Upload OligoTox_Phase2_Optional_Analysis_Notebook.ipynb

OligoTox_Phase2_Optional_Analysis_Notebook.ipynb

@@ -47,20 +47,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Notebook outputs will be written to: notebook_outputs\n"
+      "Using dataset folder: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\n",
+      "Notebook outputs will be written to: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\n"
      ]
     }
    ],
    "source": [
     "from pathlib import Path\n",
-    "\n",
-    "def display_output_path(path):\n",
-    "    \"\"\"Return a submission-safe relative path for generated notebook outputs.\"\"\"\n",
-    "    p = Path(path)\n",
-    "    return r\"\\\\notebook_outputs\\\\\" + p.name\n",
-    "\n",
     "import json\n",
     "import os\n",
+    "import sys\n",
     "import warnings\n",
     "\n",
     "import numpy as np\n",
@@ -73,8 +69,29 @@
     "pd.set_option(\"display.max_columns\", 120)\n",
     "pd.set_option(\"display.max_colwidth\", 160)\n",
     "\n",
-    "# The notebook is intended to be run from the same folder as the dataset files.\n",
-    "DATA_DIR = Path.cwd().resolve()\n",
+    "# Detect Google Colab / cloud environments where the dataset is not in the\n",
+    "# current working directory, and auto-download from Hugging Face if so.\n",
+    "def locate_dataset():\n",
+    "    cwd = Path.cwd().resolve()\n",
+    "    if (cwd / \"oligos.csv\").exists() and (cwd / \"toxicity_readouts.csv\").exists():\n",
+    "        return cwd\n",
+    "    is_colab = \"google.colab\" in sys.modules or \"COLAB_GPU\" in os.environ or \"COLAB_RELEASE_TAG\" in os.environ\n",
+    "    if is_colab or not (cwd / \"oligos.csv\").exists():\n",
+    "        try:\n",
+    "            from huggingface_hub import snapshot_download\n",
+    "        except ImportError:\n",
+    "            print(\"Installing huggingface_hub for dataset download...\")\n",
+    "            os.system(f\"{sys.executable} -m pip install --quiet huggingface_hub\")\n",
+    "            from huggingface_hub import snapshot_download\n",
+    "        print(\"Downloading dataset from Hugging Face: DBbun/oligotox-phase2-dataset ...\")\n",
+    "        local_dir = Path(snapshot_download(\n",
+    "            repo_id=\"DBbun/oligotox-phase2-dataset\",\n",
+    "            repo_type=\"dataset\",\n",
+    "        )).resolve()\n",
+    "        return local_dir\n",
+    "    return cwd\n",
+    "\n",
+    "DATA_DIR = locate_dataset()\n",
     "\n",
     "required_files = [\n",
     "    \"oligos.csv\",\n",
@@ -87,14 +104,24 @@
     "\n",
     "if missing_files:\n",
     "    raise FileNotFoundError(\n",
-    "        \"This notebook must be run from the same folder as the dataset files. \"\n",
+    "        \"Could not locate dataset files. To run this notebook, either: \"\n",
+    "        \"(1) run from a folder containing the dataset CSVs, or \"\n",
+    "        \"(2) ensure huggingface_hub is installed so the dataset can be auto-downloaded. \"\n",
     "        f\"Missing required file(s): {missing_files}\"\n",
     "    )\n",
     "\n",
-    "OUTPUT_DIR = DATA_DIR / \"notebook_outputs\"\n",
+    "OUTPUT_DIR = Path.cwd() / \"notebook_outputs\"\n",
     "OUTPUT_DIR.mkdir(exist_ok=True)\n",
     "\n",
-    "print(f\"Notebook outputs will be written to: {OUTPUT_DIR.name}\")\n"
+    "# Helper for cleanly displaying file paths in cell outputs\n",
+    "def display_output_path(p):\n",
+    "    try:\n",
+    "        return str(Path(p).relative_to(Path.cwd()))\n",
+    "    except ValueError:\n",
+    "        return str(p)\n",
+    "\n",
+    "print(f\"Using dataset folder: {DATA_DIR}\")\n",
+    "print(f\"Notebook outputs will be written to: {OUTPUT_DIR}\")\n"
    ]
   },
   {
@@ -4663,7 +4690,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_label_distribution.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_label_distribution.png\n"
      ]
     },
     {
@@ -4737,7 +4764,7 @@
     "    path = OUTPUT_DIR / name\n",
     "    plt.tight_layout()\n",
     "    plt.savefig(path, dpi=160, bbox_inches=\"tight\")\n",
-    "    print(f\"Saved: {display_output_path(path)}\")\n",
+    "    print(f\"Saved: {path}\")\n",
     "\n",
     "# Label distribution.\n",
     "label_counts = readouts[\"hepatotoxicity_label\"].value_counts().reindex([\"low\", \"moderate\", \"high\"])\n",
@@ -4760,7 +4787,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_risk_score_distribution_by_label.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_risk_score_distribution_by_label.png\n"
      ]
     },
     {
@@ -4798,7 +4825,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_label_mix_by_modality.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_label_mix_by_modality.png\n"
      ]
     },
     {
@@ -4988,7 +5015,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_median_risk_over_time.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_median_risk_over_time.png\n"
      ]
     },
     {
@@ -5179,7 +5206,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_risk_vs_dose_nM.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_risk_vs_dose_nM.png\n"
      ]
     },
     {
@@ -5196,7 +5223,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_risk_vs_phosphorothioate_fraction.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_risk_vs_phosphorothioate_fraction.png\n"
      ]
     },
     {
@@ -5213,7 +5240,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_risk_vs_GC_content.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_risk_vs_GC_content.png\n"
      ]
     },
     {
@@ -5230,7 +5257,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_risk_vs_predicted_offtarget_hybridization_burden.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_risk_vs_predicted_offtarget_hybridization_burden.png\n"
      ]
     },
     {
@@ -5498,7 +5525,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_baseline_confusion_matrix.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_baseline_confusion_matrix.png\n"
      ]
     },
     {
@@ -5826,7 +5853,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saved: \\\\notebook_outputs\\\\notebook_baseline_feature_importance.png\n"
+      "Saved: C:\\Users\\karto\\NIH-OligoTox Phase II\\dataset_root\\notebook_outputs\\notebook_baseline_feature_importance.png\n"
      ]
     },
     {
@@ -6064,14 +6091,14 @@
    "source": [
     "## 13. How this notebook supports the optional documentation package\n",
     "\n",
-    "This notebook is useful as an optional supplement because it demonstrates four things that strengthen the submission package:\n",
+    "This notebook is useful as an optional supplement because it demonstrates four things reviewers often care about:\n",
     "\n",
     "1. **Ability to solve the challenge:** the dataset can be loaded, joined, modeled, and used for immediate in silico toxicity-label prediction experiments.  \n",
     "2. **Potential impact:** the source corpus, evidence modules, and information-gap map show how the dataset addresses gaps across oligo modality, chemistry, dose/exposure, liver context, and readout structure.  \n",
     "3. **Feasibility and rigor:** the schema, validation summary, relationship checks, and reproducibility manifest make the package inspectable rather than opaque.  \n",
     "4. **Transparency and reproducibility:** the notebook uses only the released files, stores derived artifacts locally, and avoids hidden inputs.\n",
     "\n",
-    "The notebook should be presented as optional documentation support, not as a substitute for the dataset, schema, data dictionary, validation files, or source/provenance documentation."
+    "The notebook should be presented as optional reviewer support, not as a substitute for the dataset, schema, data dictionary, validation files, or source/provenance documentation."
    ]
   }
  ],