Release metadata-only ClinSeek-Bench

Remove materialized MIMIC-derived benchmark assets from the dataset repo and keep only the text and multimodal metadata files needed to reconstruct ClinSeek-Bench locally. Update the dataset README to document the metadata-only layout.

.gitattributes

@@ -2074,3 +2074,4 @@ data/mm_bench/medmod/database/patient_17132849.db filter=lfs diff=lfs merge=lfs
 data/mm_bench/medmod/database/patient_17215379.db filter=lfs diff=lfs merge=lfs -text
 data/mm_bench/medmod/database/patient_17232733.db filter=lfs diff=lfs merge=lfs -text
 rebuild/text_bench/ClinSeek-Bench_text.json filter=lfs diff=lfs merge=lfs -text
+ClinSeek-Bench_text.json filter=lfs diff=lfs merge=lfs -text

README.md

@@ -13,23 +13,24 @@ size_categories:
 - 1K<n<10K
 configs:
 - config_name: ehr_bench
-  data_files: "inputs/ehr_bench.json"
+  data_files: "ClinSeek-Bench_text.json"
 - config_name: mm_bench
-  data_files: "inputs/mm_bench.jsonl"
+  data_files: "ClinSeek-Bench_multimodal.jsonl"
 ---
 
 # ClinSeek-Bench
 
-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.
+ClinSeek-Bench provides the metadata files used to reconstruct the ClinSeekAgent
+evaluation benchmark from the original source datasets. This repository is not a
+fully materialized benchmark package: MIMIC-derived patient databases, source
+tables, 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.
 
-| Split | # data points | Modality | Released here |
+| Split | # data points | Modality | Released metadata file |
 | --- | ---: | --- | --- |
-| `ehr_bench` | 1,800 | text-only EHR | evaluation manifest |
-| `mm_bench` | 989 | EHR + chest X-ray | source manifest only |
+| `ehr_bench` | 1,800 | text-only EHR | `ClinSeek-Bench_text.json` |
+| `mm_bench` | 989 | EHR + chest X-ray | `ClinSeek-Bench_multimodal.jsonl` |
 
 `mm_bench` is restricted to image-grounded multimodal examples. It contains 497
 EHRXQA-derived CXR question-answering rows and 492 MedMod-derived ICU/CXR
@@ -39,24 +40,25 @@ prediction rows.
 
 ```text
 ClinSeek-Bench/
-├── inputs/
-│   ├── ehr_bench.json
-│   └── mm_bench.jsonl
-└── rebuild/
-    └── text_bench/
-        └── ClinSeek-Bench_text.json
+├── ClinSeek-Bench_text.json
+└── ClinSeek-Bench_multimodal.jsonl
 ```
 
-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.
+`ClinSeek-Bench_text.json` stores the text benchmark records and the patient,
+admission, task, timing, question, label, and candidate metadata needed by the
+ClinSeekAgent preparation and evaluation scripts. It does not include the
+patient-level SQLite databases or raw MIMIC source tables.
 
-## Reconstructing Multimodal Assets
+`ClinSeek-Bench_multimodal.jsonl` stores released `qid`s, questions, normalized
+labels, patient identifiers, prediction-time cutoffs, and relative CXR/report
+references for the multimodal split. It intentionally does not store rendered
+`input_text`, patient SQLite databases, CXR JPG files, or report text.
 
-Multimodal reconstruction scripts are maintained in the ClinSeekAgent GitHub
-repository, matching the text benchmark data-preparation workflow:
+## Reconstructing Benchmark Assets
 
+Reconstruction scripts are maintained in the ClinSeekAgent GitHub repository:
+
+- text benchmark documentation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_text_data_prepare.md
 - 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
 
@@ -70,7 +72,7 @@ git clone https://github.com/UCSC-VLAA/ClinSeekAgent.git
 Then run the scripts under `ClinSeekAgent/scripts/data_build/` with local paths
 to the official source datasets.
 
-Required multimodal source data:
+Required source data:
 
 | Dataset | Source |
 | --- | --- |
@@ -81,22 +83,24 @@ Required multimodal source data:
 | EHRXQA | https://physionet.org/content/ehrxqa/ |
 | MedMod code | https://github.com/nyuad-cai/MedMod |
 
-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.
+The final local reconstruction materializes the runtime benchmark assets needed
+for evaluation, including patient SQLite databases, table-description metadata,
+rendered EHR contexts, linked CXR JPGs, and radiology reports when available.
+The downloaded `ClinSeek-Bench_text.json` and `ClinSeek-Bench_multimodal.jsonl`
+remain the metadata sources of truth used to drive that reconstruction.
 
 ## Validation
 
-After cloning ClinSeekAgent, validate the released multimodal source manifest:
+After cloning ClinSeekAgent, validate the released multimodal metadata file:
 
 ```bash
 python ClinSeekAgent/scripts/data_build/validate_multimodal_release.py \
   --bench-root ClinSeek-Bench \
+  --input ClinSeek-Bench/ClinSeek-Bench_multimodal.jsonl \
   --manifest-only
 ```
 
-Expected source-manifest counts:
+Expected multimodal metadata counts:
 
 - 989 total multimodal rows.
 - 497 EHRXQA-derived rows.

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