"""Minimal exact-answer demo, not the paper's complete biomedical alias judge.""" import argparse, collections, gzip, json, unicodedata from pathlib import Path def records(path): opener=gzip.open if str(path).endswith('.gz') else open with opener(path,'rt',encoding='utf-8') as f: for line in f: if line.strip():yield json.loads(line) def norm(value): return ' '.join(unicodedata.normalize('NFKC',str(value)).casefold().split()) def evaluate(qa,predictions,aliases=None): gold={} for row in qa: qid=row['qa_id'] if qid in gold:raise ValueError('Duplicate QA ID') gold[qid]=row counts=collections.Counter(total_qa=len(gold));seen=set() for row in predictions: qid=row['qa_id'] if qid in seen:raise ValueError('Duplicate prediction ID; use one condition per file') if qid not in gold:raise ValueError('Unknown prediction QA ID') seen.add(qid) if row.get('error') or row.get('api_error'): counts['api_errors']+=1;continue prediction=row.get('answer') if isinstance(prediction,list) and len(prediction)==1:prediction=prediction[0] if not isinstance(prediction,str) or not prediction.strip(): counts['invalid_predictions']+=1;continue target=gold[qid].get('short_answer',gold[qid].get('answer')) if isinstance(target,list) and len(target)==1:target=target[0] if not isinstance(target,str):raise ValueError('Demo requires a single string answer') accepted=[target]+(aliases or {}).get(qid,[]) counts['scored']+=1 counts['correct']+=int(norm(prediction) in {norm(x) for x in accepted}) counts['missing_predictions']=len(gold)-len(seen) return dict(counts,accuracy_pct=100*counts['correct']/counts['scored'] if counts['scored'] else None, scoring='NFKC + casefold + whitespace exact match; optional explicit QA aliases', error_policy='exclude API errors and invalid/missing predictions; report counts') def main(): p=argparse.ArgumentParser(description=__doc__) p.add_argument('--qa',required=True,type=Path) p.add_argument('--predictions',required=True,type=Path) p.add_argument('--aliases',type=Path,help='JSON object: QA ID -> list of accepted answer strings') a=p.parse_args() aliases=json.loads(a.aliases.read_text(encoding='utf-8')) if a.aliases else None print(json.dumps(evaluate(records(a.qa),records(a.predictions),aliases),indent=2)) if __name__=='__main__':main()