Simplify VEPQA schema and expand provenance

README.md

@@ -36,9 +36,9 @@ Each row includes:
 - `question`: the task prompt body before the reusable answer instruction/options suffix.
 - `prompt_suffix`: the reusable answer instruction/options suffix.
 - `prompt`: the full user-facing prompt, equal to `question + "\n\n" + prompt_suffix`.
-- `options` / `choices`: allowed answer labels for the task.
+- `options`: allowed answer labels for the task.
 - `answer_index`: index of the correct option.
-- `answer_text` / `answer` / `ideal`: deterministic plain-text target.
+- `answer_text`: deterministic plain-text target.
 - `messages`: two-turn SFT messages, with the plain answer in the assistant message.
 - `gold_answer_json`: JSON-form audit target, not the primary SFT target.
 - audit metadata: ClinVar IDs, genomic position, review status, sequence hashes, and benchmark exclusion status.
@@ -63,6 +63,93 @@ Carbon eval exclusion manifest:
 
 The dataset was generated from raw ClinVar records, not from Carbon benchmark rows.
 
+Dataset-wide provenance summary:
+
+```json
+{
+  "source": {
+    "clinvar_variant_summary": 6000
+  },
+  "assembly": {
+    "GRCh38": 6000
+  },
+  "origin": {
+    "germline": 6000
+  },
+  "variant_type": {
+    "single nucleotide variant": 6000
+  },
+  "window_bp": {
+    "1024": 6000
+  },
+  "benchmark_exclusion_status": {
+    "checked": 6000
+  }
+}
+```
+
+The `all_tasks` config has 6,000 task rows but 4,000 unique variant keys. The `binary` and `clinvar_levels` configs are two views of the same 2,000 clinical-classification variants; `pathogenic_pairwise` contributes 2,000 additional pathogenic or likely pathogenic variants.
+
+Unique variant chromosome distribution across `all_tasks`:
+
+```json
+{
+  "1": 375,
+  "2": 395,
+  "3": 193,
+  "4": 100,
+  "5": 180,
+  "6": 150,
+  "7": 209,
+  "8": 109,
+  "9": 164,
+  "10": 128,
+  "11": 261,
+  "12": 209,
+  "13": 69,
+  "14": 92,
+  "15": 139,
+  "16": 205,
+  "17": 344,
+  "18": 49,
+  "19": 213,
+  "20": 81,
+  "21": 45,
+  "22": 72,
+  "X": 218
+}
+```
+
+Task-row chromosome distribution in `all_tasks`:
+
+```json
+{
+  "1": 572,
+  "2": 571,
+  "3": 283,
+  "4": 160,
+  "5": 271,
+  "6": 216,
+  "7": 316,
+  "8": 169,
+  "9": 258,
+  "10": 190,
+  "11": 386,
+  "12": 310,
+  "13": 103,
+  "14": 146,
+  "15": 198,
+  "16": 324,
+  "17": 511,
+  "18": 78,
+  "19": 321,
+  "20": 129,
+  "21": 74,
+  "22": 112,
+  "X": 302
+}
+```
+
 ## ClinVar Filtering
 
 Rows were retained from ClinVar only if they met all of the following criteria:

all_tasks/train-00000-of-00001.jsonl

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binary/train-00000-of-00001.jsonl

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clinvar_levels/train-00000-of-00001.jsonl

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pathogenic_pairwise/train-00000-of-00001.jsonl

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