import csv import json import re from typing import Dict, Tuple ALLOWED_ERROR_TYPES = { "no_error", "low_confidence_region_overtrust", "interdomain_orientation_overclaim", "disorder_as_structure", "loop_position_overtrust", "complex_negation_from_monomer", "interface_overconfidence", "cofactor_absence_misread", "low_complexity_as_domain", } def _norm(s: str) -> str: return re.sub(r"\s+", " ", (s or "").strip().lower()) def _token_set(s: str) -> set: s = _norm(s) s = re.sub(r"[^a-z0-9\s]", " ", s) return {t for t in s.split(" ") if t} def _jaccard(a: str, b: str) -> float: ta = _token_set(a) tb = _token_set(b) if not ta and not tb: return 1.0 if not ta or not tb: return 0.0 return len(ta & tb) / len(ta | tb) def _extract_json(text: str) -> Dict: if text is None: return {} text = text.strip() try: return json.loads(text) except Exception: pass m = re.search(r"\{.*\}", text, flags=re.DOTALL) if not m: return {} try: return json.loads(m.group(0)) except Exception: return {} def load_refs(test_csv_path: str) -> Dict[str, Tuple[str, str, str]]: refs = {} with open(test_csv_path, newline="", encoding="utf-8") as f: r = csv.DictReader(f) for row in r: refs[row["id"]] = ( _norm(row["gold_misinterpretation"]), row["gold_error_type"].strip(), row["gold_correction"].strip(), ) return refs def score_predictions(predictions_path: str, test_csv_path: str) -> Dict[str, float]: refs = load_refs(test_csv_path) n = 0 mis_hits = 0 type_hits = 0 corr_sim_sum = 0.0 format_hits = 0 with open(predictions_path, encoding="utf-8") as f: preds = [json.loads(line) for line in f if line.strip()] for item in preds: ex_id = item.get("id", "") raw = item.get("prediction", "") if ex_id not in refs: continue n += 1 parsed = _extract_json(raw) pred_mis = _norm(parsed.get("misinterpretation", "")) pred_type = (parsed.get("error_type") or "").strip() pred_corr = (parsed.get("correction") or "").strip() gold_mis, gold_type, gold_corr = refs[ex_id] mis_hits += 1 if pred_mis == gold_mis else 0 type_hits += 1 if pred_type == gold_type else 0 corr_sim_sum += _jaccard(pred_corr, gold_corr) has_keys = pred_mis in {"yes", "no"} and pred_type != "" and pred_corr != "" type_allowed = pred_type in ALLOWED_ERROR_TYPES consistency = (pred_mis == "no" and pred_type == "no_error") or (pred_mis == "yes" and pred_type != "no_error") format_hits += 1 if (has_keys and type_allowed and consistency) else 0 if n == 0: return { "final_score": 0.0, "misinterpretation_accuracy": 0.0, "error_type_accuracy": 0.0, "correction_similarity": 0.0, "format_pass_rate": 0.0, "n_scored": 0.0, } mis_acc = mis_hits / n type_acc = type_hits / n corr_sim = corr_sim_sum / n fmt = format_hits / n final = 0.4 * mis_acc + 0.3 * type_acc + 0.2 * corr_sim + 0.1 * fmt return { "final_score": float(final), "misinterpretation_accuracy": float(mis_acc), "error_type_accuracy": float(type_acc), "correction_similarity": float(corr_sim), "format_pass_rate": float(fmt), "n_scored": float(n), } if __name__ == "__main__": import argparse p = argparse.ArgumentParser() p.add_argument("--predictions", required=True) p.add_argument("--test_csv", required=True) args = p.parse_args() print(json.dumps(score_predictions(args.predictions, args.test_csv), indent=2))