"""Pipette mistake / error detection task.""" from __future__ import annotations from collections import Counter from pathlib import Path from typing import Any from ..io import BENCHMARK_ROOT, read_parquet, select_shard from ..metrics import bootstrap_sem, classification_scores from ..parsing import parse_choice_option from .base import BenchmarkTask, TaskSpec PMD_OPTIONS = { "CORRECT", "ERROR_REUSE", "ERROR_SURFACE", "ERROR_RELEASE", "ERROR_INSTALL", "ERROR_OTHER", } PMD_MISTAKE_TO_OPTION = { "none": "CORRECT", "reuse_tip": "ERROR_REUSE", "reuse_same_media": "ERROR_REUSE", "reuse_same_tip": "ERROR_REUSE", "surface_contamination": "ERROR_SURFACE", "early_release": "ERROR_RELEASE", "wrong_tip_for_pipette": "ERROR_INSTALL", } PMD_NUMBER_TO_OPTION = { "1": "CORRECT", "2": "ERROR_REUSE", "3": "ERROR_SURFACE", "4": "ERROR_RELEASE", "5": "ERROR_INSTALL", "6": "ERROR_OTHER", } def pmd_target_option(label: str, mistake_type: str) -> str: return "CORRECT" if label == "correct" else PMD_MISTAKE_TO_OPTION.get(mistake_type, "ERROR_OTHER") class PmdTask(BenchmarkTask): spec = TaskSpec( name="pmd", display_name="Error Detection", default_manifest=BENCHMARK_ROOT / "pmd" / "pmd.parquet", sort_key="video_id", ) primary_metric = "binary_balanced_accuracy" def load_examples( self, *, benchmark_root: Path = BENCHMARK_ROOT, manifest_path: Path | None = None, video_root: Path | None = None, num_shards: int = 1, shard_index: int = 0, limit: int | None = None, ) -> list[dict[str, Any]]: rows = read_parquet(manifest_path or self.default_manifest) selected: list[dict[str, Any]] = [] root = video_root or benchmark_root for row in rows: rel_video = str(row.get("video_path") or "") if not rel_video: continue video_path = root / rel_video target = pmd_target_option(str(row.get("label")), str(row.get("mistake_type"))) selected.append( { **row, "task": self.name, "_video_abs": str(video_path), "target_option": target, "target_binary": "CORRECT" if target == "CORRECT" else "ERROR", } ) selected = sorted(selected, key=lambda row: str(row.get("video_id") or "")) if limit is not None: selected = selected[:limit] return select_shard(selected, num_shards, shard_index) def parse_record(self, row: dict[str, Any]) -> dict[str, Any]: if row.get("error"): return row pred = parse_choice_option(str(row.get("raw_response") or ""), PMD_OPTIONS, number_map=PMD_NUMBER_TO_OPTION) pred_binary = None if pred is None else ("CORRECT" if pred == "CORRECT" else "ERROR") target = str(row.get("target_option") or pmd_target_option(str(row.get("label")), str(row.get("mistake_type")))) target_binary = "CORRECT" if target == "CORRECT" else "ERROR" row.update( { "target_option": target, "target_binary": target_binary, "pred_option": pred, "pred_binary": pred_binary, "pred_parse_ok": pred is not None, "binary_correct": pred_binary == target_binary if pred_binary is not None else False, "option_correct": pred == target if pred is not None else False, } ) return row def _summary(self, rows: list[dict[str, Any]]) -> dict[str, Any]: parsed = self.parse_rows(rows) scored = [row for row in parsed if not row.get("error")] binary_pairs: list[tuple[str, str | None]] = [] option_pairs: list[tuple[str, str | None]] = [] error_type_pairs: list[tuple[str, str | None]] = [] for row in scored: target = str(row.get("target_option")) pred = row.get("pred_option") target_binary = "CORRECT" if target == "CORRECT" else "ERROR" pred_binary = None if pred is None else ("CORRECT" if pred == "CORRECT" else "ERROR") binary_pairs.append((target_binary, pred_binary)) option_pairs.append((target, None if pred is None else str(pred))) if target != "CORRECT": error_type_pairs.append((target, None if pred in (None, "CORRECT") else str(pred))) binary = classification_scores(binary_pairs, labels=["CORRECT", "ERROR"]) option = classification_scores(option_pairs, labels=sorted(PMD_OPTIONS)) error_type = classification_scores( error_type_pairs, labels=sorted(option for option in PMD_OPTIONS if option != "CORRECT"), ) parse_errors = sum(1 for row in scored if row.get("pred_option") is None) return { "task": self.name, "display_name": self.display_name, "rows": len(rows), "scored": len(scored), "errors": sum(1 for row in rows if row.get("error")), "parse_errors": parse_errors, "parse_success_rate": (len(scored) - parse_errors) / len(scored) if scored else None, "binary_accuracy": binary["accuracy"], "binary_balanced_accuracy": binary["balanced_accuracy"], "binary_macro_f1": binary["macro_f1"], "binary_macro_precision": binary["macro_precision"], "binary_macro_recall": binary["macro_recall"], "binary_precision": binary["precision"], "binary_recall": binary["recall"], "binary_f1": binary["f1"], "binary_confusion": binary["confusion"], "option_accuracy": option["accuracy"], "option_balanced_accuracy": option["balanced_accuracy"], "option_macro_f1": option["macro_f1"], "option_confusion": option["confusion"], "error_type_accuracy": error_type["accuracy"], "error_type_balanced_accuracy": error_type["balanced_accuracy"], "error_type_macro_f1": error_type["macro_f1"], "error_type_macro_precision": error_type["macro_precision"], "error_type_macro_recall": error_type["macro_recall"], "error_type_precision": error_type["precision"], "error_type_recall": error_type["recall"], "error_type_f1": error_type["f1"], "error_type_confusion": error_type["confusion"], "target_counts": dict(Counter(str(row.get("target_option")) for row in scored)), "pred_counts": dict(Counter(str(row.get("pred_option")) for row in scored)), } def score(self, rows: list[dict[str, Any]]) -> dict[str, Any]: parsed = self.parse_rows(rows) summary = self._summary(parsed) for metric in ( "binary_accuracy", "binary_balanced_accuracy", "binary_macro_f1", "binary_macro_precision", "binary_macro_recall", "error_type_accuracy", "error_type_balanced_accuracy", "error_type_macro_f1", "error_type_macro_precision", "error_type_macro_recall", ): summary[f"{metric}_sem"] = bootstrap_sem(parsed, metric, self._summary, iterations=200) return summary