| """Rebuild the verified MedAraBench test set from QIMMA's public copy. |
| |
| Writes one file per config, <output_dir>/<config>/data.parquet, with the |
| source columns unchanged. |
| |
| Usage: |
| python apply_filter.py [output_dir] |
| """ |
| import hashlib |
| import json |
| import os |
| import sys |
|
|
| import pandas as pd |
| from huggingface_hub import hf_hub_download |
|
|
| SOURCE = "qimma/MCQ_MedAraBench" |
| SOURCE_REVISION = "c62cc54f8d9d9e9e4be5aca82982b58e2da3cf0e" |
| THIS_REPO = "IFM/MedAraBench_verified" |
| COLUMNS = ["prompt", "question", "choices", "index"] |
| EXPECTED_KEPT = { |
| "Anatomy": 830, "Histology": 188, "Histology and Anatomy": 39, |
| "Histology and Systemic Anatomy": 8, "Anesthesia": 70, "Biochemistry": 303, |
| "Cell Biology": 197, "Genetics": 176, "Physics": 521, "Chemistry": 71, |
| "Embryology": 5, "Emergency Medicine": 21, "Gastroenterology": 29, |
| "Neurology": 43, "Cardiology": 17, "Thorasic Internal": 17, "Oncology": 12, |
| "Chest Diseases": 6, "Gastroenterology & Hepatology": 38, "Microbiology": 115, |
| "Ophthalmology": 234, "Pathology": 43, "Pharmacology": 62, "Physiology": 573, |
| "Statistics": 310, "Surgery": 103, |
| } |
|
|
|
|
| def fingerprint(row): |
| values = [row["prompt"], row["question"], |
| json.dumps(list(row["choices"]), ensure_ascii=False), str(row["index"])] |
| return hashlib.sha256("\x1f".join(values).encode()).hexdigest()[:16] |
|
|
|
|
| ids = pd.read_csv(hf_hub_download(THIS_REPO, "ids.csv", repo_type="dataset")) |
| out = sys.argv[1] if len(sys.argv) > 1 else "medarabench_verified" |
| total = 0 |
| for config, expected in EXPECTED_KEPT.items(): |
| cfg = ids[ids["config"].eq(config)].sort_values("row").reset_index(drop=True) |
| source = pd.read_parquet(hf_hub_download(SOURCE, f"{config}/data.parquet", |
| repo_type="dataset", revision=SOURCE_REVISION)) |
| assert len(source) == len(cfg), f"{config}: expected {len(cfg)} source rows, got {len(source)}" |
| mismatch = [i for i, row in source.iterrows() if fingerprint(row) != cfg.at[i, "fingerprint"]] |
| assert not mismatch, f"{config}: source rows differ from the audited version: {mismatch[:10]}" |
|
|
| verified = source[cfg["status"].eq("kept").to_numpy()].reset_index(drop=True) |
| assert len(verified) == expected, f"{config}: expected {expected} rows, got {len(verified)}" |
| os.makedirs(os.path.join(out, config), exist_ok=True) |
| verified.to_parquet(os.path.join(out, config, "data.parquet")) |
| total += len(verified) |
|
|
| assert total == 4031, f"expected 4031 rows, got {total}" |
| print(f"Wrote {total} rows in {len(EXPECTED_KEPT)} configs to {out}/") |
|
|
