020fc103fb0d0..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18787238/s57000594.txt +++ /dev/null @@ -1,18 +0,0 @@ - FINAL REPORT - HISTORY: ___-year-old female with chest pain. - - COMPARISON: ___. - - FINDINGS: - - Frontal and lateral views of the chest. Lower lung volumes are seen on the - current exam with secondary crowding of the bronchovascular markings. Hazy - bibasilar opacities are likely due to atelectasis and potentially scarring - particularly on the left as seen on prior. There is no effusion. The cardiac - silhouette is enlarged but likely accentuated due to lower lung volumes. No - acute osseous abnormality detected. Surgical clips seen in the upper right - upper quadrant. - - IMPRESSION: - - No definite acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18794122/s56331259.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18794122/s56331259.txt deleted file mode 100644 index 40e6f455d6965edded2a2efd8881d8153ff44034..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18794122/s56331259.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman with recent hip fx likely fat emboli - complicated by hypoxia and CVA, now on enoxaparin and with new hypoxia, - evaluate for interval change. - - TECHNIQUE: Portable chest radiograph - - COMPARISON: Chest radiograph from ___ and ___. Chest CT - ___. - - FINDINGS: - - Since prior, there has been no significant interval change. The heart remains - mildly enlarged. There are emphysematous changes without focal lung - consolidation to suggest pneumonia. There is no evidence of pulmonary edema, - pleural effusion, or pneumothorax. - - IMPRESSION: - - No significant interval change. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50024420.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50024420.txt deleted file mode 100644 index 9c1b8727bbbe8aa733607b180f2904104977cd1f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50024420.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with CHF s/p AICD // Pulmonary edema vs - aspiration? Pulmonary edema vs aspiration? - - IMPRESSION: - - In comparison with the outside study of ___, there is now an endotracheal - tube in place with its tip approximately 4.3 cm above the carina. Nasogastric - tube extends well into the stomach. Single lead pacer device extends to the - right ventricle. - There is enlargement of the cardiac silhouette with pulmonary vascular - congestion. In the appropriate clinical setting, the possibility of - superimposed aspiration would have to be considered, especially in the left - upper and left lower lung zones. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50390234.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50390234.txt deleted file mode 100644 index 77af746a50c0760c3863bb1b3c504c428c4537dd..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18855412/s50390234.txt +++ /dev/null @@ -1,40 +0,0 @@ - WET READ: ___ ___ 5:24 PM - Endotracheal tube tip in standard position. Orogastric tube tip is seen to the - level of the gastroesophageal junction, but not clearly seen below the - diaphragm. Consider dedicated AP view of the abdomen for further assessment of - the tip of the orogastric tube. Mild pulmonary edema, worse compared to 11:03 - today. Patchy opacities in the lung upper lobes, more pronounced on the left, - may reflect areas of infection or aspiration. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: History: ___M with intubation. - - TECHNIQUE: Supine AP view of the chest - - COMPARISON: ___ at 14:34 and 11:03 - - FINDINGS: - - Assessment is somewhat limited by patient rotation. An endotracheal tube tip - terminates approximately 3.6 cm from the carina. Orogastric tube tip is seen - coursing inferiorly below the diaphragm though the tip is not well seen. - Patient is status post median sternotomy and CABG. Left-sided AICD/ pacemaker - device is noted with single lead terminating in the region of the right - ventricle. Heart is moderately enlarged with a left ventricular predominance. - The aorta remains tortuous. There is mild pulmonary edema, which has - progressed since ___:03 today. More focal ill-defined opacities within the - upper lobes bilaterally, greater on the left, may reflect areas of aspiration - or infection. No pneumothorax is identified, and no pleural effusion is seen. - - IMPRESSION: - - - - 1. Endotracheal tube tip in standard position. Orogastric tube courses below - the diaphragm. While the tip is not well seen, it is likely within the - stomach. - 2. Mild pulmonary edema, worse compared to 11:03 today. - 3. Patchy opacities in the lung upper lobes, more pronounced on the left, may - reflect areas of infection or aspiration. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s53855418.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s53855418.txt deleted file mode 100644 index 73c0eee68d60175068f9387016901b905a4343c2..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s53855418.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman s/p ct removal // r/o ptx - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiograph ___ - - FINDINGS: - - Since ___, no significant change. Bibasilar atelectasis is stable. Small - bilateral pleural effusions are unchanged. Unchanged left retrocardiac - opacity concerning for left lower lobe collapse. Median sternotomy wires in - place. The lung volumes are normal. Normal size of the cardiac silhouette. - Normal hilar and mediastinal structures. No pneumonia, no pulmonary edema. No - pneumothorax. - - IMPRESSION: - - No significant interval change from ___. Unchanged bibasilar atelectasis - with small pleural effusions. Persistent left lower lobe collapse. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s54231592.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s54231592.txt deleted file mode 100644 index f9f16c928eddd06f6f3070f2029087947d3bd468..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s54231592.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: History: ___F with post chest tube placement // check chest tube - placement - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiograph ___ 21:21, CT chest ___ - - FINDINGS: - - Left chest tube terminates at medial left lung apex. Position of the left - chest tube was better evaluated on subsequent chest CT which was available at - the time of this dictation. Consolidation of left lung is increased compared - to the radiograph prior to the chest tube placement. Diffuse left-sided - opacity is suggestive of layering of hemothorax, similar to before. Left - pneumothorax is small. Cardiac silhouette is normal size. - - IMPRESSION: - - Left chest tube terminates at medial left lung apex. Position of the left - chest tube was better evaluated on subsequent chest CT which was available at - the time of this dictation. Consolidation of left lung is increased. Small - left pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s55981123.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s55981123.txt deleted file mode 100644 index 06eab09c06fc25466a1002dedcd4e6c36ef3beac..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18881929/s55981123.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with effusion s/p tube removal // interval - change, PTX? - - IMPRESSION: - - As compared to ___, cardiomediastinal contours are within normal - limits, and left lower lobe atelectasis has substantially improved in the - interval. Multifocal linear atelectasis in the right mid and lower lung has - also slightly improved. Interval decrease in small left pleural effusion, - nearly resolved, and no evidence of pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18916144/s56836467.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18916144/s56836467.txt deleted file mode 100644 index 17945348616ac99193573b19a95f7032b4130f98..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18916144/s56836467.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: Chest pain and bradycardia. Evaluate for pneumonia. - - COMPARISONS: Chest radiograph from ___. - - TECHNIQUE: A single AP upright view of the chest was obtained. - - FINDINGS: Since prior exam, there are new interstitial opacities and vascular - congestion, most consistent with moderate pulmonary edema. There is no focal - airspace opacity, pleural effusion, or pneumothorax. The mediastinal contours - are normal. The heart size is mildly enlarged. - - IMPRESSION: New moderate pulmonary edema. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s53201922.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s53201922.txt deleted file mode 100644 index db5955127c8bac882cfeb0484ed33525d77293e9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s53201922.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old man with pigtail discontinued // ?pneumothorax? - ?pneumothorax? - - COMPARISON: Comparison to ___ at 09:28 - - FINDINGS: - - PA and lateral views the chest ___ at 17 11 are submitted. - - IMPRESSION: - - There has been interval removal of the right basilar pigtail catheter. The - lucency anteriorly on the previous lateral view is less apparent suggesting - that previously seen tiny pneumothorax has become even smaller. Streaky - opacities at the right base persist favoring atelectasis rather than - infectious process. Clinical correlation is advised. Right subclavian PICC - line is unchanged. Surgical clips are again seen overlying the left axillary - region. Overall cardiac and mediastinal contours are unchanged. A dense - nodular opacity at the left apex is unchanged consistent with a granuloma. No - evidence of pulmonary edema. No large pleural effusions. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s56566723.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s56566723.txt deleted file mode 100644 index 6e78b4a522b68ca69d0ff36cb47311a5dd2e0cf0..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s56566723.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old man with new chest tube // interval change - interval change - - IMPRESSION: - - In comparison with the study of ___, there is a right chest tube in - place. No definite residual pneumothorax. An area of increased opacification - is seen at the right base. Although this could represent merely atelectasis, - in the appropriate clinical setting superimposed pneumonia would have to be - seriously considered. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s57653161.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s57653161.txt deleted file mode 100644 index 6fda449da5d6115d79af06e03e36967066fdfa26..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s57653161.txt +++ /dev/null @@ -1,25 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ year old man with iatrogenic PTX, s/p IR pigtail placement. - Has been on WS. // evaluation of R PTX evaluation of R PTX - - COMPARISON: Comparison to prior study ___ at 10:39 - - FINDINGS: - - PA and lateral views of the chest ___ at 09:28 are submitted. - - IMPRESSION: - - Right subclavian PICC line remains in place. A right basilar pigtail catheter - is also in place. There is a tiny right-sided pneumothorax as evident by - lucency anteriorly on the lateral view. There continue be streaky opacities - at the right base which appear less confluent given interval improvement in - inspiration. Although this may represent an area of atelectasis, early - pneumonia should also be considered. The left lung is clear. Surgical clips - are again seen overlying the left axillary region. No evidence of pulmonary - edema. Overall cardiac and mediastinal contours are stable. - - NOTIFICATION: Results of this examination were called to the patient's - intern, Dr. ___, on ___ at 13 55 at the time of discovery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s58902785.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s58902785.txt deleted file mode 100644 index 914d53d7733601bd01b2f58f32e1cd5be0bce2b7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18969313/s58902785.txt +++ /dev/null @@ -1,21 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old man with persistent O2 requirement // pls eval for R - ptx pls eval for R ptx - - TECHNIQUE: AP and lateral chest views - - COMPARISON: Radiograph dated ___ - - FINDINGS: - - Likely due to technique, the prior radiograph did not show the pneumothorax. - However, there is a right-sided pneumothorax that has a its apex 2.3 cm from - the pleura. Otherwise the cardiomediastinal silhouette is unchanged. There are - no new parenchymal consolidations seen. - - IMPRESSION: - - Right-sided apical pneumothorax - - NOTIFICATION: NP, ___ was notified of the impression ___ minutes after - their discovery. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18971123/s57539379.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18971123/s57539379.txt deleted file mode 100644 index 59e32e0cd8f994ea70af4ea6b9aced3cb919f1cf..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p18/p18971123/s57539379.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT) - - INDICATION: ___ with anorexia, c. diff with new complaints of pleuritic right - flank pain // r/o PNA, PTX r/o PNA, PTX - - IMPRESSION: - - In comparison with the study of ___, the tip of the right subclavian - catheter appears to have been advanced to the cavoatrial junction or possibly - the upper portion of the right atrium. The Dobhoff tube extends at least to - the lower stomach where it crosses the inferior margin of the image. - No evidence of acute cardiopulmonary disease. Specifically, no pneumonia or - pneumothorax. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s53138804.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s53138804.txt deleted file mode 100644 index 8161f8dd3ff3acb4136805ac19129b48f7925caa..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s53138804.txt +++ /dev/null @@ -1,11 +0,0 @@ - FINAL REPORT - REASON FOR EXAMINATION: Evaluation of the patient with mental status changes. - - COMPARISON: ___ radiograph. - - Large hiatal hernia is projecting over the left lower lung behind the cardiac - silhouette. There are bibasal opacities concerning for interval increase of - areas of atelectasis. Infectious process is less likely but cannot be - excluded. Small bilateral pleural effusions are present. Mild vascular - engorgement is seen, might be consistent with interval fluid load on the - patient. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s55529237.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s55529237.txt deleted file mode 100644 index ca4bbc49a41a4cfa768b1527e136bca9a27b00a7..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19023440/s55529237.txt +++ /dev/null @@ -1,12 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old female with unresponsiveness after heatstroke. - Evaluate for infection. - - No prior examinations for comparison. - - CHEST, AP: Lung volumes are low, but there is no definite consolidation. - Heart size is at the upper limits of normal. Hiatal hernia is noted. The - aorta is tortuous and unfolded. No significant pleural effusions or - pneumothorax. No displaced rib fractures are identified. - - IMPRESSION: No acute cardiopulmonary process. Low lung volumes. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19052988/s54960496.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19052988/s54960496.txt deleted file mode 100644 index 1241d09102bb1ef34d0302c46becb3e65964abb1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19052988/s54960496.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - PORTABLE CHEST ___ - - COMPARISON: Study of earlier the same date. - - FINDINGS: Interval placement of endotracheal tube, with the tip terminating - 2.3 cm above the carina with the neck in a flexed position. Nasogastric tube - terminates in the stomach. Stable cardiomegaly with left ventricular - configuration of the heart. Pulmonary vascular congestion is accompanied by - mild edema. Worsening right lower lobe and new left lower lobe opacities may - be due to a combination of atelectasis, aspiration and potentially infectious - pneumonia. Small right and moderate left pleural effusions are new. - Previously noted right rib fractures are less well visualized on the current - study, there is no visible pneumothoraces. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s53595210.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s53595210.txt deleted file mode 100644 index 793b75c18dd9cd87f0173052196358fc956cb972..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s53595210.txt +++ /dev/null @@ -1,7 +0,0 @@ - FINAL REPORT - HISTORY: COPD and pneumonia with intubation. - - FINDINGS: In comparison with the study of ___, there is some increased - opacification in the retrocardiac region, most likely representing worsening - atelectasis. Continued hyperexpansion of the lungs with moderate cardiomegaly - and Kerley lines suggesting increased pulmonary venous pressure. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56003558.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56003558.txt deleted file mode 100644 index 68ba3ef916334b0d40a270dff20a24b378f46592..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56003558.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old female with increased secretions and worsening - respiratory function. - - COMPARISON: ___. - - TECHNIQUE: Single frontal chest radiograph was obtained portably with the - patient in an upright position. - - FINDINGS: There is increased retrocardiac density and subtle increased - opacity of the right lower lung. No pleural effusion, pneumothorax, or - pulmonary edema is detected. Evidence of emphysema corresponds with recent - chest CT findings. Cardiomegaly persists. Calcified tortuous aorta is again - noted. - - IMPRESSION: Increased bibasilar opacities, which likely reflect aspiration; - atelectasis and early infection are also possibilities. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56007548.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56007548.txt deleted file mode 100644 index 259b61efb145325d71916830c1611f91d421d344..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s56007548.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: COPD, ETT placement. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is no relevant - change. The tip of the endotracheal tube still projects 4 cm above the - carina. A nasogastric tube is in unchanged position. Moderate cardiomegaly, - mild retrocardiac atelectasis and slightly increased density of the lung - parenchyma at the right lung base is unchanged. NO newly occurred parenchymal - opacities. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s58849041.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s58849041.txt deleted file mode 100644 index f2b5c6e990b1540da50dff6448a54bf35fc5f9d9..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19103929/s58849041.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - AP CHEST, 10:53 AM ON ___ - - HISTORY: COPD. Reintubated. - - IMPRESSION: AP chest compared to ___ at 4:08 a.m.: - - Endotracheal tube ends no less than 2 cm above the carina and could be - withdrawn 2 cm to avoid unilateral intubation in the future. There is no - pneumothorax; right skin fold which should not be mistaken for a pleural edge. - Very mild interstitial edema may be present in the right lung. Consolidation - at the left base, largely pneumonia is unchanged. Heart size is top normal. - Pleural effusions are small if any. No pneumothorax. Severe emphysema is - chronic. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19280440/s58775991.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19280440/s58775991.txt deleted file mode 100644 index 1c8883aa27bef794ad753d935abfcfa1c00471c5..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19280440/s58775991.txt +++ /dev/null @@ -1,22 +0,0 @@ - FINAL REPORT - EXAM: Chest single AP upright portable view. - - CLINICAL INFORMATION: Tachycardia. - - COMPARISON: None. - - FINDINGS: Single AP upright portable view of the chest was obtained. There - are low lung volumes, which accentuate the bronchovascular markings. Given - this, there is patchy right basilar opacity which could be due to atelectasis - in combination with vascular engorgement, although consolidation from - infection is not excluded. No large pleural effusions are seen, although - trace effusions will be difficult to exclude. There is no evidence of - pneumothorax. Cardiac and mediastinal silhouettes are unremarkable. Hilar - contours are prominent, likely accentuated by low lung volumes; however, - pulmonary vascular engorgement may be present. - - IMPRESSION: - 1. Low lung volumes which accentuate the bronchovascular markings. Patchy - right basilar opacity, pneumonia not excluded versus atelectasis. - 2. Prominence of the hila, likely accentuated by low lung volumes; however, - vascular engorgement may be present. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s55489946.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s55489946.txt deleted file mode 100644 index e5ff501fdb3eeb35dac42a76f027199e92345387..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s55489946.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - EXAMINATION: Chest radiographs - - INDICATION: History: ___F with fever // eval for pneumonia - - TECHNIQUE: AP and lateral views of the chest - - COMPARISON: Chest radiographs: ___. - CT abdomen pelvis: ___. - - FINDINGS: - - The lung volumes are somewhat low, with atelectasis in the bilateral lung - bases. The heart is mildly enlarged, unchanged compared to prior studies. - There is no pneumothorax, over pulmonary edema, or focal consolidation - concerning for pneumonia. - - IMPRESSION: - - Low lung volumes, bibasilar atelectasis, and stable mild cardiomegaly. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s57907966.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s57907966.txt deleted file mode 100644 index 92522e4c27c5a724260353e3a350c2f465266e39..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s57907966.txt +++ /dev/null @@ -1,30 +0,0 @@ - WET READ: ___ ___ ___ 8:31 AM - - - Mild interstitial pulmonary edema has worsened from ___, but less - pronounced compared to ___. No new consolidation. Blunting of the - costophrenic angles suggests trace pleural effusions. - WET READ VERSION #1 ___ ___ ___ 7:31 PM - Mild interstitial pulmonary edema has worsened from ___, but less - pronounced compared to ___. No new consolidation. Blunting of the - costophrenic angles suggests trace pleural effusions. - ______________________________________________________________________________ - FINAL REPORT - EXAMINATION: CHEST ap AND LAT) - - INDICATION: ___ year old woman with chf, // interval change - - TECHNIQUE: Chest ap and lateral - - COMPARISON: None. - - FINDINGS: - - Mild cardiomegaly and tortuosity thoracic aorta are unchanged. Mild pulmonary - vascular congestion is new without overt pulmonary edema. Lungs are clear - except for linear opacities in the left mid and both lower lungs suggestive of - atelectasis. . - - IMPRESSION: - - Mild pulmonary vascular congestion. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s58352993.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s58352993.txt deleted file mode 100644 index 92dfa77a23abcd41bb7cd494d8549f2f0e2f122b..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19345192/s58352993.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (AP AND LAT) - - INDICATION: History: ___F with new dyspnea and rapid atrial flutter - - TECHNIQUE: Upright AP and lateral views of the chest - - COMPARISON: Chest radiograph ___, chest CT ___ - - FINDINGS: - - Moderate enlargement of the cardiac silhouette is unchanged. The mediastinal - contour similar. Mild pulmonary edema is worse in the interval. Hilar - contours are unchanged with prominence of the pulmonary artery suggestive of - pulmonary arterial hypertension, as seen previously. Small bilateral pleural - effusions are present. Atelectasis is seen in the lung bases without focal - consolidation. No pneumothorax is present. Osseous structures are diffusely - demineralized. - - IMPRESSION: - - Mild pulmonary edema and trace bilateral pleural effusions, worse from the - previous study. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s50515459.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s50515459.txt deleted file mode 100644 index 3afb85694251d66607401af2a3c2376ebadbf819..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s50515459.txt +++ /dev/null @@ -1,15 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Acutely hypoxic, evaluation for pulmonary edema. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is now evidence of - moderate-to-severe pulmonary edema. Marked cardiomegaly, presence of - bilateral areas of atelectasis and a left pleural effusion. Minimal blunting - of the right costophrenic sinus could suggest the presence of a small right - pleural effusion. No evidence of pneumonia. - - At the time of dictation and observation, the referring physician, ___.___ - was paged for notification, 8:47 a.m., on ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s54697052.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s54697052.txt deleted file mode 100644 index 4427fd436eb2baae0a0a7ab273679bdad21e7c2f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s54697052.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Chronic heart failure, evaluation for pulmonary edema and - interval change. - - COMPARISON: ___. - - FINDINGS: As compared to the previous radiograph, there is minimal decrease - in severity of the pre-existing evidence for pulmonary edema. However, fluid - overload is still clearly visible. The pre-existing pleural effusions have - decreased in extent. The size of the cardiac silhouette is unchanged and the - shape of the heart could suggest coexisting pericardial effusion. - Echocardiography could be helpful. No pneumothorax. No pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s58853581.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s58853581.txt deleted file mode 100644 index d7a424887a739c96cf760d3baa6443917f266788..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19352467/s58853581.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - CLINICAL HISTORY: Status post infarct. Evaluate for failure. - - AP SEMI-ERECT. - - COMPARISON: ___. - - The heart is enlarged. The size is somewhat exaggerated by the AP projection - and the semi-erect position. Some mild upper zone redistribution is present. - The perihilar edema present on the prior chest x-ray of ___ has resolved - and the lung fields overall are considerably clear. - - IMPRESSION: - Clearing failure. Heart remains enlarged. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s52311486.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s52311486.txt deleted file mode 100644 index f1b601d6247124cafbbf080b354703fe010040af..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s52311486.txt +++ /dev/null @@ -1,24 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___ year old woman with respiratory distress emergently intubated - in TICU // ETT placement - - TECHNIQUE: Portable chest radiograph - - COMPARISON: Chest radiograph from 3 hr prior - - FINDINGS: - - There has been placement of an endotracheal tube which terminates very close - to the ostium of the right mainstem bronchus and should be retracted by 2 cm - right PICC line terminates in the low SVC. Enteric tube is unchanged. Left - lower lobe atelectasis is moderate. Lungs are otherwise clear. - - IMPRESSION: - - Low position of the endotracheal tube, should be retracted by 2 cm. - - NOTIFICATION: The findings were discussed by Dr. ___ with Dr. ___ on - the telephone on ___ at 10:03 AM, 2 minutes after discovery of the - findings. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s57924863.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s57924863.txt deleted file mode 100644 index 4f68f4c6ef562ecf6ffe0232f1af391090185392..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19371747/s57924863.txt +++ /dev/null @@ -1,14 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PORTABLE AP) - - INDICATION: ___F difficult intubation, s/p c3-c6 laminectomy, c/b sever facial - edema post op. // Dobhoff placement - will need multiple films. - - IMPRESSION: - - Serial chest radiographs for performed to document feeding tube placement, - with the first image demonstrating the feeding tube in the proximal - intrathoracic esophagus, the second demonstrating the tube terminating in the - distal thoracic esophagus, in the third demonstrating positioning in the - distal stomach. Exam is otherwise remarkable for interval resolution of a - patchy right basilar opacity since ___ radiograph. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s54989798.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s54989798.txt deleted file mode 100644 index 66cbba239bcf0bbab066362efbb0c03613b43838..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s54989798.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - EXAMINATION: CHEST (PA AND LAT)CHEST (PA AND LAT) - - INDICATION: ___ year old woman with cad, AS // r/o inf, eff - - COMPARISON: None available - - FINDINGS: - - The lungs are well inflated. There is no consolidation. There is no pleural - effusion. The mediastinum is normal. The heart size is borderline. A - pacemaker is noted.. The patient has median sternotomy closures and - mediastinal clips consistent with coronary artery bypass graft. - - IMPRESSION: - - Postoperative change. No acute disease. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s55263575.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s55263575.txt deleted file mode 100644 index d2373656d7a8a1fcd37fd81fb18a8b1411b70b78..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s55263575.txt +++ /dev/null @@ -1,23 +0,0 @@ - FINAL REPORT - INDICATION: ___F with chest heaviness, AS and stent placed one month ago pls - eval for pulm edema - - TECHNIQUE: Chest PA and lateral - - COMPARISON: Chest radiograph ___. - - FINDINGS: - - The heart size is normal. Fullness in the right upper mediastinum is again - seen and may reflect a goiter. The hilar contours are unremarkable. There is - no pleural effusion or pneumothorax. The lungs are well-expanded clear without - focal consolidation. Pulmonary vasculature is within normal limits. Left - axillary dual lead pacemaker is noted with leads in stable positions. Median - sternotomy wires are intact. The upper abdomen is unremarkable. - - IMPRESSION: - - 1. No acute cardiopulmonary process. - 2. Fullness in the right upper mediastinum is noted, which may reflect a - goiter. Physical exam is recommended with consideration to additional imaging - if clinically indicated. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s58865898.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s58865898.txt deleted file mode 100644 index 2bb9e5ec0d3ae67d9c83b1690183689d6bee99fc..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19795930/s58865898.txt +++ /dev/null @@ -1,17 +0,0 @@ - FINAL REPORT - INDICATION: ___ year old woman s/pAVR // evalf or pneumo - - TECHNIQUE: Single AP view - - COMPARISON: ___ - - FINDINGS: - - Compared to ___ there is no interval change in location of - endotracheal tube, enteric tube, right-sided central line or pacemaker and - pacer wires. Multiple EKG leads overlie the chest wall. Lower lung volumes - with no evidence of pulmonary edema. Stable cardiomegaly. - - IMPRESSION: - - No significant interval change, compared to ___. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19866759/s50422139.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19866759/s50422139.txt deleted file mode 100644 index 6f587a039c6e31a94edba9c29b96ffe0f56029f1..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19866759/s50422139.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - INDICATION: Right upper lobe wedge resection for a nodule, assess for - pneumothorax - - TECHNIQUE: Portable AP upright radiograph of the chest. - - COMPARISON: CT of the chest from ___. - - FINDINGS: Right-sided chest tube is seen. There is no pleural effusion or - pneumothorax noted. Post surgical changes noted in the right juxtahilar - location including surgical clips and focal atelectasis or expected hemorrhage - following wedge resection. The heart is normal in size. Normal - cardiomediastinal silhouette. Focus of subcutaneous gas is seen in the right - lateral chest. - - IMPRESSION: No pneumothorax with expected post-surgical changes. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19875621/s56472355.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19875621/s56472355.txt deleted file mode 100644 index 5085804f4eaa774bc991e3745cca0c37f2244693..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19875621/s56472355.txt +++ /dev/null @@ -1,9 +0,0 @@ - FINAL REPORT - INDICATION: Left shoulder and chest pain, assess for pneumonia or - intrathoracic process. - - COMPARISONS: ___. - - FINDINGS/IMPRESSION: Two views of the chest were obtained. The lungs are - well expanded and clear. There is no pleural effusion or pneumothorax. The - heart is normal in size and normal cardiomediastinal contours. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s52825804.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s52825804.txt deleted file mode 100644 index c1b966bbdccca8eabd169de96e19ed1534ff0f7e..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s52825804.txt +++ /dev/null @@ -1,10 +0,0 @@ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: Fever, evaluation for pneumonia. - - COMPARISON: No comparison available at the time of dictation. - - FINDINGS: Moderate cardiomegaly with tortuosity of the thoracic aorta. No - overt pulmonary edema. No pleural effusions. No evidence of pneumonia. - Normal hilar and mediastinal structures. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s57656194.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s57656194.txt deleted file mode 100644 index 916e0a44b61bd78c12c004ac54062d67294e3844..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s57656194.txt +++ /dev/null @@ -1,21 +0,0 @@ - WET READ: ___ ___ 8:46 PM - Subdiaphragmatic lucency spanning the midline, similar to prior. This most - likely represents pannus, given similar appearance across multiple prior - exams. However, if there is clinical concern for pneumoperitoneum, CT of the - abdomen and pelvis could be obtained for further evaluation. Substantial - right middle lobe atelectasis and small left lower lobe atelectasis are - unchanged. Right PICC terminates in the lower SVC. Bilateral internal - external biliary stents are incompletely evaluated. - - ______________________________________________________________________________ - FINAL REPORT - CHEST RADIOGRAPH - - INDICATION: History of uterine cancer, evaluation. - - COMPARISON: ___, 3:03 p.m. - - FINDINGS: As compared to the previous radiograph, no relevant change. Known - intraperitoneal air after abdominal surgery. Atelectasis and low lung - volumes, right PICC line. Moderate-to-severe cardiomegaly. No evidence of - new parenchymal opacities. No pulmonary edema and no pneumonia. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s58050115.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s58050115.txt deleted file mode 100644 index 29ce03295fe41c83abaee8c6d67906c99303f876..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19936204/s58050115.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - REASON FOR EXAMINATION: Evaluation of the patient with history of uterine - cancer with questionable hilar structure. - - PA and lateral upright chest radiographs were reviewed. - - There is a substantial atelectasis of the right middle lobe, obscuring the - right hilus, new. Heart size and mediastinum are grossly stable. Left hilus - is clear. No pleural effusion or pneumothorax is seen. The right PICC line - tip is at the level of mid SVC. Biliary stent is projecting over the upper - abdomen, partially seen. - Questionable pneumoperitoneum vs. pannus projecting over upper abdomen is - seen, repeated radiograph is recommended diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19966115/s59650514.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19966115/s59650514.txt deleted file mode 100644 index 5c8a2adceddd0a0f7f0ff6673f7545fe6189bb6c..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19966115/s59650514.txt +++ /dev/null @@ -1,13 +0,0 @@ - FINAL REPORT - INDICATION: Fevers. - - COMPARISON: None. - - UPRIGHT AP VIEW OF THE CHEST: The heart size is mildly enlarged. The aorta - is tortuous and calcified. Patchy ill-defined opacities are noted at the lung - bases, which are non-specific and could represent infection, aspiration, or - atelectasis. No pleural effusion or pneumothorax is seen. Degenerative - changes of both acromioclavicular joints are noted. - - IMPRESSION: Patchy opacities at the lung bases which are nonspecific, but may - represent infection, aspiration or atelectasis. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s50515411.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s50515411.txt deleted file mode 100644 index 59ada4ff1f2a27eceb3578720732c377eaec290f..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s50515411.txt +++ /dev/null @@ -1,16 +0,0 @@ - FINAL REPORT - HISTORY: Falls. History of non-small cell lung cancer. - - COMPARISON: Chest CT ___, chest radiograph ___. - - FINDINGS: - - Again seen are signs of volume loss in the right lung with rightward shift of - the mediastinum and irregularity of the right upper chest wall after resection - of tumor. The heart size is normal. There is no pleural effusion or - pneumothorax. There is no focal consolidation concerning for pneumonia. - Nonunion of an old right clavicular fracture is again noted. - - IMPRESSION: - - No acute cardiopulmonary process. diff --git a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s54877992.txt b/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s54877992.txt deleted file mode 100644 index fec85bedaaca140cac9d3073a92eb3058c7e0faf..0000000000000000000000000000000000000000 --- a/data/mm_bench/ehrxqa/mimic-cxr/2.0.0/mimic-cxr-reports/files/p19/p19969031/s54877992.txt +++ /dev/null @@ -1,20 +0,0 @@ - FINAL REPORT - INDICATION: ___-year-old male status post fall with right chest wall - tenderness. Rule out rib fracture. - - COMPARISON: ___ chest radiograph. - - FINDINGS: Frontal and lateral views of the chest were obtained. The patient - is status post resection of a Pancoast tumor with partial right lung and chest - wall resection. Rightward shift of the mediastinum and postoperative right - lung volume loss is similar to prior, allowing for patient rotation with - respect to the film. The heart size is normal. No focal consolidation, - pleural effusion, or pneumothorax. A displaced fracture of the right clavicle - is new since ___, but similar to ___. No new displaced rib - fracture is present. - - IMPRESSION: - 1. No new displaced right rib fracture. Chronic displaced right clavicular - fracture. - 2. Stable postoperative appearance of the chest status post resection of a - Pancoast tumor. diff --git a/data/mm_bench/ehrxqa/table_description/link_information.json b/data/mm_bench/ehrxqa/table_description/link_information.json deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/data/mm_bench/ehrxqa/table_description/shorten_description.json b/data/mm_bench/ehrxqa/table_description/shorten_description.json deleted file mode 100644 index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000 diff --git a/data/mm_bench/medmod/database/patient_10001884.db b/data/mm_bench/medmod/database/patient_10001884.db deleted file mode 100644 index 6add7bb60136ac5b39a3e0faf9972dc7be455715..0000000000000000000000000000000000000000 --- a/data/mm_bench/medmod/database/patient_10001884.db +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid 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+++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:7254051a9dd88fb798751099eaed56a70cc9e4694d20003a8bfdc78f4a47fb5e -size 7668 diff --git a/data/mm_bench/medmod/table_description/link_information.json b/data/mm_bench/medmod/table_description/link_information.json deleted file mode 100644 index 2697b2f7a866fcf7bfb8ddac2dfb083938a7c393..0000000000000000000000000000000000000000 --- a/data/mm_bench/medmod/table_description/link_information.json +++ /dev/null @@ -1 +0,0 @@ -{"table_name": "events", "link_table": "d_items", "link_column": "itemid"} diff --git a/data/mm_bench/medmod/table_description/shorten_description.json b/data/mm_bench/medmod/table_description/shorten_description.json deleted file mode 100644 index 778f0f665355c3f39105855681de0dce7635d6d1..0000000000000000000000000000000000000000 --- a/data/mm_bench/medmod/table_description/shorten_description.json +++ /dev/null @@ -1,15 +0,0 @@ -{"file_name": "d_icd_diagnoses", "class": "reference", "description": "Schema extracted from the benchmark reference table 'd_icd_diagnoses'.", "columns": [{"column_name": "row_id", "description": "Column 'row_id' in table 'd_icd_diagnoses'."}, {"column_name": "icd_code", "description": "Column 'icd_code' in table 'd_icd_diagnoses'."}, {"column_name": "long_title", "description": "Column 'long_title' in table 'd_icd_diagnoses'."}]} -{"file_name": "d_icd_procedures", "class": "reference", "description": "Schema extracted from the benchmark reference table 'd_icd_procedures'.", "columns": [{"column_name": "row_id", "description": "Column 'row_id' in table 'd_icd_procedures'."}, {"column_name": "icd_code", "description": "Column 'icd_code' in table 'd_icd_procedures'."}, {"column_name": "long_title", "description": "Column 'long_title' in table 'd_icd_procedures'."}]} -{"file_name": "d_items", "class": "reference", "description": "Schema extracted from the benchmark reference table 'd_items'.", "columns": [{"column_name": "row_id", "description": "Column 'row_id' in table 'd_items'."}, {"column_name": "itemid", "description": "Column 'itemid' in table 'd_items'."}, {"column_name": "label", "description": "Column 'label' in table 'd_items'."}, {"column_name": "abbreviation", "description": "Column 'abbreviation' in table 'd_items'."}, {"column_name": "linksto", "description": "Column 'linksto' in table 'd_items'."}]} -{"file_name": "d_labitems", "class": "reference", "description": "Schema extracted from the benchmark reference table 'd_labitems'.", "columns": [{"column_name": "row_id", "description": "Column 'row_id' in table 'd_labitems'."}, {"column_name": "itemid", "description": "Column 'itemid' in table 'd_labitems'."}, {"column_name": "label", "description": "Column 'label' in table 'd_labitems'."}]} -{"file_name": "diagnoses", "class": "ehr", "description": "Schema extracted from the benchmark ehr table 'diagnoses'.", "columns": [{"column_name": "subject_id", "description": "Column 'subject_id' in table 'diagnoses'."}, {"column_name": "hadm_id", "description": "Column 'hadm_id' in table 'diagnoses'."}, {"column_name": "seq_num", "description": "Column 'seq_num' in table 'diagnoses'."}, {"column_name": "icd_code", "description": "Column 'icd_code' in table 'diagnoses'."}, {"column_name": "icd_version", "description": "Column 'icd_version' in table 'diagnoses'."}, {"column_name": "long_title", "description": "Column 'long_title' in table 'diagnoses'."}, {"column_name": "stay_id", "description": "Column 'stay_id' in table 'diagnoses'."}, {"column_name": "HCUP_CCS_2015", "description": "Column 'HCUP_CCS_2015' in table 'diagnoses'."}, {"column_name": "USE_IN_BENCHMARK", "description": "Column 'USE_IN_BENCHMARK' in table 'diagnoses'."}]} -{"file_name": "diagnoses_ccs_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'diagnoses_ccs_candidates'.", "columns": [{"column_name": "icd_code", "description": "Column 'icd_code' in table 'diagnoses_ccs_candidates'."}, {"column_name": "icd_version", "description": "Column 'icd_version' in table 'diagnoses_ccs_candidates'."}, {"column_name": "candidate", "description": "Column 'candidate' in table 'diagnoses_ccs_candidates'."}]} -{"file_name": "events", "class": "ehr", "description": "Schema extracted from the benchmark ehr table 'events'.", "columns": [{"column_name": "subject_id", "description": "Column 'subject_id' in table 'events'."}, {"column_name": "hadm_id", "description": "Column 'hadm_id' in table 'events'."}, {"column_name": "stay_id", "description": "Column 'stay_id' in table 'events'."}, {"column_name": "charttime", "description": "Column 'charttime' in table 'events'."}, {"column_name": "itemid", "description": "Column 'itemid' in table 'events'."}, {"column_name": "value", "description": "Column 'value' in table 'events'."}, {"column_name": "valuenum", "description": "Column 'valuenum' in table 'events'."}]} -{"file_name": "labevents_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'labevents_candidates'.", "columns": [{"column_name": "itemid", "description": "Column 'itemid' in table 'labevents_candidates'."}, {"column_name": "candidate", "description": "Column 'candidate' in table 'labevents_candidates'."}, {"column_name": "fluid", "description": "Column 'fluid' in table 'labevents_candidates'."}, {"column_name": "category", "description": "Column 'category' in table 'labevents_candidates'."}]} -{"file_name": "microbiologyevents_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'microbiologyevents_candidates'.", "columns": [{"column_name": "candidate", "description": "Column 'candidate' in table 'microbiologyevents_candidates'."}]} -{"file_name": "prescriptions_atc_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'prescriptions_atc_candidates'.", "columns": [{"column_name": "ndc", "description": "Column 'ndc' in table 'prescriptions_atc_candidates'."}, {"column_name": "long_drug_name", "description": "Column 'long_drug_name' in table 'prescriptions_atc_candidates'."}, {"column_name": "candidate", "description": "Column 'candidate' in table 'prescriptions_atc_candidates'."}]} -{"file_name": "procedures_ccs_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'procedures_ccs_candidates'.", "columns": [{"column_name": "icd_code", "description": "Column 'icd_code' in table 'procedures_ccs_candidates'."}, {"column_name": "icd_version", "description": "Column 'icd_version' in table 'procedures_ccs_candidates'."}, {"column_name": "candidate", "description": "Column 'candidate' in table 'procedures_ccs_candidates'."}]} -{"file_name": "radiology_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'radiology_candidates'.", "columns": [{"column_name": "candidate", "description": "Column 'candidate' in table 'radiology_candidates'."}]} -{"file_name": "stays", "class": "ehr", "description": "Schema extracted from the benchmark ehr table 'stays'.", "columns": [{"column_name": "subject_id", "description": "Column 'subject_id' in table 'stays'."}, {"column_name": "hadm_id", "description": "Column 'hadm_id' in table 'stays'."}, {"column_name": "stay_id", "description": "Column 'stay_id' in table 'stays'."}, {"column_name": "last_careunit", "description": "Column 'last_careunit' in table 'stays'."}, {"column_name": "intime", "description": "Column 'intime' in table 'stays'."}, {"column_name": "outtime", "description": "Column 'outtime' in table 'stays'."}, {"column_name": "los", "description": "Column 'los' in table 'stays'."}, {"column_name": "admittime", "description": "Column 'admittime' in table 'stays'."}, {"column_name": "dischtime", "description": "Column 'dischtime' in table 'stays'."}, {"column_name": "deathtime", "description": "Column 'deathtime' in table 'stays'."}, {"column_name": "ethnicity", "description": "Column 'ethnicity' in table 'stays'."}, {"column_name": "gender", "description": "Column 'gender' in table 'stays'."}, {"column_name": "anchor_age", "description": "Column 'anchor_age' in table 'stays'."}, {"column_name": "dod", "description": "Column 'dod' in table 'stays'."}, {"column_name": "age", "description": "Column 'age' in table 'stays'."}, {"column_name": "mortality_inunit", "description": "Column 'mortality_inunit' in table 'stays'."}, {"column_name": "mortality", "description": "Column 'mortality' in table 'stays'."}, {"column_name": "mortality_inhospital", "description": "Column 'mortality_inhospital' in table 'stays'."}]} -{"file_name": "tb_cxr", "class": "ehr", "description": "Schema extracted from the benchmark ehr table 'tb_cxr'.", "columns": [{"column_name": "subject_id", "description": "Column 'subject_id' in table 'tb_cxr'."}, {"column_name": "study_id", "description": "Column 'study_id' in table 'tb_cxr'."}, {"column_name": "studydatetime", "description": "Column 'studydatetime' in table 'tb_cxr'."}, {"column_name": "split", "description": "Column 'split' in table 'tb_cxr'."}, {"column_name": "image_id", "description": "Column 'image_id' in table 'tb_cxr'."}, {"column_name": "image_path", "description": "Column 'image_path' in table 'tb_cxr'."}, {"column_name": "viewposition", "description": "Column 'viewposition' in table 'tb_cxr'."}, {"column_name": "hadm_id", "description": "Column 'hadm_id' in table 'tb_cxr'."}, {"column_name": "stay_id", "description": "Column 'stay_id' in table 'tb_cxr'."}, {"column_name": "report_path", "description": "Column 'report_path' in table 'tb_cxr'."}]} -{"file_name": "transfers_candidates", "class": "candidate", "description": "Schema extracted from the benchmark candidate table 'transfers_candidates'.", "columns": [{"column_name": "candidate", "description": "Column 'candidate' in table 'transfers_candidates'."}]} diff --git a/rebuild/mm_bench/README.md b/rebuild/mm_bench/README.md deleted file mode 100644 index 4df3460ffc1a4ff18fd1270a06ac227949f6b10a..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/README.md +++ /dev/null @@ -1,157 +0,0 @@ -# Rebuilding ClinSeek-MM-Bench - -This directory contains the reconstruction scripts for the multimodal part of -ClinSeek-Bench. The released file `inputs/mm_bench.jsonl` is the source of -truth for the evaluated `qid`s, questions, labels, and image/report pointers. -Protected MIMIC-derived patient databases, CXR JPG files, and report text are -not redistributed. The scripts below use the manifest plus locally downloaded -PhysioNet/source datasets to rebuild the `data/mm_bench` tree on an authorized -machine. - -The scripts build two artifacts: - -1. Source-aligned subsets that preserve each upstream benchmark's own format - and pairing metadata for audit. -2. The ClinSeek-MM-Bench runtime package used by the evaluation code. - -The source-aligned subsets are provenance artifacts only. They may include -upstream labels and listfile metadata, so do not use them as model input. -Use the final `ClinSeek-MM-Bench` package for evaluation. - -## Required source data - -Download the following datasets under your own PhysioNet credentials and data -use agreements: - -- MIMIC-IV, latest available local release. -- MIMIC-CXR, with the `files/` and `mimic-cxr-reports/` folders. -- MIMIC-CXR-JPG, either v2.0.0 or v2.1.0 layout is acceptable if the JPG files - resolve by subject/study/DICOM path. -- EHRXQA release from PhysioNet, used for the EHRXQA-derived rows. -- MIMIC-IV-Note is optional for this build; the released EHRXQA rows use CXR - report text from MIMIC-CXR. - -For MedMod-derived rows, clone the official MedMod repository because the -scripts verify the released rows against its task listfiles: - -```bash -git clone https://github.com/nyuad-cai/MedMod.git /path/to/MedMod -``` - -## Configure paths - -Use paths on your machine. The examples below intentionally use placeholders. - -```bash -export CLINSEEK_BENCH=/path/to/ClinSeek-Bench -export BUILD_ROOT=/path/to/clinseek-mm-rebuild - -export EHRXQA_ROOT=/path/to/ehrxqa/1.0.0 -export MIMIC_CXR_ROOT=/path/to/mimic-cxr/2.0.0 -export MIMIC_CXR_JPG_ROOT=/path/to/mimic-cxr-jpg -export MIMICIV_ROOT=/path/to/mimiciv -export MIMIC_IV_NOTE_ROOT=/path/to/mimic-iv-note - -export MEDMOD_REPO_ROOT=/path/to/MedMod -``` - -## Build source-aligned subsets - -```bash -python "$CLINSEEK_BENCH/rebuild/mm_bench/build_ehrxqa_release_original_subset.py" \ - --input "$CLINSEEK_BENCH/inputs/mm_bench.jsonl" \ - --output-root "$BUILD_ROOT/source/EHRXQA" \ - --ehrxqa-root "$EHRXQA_ROOT" \ - --cxr-root "$MIMIC_CXR_ROOT" \ - --cxr-jpg-root "$MIMIC_CXR_JPG_ROOT" \ - --mimiciv-root "$MIMICIV_ROOT" \ - --mimic-iv-note-root "$MIMIC_IV_NOTE_ROOT" \ - --overwrite - -python "$CLINSEEK_BENCH/rebuild/mm_bench/build_medmod_release_original_subset.py" \ - --input "$CLINSEEK_BENCH/inputs/mm_bench.jsonl" \ - --output-root "$BUILD_ROOT/source/MedMod" \ - --medmod-repo-root "$MEDMOD_REPO_ROOT" \ - --cxr-jpg-root "$MIMIC_CXR_JPG_ROOT" \ - --cxr-meta-root "$MIMIC_CXR_ROOT" \ - --mimiciv-root "$MIMICIV_ROOT" \ - --overwrite -``` - -The MedMod script intentionally rebuilds only the rows present in -`inputs/mm_bench.jsonl`; it does not rebuild the full MedMod benchmark. -It also writes audit warnings when a frozen released row differs from the -script's latest-AP CXR pairing check. These warnings are preserved in metadata; -use `--strict-official-match` if you want such rows to fail reconstruction. - -## Convert to ClinSeek-MM-Bench format - -```bash -python "$CLINSEEK_BENCH/rebuild/mm_bench/build_ehrxqa_clinseek_mm_subset.py" \ - --original-root "$BUILD_ROOT/source/EHRXQA" \ - --output-root "$BUILD_ROOT/runtime/EHRXQA" \ - --overwrite - -python "$CLINSEEK_BENCH/rebuild/mm_bench/build_medmod_clinseek_mm_subset.py" \ - --original-root "$BUILD_ROOT/source/MedMod" \ - --output-root "$BUILD_ROOT/runtime/MedMod" \ - --overwrite - -python "$CLINSEEK_BENCH/rebuild/mm_bench/combine_clinseek_mm_bench.py" \ - --reference-input "$CLINSEEK_BENCH/inputs/mm_bench.jsonl" \ - --ehrxqa-root "$BUILD_ROOT/runtime/EHRXQA" \ - --medmod-root "$BUILD_ROOT/runtime/MedMod" \ - --output-root "$BUILD_ROOT/final/ClinSeek-MM-Bench" \ - --overwrite -``` - -The final package will be: - -```text -$BUILD_ROOT/final/ClinSeek-MM-Bench/ -├── inputs/mm_bench.jsonl -└── data/mm_bench/ - ├── ehrxqa/ - └── medmod/ -``` - -The source-only `inputs/mm_bench.jsonl` does not store pre-rendered -`input_text`, because that field contains MIMIC-derived EHR table rows. During -conversion, the scripts render `input_text` locally from the rebuilt patient -databases and CXR asset pointers. - -## Validate - -Validate either a local rebuilt package: - -```bash -python "$CLINSEEK_BENCH/rebuild/mm_bench/validate_multimodal_release.py" \ - --bench-root "$BUILD_ROOT/final/ClinSeek-MM-Bench" -``` - -Validate this source-only Hugging Face checkout without requiring protected -assets: - -```bash -python "$CLINSEEK_BENCH/rebuild/mm_bench/validate_multimodal_release.py" \ - --bench-root "$CLINSEEK_BENCH" \ - --manifest-only -``` - -If you have a local checkout that also materializes rebuilt assets, you can -validate by file names in the git tree: - -```bash -python "$CLINSEEK_BENCH/rebuild/mm_bench/validate_multimodal_release.py" \ - --bench-root "$CLINSEEK_BENCH" \ - --use-git-tree -``` - -Expected release counts: - -- 989 total rows. -- 497 EHRXQA-derived rows and 492 MedMod-derived rows. -- 165 EHRXQA patient DBs and 395 MedMod patient DBs. -- 350 EHRXQA JPG files and 477 MedMod JPG files. -- 356 EHRXQA CXR report text files. -- 0 missing DB/image/report references. diff --git a/rebuild/mm_bench/build_ehrxqa_clinseek_mm_subset.py b/rebuild/mm_bench/build_ehrxqa_clinseek_mm_subset.py deleted file mode 100644 index 4060ad51d8f4c41b73ae76f4a057e1b71662f8e6..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/build_ehrxqa_clinseek_mm_subset.py +++ /dev/null @@ -1,744 +0,0 @@ -#!/usr/bin/env python3 -"""Convert a source-aligned EHRXQA subset into ClinSeek-MM-Bench format.""" - -from __future__ import annotations - -import argparse -import csv -import json -import os -import shutil -import sqlite3 -import sys -from collections import Counter -from pathlib import Path -from typing import Any - -import pandas as pd - - -REPO_ROOT = Path(__file__).resolve().parents[2] -SRC_ROOT = REPO_ROOT / "src" -if str(SRC_ROOT) not in sys.path: - sys.path.insert(0, str(SRC_ROOT)) - -DEFAULT_ORIGINAL_ROOT = Path( - os.environ.get( - "EHRXQA_ORIGINAL_SUBSET_ROOT", - "data/build/ClinSeek-MM-Bench-EHRXQA-source", - ) -) -DEFAULT_OUTPUT_ROOT = Path( - os.environ.get( - "CLINSEEK_EHRXQA_MM_ROOT", - "data/build/ClinSeek-MM-Bench-EHRXQA", - ) -) - -TIME_COLUMNS = { - "admissions": "admittime", - "chartevents": "charttime", - "cost": "chargetime", - "diagnoses_icd": "charttime", - "icustays": "intime", - "inputevents": "starttime", - "labevents": "charttime", - "microbiologyevents": "charttime", - "outputevents": "charttime", - "prescriptions": "starttime", - "procedures_icd": "charttime", - "tb_cxr": "studydatetime", - "transfers": "intime", -} - -LEAKAGE_POLICY = { - "sanitize_datetime_columns": True, - "mask_future_datetime_columns": True, - "row_timestamp_columns": TIME_COLUMNS, - "datetime_columns": { - "admissions": ["admittime", "dischtime"], - "chartevents": ["charttime"], - "cost": ["chargetime"], - "diagnoses_icd": ["charttime"], - "icustays": ["intime", "outtime"], - "inputevents": ["starttime"], - "labevents": ["charttime"], - "microbiologyevents": ["charttime"], - "outputevents": ["charttime"], - "patients": ["dod"], - "prescriptions": ["starttime", "stoptime"], - "procedures_icd": ["charttime"], - "tb_cxr": ["studydatetime"], - "transfers": ["intime", "outtime"], - }, -} - -REFERENCE_TABLES = {"d_icd_diagnoses", "d_icd_procedures", "d_items", "d_labitems"} - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument("--original-root", type=Path, default=DEFAULT_ORIGINAL_ROOT) - parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT) - parser.add_argument("--asset-prefix", default="EHRXQAOriginalLinked_v1") - parser.add_argument("--max-table-rows", type=int, default=80) - parser.add_argument( - "--render-input-text", - action="store_true", - help="Render input_text from the rebuilt patient DB instead of preserving the released HF JSONL field.", - ) - parser.add_argument( - "--copy-cxr-context", - choices=("linked", "all"), - default="linked", - help="Copy only JSONL-linked assets or all CXR assets packaged by the source-aligned subset.", - ) - parser.add_argument("--overwrite", action="store_true") - return parser.parse_args() - - -def ensure_dir(path: Path) -> None: - path.mkdir(parents=True, exist_ok=True) - - -def reset_dir(path: Path, overwrite: bool) -> None: - if path.exists(): - if not overwrite: - raise FileExistsError(f"Output root already exists: {path}") - shutil.rmtree(path) - path.mkdir(parents=True, exist_ok=True) - - -def link_or_copy(src: Path, dst: Path) -> None: - src = src.resolve() - ensure_dir(dst.parent) - if dst.exists(): - return - try: - os.link(src, dst) - except OSError: - shutil.copy2(src, dst) - - -def copytree_links(src: Path, dst: Path) -> None: - if not src.exists(): - return - if dst.exists(): - return - shutil.copytree(src, dst, copy_function=lambda s, d: (link_or_copy(Path(s), Path(d)) or str(d))) - - -def write_json(path: Path, payload: Any) -> None: - ensure_dir(path.parent) - path.write_text(json.dumps(payload, ensure_ascii=False, indent=2) + "\n", encoding="utf-8") - - -def read_jsonl(path: Path) -> list[dict[str, Any]]: - rows: list[dict[str, Any]] = [] - with path.open("r", encoding="utf-8") as handle: - for line in handle: - if line.strip(): - rows.append(json.loads(line)) - return rows - - -def safe_int(value: Any) -> int | None: - if value is None or value == "": - return None - try: - if pd.isna(value): - return None - except TypeError: - pass - try: - return int(float(str(value).strip())) - except ValueError: - return None - - -def compact_value(value: Any) -> Any: - try: - if pd.isna(value): - return "" - except TypeError: - pass - if hasattr(value, "isoformat"): - return value.isoformat(sep=" ") - return value - - -def table_to_text(table_name: str, frame: pd.DataFrame, max_rows: int) -> str: - total = len(frame) - if total == 0: - return f"### {table_name}\nRows visible before cutoff: 0\n" - display = frame - sort_col = TIME_COLUMNS.get(table_name) - if sort_col and sort_col in display.columns: - display = display.sort_values(sort_col, kind="stable") - if max_rows and len(display) > max_rows: - display = display.tail(max_rows) - shown = f"latest {len(display)} of {total}" - else: - shown = f"{total} of {total}" - clean = display.copy() - for column in clean.columns: - clean[column] = clean[column].map(compact_value) - return ( - f"### {table_name}\n" - f"Rows visible before cutoff: {total}; rows included below: {shown}\n" - f"{clean.to_csv(index=False)}" - ) - - -def render_ehr_context_from_manager(manager: Any, sample: dict[str, Any], max_table_rows: int) -> str: - manager.load_ehr_for_sample(str(sample["subject_id"]), sample["prediction_time"]) - blocks = [] - for table_name in sorted(manager.ehr_data): - blocks.append(table_to_text(table_name, manager.ehr_data[table_name], max_table_rows)) - return "\n".join(blocks).strip() - - -def parse_datetime(value: Any) -> pd.Timestamp | None: - if value in (None, ""): - return None - try: - parsed = pd.Timestamp(value) - except (TypeError, ValueError): - return None - if pd.isna(parsed): - return None - return parsed - - -def filter_by_cutoff(table_name: str, frame: pd.DataFrame, cutoff: pd.Timestamp | None) -> pd.DataFrame: - if cutoff is None: - return frame - time_column = TIME_COLUMNS.get(table_name) - if not time_column or time_column not in frame.columns: - return frame - parsed = pd.to_datetime(frame[time_column], errors="coerce") - return frame.loc[parsed.notna() & (parsed <= cutoff)].copy() - - -def render_ehr_context(db_path: Path, prediction_time: str, max_table_rows: int) -> str: - cutoff = parse_datetime(prediction_time) - blocks: list[str] = [] - with sqlite3.connect(db_path) as conn: - table_names = [ - row[0] - for row in conn.execute("SELECT name FROM sqlite_master WHERE type='table' ORDER BY name") - ] - for table_name in table_names: - frame = pd.read_sql_query(f'SELECT * FROM "{table_name}"', conn) - visible = filter_by_cutoff(table_name, frame, cutoff) - blocks.append(table_to_text(table_name, visible, max_table_rows)) - return "\n".join(blocks).strip() - - -def build_input_text(sample: dict[str, Any], image_paths: list[str], ehr_text: str) -> str: - return "\n\n".join( - [ - str(sample.get("question") or "").strip(), - "", - ehr_text, - "", - "", - "\n".join(f"- {path}" for path in image_paths) if image_paths else "NONE", - "", - ] - ) - - -def strip_asset_prefix(path: str) -> str: - text = str(path).replace("\\", "/") - if "/" in text and text.split("/", 1)[0].endswith("OriginalLinked_v1"): - return text.split("/", 1)[1] - return text - - -def load_manifest(original_root: Path) -> list[dict[str, Any]]: - manifest = original_root / "linked_manifests" / "test.jsonl" - if not manifest.exists(): - raise FileNotFoundError(f"Missing source manifest: {manifest}") - return read_jsonl(manifest) - - -def source_tables_dir(original_root: Path) -> Path: - path = original_root / "source_release" / "1.0.0" / "ehrxqa" / "database" / "gold" - if not path.is_dir(): - raise FileNotFoundError(f"Missing EHRXQA gold table root: {path}") - return path - - -def table_is_reference(table_name: str) -> bool: - return table_name in REFERENCE_TABLES or table_name.startswith("d_") - - -def write_frame(conn: sqlite3.Connection, table_name: str, frame: pd.DataFrame, *, append: bool = False) -> None: - clean = frame.where(pd.notna(frame), None) - clean.to_sql(table_name, conn, if_exists="append" if append else "replace", index=False) - - -def quote_identifier(name: str) -> str: - return '"' + name.replace('"', '""') + '"' - - -def list_sqlite_tables(conn: sqlite3.Connection) -> list[str]: - return [ - row[0] - for row in conn.execute("SELECT name FROM sqlite_master WHERE type='table' ORDER BY name") - ] - - -def list_attached_sqlite_tables(conn: sqlite3.Connection, schema: str) -> list[str]: - q_schema = quote_identifier(schema) - return [ - row[0] - for row in conn.execute(f"SELECT name FROM {q_schema}.sqlite_master WHERE type='table' ORDER BY name") - ] - - -def sqlite_table_columns(conn: sqlite3.Connection, table_name: str) -> list[str]: - return [row[1] for row in conn.execute(f"PRAGMA table_info({quote_identifier(table_name)})")] - - -def source_sqlite_path(original_root: Path) -> Path: - return source_tables_dir(original_root) / "mimic_iv_cxr.sqlite" - - -def build_reference_database(tables_dir: Path, output_db: Path) -> list[str]: - written: list[str] = [] - if output_db.exists(): - output_db.unlink() - with sqlite3.connect(output_db) as conn: - for csv_path in sorted(tables_dir.glob("*.csv")): - table_name = csv_path.stem - if not table_is_reference(table_name): - continue - write_frame(conn, table_name, pd.read_csv(csv_path, low_memory=False)) - written.append(table_name) - return written - - -def create_text_table( - conn: sqlite3.Connection, - table_name: str, - columns: list[str], - rows: list[list[Any]], -) -> None: - q_table = quote_identifier(table_name) - column_sql = ", ".join(f"{quote_identifier(column)} TEXT" for column in columns) - conn.execute(f"CREATE TABLE {q_table} ({column_sql})") - if not rows: - return - placeholders = ", ".join(["?"] * len(columns)) - conn.executemany(f"INSERT INTO {q_table} VALUES ({placeholders})", rows) - - -def csv_value(value: Any) -> Any: - if value is None or value == "": - return None - return value - - -def build_reference_database_from_csvs(tables_dir: Path, output_db: Path) -> list[str]: - written: list[str] = [] - if output_db.exists(): - output_db.unlink() - with sqlite3.connect(output_db) as conn: - for csv_path in sorted(tables_dir.glob("*.csv")): - table_name = csv_path.stem - if not table_is_reference(table_name): - continue - with csv_path.open("r", encoding="utf-8", newline="") as handle: - reader = csv.reader(handle) - columns = next(reader) - rows = [[csv_value(value) for value in row] for row in reader] - create_text_table(conn, table_name, columns, rows) - written.append(table_name) - conn.commit() - return written - - -def build_patient_databases_from_source_csvs( - *, - original_root: Path, - database_root: Path, - subject_ids: set[int], -) -> dict[str, Any]: - tables_dir = source_tables_dir(original_root) - subject_lookup = {str(subject_id): subject_id for subject_id in subject_ids} - subject_tables: dict[int, list[tuple[str, list[str], list[list[Any]]]]] = { - subject_id: [] for subject_id in subject_ids - } - built_tables: list[str] = [] - for csv_path in sorted(tables_dir.glob("*.csv")): - table_name = csv_path.stem - if table_is_reference(table_name): - continue - with csv_path.open("r", encoding="utf-8", newline="") as handle: - reader = csv.DictReader(handle) - if not reader.fieldnames or "subject_id" not in reader.fieldnames: - continue - columns = list(reader.fieldnames) - if table_name == "patients": - columns = [column for column in columns if column != "dod"] - grouped: dict[int, list[list[Any]]] = {} - for row in reader: - subject_id = subject_lookup.get(str(row.get("subject_id") or "")) - if subject_id is None: - continue - grouped.setdefault(subject_id, []).append([csv_value(row.get(column)) for column in columns]) - if not grouped: - continue - built_tables.append(table_name) - for subject_id, rows in grouped.items(): - subject_tables[subject_id].append((table_name, columns, rows)) - - built_subjects = {subject_id for subject_id, tables in subject_tables.items() if tables} - missing = sorted(subject_ids - built_subjects) - if missing: - raise FileNotFoundError(f"Missing built patient DBs for subjects: {missing[:20]}") - ensure_dir(database_root) - for subject_id, tables in sorted(subject_tables.items()): - db_path = database_root / f"patient_{subject_id}.db" - if db_path.exists(): - db_path.unlink() - with sqlite3.connect(db_path) as conn: - conn.execute("PRAGMA journal_mode=OFF") - conn.execute("PRAGMA synchronous=OFF") - for table_name, columns, rows in tables: - create_text_table(conn, table_name, columns, rows) - conn.commit() - reference_tables = build_reference_database_from_csvs(tables_dir, database_root / "reference_table.db") - return { - "patient_db_source": "source_aligned_subset_csv", - "source_table_root": "source_release/1.0.0/ehrxqa/database/gold", - "built_subjects": len(built_subjects), - "built_tables": built_tables, - "reference_tables": reference_tables, - } - - -def build_reference_database_from_sqlite(source_db: Path, output_db: Path) -> list[str]: - written: list[str] = [] - if output_db.exists(): - output_db.unlink() - with sqlite3.connect(output_db) as conn: - conn.execute("ATTACH DATABASE ? AS src", (str(source_db),)) - for table_name in list_attached_sqlite_tables(conn, "src"): - if not table_is_reference(table_name): - continue - q_table = quote_identifier(table_name) - conn.execute(f"CREATE TABLE {q_table} AS SELECT * FROM src.{q_table}") - written.append(table_name) - conn.commit() - return written - - -def build_patient_databases_from_source_sqlite( - *, - original_root: Path, - database_root: Path, - subject_ids: set[int], -) -> dict[str, Any]: - source_db = source_sqlite_path(original_root) - if not source_db.exists(): - raise FileNotFoundError(f"Missing EHRXQA source SQLite: {source_db}") - ensure_dir(database_root) - with sqlite3.connect(source_db) as src_conn: - table_names = list_sqlite_tables(src_conn) - patient_tables = [ - table_name - for table_name in table_names - if not table_is_reference(table_name) - and "subject_id" in sqlite_table_columns(src_conn, table_name) - ] - - built_subjects = set() - for subject_id in sorted(subject_ids): - db_path = database_root / f"patient_{subject_id}.db" - if db_path.exists(): - db_path.unlink() - with sqlite3.connect(db_path) as dst_conn: - dst_conn.execute("PRAGMA journal_mode=OFF") - dst_conn.execute("PRAGMA synchronous=OFF") - dst_conn.execute("ATTACH DATABASE ? AS src", (str(source_db),)) - rows_written = 0 - for table_name in patient_tables: - q_table = quote_identifier(table_name) - row_count = dst_conn.execute( - f"SELECT COUNT(*) FROM src.{q_table} WHERE subject_id = ?", - (subject_id,), - ).fetchone()[0] - if row_count == 0: - continue - columns = [ - row[1] - for row in dst_conn.execute(f"PRAGMA src.table_info({quote_identifier(table_name)})") - ] - if table_name == "patients": - columns = [column for column in columns if column != "dod"] - select_columns = ", ".join(quote_identifier(column) for column in columns) - dst_conn.execute( - f"CREATE TABLE {q_table} AS SELECT {select_columns} FROM src.{q_table} WHERE subject_id = ?", - (subject_id,), - ) - rows_written += row_count - dst_conn.commit() - if rows_written: - built_subjects.add(subject_id) - - missing = sorted(subject_ids - built_subjects) - if missing: - raise FileNotFoundError(f"Missing built patient DBs for subjects: {missing[:20]}") - reference_tables = build_reference_database_from_sqlite(source_db, database_root / "reference_table.db") - return { - "patient_db_source": "source_aligned_subset_sqlite", - "source_sqlite": "source_release/1.0.0/ehrxqa/database/gold/mimic_iv_cxr.sqlite", - "built_subjects": len(built_subjects), - "built_tables": patient_tables, - "reference_tables": reference_tables, - } - - -def build_patient_databases_from_source( - *, - original_root: Path, - database_root: Path, - subject_ids: set[int], -) -> dict[str, Any]: - tables_dir = source_tables_dir(original_root) - if any(tables_dir.glob("*.csv")): - return build_patient_databases_from_source_csvs( - original_root=original_root, - database_root=database_root, - subject_ids=subject_ids, - ) - - sqlite_path = source_sqlite_path(original_root) - if sqlite_path.exists(): - return build_patient_databases_from_source_sqlite( - original_root=original_root, - database_root=database_root, - subject_ids=subject_ids, - ) - - built_tables: list[str] = [] - subject_frames: dict[int, list[tuple[str, pd.DataFrame]]] = {subject_id: [] for subject_id in subject_ids} - for csv_path in sorted(tables_dir.glob("*.csv")): - table_name = csv_path.stem - if table_is_reference(table_name): - continue - header = pd.read_csv(csv_path, nrows=0) - if "subject_id" not in header.columns: - continue - built_tables.append(table_name) - frame = pd.read_csv(csv_path, low_memory=False) - subset = frame[frame["subject_id"].isin(subject_ids)] - if subset.empty: - continue - for subject_id, group in subset.groupby("subject_id", sort=True): - subject_frames[int(subject_id)].append((table_name, group.copy())) - - built_subjects = {subject_id for subject_id, frames in subject_frames.items() if frames} - missing = sorted(subject_ids - built_subjects) - if missing: - raise FileNotFoundError(f"Missing built patient DBs for subjects: {missing[:20]}") - ensure_dir(database_root) - for subject_id, frames in sorted(subject_frames.items()): - db_path = database_root / f"patient_{subject_id}.db" - if db_path.exists(): - db_path.unlink() - with sqlite3.connect(db_path) as conn: - for table_name, frame in frames: - write_frame(conn, table_name, frame) - reference_tables = build_reference_database(tables_dir, database_root / "reference_table.db") - return { - "patient_db_source": "source_aligned_subset", - "built_subjects": len(built_subjects), - "built_tables": built_tables, - "reference_tables": reference_tables, - } - - -def write_runtime_metadata(bench_root: Path) -> None: - write_json( - bench_root / "metadata.json", - { - "package_name": "ClinSeek-MM-Bench-EHRXQA-runtime", - "leakage_policy": LEAKAGE_POLICY, - "path_contract": { - "db_path_hint": "relative_to_benchmark_root", - "image_paths": "relative_to_benchmark_root", - "report_paths": "relative_to_benchmark_root", - "tb_cxr.image_path": "relative_to_benchmark_root", - "tb_cxr.report_path": "relative_to_benchmark_root", - }, - }, - ) - - -def copy_linked_assets(original_root: Path, bench_root: Path, row: dict[str, Any]) -> tuple[list[str], list[str]]: - rel_images = [strip_asset_prefix(path) for path in row.get("packaged_image_relpaths") or []] - rel_reports = [strip_asset_prefix(path) for path in row.get("packaged_report_relpaths") or []] - for relpath in rel_images + rel_reports: - link_or_copy(original_root / relpath, bench_root / relpath) - return rel_images, rel_reports - - -def copy_all_cxr_context(original_root: Path, bench_root: Path) -> None: - copytree_links(original_root / "mimic-cxr", bench_root / "mimic-cxr") - - -def write_table_descriptions(bench_root: Path) -> None: - dst = bench_root / "table_description" - ensure_dir(dst) - (dst / "link_information.json").write_text("", encoding="utf-8") - (dst / "shorten_description.json").write_text("", encoding="utf-8") - - -def main() -> None: - args = parse_args() - reset_dir(args.output_root, args.overwrite) - manifest_rows = load_manifest(args.original_root) - - bench_root = args.output_root / "data" / "mm_bench" / "ehrxqa" - database_root = bench_root / "database" - inputs_root = args.output_root / "inputs" - ensure_dir(database_root) - ensure_dir(inputs_root) - - by_subject: dict[int, dict[str, Any]] = {} - for row in manifest_rows: - subject_id = safe_int(row.get("subject_id")) - if subject_id is None: - raise ValueError(f"Missing subject_id: {row.get('qid')}") - by_subject.setdefault(subject_id, row) - - db_build_summary = build_patient_databases_from_source( - original_root=args.original_root, - database_root=database_root, - subject_ids=set(by_subject), - ) - write_table_descriptions(bench_root) - ehr_manager_root = bench_root - write_runtime_metadata(bench_root) - - if args.copy_cxr_context == "all": - copy_all_cxr_context(args.original_root, bench_root) - - ehr_manager = None - need_rendered_input_text = args.render_input_text or any( - not row.get("released_input_text") for row in manifest_rows - ) - if need_rendered_input_text: - try: - from agentlite.commons.EHRManager import EHRManager # type: ignore - - ehr_manager = EHRManager(str(ehr_manager_root)) - except Exception as exc: # pragma: no cover - fallback for portable envs - print({"ehr_manager_unavailable": repr(exc)}, flush=True) - output_rows: list[dict[str, Any]] = [] - stats = Counter() - linked_image_count = 0 - linked_report_count = 0 - for index, row in enumerate(manifest_rows): - rel_images, rel_reports = copy_linked_assets(args.original_root, bench_root, row) - linked_image_count += len(rel_images) - linked_report_count += len(rel_reports) - prefixed_images = [f"{args.asset_prefix}/{relpath}" for relpath in rel_images] - prefixed_reports = [f"{args.asset_prefix}/{relpath}" for relpath in rel_reports] - if args.render_input_text or not row.get("released_input_text"): - if ehr_manager is not None: - ehr_text = render_ehr_context_from_manager(ehr_manager, row, args.max_table_rows) - else: - subject_id = safe_int(row.get("subject_id")) - if subject_id is None: - raise ValueError(f"Missing subject_id: {row.get('qid')}") - ehr_text = render_ehr_context( - database_root / f"patient_{subject_id}.db", - str(row.get("prediction_time")), - args.max_table_rows, - ) - input_text = build_input_text(row, prefixed_images, ehr_text) - else: - input_text = row.get("released_input_text") - output_rows.append( - { - "qid": row.get("qid"), - "source_index": row.get("source_index"), - "source_benchmark": "ehrxqa", - "task": row.get("task"), - "source_split": row.get("source_split"), - "subject_id": row.get("subject_id"), - "hadm_id": row.get("hadm_id"), - "stay_id": row.get("stay_id"), - "prediction_time": row.get("prediction_time"), - "question": row.get("question"), - "input_text": input_text, - "image_paths": prefixed_images, - "report_paths": prefixed_reports, - "ground_truth": row.get("ground_truth"), - "answer_type": row.get("answer_type"), - "modalities": row.get("modalities") or ["cxr_table", "cxr_image"], - } - ) - stats[f"task:{row.get('task')}"] += 1 - if (index + 1) % 100 == 0: - print({"rendered_rows": index + 1, "total": len(manifest_rows)}, flush=True) - - output_path = inputs_root / "mm_bench_ehrxqa.jsonl" - with output_path.open("w", encoding="utf-8") as handle: - for row in output_rows: - handle.write(json.dumps(row, ensure_ascii=False, separators=(",", ":")) + "\n") - - metadata = { - "package_name": "ClinSeek-MM-Bench-EHRXQA", - "original_root": "EHRXQA_ORIGINAL_SUBSET_ROOT", - "records": len(output_rows), - "subjects": len(by_subject), - "patient_dbs": len(list(database_root.glob("patient_*.db"))), - "db_build_summary": db_build_summary, - "unique_linked_images": len({p for row in output_rows for p in row["image_paths"]}), - "unique_linked_reports": len({p for row in output_rows for p in row["report_paths"]}), - "linked_image_refs": linked_image_count, - "linked_report_refs": linked_report_count, - "copy_cxr_context": args.copy_cxr_context, - "input_text_source": "rendered_from_db" if need_rendered_input_text else "released_hf_jsonl", - "input_file": "inputs/mm_bench_ehrxqa.jsonl", - "bench_root": "data/mm_bench/ehrxqa", - "asset_prefix": args.asset_prefix, - "stats": dict(sorted(stats.items())), - "path_contract": { - "image_paths": "strip asset_prefix, then resolve relative to bench_root", - "report_paths": "strip asset_prefix, then resolve relative to bench_root", - "patient_db": "data/mm_bench/ehrxqa/database/patient_.db", - }, - "leakage_policy": { - "ground_truth": "kept only in output JSONL field, never in input_text", - "patient_db_source": db_build_summary.get("patient_db_source"), - "runtime_policy": "EHRManager uses benchmark metadata leakage_policy at load time", - }, - } - write_json(args.output_root / "metadata.json", metadata) - - readme = """# ClinSeek-MM-Bench-EHRXQA - -This directory contains the EHRXQA-derived portion of ClinSeek-MM-Bench. - -Use: - -- `inputs/mm_bench_ehrxqa.jsonl` -- `data/mm_bench/ehrxqa` - -The JSONL contains both agentic fields (`question`, `image_paths`, `subject_id`) -and curated-input fields (`input_text`, `image_paths`). Patient SQLite DBs are -under `data/mm_bench/ehrxqa/database`. -""" - (args.output_root / "README.md").write_text(readme, encoding="utf-8") - print(json.dumps(metadata, ensure_ascii=False, indent=2)) - - -if __name__ == "__main__": - main() diff --git a/rebuild/mm_bench/build_ehrxqa_release_original_subset.py b/rebuild/mm_bench/build_ehrxqa_release_original_subset.py deleted file mode 100644 index cbf0b02a120c8e5721aefac594b8379ce02800dc..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/build_ehrxqa_release_original_subset.py +++ /dev/null @@ -1,570 +0,0 @@ -#!/usr/bin/env python3 -"""Build the source-aligned EHRXQA subset used by ClinSeek MM-Bench. - -This script rebuilds only the EHRXQA rows present in the released -inputs/mm_bench.jsonl. It keeps the official EHRXQA schema, writes subset -CSV/SQLite tables, and packages the CXR files needed by the selected patients -using relative paths. -""" - -from __future__ import annotations - -import argparse -import json -import os -import re -import shutil -import sqlite3 -from collections import Counter -from pathlib import Path -from typing import Any - -import pandas as pd - - -DEFAULT_INPUT = Path( - os.environ.get( - "CLINSEEK_MM_BENCH_JSONL", - "data/ClinSeek-Bench/inputs/mm_bench.jsonl", - ) -) -DEFAULT_OUTPUT_ROOT = Path( - os.environ.get( - "EHRXQA_ORIGINAL_SUBSET_ROOT", - "data/build/ClinSeek-MM-Bench-EHRXQA-source", - ) -) -DEFAULT_EHRXQA_ROOT = Path( - os.environ.get("EHRXQA_ROOT", "external/ehrxqa/1.0.0") -) -DEFAULT_CXR_ROOT = Path( - os.environ.get("MIMIC_CXR_ROOT", "external/mimic-cxr/2.0.0") -) -DEFAULT_CXR_JPG_ROOT = Path( - os.environ.get("MIMIC_CXR_JPG_ROOT", "external/mimic-cxr-jpg") -) -DEFAULT_MIMICIV_ROOT = Path(os.environ.get("MIMICIV_ROOT", "external/mimiciv/3.1")) -DEFAULT_MIMIC_IV_NOTE_ROOT = Path( - os.environ.get("MIMIC_IV_NOTE_ROOT", "external/mimic-iv-note/2.2") -) - -QID_RE = re.compile(r"^ehrxqa_(?P[a-zA-Z0-9-]+)_(?P\d+)$") -IMAGE_RE = re.compile( - r"(?:^|/)files/p\d+/p(?P\d+)/s(?P\d+)/(?P[^/]+)\.jpg$" -) - -REFERENCE_TABLE_PREFIXES = ("d_",) -REFERENCE_TABLES = {"d_icd_diagnoses", "d_icd_procedures", "d_items", "d_labitems"} - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument("--input", type=Path, default=DEFAULT_INPUT) - parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT) - parser.add_argument("--ehrxqa-root", type=Path, default=DEFAULT_EHRXQA_ROOT) - parser.add_argument( - "--cxr-root", - type=Path, - default=DEFAULT_CXR_ROOT, - help="MIMIC-CXR root containing files/ and mimic-cxr-reports/.", - ) - parser.add_argument( - "--cxr-jpg-root", - type=Path, - default=DEFAULT_CXR_JPG_ROOT, - help="Optional MIMIC-CXR-JPG root or flat mimic-cxr2 export used as an image fallback.", - ) - parser.add_argument("--mimiciv-root", type=Path, default=DEFAULT_MIMICIV_ROOT) - parser.add_argument( - "--mimic-iv-note-root", - type=Path, - default=DEFAULT_MIMIC_IV_NOTE_ROOT, - help="Optional MIMIC-IV-Note root kept for provenance; this EHRXQA build uses CXR report TXT files.", - ) - parser.add_argument("--overwrite", action="store_true") - parser.add_argument( - "--allow-missing-nonlinked-assets", - action="store_true", - help=( - "Deprecated compatibility flag. Non-linked patient-context CXR assets " - "are optional; linked benchmark assets are still required." - ), - ) - return parser.parse_args() - - -def ensure_dir(path: Path) -> None: - path.mkdir(parents=True, exist_ok=True) - - -def reset_dir(path: Path, overwrite: bool) -> None: - if path.exists(): - if not overwrite: - raise FileExistsError(f"Output root already exists: {path}") - shutil.rmtree(path) - path.mkdir(parents=True, exist_ok=True) - - -def link_or_copy(src: Path, dst: Path) -> None: - src = src.resolve() - ensure_dir(dst.parent) - if dst.exists(): - return - try: - os.link(src, dst) - except OSError: - shutil.copy2(src, dst) - - -def write_json(path: Path, payload: Any, *, compact: bool = False) -> None: - ensure_dir(path.parent) - kwargs = {"ensure_ascii": False} - if not compact: - kwargs["indent"] = 2 - path.write_text(json.dumps(payload, **kwargs) + "\n", encoding="utf-8") - - -def write_jsonl(path: Path, rows: list[dict[str, Any]]) -> None: - ensure_dir(path.parent) - with path.open("w", encoding="utf-8") as handle: - for row in rows: - handle.write(json.dumps(row, ensure_ascii=False, separators=(",", ":")) + "\n") - - -def safe_int(value: Any) -> int | None: - if value is None or value == "": - return None - try: - if pd.isna(value): - return None - except TypeError: - pass - try: - return int(float(str(value).strip())) - except ValueError: - return None - - -def normalize_ehrxqa_root(path: Path) -> tuple[Path, Path]: - """Return (release_root, ehrxqa_dir).""" - if (path / "ehrxqa" / "dataset").is_dir(): - return path, path / "ehrxqa" - if (path / "dataset").is_dir() and (path / "database").is_dir(): - return path.parent, path - raise FileNotFoundError( - f"Could not find EHRXQA dataset/database under {path}. " - "Pass either the 1.0.0 root or the 1.0.0/ehrxqa directory." - ) - - -def load_release_rows(input_path: Path) -> list[dict[str, Any]]: - rows: list[dict[str, Any]] = [] - with input_path.open("r", encoding="utf-8") as handle: - for line_index, line in enumerate(handle): - if not line.strip(): - continue - row = json.loads(line) - if row.get("source_benchmark") != "ehrxqa": - continue - match = QID_RE.match(str(row.get("qid") or "")) - if not match: - raise ValueError(f"Cannot parse EHRXQA qid: {row.get('qid')}") - row["_source_line_index"] = line_index - row["_source_split_from_qid"] = match.group("split") - row["_source_id_from_qid"] = int(match.group("source_id")) - rows.append(row) - return rows - - -def strip_asset_prefix(path: str) -> str: - text = path.replace("\\", "/") - if "/" in text and text.split("/", 1)[0].endswith("OriginalLinked_v1"): - return text.split("/", 1)[1] - return text - - -def parse_image_ref(path: str) -> dict[str, Any]: - stripped = strip_asset_prefix(path) - match = IMAGE_RE.search(stripped) - if not match: - raise ValueError(f"Cannot parse EHRXQA image path: {path}") - subject_id = int(match.group("subject_id")) - study_id = int(match.group("study_id")) - dicom_id = match.group("dicom_id") - nested_relpath = ( - f"mimic-cxr/2.0.0/files/p{str(subject_id)[:2]}/p{subject_id}/" - f"s{study_id}/{dicom_id}.jpg" - ) - report_relpath = ( - f"mimic-cxr/2.0.0/mimic-cxr-reports/files/p{str(subject_id)[:2]}/" - f"p{subject_id}/s{study_id}.txt" - ) - return { - "subject_id": subject_id, - "study_id": study_id, - "dicom_id": dicom_id, - "image_relpath": nested_relpath, - "report_relpath": report_relpath, - } - - -def nested_file_relpath(subject_id: int, study_id: int, dicom_id: str) -> str: - return ( - f"mimic-cxr/2.0.0/files/p{str(subject_id)[:2]}/p{subject_id}/" - f"s{study_id}/{dicom_id}.jpg" - ) - - -def nested_report_relpath(subject_id: int, study_id: int) -> str: - return ( - f"mimic-cxr/2.0.0/mimic-cxr-reports/files/p{str(subject_id)[:2]}/" - f"p{subject_id}/s{study_id}.txt" - ) - - -def find_cxr_image( - cxr_root: Path, - cxr_jpg_root: Path, - subject_id: int, - study_id: int, - dicom_id: str, -) -> Path | None: - nested = Path(nested_file_relpath(subject_id, study_id, dicom_id)).relative_to("mimic-cxr/2.0.0") - flat_name = f"p{str(subject_id)[:2]}_p{subject_id}_s{study_id}_{dicom_id}.jpg" - candidates = [ - cxr_root / nested, - cxr_root / "files" / nested.relative_to("files"), - cxr_root / "mimic-cxr" / "2.0.0" / nested, - cxr_root / "2.0.0" / nested, - cxr_root / "2.1.0" / nested, - cxr_root / "2.1.0-lite" / nested, - cxr_root / "2.1.0-working-subset" / nested, - cxr_root / "mimic-cxr2" / flat_name, - cxr_root / flat_name, - cxr_jpg_root / nested, - cxr_jpg_root / "files" / nested.relative_to("files"), - cxr_jpg_root / "2.0.0" / nested, - cxr_jpg_root / "2.1.0" / nested, - cxr_jpg_root / "2.1.0-lite" / nested, - cxr_jpg_root / "2.1.0-working-subset" / nested, - cxr_jpg_root / "mimic-cxr2" / flat_name, - cxr_jpg_root / flat_name, - ] - for candidate in candidates: - if candidate.exists(): - return candidate - return None - - -def find_cxr_report(cxr_root: Path, subject_id: int, study_id: int) -> Path | None: - nested = Path(nested_report_relpath(subject_id, study_id)).relative_to("mimic-cxr/2.0.0") - candidates = [ - cxr_root / nested, - cxr_root / "mimic-cxr-reports" / nested.relative_to("mimic-cxr-reports"), - cxr_root / "mimic-cxr" / "2.0.0" / nested, - cxr_root / "2.0.0" / nested, - ] - for candidate in candidates: - if candidate.exists(): - return candidate - return None - - -def table_is_reference(table_name: str) -> bool: - return table_name in REFERENCE_TABLES or table_name.startswith(REFERENCE_TABLE_PREFIXES) - - -def load_source_records(ehrxqa_dir: Path, split: str, source_ids: set[int]) -> dict[int, dict[str, Any]]: - path = ehrxqa_dir / "dataset" / f"{split}.json" - rows = json.loads(path.read_text(encoding="utf-8")) - by_id = {int(row["id"]): row for row in rows if int(row["id"]) in source_ids} - missing = sorted(source_ids - set(by_id)) - if missing: - raise ValueError(f"Missing EHRXQA source ids in {path}: {missing[:20]}") - return by_id - - -def load_tb_cxr( - table_path: Path, - selected_subjects: set[int], - cxr_root: Path, - cxr_jpg_root: Path, -) -> pd.DataFrame: - frame = pd.read_csv(table_path) - frame = frame[frame["subject_id"].isin(selected_subjects)].copy() - frame = frame.where(pd.notna(frame), None) - image_paths: list[str | None] = [] - report_paths: list[str | None] = [] - for row in frame.to_dict(orient="records"): - subject_id = safe_int(row.get("subject_id")) - study_id = safe_int(row.get("study_id")) - dicom_id = str(row.get("image_id") or "").strip() - if subject_id is None or study_id is None or not dicom_id: - image_paths.append(None) - report_paths.append(None) - continue - image_paths.append( - nested_file_relpath(subject_id, study_id, dicom_id) - if find_cxr_image(cxr_root, cxr_jpg_root, subject_id, study_id, dicom_id) is not None - else None - ) - report_paths.append(nested_report_relpath(subject_id, study_id)) - frame["image_path"] = image_paths - frame["report_path"] = report_paths - return frame - - -def write_subset_tables( - *, - source_tables_dir: Path, - output_tables_dir: Path, - selected_subjects: set[int], - selected_tb_cxr: pd.DataFrame, -) -> list[str]: - ensure_dir(output_tables_dir) - written: list[str] = [] - for csv_path in sorted(source_tables_dir.glob("*.csv")): - table_name = csv_path.stem - if table_name == "tb_cxr": - frame = selected_tb_cxr - else: - header = pd.read_csv(csv_path, nrows=0) - if table_is_reference(table_name) or "subject_id" not in header.columns: - frame = pd.read_csv(csv_path) - else: - chunks = [] - for chunk in pd.read_csv(csv_path, chunksize=200_000): - chunks.append(chunk[chunk["subject_id"].isin(selected_subjects)]) - frame = pd.concat(chunks, ignore_index=True) if chunks else header - frame = frame.where(pd.notna(frame), None) - out_path = output_tables_dir / csv_path.name - frame.to_csv(out_path, index=False) - written.append(table_name) - for extra_name in ("mimic_iv_cxr.sql", "index.html"): - src = source_tables_dir / extra_name - if src.exists(): - link_or_copy(src, output_tables_dir / extra_name) - return written - - -def write_sqlite_from_csvs(tables_dir: Path, sqlite_path: Path) -> None: - if sqlite_path.exists(): - sqlite_path.unlink() - with sqlite3.connect(sqlite_path) as conn: - for csv_path in sorted(tables_dir.glob("*.csv")): - frame = pd.read_csv(csv_path) - frame = frame.where(pd.notna(frame), None) - frame.to_sql(csv_path.stem, conn, if_exists="replace", index=False) - - -def copy_asset(src: Path | None, dst: Path, *, required: bool, label: str) -> bool: - if src is None: - if required: - raise FileNotFoundError(f"Missing required {label}: {dst}") - return False - link_or_copy(src, dst) - return True - - -def main() -> None: - args = parse_args() - reset_dir(args.output_root, args.overwrite) - - release_root, ehrxqa_dir = normalize_ehrxqa_root(args.ehrxqa_root) - rows = load_release_rows(args.input) - if not rows: - raise ValueError(f"No EHRXQA rows found in {args.input}") - - split_ids: dict[str, set[int]] = {} - for row in rows: - split_ids.setdefault(row["_source_split_from_qid"], set()).add(row["_source_id_from_qid"]) - if set(split_ids) != {"test"}: - raise ValueError(f"This release subset expects only EHRXQA test rows, got {sorted(split_ids)}") - source_by_id = load_source_records(ehrxqa_dir, "test", split_ids["test"]) - - linked_study_ids: set[int] = set() - linked_image_refs: dict[tuple[int, int, str], dict[str, Any]] = {} - for row in rows: - for image_path in row.get("image_paths") or []: - ref = parse_image_ref(image_path) - linked_study_ids.add(ref["study_id"]) - linked_image_refs[(ref["subject_id"], ref["study_id"], ref["dicom_id"])] = ref - - selected_subjects = {int(row["subject_id"]) for row in rows} - source_tables_dir = ehrxqa_dir / "database" / "gold" - selected_tb_cxr = load_tb_cxr( - source_tables_dir / "tb_cxr.csv", - selected_subjects, - args.cxr_root, - args.cxr_jpg_root, - ) - tb_cxr_by_study = { - int(record["study_id"]): record - for record in selected_tb_cxr.to_dict(orient="records") - if safe_int(record.get("study_id")) is not None - } - - output_ehrxqa_dir = args.output_root / "source_release" / "1.0.0" / "ehrxqa" - output_dataset_dir = output_ehrxqa_dir / "dataset" - output_tables_dir = output_ehrxqa_dir / "database" / "gold" - subset_source_rows = [source_by_id[row["_source_id_from_qid"]] for row in rows] - write_json(output_dataset_dir / "test.json", subset_source_rows) - written_tables = write_subset_tables( - source_tables_dir=source_tables_dir, - output_tables_dir=output_tables_dir, - selected_subjects=selected_subjects, - selected_tb_cxr=selected_tb_cxr, - ) - sqlite_relpath = "source_release/1.0.0/ehrxqa/database/gold/mimic_iv_cxr.sqlite" - write_sqlite_from_csvs(output_tables_dir, args.output_root / sqlite_relpath) - - for rel in ("index.html", "LICENSE.txt", "SHA256SUMS.txt"): - src = release_root / rel - if src.exists(): - link_or_copy(src, args.output_root / "source_release" / "1.0.0" / rel) - - copied_images = 0 - copied_reports = 0 - missing_nonlinked_assets = 0 - asset_rows = selected_tb_cxr.to_dict(orient="records") - for asset_row in asset_rows: - subject_id = safe_int(asset_row.get("subject_id")) - study_id = safe_int(asset_row.get("study_id")) - dicom_id = str(asset_row.get("image_id") or "").strip() - if subject_id is None or study_id is None or not dicom_id: - continue - linked = (subject_id, study_id, dicom_id) in linked_image_refs - image_rel = nested_file_relpath(subject_id, study_id, dicom_id) - report_rel = nested_report_relpath(subject_id, study_id) - image_src = find_cxr_image(args.cxr_root, args.cxr_jpg_root, subject_id, study_id, dicom_id) - report_src = find_cxr_report(args.cxr_root, subject_id, study_id) - if copy_asset(image_src, args.output_root / image_rel, required=linked, label="CXR image"): - copied_images += 1 - else: - missing_nonlinked_assets += 1 - if copy_asset(report_src, args.output_root / report_rel, required=linked, label="CXR report"): - copied_reports += 1 - else: - missing_nonlinked_assets += 1 - - manifest_rows: list[dict[str, Any]] = [] - for row in rows: - source_id = row["_source_id_from_qid"] - source_row = source_by_id[source_id] - packaged_images = [strip_asset_prefix(path) for path in row.get("image_paths") or []] - packaged_reports = [strip_asset_prefix(path) for path in row.get("report_paths") or []] - study_ids = [] - dicom_ids = [] - raw_images = [] - raw_reports = [] - for image_path in packaged_images: - ref = parse_image_ref(image_path) - study_ids.append(ref["study_id"]) - dicom_ids.append(ref["dicom_id"]) - raw_images.append(str(Path("files") / Path(ref["image_relpath"]).relative_to("mimic-cxr/2.0.0/files"))) - for report_path in packaged_reports: - raw_reports.append( - str(Path("mimic-cxr-reports") / Path(report_path).relative_to("mimic-cxr/2.0.0/mimic-cxr-reports")) - ) - manifest_rows.append( - { - "qid": row.get("qid"), - "source_line_index": row.get("_source_line_index"), - "source_index": row.get("source_index"), - "source_benchmark": "ehrxqa", - "task": row.get("task"), - "source_split": row.get("source_split"), - "source_id": source_id, - "variant": "gold", - "subject_id": row.get("subject_id"), - "hadm_id": row.get("hadm_id"), - "stay_id": row.get("stay_id"), - "prediction_time": row.get("prediction_time"), - "question": row.get("question"), - "released_input_text": row.get("input_text"), - "source_question": source_row.get("question"), - "source_sql": source_row.get("query"), - "source_template": source_row.get("template"), - "source_value": source_row.get("value"), - "source_answer": source_row.get("answer"), - "ground_truth": row.get("ground_truth"), - "answer_type": row.get("answer_type"), - "modalities": row.get("modalities") or ["cxr_table", "cxr_image"], - "study_ids": study_ids, - "dicom_ids": dicom_ids, - "packaged_db_relpath": sqlite_relpath, - "packaged_table_root_relpath": "source_release/1.0.0/ehrxqa/database/gold", - "packaged_image_relpaths": packaged_images, - "packaged_report_relpaths": packaged_reports, - "raw_image_source_relpaths": raw_images, - "raw_report_source_relpaths": raw_reports, - "source_dataset_relpath": "source_release/1.0.0/ehrxqa/dataset/test.json", - "tb_cxr_context_rows": len( - [record for record in asset_rows if safe_int(record.get("subject_id")) == row.get("subject_id")] - ), - } - ) - - write_jsonl(args.output_root / "linked_manifests" / "test.jsonl", manifest_rows) - - readme = """# ClinSeek-MM-Bench-EHRXQA-source - -This package is the source-aligned EHRXQA subset used by ClinSeek MM-Bench. -It contains only the EHRXQA rows present in `inputs/mm_bench.jsonl`. - -Required source downloads: - -- EHRXQA 1.0.0 answered release: `$EHRXQA_ROOT` -- MIMIC-CXR / MIMIC-CXR-JPG files and reports: `$MIMIC_CXR_ROOT` -- MIMIC-CXR-JPG fallback root: `$MIMIC_CXR_JPG_ROOT` -- MIMIC-IV latest local release kept for provenance: `$MIMICIV_ROOT` -- MIMIC-IV-Note kept for provenance when local notes are inspected: `$MIMIC_IV_NOTE_ROOT` - -Contents: - -- `source_release/1.0.0/ehrxqa/dataset/test.json`: official EHRXQA rows selected by ClinSeek. -- `source_release/1.0.0/ehrxqa/database/gold/`: official-schema subset tables. -- `source_release/1.0.0/ehrxqa/database/gold/mimic_iv_cxr.sqlite`: SQLite materialization of the subset tables. - - `linked_manifests/test.jsonl`: row-level provenance and package-relative asset paths. - - `mimic-cxr/2.0.0/...`: packaged CXR JPG and report TXT assets for selected patient context. - -The linked manifest is a provenance artifact. It contains gold answers and the -original EHRXQA SQL fields, so it must not be used as the runtime model input. - """ - (args.output_root / "README.md").write_text(readme, encoding="utf-8") - - metadata = { - "package_name": "ClinSeek-MM-Bench-EHRXQA-source", - "input": "CLINSEEK_MM_BENCH_JSONL", - "records": len(manifest_rows), - "subjects": len(selected_subjects), - "variant": "gold", - "source_splits": dict(Counter(row["source_split"] for row in manifest_rows)), - "written_tables": written_tables, - "tb_cxr_context_rows": len(asset_rows), - "unique_linked_images": len({p for row in manifest_rows for p in row["packaged_image_relpaths"]}), - "unique_linked_reports": len({p for row in manifest_rows for p in row["packaged_report_relpaths"]}), - "copied_images": copied_images, - "copied_reports": copied_reports, - "missing_nonlinked_context_assets": missing_nonlinked_assets, - "source_path_env_vars": { - "ehrxqa_root": "EHRXQA_ROOT", - "cxr_root": "MIMIC_CXR_ROOT", - "cxr_jpg_root": "MIMIC_CXR_JPG_ROOT", - "mimiciv_root": "MIMICIV_ROOT", - "mimic_iv_note_root": "MIMIC_IV_NOTE_ROOT", - }, - "path_contract": { - "manifest_paths": "relative_to_package_root", - "packaged_image_relpaths": "relative_to_package_root", - "packaged_report_relpaths": "relative_to_package_root", - "raw_image_source_relpaths": "relative_to_MIMIC_CXR_ROOT_or_MIMIC_CXR_JPG_ROOT", - "raw_report_source_relpaths": "relative_to_MIMIC_CXR_ROOT", - }, - } - write_json(args.output_root / "metadata.json", metadata) - print(json.dumps(metadata, ensure_ascii=False, indent=2)) - - -if __name__ == "__main__": - main() diff --git a/rebuild/mm_bench/build_medmod_clinseek_mm_subset.py b/rebuild/mm_bench/build_medmod_clinseek_mm_subset.py deleted file mode 100644 index c5134e1405600fa9744d966c9d58f08634c466ce..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/build_medmod_clinseek_mm_subset.py +++ /dev/null @@ -1,679 +0,0 @@ -#!/usr/bin/env python3 -"""Convert a source-aligned MedMod subset into ClinSeek-MM-Bench format. - -Input is the package produced by build_medmod_release_original_subset.py. -Output is a compact release tree with: - -- inputs/mm_bench_medmod.jsonl -- data/mm_bench/medmod/database/patient_.db -- data/mm_bench/medmod/mimic-cxr/2.0.0/files/... -- data/mm_bench/medmod/table_description/* -""" - -from __future__ import annotations - -import argparse -import csv -import json -import os -import shutil -import sqlite3 -import sys -from collections import Counter, defaultdict -from datetime import datetime -from pathlib import Path -from typing import Any - -import pandas as pd - - -REPO_ROOT = Path(__file__).resolve().parents[2] -SRC_ROOT = REPO_ROOT / "src" -if str(SRC_ROOT) not in sys.path: - sys.path.insert(0, str(SRC_ROOT)) - -DEFAULT_ORIGINAL_ROOT = Path( - os.environ.get( - "MEDMOD_ORIGINAL_SUBSET_ROOT", - "data/build/ClinSeek-MM-Bench-MedMod-source", - ) -) -DEFAULT_OUTPUT_ROOT = Path( - os.environ.get( - "CLINSEEK_MEDMOD_MM_ROOT", - "data/build/ClinSeek-MM-Bench-MedMod", - ) -) - -LEAKY_STAY_COLUMNS = { - "outtime", - "los", - "dischtime", - "deathtime", - "dod", - "mortality_inunit", - "mortality", - "mortality_inhospital", -} - -TIME_COLUMNS = { - "events": "charttime", - "stays": "intime", - "tb_cxr": "studydatetime", -} - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument("--original-root", type=Path, default=DEFAULT_ORIGINAL_ROOT) - parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT) - parser.add_argument("--asset-prefix", default="MedModOriginalLinked_v1") - parser.add_argument("--max-table-rows", type=int, default=80) - parser.add_argument( - "--patient-db-scope", - choices=("selected_stays", "full_subject"), - default="selected_stays", - help=( - "Build patient DBs from only the official stays selected by the release manifest, or from the " - "whole extracted subject folder." - ), - ) - parser.add_argument("--overwrite", action="store_true") - parser.add_argument( - "--render-input-text", - action="store_true", - help="Render input_text from the rebuilt patient DB instead of preserving the released HF JSONL field.", - ) - return parser.parse_args() - - -def ensure_dir(path: Path) -> None: - path.mkdir(parents=True, exist_ok=True) - - -def reset_dir(path: Path, overwrite: bool) -> None: - if path.exists(): - if not overwrite: - raise FileExistsError(f"Output root already exists: {path}") - shutil.rmtree(path) - path.mkdir(parents=True, exist_ok=True) - - -def link_or_copy(src: Path, dst: Path) -> None: - src = src.resolve() - ensure_dir(dst.parent) - if dst.exists(): - return - try: - os.link(src, dst) - except OSError: - shutil.copy2(src, dst) - - -def write_json(path: Path, payload: Any) -> None: - ensure_dir(path.parent) - path.write_text(json.dumps(payload, ensure_ascii=False, indent=2) + "\n", encoding="utf-8") - - -def read_jsonl(path: Path) -> list[dict[str, Any]]: - rows = [] - with path.open("r", encoding="utf-8") as handle: - for line in handle: - rows.append(json.loads(line)) - return rows - - -def safe_int(value: Any) -> int | None: - if value is None or value == "": - return None - try: - if pd.isna(value): - return None - except TypeError: - pass - try: - return int(float(str(value).strip())) - except ValueError: - return None - - -def compact_value(value: Any) -> Any: - try: - if pd.isna(value): - return "" - except TypeError: - pass - if hasattr(value, "isoformat"): - return value.isoformat(sep=" ") - return value - - -def parse_datetime(value: Any) -> datetime | None: - if not value: - return None - if isinstance(value, datetime): - return value - text = str(value) - for fmt in ("%Y-%m-%d %H:%M:%S", "%Y-%m-%d %H:%M:%S.%f"): - try: - return datetime.strptime(text, fmt) - except ValueError: - pass - return None - - -def study_datetime_from_metadata(record: dict[str, Any]) -> str | None: - date = record.get("StudyDate") - time = record.get("StudyTime") - if date in (None, "") or time in (None, ""): - return None - try: - time_text = f"{int(float(time)):06d}" - dt = datetime.strptime(f"{int(float(date))} {time_text}", "%Y%m%d %H%M%S") - return dt.strftime("%Y-%m-%d %H:%M:%S") - except (TypeError, ValueError): - return None - - -def load_manifest(original_root: Path) -> list[dict[str, Any]]: - manifest = original_root / "linked_manifests" / "all.jsonl" - if not manifest.exists(): - raise FileNotFoundError(f"Missing source manifest: {manifest}") - return read_jsonl(manifest) - - -def load_cxr_metadata(original_root: Path) -> tuple[dict[str, dict[str, Any]], dict[str, str]]: - meta_root = original_root / "source_release" / "cxr_metadata" - metadata_path = meta_root / "mimic-cxr-2.0.0-metadata.csv" - if not metadata_path.exists(): - raise FileNotFoundError(f"Missing packaged CXR metadata: {metadata_path}") - metadata_df = pd.read_csv(metadata_path) - metadata_by_dicom = { - str(record["dicom_id"]): record for record in metadata_df.to_dict(orient="records") - } - - split_by_dicom: dict[str, str] = {} - split_path = meta_root / "mimic-cxr-2.0.0-split.csv" - if split_path.exists(): - split_df = pd.read_csv(split_path) - if {"dicom_id", "split"}.issubset(split_df.columns): - split_by_dicom = { - str(record["dicom_id"]): str(record["split"]) - for record in split_df.to_dict(orient="records") - } - return metadata_by_dicom, split_by_dicom - - -def build_tb_cxr_rows( - manifest_rows: list[dict[str, Any]], - metadata_by_dicom: dict[str, dict[str, Any]], - split_by_dicom: dict[str, str], -) -> dict[int, pd.DataFrame]: - rows_by_subject: dict[int, list[dict[str, Any]]] = defaultdict(list) - seen: set[tuple[int, int, str, int | None]] = set() - for sample in manifest_rows: - subject_id = safe_int(sample.get("subject_id")) - hadm_id = safe_int(sample.get("hadm_id")) - stay_id = safe_int(sample.get("stay_id")) - if subject_id is None: - continue - for study_id, dicom_id, image_relpath in zip( - sample.get("study_ids") or [], - sample.get("dicom_ids") or [], - sample.get("packaged_image_relpaths") or [], - ): - study_id_int = safe_int(study_id) - if study_id_int is None: - continue - key = (subject_id, study_id_int, str(dicom_id), stay_id) - if key in seen: - continue - seen.add(key) - metadata = metadata_by_dicom.get(str(dicom_id), {}) - rows_by_subject[subject_id].append( - { - "subject_id": subject_id, - "study_id": study_id_int, - "studydatetime": study_datetime_from_metadata(metadata) - or sample.get("prediction_time"), - "split": split_by_dicom.get(str(dicom_id), sample.get("source_split") or "test"), - "image_id": str(dicom_id), - "image_path": image_relpath, - "viewposition": str(metadata.get("ViewPosition") or "AP"), - "hadm_id": hadm_id, - "stay_id": stay_id, - } - ) - return { - subject_id: pd.DataFrame(rows).sort_values(["studydatetime", "study_id", "image_id"]) - for subject_id, rows in rows_by_subject.items() - } - - -def sanitize_stays(frame: pd.DataFrame) -> pd.DataFrame: - drop_cols = [col for col in frame.columns if col.lower() in LEAKY_STAY_COLUMNS] - return frame.drop(columns=drop_cols) if drop_cols else frame - - -def write_frame(conn: sqlite3.Connection, table_name: str, frame: pd.DataFrame) -> None: - clean = frame.where(pd.notna(frame), None) - clean.to_sql(table_name, conn, if_exists="replace", index=False) - - -def quote_identifier(name: str) -> str: - return '"' + name.replace('"', '""') + '"' - - -def csv_value(value: Any) -> Any: - if value is None or value == "": - return None - return value - - -def create_text_table( - conn: sqlite3.Connection, - table_name: str, - columns: list[str], - rows: list[list[Any]], -) -> None: - q_table = quote_identifier(table_name) - column_sql = ", ".join(f"{quote_identifier(column)} TEXT" for column in columns) - conn.execute(f"CREATE TABLE {q_table} ({column_sql})") - if not rows: - return - placeholders = ", ".join(["?"] * len(columns)) - conn.executemany(f"INSERT INTO {q_table} VALUES ({placeholders})", rows) - - -def sample_stay_ids(samples: list[dict[str, Any]]) -> set[int]: - stay_ids: set[int] = set() - for sample in samples: - for candidate in ( - sample.get("stay_id"), - (sample.get("official_data_full_row") or {}).get("stay_id") - if isinstance(sample.get("official_data_full_row"), dict) - else None, - (sample.get("official_listfile_row") or {}).get("stay_id") - if isinstance(sample.get("official_listfile_row"), dict) - else None, - ): - stay_id = safe_int(candidate) - if stay_id is not None: - stay_ids.add(stay_id) - return stay_ids - - -def filter_frame_to_stays(frame: pd.DataFrame, stay_ids: set[int]) -> pd.DataFrame: - if not stay_ids or "stay_id" not in frame.columns: - return frame - numeric_stay_ids = pd.to_numeric(frame["stay_id"], errors="coerce").astype("Int64") - return frame[numeric_stay_ids.isin(stay_ids)].copy() - - -def write_csv_table( - conn: sqlite3.Connection, - table_name: str, - csv_path: Path, - *, - stay_ids: set[int], - drop_lower_columns: set[str] | None = None, -) -> None: - drop_lower_columns = drop_lower_columns or set() - with csv_path.open("r", encoding="utf-8", newline="") as handle: - reader = csv.reader(handle) - source_columns = next(reader) - keep_indexes = [ - index - for index, column in enumerate(source_columns) - if column.lower() not in drop_lower_columns - ] - columns = [source_columns[index] for index in keep_indexes] - stay_index = source_columns.index("stay_id") if "stay_id" in source_columns else None - rows: list[list[Any]] = [] - for row in reader: - if stay_ids and stay_index is not None: - stay_id = safe_int(row[stay_index] if stay_index < len(row) else None) - if stay_id not in stay_ids: - continue - rows.append([csv_value(row[index]) if index < len(row) else None for index in keep_indexes]) - create_text_table(conn, table_name, columns, rows) - - -def build_patient_db( - *, - original_root: Path, - samples: list[dict[str, Any]], - output_db: Path, - tb_cxr: pd.DataFrame | None, - patient_db_scope: str, -) -> None: - ensure_dir(output_db.parent) - if not samples: - raise ValueError("Cannot build MedMod patient DB from an empty sample list") - sample = samples[0] - subject_dirs = sample.get("ehr_subject_relpaths") or [] - if not subject_dirs: - raise FileNotFoundError(f"Sample has no EHR subject path: {sample.get('qid')}") - subject_dir = original_root / subject_dirs[0] - if not subject_dir.is_dir(): - raise FileNotFoundError(f"Missing EHR subject dir: {subject_dir}") - stay_ids = sample_stay_ids(samples) if patient_db_scope == "selected_stays" else set() - with sqlite3.connect(output_db) as conn: - conn.execute("PRAGMA journal_mode=OFF") - conn.execute("PRAGMA synchronous=OFF") - events_path = subject_dir / "events.csv" - stays_path = subject_dir / "stays.csv" - if events_path.exists(): - write_csv_table(conn, "events", events_path, stay_ids=stay_ids) - if stays_path.exists(): - write_csv_table( - conn, - "stays", - stays_path, - stay_ids=stay_ids, - drop_lower_columns=LEAKY_STAY_COLUMNS, - ) - if tb_cxr is not None and not tb_cxr.empty: - write_frame(conn, "tb_cxr", filter_frame_to_stays(tb_cxr, stay_ids)) - conn.commit() - - -def materialize_patient_db( - *, - original_root: Path, - samples: list[dict[str, Any]], - output_db: Path, - tb_cxr: pd.DataFrame | None, - patient_db_scope: str, -) -> str: - if not samples: - raise ValueError("Cannot materialize MedMod patient DB from an empty sample list") - sample = samples[0] - subject_id = safe_int(sample.get("subject_id")) - if subject_id is None: - raise ValueError(f"Missing subject_id for {sample.get('qid')}") - build_patient_db( - original_root=original_root, - samples=samples, - output_db=output_db, - tb_cxr=tb_cxr, - patient_db_scope=patient_db_scope, - ) - return f"source_aligned_{patient_db_scope}" - - -def filter_by_cutoff(table_name: str, frame: pd.DataFrame, cutoff: datetime | None) -> pd.DataFrame: - if cutoff is None: - return frame.copy() - column = TIME_COLUMNS.get(table_name) - if not column or column not in frame.columns: - return frame.copy() - parsed = pd.to_datetime(frame[column], errors="coerce") - return frame[parsed.isna() | (parsed <= pd.Timestamp(cutoff))].copy() - - -def table_to_text(table_name: str, frame: pd.DataFrame, max_rows: int) -> str: - total = len(frame) - if total == 0: - return f"### {table_name}\nRows visible before cutoff: 0\n" - sort_col = TIME_COLUMNS.get(table_name) - display = frame - if sort_col and sort_col in display.columns: - display = display.sort_values(sort_col, kind="stable") - if max_rows and len(display) > max_rows: - display = display.tail(max_rows) - shown = f"latest {len(display)} of {total}" - else: - shown = f"{total} of {total}" - clean = display.copy() - for column in clean.columns: - clean[column] = clean[column].map(compact_value) - return ( - f"### {table_name}\n" - f"Rows visible before cutoff: {total}; rows included below: {shown}\n" - f"{clean.to_csv(index=False)}" - ) - - -def render_ehr_context_from_manager(manager: Any, sample: dict[str, Any], max_table_rows: int) -> str: - manager.load_ehr_for_sample(str(sample["subject_id"]), sample["prediction_time"]) - blocks = [] - for table_name in sorted(manager.ehr_data): - blocks.append(table_to_text(table_name, manager.ehr_data[table_name], max_table_rows)) - return "\n".join(blocks).strip() - - -def render_ehr_context(db_path: Path, prediction_time: str, max_table_rows: int) -> str: - cutoff = parse_datetime(prediction_time) - blocks: list[str] = [] - with sqlite3.connect(db_path) as conn: - table_names = [ - row[0] - for row in conn.execute("SELECT name FROM sqlite_master WHERE type='table' ORDER BY name") - ] - for table_name in table_names: - frame = pd.read_sql_query(f'SELECT * FROM "{table_name}"', conn) - visible = filter_by_cutoff(table_name, frame, cutoff) - blocks.append(table_to_text(table_name, visible, max_table_rows)) - return "\n".join(blocks).strip() - - -def build_input_text(sample: dict[str, Any], image_paths: list[str], ehr_text: str) -> str: - return "\n\n".join( - [ - str(sample.get("question") or "").strip(), - "", - ehr_text, - "", - "", - "\n".join(f"- {path}" for path in image_paths) if image_paths else "NONE", - "", - ] - ) - - -def write_table_descriptions(benchmark_root: Path) -> None: - database_root = benchmark_root / "database" - table_desc_root = benchmark_root / "table_description" - ensure_dir(table_desc_root) - schemas: dict[str, list[str]] = {} - for db_path in sorted(database_root.glob("patient_*.db"))[:50]: - with sqlite3.connect(db_path) as conn: - for (table_name,) in conn.execute("SELECT name FROM sqlite_master WHERE type='table'"): - columns = [row[1] for row in conn.execute(f'PRAGMA table_info("{table_name}")')] - known = schemas.setdefault(table_name, []) - for column in columns: - if column not in known: - known.append(column) - desc_records = [ - { - "file_name": table_name, - "class": "ehr", - "description": f"Schema extracted from MedMod subset table '{table_name}'.", - "columns": [ - { - "column_name": column, - "description": f"Column '{column}' in table '{table_name}'.", - } - for column in columns - ], - } - for table_name, columns in sorted(schemas.items()) - ] - with (table_desc_root / "shorten_description.json").open("w", encoding="utf-8") as handle: - for record in desc_records: - handle.write(json.dumps(record, ensure_ascii=False) + "\n") - (table_desc_root / "link_information.json").write_text("", encoding="utf-8") - - -def write_runtime_metadata(benchmark_root: Path) -> None: - write_json( - benchmark_root / "metadata.json", - { - "package_name": "ClinSeek-MM-Bench-MedMod-runtime", - "leakage_policy": { - "sanitize_datetime_columns": True, - "mask_future_datetime_columns": True, - "row_timestamp_columns": TIME_COLUMNS, - "datetime_columns": { - "events": ["charttime"], - "stays": ["intime", "admittime"], - "tb_cxr": ["studydatetime"], - }, - "drop_columns": { - "stays": sorted(LEAKY_STAY_COLUMNS), - }, - }, - "path_contract": { - "db_path_hint": "relative_to_benchmark_root", - "image_paths": "relative_to_benchmark_root", - "report_paths": "relative_to_benchmark_root", - "tb_cxr.image_path": "relative_to_benchmark_root", - }, - }, - ) - - -def main() -> None: - args = parse_args() - reset_dir(args.output_root, args.overwrite) - manifest_rows = load_manifest(args.original_root) - metadata_by_dicom, split_by_dicom = load_cxr_metadata(args.original_root) - tb_cxr_by_subject = build_tb_cxr_rows(manifest_rows, metadata_by_dicom, split_by_dicom) - - bench_root = args.output_root / "data" / "mm_bench" / "medmod" - database_root = bench_root / "database" - inputs_root = args.output_root / "inputs" - ensure_dir(database_root) - ensure_dir(inputs_root) - - by_subject: dict[int, list[dict[str, Any]]] = defaultdict(list) - for sample in manifest_rows: - subject_id = safe_int(sample.get("subject_id")) - if subject_id is not None: - by_subject[subject_id].append(sample) - - db_source_counts = Counter() - for subject_id, samples in sorted(by_subject.items()): - source = materialize_patient_db( - original_root=args.original_root, - samples=samples, - output_db=database_root / f"patient_{subject_id}.db", - tb_cxr=tb_cxr_by_subject.get(subject_id), - patient_db_scope=args.patient_db_scope, - ) - db_source_counts[source] += 1 - - write_table_descriptions(bench_root) - write_runtime_metadata(bench_root) - - ehr_manager = None - need_rendered_input_text = args.render_input_text or any( - not sample.get("released_input_text") for sample in manifest_rows - ) - if need_rendered_input_text: - try: - from agentlite.commons.EHRManager import EHRManager # type: ignore - - ehr_manager = EHRManager(str(bench_root)) - except Exception as exc: # pragma: no cover - fallback for portable envs - print({"ehr_manager_unavailable": repr(exc)}, flush=True) - - output_rows: list[dict[str, Any]] = [] - stats = Counter() - for index, sample in enumerate(manifest_rows): - subject_id = safe_int(sample.get("subject_id")) - if subject_id is None: - raise ValueError(f"Missing subject_id: {sample.get('qid')}") - rel_images = list(sample.get("packaged_image_relpaths") or []) - rel_reports = list(sample.get("packaged_report_relpaths") or []) - for relpath in rel_images + rel_reports: - link_or_copy(args.original_root / relpath, bench_root / relpath) - prefixed_images = [f"{args.asset_prefix}/{relpath}" for relpath in rel_images] - prefixed_reports = [f"{args.asset_prefix}/{relpath}" for relpath in rel_reports] - db_path = database_root / f"patient_{subject_id}.db" - if args.render_input_text or not sample.get("released_input_text"): - if ehr_manager is not None: - ehr_text = render_ehr_context_from_manager(ehr_manager, sample, args.max_table_rows) - else: - ehr_text = render_ehr_context(db_path, str(sample.get("prediction_time")), args.max_table_rows) - input_text = build_input_text(sample, prefixed_images, ehr_text) - else: - input_text = sample.get("released_input_text") - output_rows.append( - { - "qid": sample.get("qid"), - "source_index": sample.get("source_index"), - "source_benchmark": "medmod", - "task": sample.get("source_task"), - "source_split": sample.get("source_split"), - "subject_id": sample.get("subject_id"), - "hadm_id": sample.get("hadm_id"), - "stay_id": sample.get("stay_id"), - "prediction_time": sample.get("prediction_time"), - "question": sample.get("question"), - "input_text": input_text, - "image_paths": prefixed_images, - "report_paths": prefixed_reports, - "ground_truth": sample.get("ground_truth"), - "answer_type": sample.get("answer_type"), - "modalities": sample.get("modalities") or ["ehr", "cxr"], - } - ) - stats[f"task:{sample.get('source_task')}"] += 1 - if (index + 1) % 100 == 0: - print({"rendered_rows": index + 1, "total": len(manifest_rows)}, flush=True) - - output_path = inputs_root / "mm_bench_medmod.jsonl" - with output_path.open("w", encoding="utf-8") as handle: - for row in output_rows: - handle.write(json.dumps(row, ensure_ascii=False, separators=(",", ":")) + "\n") - - metadata = { - "package_name": "ClinSeek-MM-Bench-MedMod", - "original_root": "MEDMOD_ORIGINAL_SUBSET_ROOT", - "records": len(output_rows), - "subjects": len(by_subject), - "patient_dbs": len(list(database_root.glob("patient_*.db"))), - "patient_db_sources": dict(sorted(db_source_counts.items())), - "patient_db_scope": args.patient_db_scope, - "unique_images": len({p for row in output_rows for p in row["image_paths"]}), - "unique_reports": len({p for row in output_rows for p in row["report_paths"]}), - "input_file": "inputs/mm_bench_medmod.jsonl", - "bench_root": "data/mm_bench/medmod", - "asset_prefix": args.asset_prefix, - "input_text_source": "rendered_from_db" if need_rendered_input_text else "released_hf_jsonl", - "stats": dict(sorted(stats.items())), - "path_contract": { - "image_paths": "strip asset_prefix, then resolve relative to bench_root", - "report_paths": "strip asset_prefix, then resolve relative to bench_root", - "patient_db": "data/mm_bench/medmod/database/patient_.db", - }, - "leakage_policy": { - "ground_truth": "kept only in output JSONL field, never in input_text", - "stays_dropped_columns": sorted(LEAKY_STAY_COLUMNS), - "diagnoses_table": "not materialized in patient DB", - "runtime_cutoff_columns": TIME_COLUMNS, - }, - } - write_json(args.output_root / "metadata.json", metadata) - - readme = f"""# ClinSeek-MM-Bench-MedMod - -This directory contains the MedMod-derived portion of ClinSeek-MM-Bench. - -Use: - -- `inputs/mm_bench_medmod.jsonl` -- `data/mm_bench/medmod` - -The JSONL contains both agentic fields (`question`, `image_paths`, `subject_id`) -and one-shot fields (`input_text`, `image_paths`). Patient SQLite DBs are under -`data/mm_bench/medmod/database`. -""" - (args.output_root / "README.md").write_text(readme, encoding="utf-8") - print(json.dumps(metadata, ensure_ascii=False, indent=2)) - - -if __name__ == "__main__": - main() diff --git a/rebuild/mm_bench/build_medmod_release_original_subset.py b/rebuild/mm_bench/build_medmod_release_original_subset.py deleted file mode 100644 index 6e0fc223944626a11fc9b3f3cbd874fc0c5698c0..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/build_medmod_release_original_subset.py +++ /dev/null @@ -1,929 +0,0 @@ -#!/usr/bin/env python3 -"""Build the source-aligned MedMod subset used by ClinSeek MM-Bench. - -This script intentionally does not rebuild the full MedMod benchmark. It reads -the released ClinSeek multimodal input file, keeps only the MedMod rows that are -actually evaluated, verifies them against the official MedMod listfiles and -MIMIC-CXR labels/metadata, and packages the required source-format EHR folders -and CXR files with relative paths. -""" - -from __future__ import annotations - -import argparse -import json -import os -import re -import shutil -import sqlite3 -from collections import Counter, defaultdict -from datetime import datetime -from pathlib import Path -from typing import Any - -import pandas as pd - - -DEFAULT_INPUT = Path( - os.environ.get( - "CLINSEEK_MM_BENCH_JSONL", - "data/ClinSeek-Bench/inputs/mm_bench.jsonl", - ) -) -DEFAULT_OUTPUT_ROOT = Path( - os.environ.get( - "MEDMOD_ORIGINAL_SUBSET_ROOT", - "data/build/ClinSeek-MM-Bench-MedMod-source", - ) -) -DEFAULT_MEDMOD_REPO = Path(os.environ.get("MEDMOD_REPO_ROOT", "external/MedMod")) -DEFAULT_CXR_JPG_ROOT = Path( - os.environ.get("MIMIC_CXR_JPG_ROOT", "external/mimic-cxr-jpg") -) -DEFAULT_CXR_META_ROOT = Path( - os.environ.get("MIMIC_CXR_META_ROOT", "external/mimic-cxr/2.0.0") -) -DEFAULT_MIMICIV_ROOT = Path(os.environ.get("MIMICIV_ROOT", "external/mimiciv/3.1")) - -IMAGE_RE = re.compile( - r"(?:^|/)files/p\d+/p(?P\d+)/s(?P\d+)/(?P[^/]+)\.jpg$" -) - -TASK_MAP = { - "medmod_decompensation": "decompensation", - "medmod_in_hospital_mortality": "in-hospital-mortality", - "medmod_length_of_stay": "length-of-stay", - "medmod_phenotyping": "phenotyping", - "medmod_radiology": "radiology", - "decompensation": "decompensation", - "in-hospital-mortality": "in-hospital-mortality", - "length-of-stay": "length-of-stay", - "phenotyping": "phenotyping", - "radiology": "radiology", -} - -PHENOTYPE_CLASSES = [ - "Acute and unspecified renal failure", - "Acute cerebrovascular disease", - "Acute myocardial infarction", - "Cardiac dysrhythmias", - "Chronic kidney disease", - "Chronic obstructive pulmonary disease and bronchiectasis", - "Complications of surgical procedures or medical care", - "Conduction disorders", - "Congestive heart failure; nonhypertensive", - "Coronary atherosclerosis and other heart disease", - "Diabetes mellitus with complications", - "Diabetes mellitus without complication", - "Disorders of lipid metabolism", - "Essential hypertension", - "Fluid and electrolyte disorders", - "Gastrointestinal hemorrhage", - "Hypertension with complications and secondary hypertension", - "Other liver diseases", - "Other lower respiratory disease", - "Other upper respiratory disease", - "Pleurisy; pneumothorax; pulmonary collapse", - "Pneumonia (except that caused by tuberculosis or sexually transmitted disease)", - "Respiratory failure; insufficiency; arrest (adult)", - "Septicemia (except in labor)", - "Shock", -] - -RADIOLOGY_CLASSES = [ - "Atelectasis", - "Cardiomegaly", - "Consolidation", - "Edema", - "Enlarged Cardiomediastinum", - "Fracture", - "Lung Lesion", - "Lung Opacity", - "No Finding", - "Pleural Effusion", - "Pleural Other", - "Pneumonia", - "Pneumothorax", - "Support Devices", -] - -LEAKY_STAY_COLUMNS = { - "outtime", - "los", - "dischtime", - "deathtime", - "dod", - "mortality_inunit", - "mortality", - "mortality_inhospital", -} - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument("--input", type=Path, default=DEFAULT_INPUT) - parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT) - parser.add_argument("--medmod-repo-root", type=Path, default=DEFAULT_MEDMOD_REPO) - parser.add_argument("--cxr-jpg-root", type=Path, default=DEFAULT_CXR_JPG_ROOT) - parser.add_argument("--cxr-meta-root", type=Path, default=DEFAULT_CXR_META_ROOT) - parser.add_argument("--mimiciv-root", type=Path, default=DEFAULT_MIMICIV_ROOT) - parser.add_argument("--overwrite", action="store_true") - parser.add_argument( - "--include-reports", - action="store_true", - help="Also package CXR report TXT files. Keep disabled for the ClinSeek MedMod release.", - ) - parser.add_argument( - "--allow-warnings", - action="store_true", - help="Deprecated compatibility flag; warnings are non-fatal unless --strict-official-match is set.", - ) - parser.add_argument( - "--strict-official-match", - action="store_true", - help="Exit non-zero if official pairing/label validation warnings are found.", - ) - return parser.parse_args() - - -def ensure_dir(path: Path) -> None: - path.mkdir(parents=True, exist_ok=True) - - -def reset_dir(path: Path, overwrite: bool) -> None: - if path.exists(): - if not overwrite: - raise FileExistsError(f"Output root already exists: {path}") - shutil.rmtree(path) - path.mkdir(parents=True, exist_ok=True) - - -def link_or_copy(src: Path, dst: Path) -> None: - src = src.resolve() - ensure_dir(dst.parent) - if dst.exists(): - return - try: - os.link(src, dst) - except OSError: - shutil.copy2(src, dst) - - -def copytree_links(src: Path, dst: Path) -> None: - if dst.exists(): - return - shutil.copytree(src, dst, copy_function=lambda s, d: (link_or_copy(Path(s), Path(d)) or str(d))) - - -def relpath_or_name(path: Path, root: Path) -> str: - try: - return str(path.resolve().relative_to(root.resolve())) - except ValueError: - return path.name - - -def write_json(path: Path, payload: Any) -> None: - ensure_dir(path.parent) - path.write_text(json.dumps(payload, ensure_ascii=False, indent=2) + "\n", encoding="utf-8") - - -def write_jsonl(path: Path, rows: list[dict[str, Any]]) -> None: - ensure_dir(path.parent) - with path.open("w", encoding="utf-8") as handle: - for row in rows: - handle.write(json.dumps(row, ensure_ascii=False, separators=(",", ":")) + "\n") - - -def safe_int(value: Any) -> int | None: - if value is None or value == "": - return None - try: - if pd.isna(value): - return None - except TypeError: - pass - try: - return int(float(str(value).strip())) - except ValueError: - return None - - -def safe_float(value: Any) -> float | None: - if value is None or value == "": - return None - try: - if pd.isna(value): - return None - except TypeError: - pass - try: - return float(str(value).strip()) - except ValueError: - return None - - -def normalize_split(split: str) -> str: - return "valid" if split in {"val", "validate", "validation"} else split - - -def medmod_listfile_name(split: str, *, mml_ssl: bool) -> str: - split = normalize_split(split) - if split == "valid": - return "validate_listfile.csv" if mml_ssl else "val_listfile.csv" - return f"{split}_listfile.csv" - - -def canonical_task(task: str) -> str: - if task not in TASK_MAP: - raise ValueError(f"Unsupported MedMod task: {task}") - return TASK_MAP[task] - - -def ground_truth_names(row: dict[str, Any]) -> list[str]: - values = row.get("ground_truth") - if values is None: - values = row.get("label") - if isinstance(values, list): - names = [] - for item in values: - if isinstance(item, dict) and item.get("name") is not None: - names.append(str(item["name"])) - elif item is not None: - names.append(str(item)) - return names - if values is None: - return [] - return [str(values)] - - -def parse_image_ref(path: str) -> dict[str, Any]: - stripped = path - if "/" in stripped and stripped.split("/", 1)[0].endswith("OriginalLinked_v1"): - stripped = stripped.split("/", 1)[1] - match = IMAGE_RE.search(stripped) - if not match: - raise ValueError(f"Cannot parse CXR image path: {path}") - subject_id = int(match.group("subject_id")) - study_id = int(match.group("study_id")) - dicom_id = match.group("dicom_id") - nested_relpath = ( - f"mimic-cxr/2.0.0/files/p{str(subject_id)[:2]}/p{subject_id}/" - f"s{study_id}/{dicom_id}.jpg" - ) - return { - "subject_id": subject_id, - "study_id": study_id, - "dicom_id": dicom_id, - "nested_relpath": nested_relpath, - } - - -def parse_stay_period_from_qid(qid: str, task: str) -> tuple[int | None, float | None]: - if task == "radiology": - return None, None - try: - _, stay_text, period_text = qid.rsplit("_", 2) - except ValueError: - return None, None - return safe_int(stay_text), safe_float(period_text) - - -def load_medmod_rows(input_path: Path) -> list[dict[str, Any]]: - rows: list[dict[str, Any]] = [] - with input_path.open("r", encoding="utf-8") as handle: - for line_index, line in enumerate(handle): - row = json.loads(line) - if row.get("source_benchmark") != "medmod": - continue - task = canonical_task(str(row.get("task"))) - stay_from_qid, period_from_qid = parse_stay_period_from_qid(str(row.get("qid")), task) - image_refs = [parse_image_ref(path) for path in row.get("image_paths") or []] - row["_source_line_index"] = line_index - row["_canonical_task"] = task - row["_stay_id_from_qid"] = stay_from_qid - row["_period_length_from_qid"] = period_from_qid - row["_image_refs"] = image_refs - rows.append(row) - return rows - - -def row_key(row: dict[str, Any], task: str) -> tuple[int, float | None]: - stay_id = safe_int(row.get("stay_id")) - if stay_id is None: - raise ValueError(f"Listfile row missing stay_id: {row}") - if task in {"decompensation", "length-of-stay", "phenotyping"}: - period = safe_float(row.get("period_length")) - return stay_id, period - return stay_id, None - - -def sample_key(sample: dict[str, Any]) -> tuple[int, float | None]: - task = sample["_canonical_task"] - stay_id = safe_int(sample.get("stay_id")) or sample.get("_stay_id_from_qid") - if stay_id is None: - raise ValueError(f"Sample missing stay_id: {sample.get('qid')}") - if task in {"decompensation", "length-of-stay", "phenotyping"}: - return int(stay_id), safe_float(sample.get("_period_length_from_qid")) - return int(stay_id), None - - -def load_filtered_csv_index( - path: Path, - *, - task: str, - needed_keys: set[tuple[int, float | None]], -) -> tuple[dict[tuple[int, float | None], dict[str, Any]], list[str]]: - if not path.exists(): - return {}, [] - rows: dict[tuple[int, float | None], dict[str, Any]] = {} - columns: list[str] = [] - for chunk in pd.read_csv(path, chunksize=200_000): - if not columns: - columns = list(chunk.columns) - for record in chunk.to_dict(orient="records"): - key = row_key(record, task) - if key in needed_keys and key not in rows: - rows[key] = record - if len(rows) == len(needed_keys): - break - return rows, columns - - -def load_listfile_index( - repo_root: Path, - task: str, - split: str, - needed_keys: set[tuple[int, float | None]], -) -> dict[str, Any]: - split_name = normalize_split(split) - mml_path = repo_root / "mml-ssl-full" / task / medmod_listfile_name(split_name, mml_ssl=True) - data_path = repo_root / "data_full" / task / medmod_listfile_name(split_name, mml_ssl=False) - if not mml_path.exists(): - raise FileNotFoundError(f"Missing official MedMod mml-ssl listfile: {mml_path}") - mml_by_key, mml_columns = load_filtered_csv_index( - mml_path, - task=task, - needed_keys=needed_keys, - ) - data_by_key, data_columns = load_filtered_csv_index( - data_path, - task=task, - needed_keys=needed_keys, - ) - - return { - "mml_path": mml_path, - "data_path": data_path if data_path.exists() else None, - "mml_by_key": mml_by_key, - "data_by_key": data_by_key, - "mml_columns": mml_columns, - "data_columns": data_columns, - } - - -def expected_label_from_listfile(task: str, record: dict[str, Any]) -> list[str]: - if task in {"decompensation", "in-hospital-mortality"}: - return ["yes" if safe_int(record.get("y_true")) == 1 else "no"] - if task == "phenotyping": - return [label for label in PHENOTYPE_CLASSES if safe_int(record.get(label)) == 1] - if task == "length-of-stay": - value = safe_float(record.get("y_true")) - return [] if value is None else [str(value)] - raise ValueError(f"No listfile label parser for task: {task}") - - -def find_subject_dir(repo_root: Path, subject_id: int) -> tuple[Path, str]: - for split in ("test", "train"): - path = repo_root / "data_full" / "root" / split / str(subject_id) - if path.is_dir(): - return path, split - raise FileNotFoundError(f"Missing MedMod subject directory for subject_id={subject_id}") - - -def local_episode_filename(subject_id: int, official_stay: str | None) -> str | None: - if not official_stay: - return None - prefix = f"{subject_id}_" - if official_stay.startswith(prefix): - return official_stay[len(prefix) :] - return official_stay - - -def task_data_split_dir(split: str) -> str: - split = normalize_split(split) - if split == "valid": - return "train" - return split - - -def find_cxr_file(cxr_jpg_root: Path, image_ref: dict[str, Any], suffix: str) -> Path | None: - subject_id = image_ref["subject_id"] - study_id = image_ref["study_id"] - dicom_id = image_ref["dicom_id"] - flat_name = f"p{str(subject_id)[:2]}_p{subject_id}_s{study_id}_{dicom_id}.{suffix}" - nested = Path(image_ref["nested_relpath"]).with_suffix(f".{suffix}") - candidates = [ - cxr_jpg_root / "mimic-cxr2" / flat_name, - cxr_jpg_root / nested.relative_to("mimic-cxr/2.0.0"), - cxr_jpg_root / "2.1.0-lite" / nested.relative_to("mimic-cxr/2.0.0"), - cxr_jpg_root / "2.1.0-working-subset" / nested.relative_to("mimic-cxr/2.0.0"), - cxr_jpg_root / nested, - ] - for candidate in candidates: - if candidate.exists(): - return candidate - return None - - -def read_csv_subset(path: Path, column: str, values: set[Any]) -> pd.DataFrame: - if not path.exists(): - return pd.DataFrame() - df = pd.read_csv(path) - if column not in df.columns: - return df.iloc[0:0].copy() - return df[df[column].isin(values)].copy() - - -def build_metadata_indexes(cxr_meta_root: Path) -> dict[str, Any]: - metadata_path = cxr_meta_root / "mimic-cxr-2.0.0-metadata.csv" - chexpert_path = cxr_meta_root / "mimic-cxr-2.0.0-chexpert.csv" - if not metadata_path.exists(): - raise FileNotFoundError(f"Missing MIMIC-CXR metadata: {metadata_path}") - if not chexpert_path.exists(): - raise FileNotFoundError(f"Missing MIMIC-CXR CheXpert labels: {chexpert_path}") - - metadata_df = pd.read_csv(metadata_path) - chexpert_df = pd.read_csv(chexpert_path) - chexpert_df[RADIOLOGY_CLASSES] = chexpert_df[RADIOLOGY_CLASSES].fillna(0) - chexpert_df = chexpert_df.replace(-1.0, 0.0) - metadata_by_dicom = { - str(record["dicom_id"]): record for record in metadata_df.to_dict(orient="records") - } - ap_rows_by_subject: dict[int, list[dict[str, Any]]] = defaultdict(list) - for record in metadata_df.to_dict(orient="records"): - if str(record.get("ViewPosition") or "").upper() != "AP": - continue - subject_id = safe_int(record.get("subject_id")) - study_id = safe_int(record.get("study_id")) - if subject_id is None or study_id is None: - continue - study_datetime = parse_cxr_datetime(record) - if study_datetime is None: - continue - ap_rows_by_subject[subject_id].append( - { - "subject_id": subject_id, - "study_id": study_id, - "dicom_id": str(record.get("dicom_id") or ""), - "study_datetime": study_datetime, - "view_position": "AP", - } - ) - for rows in ap_rows_by_subject.values(): - rows.sort(key=lambda item: item["study_datetime"]) - chexpert_by_study: dict[int, list[str]] = {} - for record in chexpert_df.to_dict(orient="records"): - study_id = safe_int(record.get("study_id")) - if study_id is None: - continue - chexpert_by_study[study_id] = [ - label for label in RADIOLOGY_CLASSES if safe_float(record.get(label)) == 1.0 - ] - return { - "metadata_path": metadata_path, - "chexpert_path": chexpert_path, - "metadata_df": metadata_df, - "chexpert_df": chexpert_df, - "metadata_by_dicom": metadata_by_dicom, - "ap_rows_by_subject": ap_rows_by_subject, - "chexpert_by_study": chexpert_by_study, - } - - -def parse_cxr_datetime(record: dict[str, Any]) -> pd.Timestamp | None: - date = record.get("StudyDate") - time = record.get("StudyTime") - if date in (None, "") or time in (None, ""): - return None - try: - time_text = f"{int(float(time)):06d}" - return pd.Timestamp(datetime.strptime(f"{int(float(date))} {time_text}", "%Y%m%d %H%M%S")) - except (TypeError, ValueError): - return None - - -def parse_timestamp(value: Any) -> pd.Timestamp | None: - if value in (None, ""): - return None - try: - parsed = pd.Timestamp(value) - except (TypeError, ValueError): - return None - if pd.isna(parsed): - return None - return parsed - - -def validate_latest_ap_pairing( - sample: dict[str, Any], - official_row: dict[str, Any] | None, - cxr_indexes: dict[str, Any], -) -> list[str]: - if official_row is None: - return [] - task = sample["_canonical_task"] - if task == "radiology": - return [] - - subject_id = safe_int(sample.get("subject_id")) - selected_study_ids = {ref["study_id"] for ref in sample["_image_refs"]} - intime = parse_timestamp(official_row.get("intime")) - prediction_time = parse_timestamp(sample.get("prediction_time") or official_row.get("prediction_time")) - if subject_id is None or intime is None or prediction_time is None or not selected_study_ids: - return ["pairing_window_unverifiable"] - - in_window = [ - row - for row in cxr_indexes["ap_rows_by_subject"].get(subject_id, []) - if row["study_datetime"] >= intime and row["study_datetime"] <= prediction_time - ] - if not in_window: - return ["official_pairing_no_ap_in_window"] - latest_time = max(row["study_datetime"] for row in in_window) - latest_studies = {row["study_id"] for row in in_window if row["study_datetime"] == latest_time} - if selected_study_ids.isdisjoint(latest_studies): - return [ - "official_pairing_latest_ap_mismatch " - f"expected_study_ids={sorted(latest_studies)} got={sorted(selected_study_ids)}" - ] - return [] - - -def same_label_set(left: list[str], right: list[str]) -> bool: - return set(left) == set(right) - - -def validate_sample( - sample: dict[str, Any], - *, - list_indexes: dict[tuple[str, str], dict[str, Any]], - cxr_indexes: dict[str, Any], -) -> tuple[dict[str, Any], list[str], dict[str, Any] | None, dict[str, Any] | None]: - task = sample["_canonical_task"] - split = normalize_split(str(sample.get("source_split") or "test")) - gt = ground_truth_names(sample) - warnings: list[str] = [] - official_row = None - official_source_row = None - - if task == "radiology": - study_ids = [ref["study_id"] for ref in sample["_image_refs"]] - expected = sorted({label for study_id in study_ids for label in cxr_indexes["chexpert_by_study"].get(study_id, [])}) - if not same_label_set(gt, expected): - warnings.append(f"radiology_label_mismatch expected={expected} got={gt}") - else: - index = list_indexes[(task, split)] - key = sample_key(sample) - official_row = index["mml_by_key"].get(key) - official_source_row = index["data_by_key"].get(key) - if official_row is None: - warnings.append(f"missing_official_listfile_row key={key}") - else: - expected = expected_label_from_listfile(task, official_row) - if not same_label_set(gt, expected): - warnings.append(f"listfile_label_mismatch expected={expected} got={gt}") - for field in ("subject_id", "hadm_id", "prediction_time"): - if field in official_row and sample.get(field) is not None: - if str(official_row.get(field)) != str(sample.get(field)): - warnings.append( - f"{field}_mismatch official={official_row.get(field)} got={sample.get(field)}" - ) - warnings.extend(validate_latest_ap_pairing(sample, official_row, cxr_indexes)) - - for image_ref in sample["_image_refs"]: - metadata = cxr_indexes["metadata_by_dicom"].get(image_ref["dicom_id"]) - if metadata is None: - warnings.append(f"missing_cxr_metadata dicom_id={image_ref['dicom_id']}") - continue - if safe_int(metadata.get("study_id")) != image_ref["study_id"]: - warnings.append(f"cxr_metadata_study_mismatch dicom_id={image_ref['dicom_id']}") - if str(metadata.get("ViewPosition") or "").upper() != "AP": - warnings.append(f"cxr_not_ap dicom_id={image_ref['dicom_id']}") - - validation = { - "official_match_ok": not warnings, - "warnings": warnings, - } - return validation, warnings, official_row, official_source_row - - -def write_subset_csvs( - *, - output_root: Path, - medmod_repo_root: Path, - rows_by_task_split: dict[tuple[str, str], list[dict[str, Any]]], - list_indexes: dict[tuple[str, str], dict[str, Any]], -) -> None: - for (task, split), rows in sorted(rows_by_task_split.items()): - if task == "radiology": - continue - index = list_indexes[(task, split)] - mml_rows = [row["official_listfile_row"] for row in rows if row.get("official_listfile_row")] - data_rows = [row["official_data_full_row"] for row in rows if row.get("official_data_full_row")] - mml_out = ( - output_root - / "source_release" - / "mml-ssl-full" - / task - / medmod_listfile_name(split, mml_ssl=True) - ) - ensure_dir(mml_out.parent) - pd.DataFrame(mml_rows, columns=index["mml_columns"]).to_csv(mml_out, index=False) - if data_rows: - data_out = ( - output_root - / "source_release" - / "data_full" - / task - / medmod_listfile_name(split, mml_ssl=False) - ) - ensure_dir(data_out.parent) - pd.DataFrame(data_rows, columns=index["data_columns"]).to_csv(data_out, index=False) - - for name in ("README.md", "LICENSE"): - src = medmod_repo_root / name - if src.exists(): - link_or_copy(src, output_root / "source_release" / "repo_docs" / name) - - -def write_root_table_subsets(output_root: Path, repo_root: Path, subject_ids: set[int], stay_ids: set[int]) -> None: - root_out = output_root / "source_release" / "root_tables" - ensure_dir(root_out) - for table_name in ("all_stays.csv", "all_diagnoses.csv", "diagnosis_counts.csv", "phenotype_labels.csv"): - src = repo_root / "data_full" / "root" / table_name - if not src.exists(): - continue - df = pd.read_csv(src) - if "subject_id" in df.columns: - df = df[df["subject_id"].isin(subject_ids)].copy() - if "stay_id" in df.columns and stay_ids: - stay_filtered = df[df["stay_id"].isin(stay_ids)].copy() - if not stay_filtered.empty: - df = stay_filtered - df.to_csv(root_out / table_name, index=False) - - -def write_cxr_metadata_subsets(output_root: Path, cxr_meta_root: Path, cxr_indexes: dict[str, Any], image_refs: list[dict[str, Any]]) -> None: - meta_out = output_root / "source_release" / "cxr_metadata" - ensure_dir(meta_out) - dicom_ids = {ref["dicom_id"] for ref in image_refs} - study_ids = {ref["study_id"] for ref in image_refs} - - cxr_indexes["metadata_df"][cxr_indexes["metadata_df"]["dicom_id"].isin(dicom_ids)].to_csv( - meta_out / "mimic-cxr-2.0.0-metadata.csv", index=False - ) - cxr_indexes["chexpert_df"][cxr_indexes["chexpert_df"]["study_id"].isin(study_ids)].to_csv( - meta_out / "mimic-cxr-2.0.0-chexpert.csv", index=False - ) - - optional_specs = [ - ("mimic-cxr-2.0.0-split.csv", "dicom_id", dicom_ids), - ("mimic-cxr-ehr-split.csv", "dicom_id", dicom_ids), - ] - for filename, column, values in optional_specs: - subset = read_csv_subset(cxr_meta_root / filename, column, values) - if not subset.empty: - subset.to_csv(meta_out / filename, index=False) - - -def main() -> None: - args = parse_args() - reset_dir(args.output_root, args.overwrite) - - rows = load_medmod_rows(args.input) - if not rows: - raise ValueError(f"No MedMod rows found in {args.input}") - - needed_keys_by_index: dict[tuple[str, str], set[tuple[int, float | None]]] = defaultdict(set) - for row in rows: - task = row["_canonical_task"] - if task == "radiology": - continue - split = normalize_split(str(row.get("source_split") or "test")) - needed_keys_by_index[(task, split)].add(sample_key(row)) - - list_indexes = { - key: load_listfile_index( - args.medmod_repo_root, - key[0], - key[1], - needed_keys=needed_keys, - ) - for key, needed_keys in sorted(needed_keys_by_index.items()) - } - cxr_indexes = build_metadata_indexes(args.cxr_meta_root) - - manifest_rows: list[dict[str, Any]] = [] - rows_by_task_split: dict[tuple[str, str], list[dict[str, Any]]] = defaultdict(list) - subject_ids: set[int] = set() - stay_ids: set[int] = set() - all_image_refs: list[dict[str, Any]] = [] - stats = Counter() - warning_rows: list[dict[str, Any]] = [] - - for row in rows: - task = row["_canonical_task"] - split = normalize_split(str(row.get("source_split") or "test")) - validation, warnings, official_row, official_source_row = validate_sample( - row, - list_indexes=list_indexes, - cxr_indexes=cxr_indexes, - ) - if warnings: - stats["rows_with_warnings"] += 1 - warning_rows.append({"qid": row.get("qid"), "warnings": warnings}) - - subject_id = safe_int(row.get("subject_id")) - stay_id = safe_int(row.get("stay_id")) - if subject_id is None: - raise ValueError(f"Sample missing subject_id: {row.get('qid')}") - subject_ids.add(subject_id) - if stay_id is not None: - stay_ids.add(stay_id) - - subject_dir, subject_partition = find_subject_dir(args.medmod_repo_root, subject_id) - subject_rel = f"source_release/data_full/root/{subject_partition}/{subject_id}" - copytree_links(subject_dir, args.output_root / subject_rel) - - official_stay = None - if official_row is not None: - official_stay = official_row.get("stay") - if official_stay is None and official_source_row is not None: - official_stay = official_source_row.get("stay") - official_stay = str(official_stay) if official_stay not in (None, "") else None - official_period = None - if official_row is not None: - official_period = official_row.get("period_length") - if official_period is None and official_source_row is not None: - official_period = official_source_row.get("period_length") - local_stay = local_episode_filename(subject_id, official_stay) - ehr_timeseries_relpath = f"{subject_rel}/{local_stay}" if local_stay else None - ehr_episode_relpath = None - if local_stay and local_stay.endswith("_timeseries.csv"): - candidate_episode = f"{subject_rel}/{local_stay.replace('_timeseries.csv', '.csv')}" - if (args.output_root / candidate_episode).exists(): - ehr_episode_relpath = candidate_episode - ehr_task_timeseries_relpath = None - if official_stay and task != "radiology": - split_dir = task_data_split_dir(split) - task_src = args.medmod_repo_root / "data_full" / task / split_dir / official_stay - if task_src.exists(): - ehr_task_timeseries_relpath = ( - f"source_release/data_full/{task}/{split_dir}/{official_stay}" - ) - link_or_copy(task_src, args.output_root / ehr_task_timeseries_relpath) - - packaged_images: list[str] = [] - packaged_reports: list[str] = [] - raw_images: list[str] = [] - raw_reports: list[str] = [] - for image_ref in row["_image_refs"]: - all_image_refs.append(image_ref) - jpg_src = find_cxr_file(args.cxr_jpg_root, image_ref, "jpg") - if jpg_src is None: - raise FileNotFoundError(f"Missing CXR JPG for {row.get('qid')}: {image_ref}") - jpg_rel = image_ref["nested_relpath"] - link_or_copy(jpg_src, args.output_root / jpg_rel) - packaged_images.append(jpg_rel) - raw_images.append(relpath_or_name(jpg_src, args.cxr_jpg_root)) - - txt_src = find_cxr_file(args.cxr_jpg_root, image_ref, "txt") if args.include_reports else None - if txt_src is not None: - txt_rel = str(Path(jpg_rel).with_suffix(".txt")) - link_or_copy(txt_src, args.output_root / txt_rel) - packaged_reports.append(txt_rel) - raw_reports.append(relpath_or_name(txt_src, args.cxr_jpg_root)) - - sidecar = { - "qid": row.get("qid"), - "source_line_index": row.get("_source_line_index"), - "source_index": row.get("source_index"), - "task": task, - "source_task": row.get("task"), - "source_split": split, - "subject_id": row.get("subject_id"), - "hadm_id": row.get("hadm_id"), - "stay_id": row.get("stay_id"), - "prediction_time": row.get("prediction_time"), - "question": row.get("question"), - "released_input_text": row.get("input_text"), - "ground_truth": row.get("ground_truth"), - "answer_type": row.get("answer_type"), - "modalities": row.get("modalities") or ["ehr", "cxr"], - "study_ids": [ref["study_id"] for ref in row["_image_refs"]], - "dicom_ids": [ref["dicom_id"] for ref in row["_image_refs"]], - "packaged_image_relpaths": packaged_images, - "packaged_report_relpaths": packaged_reports, - "raw_image_source_relpaths": raw_images, - "raw_report_source_relpaths": raw_reports, - "ehr_subject_relpaths": [subject_rel], - "official_stay": official_stay, - "official_period_length": official_period, - "ehr_timeseries_relpath": ehr_timeseries_relpath, - "ehr_episode_relpath": ehr_episode_relpath, - "ehr_task_timeseries_relpath": ehr_task_timeseries_relpath, - "official_listfile_row": official_row, - "official_data_full_row": official_source_row, - "official_validation": validation, - "raw_join_key": { - "stay_id": row.get("stay_id"), - "period_length_hours": row.get("_period_length_from_qid"), - }, - } - manifest_rows.append(sidecar) - rows_by_task_split[(task, split)].append(sidecar) - stats[f"task:{task}"] += 1 - stats[f"split:{split}"] += 1 - - write_subset_csvs( - output_root=args.output_root, - medmod_repo_root=args.medmod_repo_root, - rows_by_task_split=rows_by_task_split, - list_indexes=list_indexes, - ) - write_root_table_subsets(args.output_root, args.medmod_repo_root, subject_ids, stay_ids) - write_cxr_metadata_subsets(args.output_root, args.cxr_meta_root, cxr_indexes, all_image_refs) - - write_jsonl(args.output_root / "linked_manifests" / "all.jsonl", manifest_rows) - for (task, split), task_rows in sorted(rows_by_task_split.items()): - write_jsonl(args.output_root / "linked_manifests" / task / f"{split}.jsonl", task_rows) - - readme = f"""# ClinSeek-MM-Bench-MedMod-source - -This package is the source-aligned MedMod subset used by ClinSeek MM-Bench. -It contains only the MedMod rows present in `$CLINSEEK_MM_BENCH_JSONL`. - -The layout preserves the official MedMod task/listfile style where possible: - -- `source_release/mml-ssl-full//*_listfile.csv`: subset of official MedMod rows. -- `source_release/data_full//*_listfile.csv`: subset of original task listfiles when available. -- `source_release/data_full/root///`: official extracted MedMod EHR folders. -- `source_release/root_tables/`: filtered MedMod root tables kept only for provenance. - Some files in this directory contain labels and must not be mounted as runtime - EHR tables for agent inference. -- `source_release/cxr_metadata/`: subset MIMIC-CXR metadata and CheXpert labels. -- `mimic-cxr/2.0.0/files/...`: packaged JPG files. TXT reports are only included - when `--include-reports` is explicitly set. -- `linked_manifests/`: row-level sidecar manifests with questions, gold labels, and relative paths. - -Important: each manifest row records `official_stay`, `ehr_timeseries_relpath`, -and `ehr_episode_relpath` so downstream rendering can use the exact MedMod -episode from the official listfile instead of all episodes for the same subject. - -Input root contract: - -- ClinSeek multimodal input: `$CLINSEEK_MM_BENCH_JSONL` -- MedMod repository: `$MEDMOD_REPO_ROOT` -- Raw MIMIC-CXR JPG root: `$MIMIC_CXR_JPG_ROOT` -- Raw MIMIC-CXR metadata root: `$MIMIC_CXR_META_ROOT` -- Raw MIMIC-IV latest local release kept for provenance: `$MIMICIV_ROOT` -""" - (args.output_root / "README.md").write_text(readme, encoding="utf-8") - - metadata = { - "package_name": "ClinSeek-MM-Bench-MedMod-source", - "input": "CLINSEEK_MM_BENCH_JSONL", - "records": len(manifest_rows), - "subjects": len(subject_ids), - "unique_images": len({p for row in manifest_rows for p in row["packaged_image_relpaths"]}), - "unique_reports": len({p for row in manifest_rows for p in row["packaged_report_relpaths"]}), - "reports_included": bool(args.include_reports), - "stats": dict(sorted(stats.items())), - "warning_rows": warning_rows, - "source_path_env_vars": { - "medmod_repo_root": "MEDMOD_REPO_ROOT", - "cxr_jpg_root": "MIMIC_CXR_JPG_ROOT", - "cxr_meta_root": "MIMIC_CXR_META_ROOT", - "mimiciv_root": "MIMICIV_ROOT", - }, - "path_contract": { - "manifest_paths": "relative_to_package_root", - "packaged_image_relpaths": "relative_to_package_root", - "packaged_report_relpaths": "relative_to_package_root", - "ehr_subject_relpaths": "relative_to_package_root", - "raw_image_source_relpaths": "relative_to_MIMIC_CXR_JPG_ROOT", - "raw_report_source_relpaths": "relative_to_MIMIC_CXR_JPG_ROOT", - }, - } - write_json(args.output_root / "metadata.json", metadata) - - if warning_rows and args.strict_official_match and not args.allow_warnings: - raise SystemExit( - f"Built package but found {len(warning_rows)} validation warning rows. " - "Inspect metadata.json or rerun without --strict-official-match." - ) - print(json.dumps(metadata, ensure_ascii=False, indent=2)) - - -if __name__ == "__main__": - main() diff --git a/rebuild/mm_bench/combine_clinseek_mm_bench.py b/rebuild/mm_bench/combine_clinseek_mm_bench.py deleted file mode 100644 index 869cfab56f1e83592aa73acee1cad9bd7dcbb5be..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/combine_clinseek_mm_bench.py +++ /dev/null @@ -1,169 +0,0 @@ -#!/usr/bin/env python3 -"""Combine EHRXQA and MedMod subsets into the ClinSeek-MM-Bench package.""" - -from __future__ import annotations - -import argparse -import json -import os -import shutil -from pathlib import Path -from typing import Any - - -REPO_ROOT = Path(__file__).resolve().parents[2] -DEFAULT_REFERENCE_INPUT = Path( - os.environ.get( - "CLINSEEK_MM_BENCH_JSONL", - str(REPO_ROOT / "inputs" / "mm_bench.jsonl"), - ) -) -DEFAULT_EHRXQA_SUBSET_ROOT = Path( - os.environ.get("CLINSEEK_EHRXQA_MM_ROOT", "data/build/ClinSeek-MM-Bench-EHRXQA") -) -DEFAULT_MEDMOD_SUBSET_ROOT = Path( - os.environ.get("CLINSEEK_MEDMOD_MM_ROOT", "data/build/ClinSeek-MM-Bench-MedMod") -) -DEFAULT_OUTPUT_ROOT = Path( - os.environ.get("CLINSEEK_MM_RELEASE_ROOT", "data/build/ClinSeek-MM-Bench") -) - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument("--reference-input", type=Path, default=DEFAULT_REFERENCE_INPUT) - parser.add_argument("--ehrxqa-root", type=Path, default=DEFAULT_EHRXQA_SUBSET_ROOT) - parser.add_argument("--medmod-root", type=Path, default=DEFAULT_MEDMOD_SUBSET_ROOT) - parser.add_argument("--output-root", type=Path, default=DEFAULT_OUTPUT_ROOT) - parser.add_argument("--overwrite", action="store_true") - return parser.parse_args() - - -def ensure_dir(path: Path) -> None: - path.mkdir(parents=True, exist_ok=True) - - -def reset_dir(path: Path, overwrite: bool) -> None: - if path.exists(): - if not overwrite: - raise FileExistsError(f"Output root already exists: {path}") - shutil.rmtree(path) - path.mkdir(parents=True, exist_ok=True) - - -def link_or_copy(src: Path, dst: Path) -> None: - src = src.resolve() - ensure_dir(dst.parent) - if dst.exists(): - return - try: - os.link(src, dst) - except OSError: - shutil.copy2(src, dst) - - -def copytree_links(src: Path, dst: Path) -> None: - if not src.exists(): - raise FileNotFoundError(f"Missing source directory: {src}") - if dst.exists(): - return - shutil.copytree(src, dst, copy_function=lambda s, d: (link_or_copy(Path(s), Path(d)) or str(d))) - - -def drop_runtime_sidecars(output_root: Path) -> None: - """Keep final data/mm_bench file layout aligned with the HF release tree.""" - for relpath in ( - "data/mm_bench/ehrxqa/database/reference_table.db", - "data/mm_bench/ehrxqa/metadata.json", - "data/mm_bench/medmod/metadata.json", - ): - path = output_root / relpath - if path.exists(): - path.unlink() - - -def read_jsonl(path: Path) -> list[dict[str, Any]]: - rows: list[dict[str, Any]] = [] - with path.open("r", encoding="utf-8") as handle: - for line in handle: - if line.strip(): - rows.append(json.loads(line)) - return rows - - -def write_json(path: Path, payload: Any) -> None: - ensure_dir(path.parent) - path.write_text(json.dumps(payload, ensure_ascii=False, indent=2) + "\n", encoding="utf-8") - - -def write_jsonl(path: Path, rows: list[dict[str, Any]]) -> None: - ensure_dir(path.parent) - with path.open("w", encoding="utf-8") as handle: - for row in rows: - handle.write(json.dumps(row, ensure_ascii=False, separators=(",", ":")) + "\n") - - -def load_subset_rows(root: Path, filename: str) -> dict[str, dict[str, Any]]: - path = root / "inputs" / filename - rows = read_jsonl(path) - return {str(row["qid"]): row for row in rows} - - -def main() -> None: - args = parse_args() - reset_dir(args.output_root, args.overwrite) - - reference_rows = read_jsonl(args.reference_input) - ehrxqa_by_qid = load_subset_rows(args.ehrxqa_root, "mm_bench_ehrxqa.jsonl") - medmod_by_qid = load_subset_rows(args.medmod_root, "mm_bench_medmod.jsonl") - by_qid = {**ehrxqa_by_qid, **medmod_by_qid} - - missing = [row["qid"] for row in reference_rows if row.get("qid") not in by_qid] - extra = sorted(set(by_qid) - {row.get("qid") for row in reference_rows}) - if missing or extra: - raise ValueError({"missing": missing[:20], "extra": extra[:20]}) - - output_rows = [by_qid[str(row["qid"])] for row in reference_rows] - write_jsonl(args.output_root / "inputs" / "mm_bench.jsonl", output_rows) - - copytree_links( - args.ehrxqa_root / "data" / "mm_bench" / "ehrxqa", - args.output_root / "data" / "mm_bench" / "ehrxqa", - ) - copytree_links( - args.medmod_root / "data" / "mm_bench" / "medmod", - args.output_root / "data" / "mm_bench" / "medmod", - ) - drop_runtime_sidecars(args.output_root) - - metadata = { - "package_name": "ClinSeek-MM-Bench", - "reference_input": "CLINSEEK_MM_BENCH_JSONL", - "ehrxqa_root": "CLINSEEK_EHRXQA_MM_ROOT", - "medmod_root": "CLINSEEK_MEDMOD_MM_ROOT", - "records": len(output_rows), - "source_counts": { - "ehrxqa": len(ehrxqa_by_qid), - "medmod": len(medmod_by_qid), - }, - "input_file": "inputs/mm_bench.jsonl", - "bench_root": "data/mm_bench", - } - write_json(args.output_root / "metadata.json", metadata) - - readme = """# ClinSeek-MM-Bench - -This package combines the EHRXQA-derived and MedMod-derived subsets into the -final ClinSeek multimodal benchmark layout. - -Use: - -- `inputs/mm_bench.jsonl` -- `data/mm_bench` -""" - (args.output_root / "README.md").write_text(readme, encoding="utf-8") - print(json.dumps(metadata, ensure_ascii=False, indent=2)) - - -if __name__ == "__main__": - main() diff --git a/rebuild/mm_bench/validate_multimodal_release.py b/rebuild/mm_bench/validate_multimodal_release.py deleted file mode 100644 index 22a7a0071846f2ef861e11a6c222572735989a90..0000000000000000000000000000000000000000 --- a/rebuild/mm_bench/validate_multimodal_release.py +++ /dev/null @@ -1,207 +0,0 @@ -#!/usr/bin/env python3 -"""Validate the released ClinSeek multimodal benchmark manifest or package. - -The validator checks the ClinSeek-MM-Bench release tree: - -- every row in inputs/mm_bench.jsonl has an expected source/task distribution; -- in package mode, every referenced patient database exists; -- in package mode, every referenced image/report path resolves under data/mm_bench//; -- in manifest-only mode, protected MIMIC-derived assets are not required; -- optional git-tree mode can validate a Hugging Face repository checkout without - downloading all LFS file contents. -""" - -from __future__ import annotations - -import argparse -import json -import subprocess -import sys -from collections import Counter, defaultdict -from pathlib import Path -from typing import Any - - -EXPECTED_SOURCE_COUNTS = {"ehrxqa": 497, "medmod": 492} -EXPECTED_TASK_COUNTS = { - "ehrxqa_image": 497, - "medmod_decompensation": 125, - "medmod_in_hospital_mortality": 125, - "medmod_phenotyping": 120, - "medmod_radiology": 122, -} - - -def parse_args() -> argparse.Namespace: - parser = argparse.ArgumentParser(description=__doc__) - parser.add_argument( - "--bench-root", - type=Path, - default=Path("data/ClinSeek-Bench"), - help="Root of the ClinSeek-Bench repository or downloaded package.", - ) - parser.add_argument( - "--input", - type=Path, - default=None, - help="Optional explicit mm_bench.jsonl path. Defaults to /inputs/mm_bench.jsonl.", - ) - parser.add_argument( - "--use-git-tree", - action="store_true", - help="Validate file presence against git ls-tree instead of local filesystem contents.", - ) - parser.add_argument( - "--manifest-only", - action="store_true", - help="Validate only inputs/mm_bench.jsonl counts/schema and referenced path strings. Do not require DB/JPG/report files.", - ) - parser.add_argument( - "--allow-unexpected-counts", - action="store_true", - help="Do not fail if source/task counts differ from the frozen release counts.", - ) - return parser.parse_args() - - -def read_jsonl(path: Path) -> list[dict[str, Any]]: - rows: list[dict[str, Any]] = [] - with path.open("r", encoding="utf-8") as handle: - for line in handle: - if line.strip(): - rows.append(json.loads(line)) - return rows - - -def safe_int(value: Any) -> int | None: - if value is None or value == "": - return None - try: - return int(float(str(value))) - except ValueError: - return None - - -def git_tree_paths(root: Path) -> set[str]: - output = subprocess.check_output( - ["git", "-C", str(root), "ls-tree", "-r", "--name-only", "HEAD"], - text=True, - ) - return {line.strip() for line in output.splitlines() if line.strip()} - - -def release_asset_relpath(source: str, raw_path: str) -> str: - """Map JSONL asset paths to their release-relative locations. - - The JSONL preserves original package prefixes such as - EHRXQAOriginalLinked_v1/ or MedModOriginalLinked_v1/. The released HF tree - stores the actual assets under data/mm_bench//. - """ - parts = Path(raw_path).parts - if parts and parts[0].endswith("OriginalLinked_v1"): - parts = parts[1:] - return str(Path("data") / "mm_bench" / source / Path(*parts)) - - -def exists(path: str, *, root: Path, tree: set[str] | None) -> bool: - if tree is not None: - return path in tree - return (root / path).exists() - - -def validate(args: argparse.Namespace) -> tuple[dict[str, Any], list[dict[str, Any]]]: - bench_root = args.bench_root - input_path = args.input or bench_root / "inputs" / "mm_bench.jsonl" - rows = read_jsonl(input_path) - tree = git_tree_paths(bench_root) if args.use_git_tree and not args.manifest_only else None - - source_counts = Counter(row.get("source_benchmark") for row in rows) - task_counts = Counter(row.get("task") for row in rows) - subjects_by_source: dict[str, set[int]] = defaultdict(set) - images_by_source: dict[str, set[str]] = defaultdict(set) - reports_by_source: dict[str, set[str]] = defaultdict(set) - - errors: list[dict[str, Any]] = [] - missing_by_kind = Counter() - - for row in rows: - qid = row.get("qid") - source = str(row.get("source_benchmark") or "") - subject_id = safe_int(row.get("subject_id")) - if source not in {"ehrxqa", "medmod"}: - errors.append({"qid": qid, "kind": "bad_source", "value": source}) - continue - if subject_id is None: - errors.append({"qid": qid, "kind": "missing_subject_id"}) - continue - - subjects_by_source[source].add(subject_id) - db_rel = str(Path("data") / "mm_bench" / source / "database" / f"patient_{subject_id}.db") - if not args.manifest_only and not exists(db_rel, root=bench_root, tree=tree): - missing_by_kind["database"] += 1 - errors.append({"qid": qid, "kind": "missing_database", "path": db_rel}) - - for raw_path in row.get("image_paths") or []: - rel = release_asset_relpath(source, str(raw_path)) - images_by_source[source].add(rel) - if not args.manifest_only and not exists(rel, root=bench_root, tree=tree): - missing_by_kind["image"] += 1 - errors.append({"qid": qid, "kind": "missing_image", "path": rel}) - - for raw_path in row.get("report_paths") or []: - rel = release_asset_relpath(source, str(raw_path)) - reports_by_source[source].add(rel) - if not args.manifest_only and not exists(rel, root=bench_root, tree=tree): - missing_by_kind["report"] += 1 - errors.append({"qid": qid, "kind": "missing_report", "path": rel}) - - if not args.allow_unexpected_counts: - if dict(source_counts) != EXPECTED_SOURCE_COUNTS: - errors.append( - { - "kind": "unexpected_source_counts", - "actual": dict(source_counts), - "expected": EXPECTED_SOURCE_COUNTS, - } - ) - if dict(task_counts) != EXPECTED_TASK_COUNTS: - errors.append( - { - "kind": "unexpected_task_counts", - "actual": dict(task_counts), - "expected": EXPECTED_TASK_COUNTS, - } - ) - - summary = { - "rows": len(rows), - "source_counts": dict(source_counts), - "task_counts": dict(task_counts), - "subjects": {key: len(value) for key, value in subjects_by_source.items()}, - "unique_images": {key: len(value) for key, value in images_by_source.items()}, - "unique_reports": {key: len(value) for key, value in reports_by_source.items()}, - "missing_by_kind": dict(missing_by_kind), - "error_count": len(errors), - "validated_against": "manifest_only" - if args.manifest_only - else ("git_tree" if args.use_git_tree else "filesystem"), - "bench_root": str(bench_root), - "input": str(input_path), - } - return summary, errors - - -def main() -> int: - args = parse_args() - summary, errors = validate(args) - print(json.dumps(summary, ensure_ascii=False, indent=2)) - if errors: - print("First errors:", file=sys.stderr) - for error in errors[:20]: - print(json.dumps(error, ensure_ascii=False), file=sys.stderr) - return 1 - return 0 - - -if __name__ == "__main__": - raise SystemExit(main())