| from __future__ import annotations |
|
|
| import argparse |
| import json |
| import math |
| import shutil |
| from argparse import Namespace |
| from pathlib import Path |
| from typing import Any |
|
|
| try: |
| from tqdm import tqdm |
| except Exception: |
| tqdm = None |
|
|
| from .benchmark_triage_repeated import _build_config, _ensure_matplotlib, _median, _read_rows |
| from .benchmark_triage_strategies import ( |
| DIRECT_BASELINES, |
| _collect_runner_result, |
| _dock_reference_ligand_baseline, |
| _ensure_reference_sample, |
| _executive_decision, |
| _json_or_empty, |
| _numeric_median, |
| _run_direct_baseline, |
| _run_runner_strategy, |
| _score_or_inf, |
| _strategy_base_name, |
| ) |
| from .dataset import validate_dataset_dir |
| from .provenance import RDockPipelineError |
| from .sdf import write_rows_csv |
|
|
|
|
| ABALATION_VARIANTS = ( |
| "classifier_only_no_fallback", |
| "classifier_only_union_fallback", |
| "classifier_regressor_no_fallback", |
| "classifier_regressor_union_fallback", |
| "cluster_only_triage", |
| "diverse_random_cost_balanced", |
| "single_fidelity_cost_balanced", |
| ) |
|
|
|
|
| def _mean(values: list[float]) -> float | None: |
| if not values: |
| return None |
| return sum(values) / len(values) |
|
|
|
|
| def _float(value: Any, default: float | None = None) -> float | None: |
| try: |
| text = str(value).strip() |
| if not text: |
| return default |
| return float(text) |
| except Exception: |
| return default |
|
|
|
|
| def _variant_config(args: argparse.Namespace, variant: str) -> tuple[str, Namespace]: |
| payload = Namespace(**vars(args)) |
| payload.strategy = "reference_free_active_learning_v2" |
| payload.adaptive_policy = "classifier_only" |
| payload.regressor_contribution_mode = "none" |
| payload.model_fallback_if_worse = "none" |
| payload.survivor_combination_policy = "model_only" |
| payload.classifier_weight = float(getattr(args, "classifier_weight", 1.0)) |
| payload.regressor_weight = float(getattr(args, "regressor_weight", 0.35)) |
| payload.cluster_quality_weight = float(getattr(args, "cluster_quality_weight", 0.5)) |
| if variant == "classifier_only_union_fallback": |
| payload.model_fallback_if_worse = "union_with_cluster_only" |
| payload.survivor_combination_policy = "union" |
| elif variant == "classifier_regressor_no_fallback": |
| payload.regressor_contribution_mode = str(getattr(args, "regressor_contribution_mode", "gate")) |
| elif variant == "classifier_regressor_union_fallback": |
| payload.regressor_contribution_mode = str(getattr(args, "regressor_contribution_mode", "gate")) |
| payload.model_fallback_if_worse = "union_with_cluster_only" |
| payload.survivor_combination_policy = "union" |
| return payload.strategy, payload |
|
|
|
|
| def _variant_label(variant: str, policy: str = "classifier_only") -> str: |
| if variant.startswith("classifier_"): |
| return f"reference_free_active_learning_v2::{policy}::{variant}" |
| return variant |
|
|
|
|
| def _summary_rows(results: list[dict[str, Any]], estimated_full_runs: int, has_reference: bool) -> list[dict[str, Any]]: |
| rows: list[dict[str, Any]] = [] |
| for strategy in sorted({str(item["strategy"]) for item in results}): |
| items = [row for row in results if str(row["strategy"]) == strategy] |
| rows.append( |
| { |
| "strategy": strategy, |
| "median_best_filtered_score": _numeric_median([row.get("best_filtered_hit_score") for row in items]), |
| "median_top5_mean_filtered_score": _numeric_median([row.get("top5_mean_filtered_score") for row in items]), |
| "median_top10_mean_filtered_score": _numeric_median([row.get("top10_mean_filtered_score") for row in items]), |
| "median_reduction_fraction": _numeric_median([row.get("reduction_fraction") for row in items]), |
| "median_total_runs_spent": _numeric_median([row.get("total_runs_spent") for row in items]), |
| "median_walltime_total_seconds": _numeric_median([row.get("walltime_total_seconds") for row in items]), |
| "median_top5pct_recall": _numeric_median([row.get("top5pct_recall") for row in items]) if has_reference else None, |
| "median_false_negative_rate": _numeric_median([row.get("false_negative_rate") for row in items]) if has_reference else None, |
| "median_survivors": _numeric_median([row.get("triage_survivor_count") for row in items]), |
| "median_initial_ligands": _numeric_median([row.get("initial_ligands") for row in items]), |
| "median_cost_saved_vs_full": _numeric_median([max(0.0, float(estimated_full_runs) - float(row.get("total_runs_spent") or 0.0)) for row in items]), |
| "classifier_precision": _numeric_median([row.get("classifier_precision") for row in items]), |
| "classifier_recall": _numeric_median([row.get("classifier_recall") for row in items]), |
| "classifier_auc_pr": _numeric_median([row.get("classifier_auc_pr") for row in items]), |
| } |
| ) |
| return rows |
|
|
|
|
| def _regressor_value_added(summary_map: dict[str, dict[str, Any]]) -> tuple[bool, str]: |
| cls = summary_map.get("classifier_only_no_fallback", {}) |
| reg = summary_map.get("classifier_regressor_no_fallback", {}) |
| if not cls or not reg: |
| return False, "Missing ablation variants." |
| cls_top5 = _float(cls.get("median_top5_mean_filtered_score"), None) |
| reg_top5 = _float(reg.get("median_top5_mean_filtered_score"), None) |
| cls_top10 = _float(cls.get("median_top10_mean_filtered_score"), None) |
| reg_top10 = _float(reg.get("median_top10_mean_filtered_score"), None) |
| cls_red = _float(cls.get("median_reduction_fraction"), None) |
| reg_red = _float(reg.get("median_reduction_fraction"), None) |
| if cls_top5 is None or reg_top5 is None or cls_top10 is None or reg_top10 is None: |
| return False, "REGRESSOR_NOT_PROVEN_USEFUL" |
| topk_better = reg_top5 < cls_top5 and reg_top10 < cls_top10 |
| reduction_ok = cls_red is None or reg_red is None or reg_red >= cls_red * 0.9 |
| if topk_better and reduction_ok: |
| return True, "REGRESSOR_ADDS_VALUE" |
| return False, "REGRESSOR_NOT_PROVEN_USEFUL" |
|
|
|
|
| def _write_ablation_plots(out_dir: Path, summary_rows: list[dict[str, Any]], results: list[dict[str, Any]]) -> list[str]: |
| plot_dir = out_dir / "plots" |
| plot_dir.mkdir(parents=True, exist_ok=True) |
| paths: list[str] = [] |
| plt = _ensure_matplotlib() |
| if plt is None: |
| return paths |
|
|
| def _save(name: str, fn) -> None: |
| fig = fn(plt) |
| fig.tight_layout() |
| path = plot_dir / name |
| fig.savefig(path, dpi=160) |
| plt.close(fig) |
| paths.append(str(path)) |
|
|
| def _bar(key: str, title: str, ylabel: str, name: str): |
| def _fn(plt): |
| fig, ax = plt.subplots(figsize=(10, 4)) |
| labels = [row["strategy"] for row in summary_rows] |
| vals = [float(row.get(key) or 0.0) for row in summary_rows] |
| ax.bar(labels, vals, color="#4f7d3a") |
| ax.set_title(title) |
| ax.set_xlabel("Wariant / strategia") |
| ax.set_ylabel(ylabel) |
| ax.tick_params(axis="x", rotation=25) |
| return fig |
| _save(name, _fn) |
|
|
| def _scatter(x_key: str, y_key: str, title: str, name: str): |
| def _fn(plt): |
| fig, ax = plt.subplots(figsize=(8, 5)) |
| for row in summary_rows: |
| x_val = _float(row.get(x_key), None) |
| y_val = _float(row.get(y_key), None) |
| if x_val is None or y_val is None: |
| continue |
| ax.scatter(x_val, y_val, alpha=0.7) |
| ax.text(x_val, y_val, str(row["strategy"]), fontsize=7) |
| ax.set_title(title) |
| ax.set_xlabel(x_key.replace("_", " ")) |
| ax.set_ylabel(y_key.replace("_", " ")) |
| ax.grid(True, alpha=0.25) |
| return fig |
| _save(name, _fn) |
|
|
| _bar("median_best_filtered_score", "Ablation: best filtered score", "Median best filtered SCORE", "ablation_best_score_by_strategy.png") |
| _bar("median_top5_mean_filtered_score", "Ablation: top-5 mean filtered score", "Median top-5 mean filtered SCORE", "ablation_top5_mean_by_strategy.png") |
| _bar("median_top10_mean_filtered_score", "Ablation: top-10 mean filtered score", "Median top-10 mean filtered SCORE", "ablation_top10_mean_by_strategy.png") |
| _scatter("median_reduction_fraction", "median_top10_mean_filtered_score", "Ablation: reduction versus top-10 mean score", "ablation_reduction_vs_top10.png") |
| _scatter("median_cost_saved_vs_full", "median_top10_mean_filtered_score", "Ablation: cost saved versus top-10 mean score", "ablation_cost_vs_top10.png") |
|
|
| pred_rows = [row for row in _concat_csv_tables(results, "tables/regressor_validation_predictions.csv") if _float(row.get("predicted_score"), None) is not None and _float(row.get("observed_component_sane_score"), None) is not None] |
| if pred_rows: |
| def _pred_obs(plt): |
| fig, ax = plt.subplots(figsize=(5, 5)) |
| xs = [float(row["predicted_score"]) for row in pred_rows] |
| ys = [float(row["observed_component_sane_score"]) for row in pred_rows] |
| ax.scatter(xs, ys, alpha=0.5) |
| lo = min(xs + ys) |
| hi = max(xs + ys) |
| ax.plot([lo, hi], [lo, hi], linestyle="--", color="gray") |
| ax.set_title("Regressor: predicted vs observed") |
| ax.set_xlabel("Predicted component-sane score") |
| ax.set_ylabel("Observed component-sane score") |
| return fig |
| _save("regressor_predicted_vs_observed.png", _pred_obs) |
|
|
| def _pred_rank(plt): |
| fig, ax = plt.subplots(figsize=(5, 5)) |
| ordered_pred = sorted(enumerate(pred_rows, start=1), key=lambda item: float(item[1]["predicted_score"])) |
| ordered_obs = sorted(enumerate(pred_rows, start=1), key=lambda item: float(item[1]["observed_component_sane_score"])) |
| pred_rank = {str(item[1]["ligand_id"]): idx for idx, item in enumerate(ordered_pred, start=1)} |
| obs_rank = {str(item[1]["ligand_id"]): idx for idx, item in enumerate(ordered_obs, start=1)} |
| xs = [] |
| ys = [] |
| for ligand_id in pred_rank: |
| if ligand_id not in obs_rank: |
| continue |
| xs.append(pred_rank[ligand_id]) |
| ys.append(obs_rank[ligand_id]) |
| ax.scatter(xs, ys, alpha=0.5) |
| ax.set_title("Regressor rank: predicted vs observed") |
| ax.set_xlabel("Predicted rank") |
| ax.set_ylabel("Observed rank") |
| return fig |
| _save("regressor_rank_predicted_vs_observed.png", _pred_rank) |
|
|
| def _pred_dist(plt): |
| fig, ax = plt.subplots(figsize=(6, 4)) |
| xs = [float(row["predicted_score"]) for row in pred_rows] |
| ax.hist(xs, bins=30, color="#3b6ea8", alpha=0.8) |
| ax.set_title("Regressor prediction distribution") |
| ax.set_xlabel("Predicted component-sane score") |
| ax.set_ylabel("Count") |
| return fig |
| _save("regressor_prediction_distribution.png", _pred_dist) |
|
|
| sign_rows = _concat_csv_tables(results, "tables/regressor_sign_check.csv") |
| if sign_rows: |
| def _target_compare(plt): |
| fig, ax = plt.subplots(figsize=(8, 4)) |
| labels = [str(row.get("comparison", "")) for row in sign_rows] |
| vals = [float(_float(row.get("value"), 0.0) or 0.0) for row in sign_rows] |
| ax.bar(labels, vals, color="#7a4f9d") |
| ax.set_title("Regressor sign comparison") |
| ax.set_ylabel("Spearman") |
| ax.tick_params(axis="x", rotation=35) |
| return fig |
| _save("regressor_target_comparison_spearman.png", _target_compare) |
|
|
| def _value_seed(plt): |
| fig, ax = plt.subplots(figsize=(9, 4)) |
| groups: dict[str, list[dict[str, Any]]] = {} |
| for row in results: |
| groups.setdefault(str(row["strategy"]), []).append(row) |
| for label, items in groups.items(): |
| xs = [int(_float(item.get("seed"), 0.0) or 0) for item in items] |
| ys = [float(_float(item.get("top10_mean_filtered_score"), 0.0) or 0.0) for item in items] |
| if xs and ys: |
| ax.plot(xs, ys, marker="o", label=label) |
| ax.set_title("Regressor value added by seed") |
| ax.set_xlabel("Seed") |
| ax.set_ylabel("Top-10 mean filtered SCORE") |
| handles, labels = ax.get_legend_handles_labels() |
| if handles and labels: |
| ax.legend(fontsize=8) |
| return fig |
| _save("regressor_value_added_by_seed.png", _value_seed) |
|
|
| return paths |
|
|
|
|
| def _concat_csv_tables(results: list[dict[str, Any]], relative_path: str) -> list[dict[str, Any]]: |
| rows: list[dict[str, Any]] = [] |
| rel = Path(relative_path) |
| for result in results: |
| run_dir = Path(str(result.get("run_dir", ""))) |
| path = run_dir / rel |
| if not path.exists(): |
| continue |
| for row in _read_rows(path): |
| item = dict(row) |
| item.setdefault("strategy", str(result.get("strategy", ""))) |
| item.setdefault("seed", str(result.get("seed", ""))) |
| rows.append(item) |
| return rows |
|
|
|
|
| def benchmark_regressor_ablation(args: argparse.Namespace) -> dict[str, Any]: |
| dataset_dir = Path(args.dataset_dir) |
| dataset_validation = validate_dataset_dir(dataset_dir, check_rdock_tools=False) |
| out_dir = Path(args.out) |
| if args.force and args.resume: |
| raise RDockPipelineError("benchmark-regressor-ablation does not allow using --force and --resume together") |
| if args.force and out_dir.exists(): |
| shutil.rmtree(out_dir) |
| out_dir.mkdir(parents=True, exist_ok=True) |
| seeds = [int(part.strip()) for part in str(args.seeds).split(",") if part.strip()] |
| variants = [part.strip() for part in str(args.variants).split(",") if part.strip()] if getattr(args, "variants", "") else list(ABALATION_VARIANTS) |
| invalid = [variant for variant in variants if variant not in ABALATION_VARIANTS] |
| if invalid: |
| raise RDockPipelineError(f"Unsupported regressor ablation variants: {invalid}") |
|
|
| reference_rows = _ensure_reference_sample( |
| dataset_dir, |
| out_dir, |
| args.jobs, |
| float(args.cpu_fraction), |
| int(args.reference_sample_size), |
| int(args.reference_sample_seed), |
| int(args.rdock_timeout_seconds), |
| bool(args.resume), |
| False, |
| ) if str(args.reference_mode).lower() == "sampled" and int(args.reference_sample_size) > 0 else [] |
| reference_ligand_baseline = _dock_reference_ligand_baseline( |
| dataset_dir, |
| out_dir, |
| args.jobs, |
| float(args.cpu_fraction), |
| int(args.rdock_timeout_seconds), |
| bool(args.resume), |
| ) |
|
|
| all_results: list[dict[str, Any]] = [] |
| progress = tqdm(total=len(seeds) * len(variants), desc="Regressor ablation", unit="run") if tqdm is not None else None |
| for seed in seeds: |
| for variant in variants: |
| run_dir = out_dir / f"seed_{seed:02d}" / variant |
| run_dir.mkdir(parents=True, exist_ok=True) |
| if variant in DIRECT_BASELINES: |
| baseline_payload = _run_direct_baseline(dataset_dir, run_dir, args, variant, seed) |
| result = _collect_runner_result(variant, seed, run_dir, reference_rows, set(baseline_payload.get("selected_ids", []))) |
| elif variant == "cluster_only_triage": |
| variant_args = Namespace(**vars(args)) |
| variant_args.adaptive_policy = "classifier_only" |
| variant_args.regressor_contribution_mode = "none" |
| _run_runner_strategy(dataset_dir, run_dir, variant_args, "cluster_only_triage", seed) |
| result = _collect_runner_result(variant, seed, run_dir, reference_rows) |
| else: |
| strategy_name, variant_args = _variant_config(args, variant) |
| _run_runner_strategy(dataset_dir, run_dir, variant_args, strategy_name, seed) |
| result = _collect_runner_result(_variant_label(variant), seed, run_dir, reference_rows) |
| result["variant_name"] = variant |
| result["strategy"] = variant |
| all_results.append(result) |
| if progress is not None: |
| progress.update(1) |
| progress.set_postfix(seed=seed, variant=variant) |
| if progress is not None: |
| progress.close() |
|
|
| estimated_full_runs = len(_read_rows(dataset_dir / "ligands" / "ligand_metadata.csv")) * max(int(part) for part in str(args.fidelity_levels).split(",") if part.strip()) |
| summary_rows = _summary_rows(all_results, estimated_full_runs, bool(reference_rows)) |
| summary_map = {str(row["strategy"]): row for row in summary_rows} |
| regressor_useful, regressor_reason = _regressor_value_added(summary_map) |
|
|
| strategy_csv_rows = [] |
| for row in summary_rows: |
| item = dict(row) |
| item["regressor_value_added"] = regressor_useful if str(row["strategy"]).startswith("classifier_regressor_") else "" |
| strategy_csv_rows.append(item) |
|
|
| write_rows_csv(all_results, out_dir / "tables" / "regressor_ablation_results.csv") |
| write_rows_csv(strategy_csv_rows, out_dir / "tables" / "strategy_comparison_ablation.csv") |
| write_rows_csv(_concat_csv_tables(all_results, "tables/regressor_validation_predictions.csv"), out_dir / "tables" / "regressor_validation_predictions.csv") |
| write_rows_csv(_concat_csv_tables(all_results, "tables/regressor_sign_check.csv"), out_dir / "tables" / "regressor_sign_check.csv") |
| write_rows_csv(_concat_csv_tables(all_results, "tables/regressor_target_comparison.csv"), out_dir / "tables" / "regressor_target_comparison.csv") |
| write_rows_csv( |
| [ |
| { |
| "strategy": row["strategy"], |
| "best_filtered_hit_ligand_id": row.get("best_filtered_hit_ligand_id"), |
| "best_filtered_hit_score": row.get("best_filtered_hit_score"), |
| "top5_mean_filtered_score": row.get("top5_mean_filtered_score"), |
| "top10_mean_filtered_score": row.get("top10_mean_filtered_score"), |
| } |
| for row in all_results |
| ], |
| out_dir / "tables" / "top_hits_by_ablation_strategy.csv", |
| ) |
| write_rows_csv( |
| _concat_csv_tables(all_results, "tables/final_hits_raw.csv"), |
| out_dir / "tables" / "top_hits_component_sanity_by_ablation_strategy.csv", |
| ) |
|
|
| cluster = summary_map.get("cluster_only_triage", {}) |
| diverse = summary_map.get("diverse_random_cost_balanced", {}) |
| single = summary_map.get("single_fidelity_cost_balanced", {}) |
| for key in ("classifier_only_no_fallback", "classifier_only_union_fallback", "classifier_regressor_no_fallback", "classifier_regressor_union_fallback"): |
| item = summary_map.get(key, {}) |
| if not item: |
| continue |
| item["model_beats_cluster_only"] = _score_or_inf(item.get("median_best_filtered_score")) < _score_or_inf(cluster.get("median_best_filtered_score")) |
| item["model_beats_diverse_random"] = _score_or_inf(item.get("median_best_filtered_score")) < _score_or_inf(diverse.get("median_best_filtered_score")) |
| item["model_beats_single_fidelity"] = _score_or_inf(item.get("median_best_filtered_score")) < _score_or_inf(single.get("median_best_filtered_score")) |
|
|
| if regressor_useful and summary_map.get("classifier_regressor_no_fallback"): |
| recommended_final = "classifier_regressor_no_fallback" |
| recommended_reason = "REGRESSOR_ADDS_VALUE" |
| elif summary_map.get("classifier_only_no_fallback"): |
| recommended_final = "classifier_only_no_fallback" |
| recommended_reason = regressor_reason |
| else: |
| recommended_final = "cluster_only_triage" |
| recommended_reason = regressor_reason |
|
|
| regressor_audit_payload = { |
| "fixed_score_regressor_name": str(getattr(args, "fixed_score_regressor_name", "fixed_score_regressor_v1")), |
| "fixed_score_regressor_target": str(getattr(args, "fixed_score_regressor_target", "component_sane_affinity_like")), |
| "regressor_model_type": str(getattr(args, "regressor_model_type", "extra_trees")), |
| "regressor_useful": regressor_useful, |
| "regressor_reason": regressor_reason, |
| "per_variant": { |
| variant: _json_or_empty(out_dir / f"seed_{seed:02d}" / variant / "metrics" / "regressor_audit_metrics.json") |
| for variant in variants |
| for seed in seeds[:1] |
| if (out_dir / f"seed_{seed:02d}" / variant / "metrics" / "regressor_audit_metrics.json").exists() |
| }, |
| } |
| summary = { |
| "dataset_dir": str(dataset_dir), |
| "reference_mode": str(args.reference_mode), |
| "reference_sample_size": int(args.reference_sample_size), |
| "reference_sample_docked_once_for_evaluation": bool(reference_rows), |
| "scientifically_valid_model_benchmark": not bool(dataset_validation["manifest"].get("synthetic_expansion") or dataset_validation["manifest"].get("synthetic_stress_test_only")), |
| "variants": variants, |
| "seeds": seeds, |
| "reference_ligand_baseline": reference_ligand_baseline, |
| "by_strategy": summary_map, |
| "recommended_strategy_final": recommended_final, |
| "recommended_reason": recommended_reason, |
| "regressor_adds_value": regressor_useful, |
| } |
| comparability = { |
| "dataset_dir": str(dataset_dir), |
| "reference_mode": str(args.reference_mode), |
| "reference_sample_size": int(args.reference_sample_size), |
| "reference_sample_seed": int(args.reference_sample_seed), |
| "fidelity_levels": str(args.fidelity_levels), |
| "cost_budget_runs": int(args.cost_budget_runs), |
| "seeds": seeds, |
| "variants": variants, |
| } |
| plots = _write_ablation_plots(out_dir, summary_rows, all_results) |
| (out_dir / "metrics").mkdir(parents=True, exist_ok=True) |
| _write_json(out_dir / "metrics" / "regressor_ablation_summary.json", summary) |
| _write_json(out_dir / "metrics" / "regressor_audit_metrics.json", regressor_audit_payload) |
| _write_json(out_dir / "metrics" / "ablation_comparability_manifest.json", comparability) |
|
|
| report_lines = [ |
| "# benchmark-regressor-ablation", |
| "", |
| "## Executive", |
| f"- recommended_strategy_final: `{recommended_final}`", |
| f"- recommended_reason: `{recommended_reason}`", |
| f"- regressor_adds_value: `{regressor_useful}`", |
| "", |
| "## Variants", |
| ] |
| for row in summary_rows: |
| report_lines.append( |
| f"- {row['strategy']}: best `{row.get('median_best_filtered_score')}`, top5 `{row.get('median_top5_mean_filtered_score')}`, " |
| f"top10 `{row.get('median_top10_mean_filtered_score')}`, reduction `{row.get('median_reduction_fraction')}`, " |
| f"runs `{row.get('median_total_runs_spent')}`" |
| ) |
| report_lines.extend(["", "## Plots"]) |
| report_lines.extend([f"- `{path}`" for path in plots] or ["- no_plots"]) |
| (out_dir / "report.md").write_text("\n".join(report_lines) + "\n", encoding="utf-8") |
| return {"run_dir": str(out_dir), "summary": summary, "plots": plots} |
|
|
|
|
| def build_arg_parser() -> argparse.ArgumentParser: |
| parser = argparse.ArgumentParser(description="Run real rDock regressor ablation benchmark on independent adaptive variants.") |
| parser.add_argument("--dataset-dir", required=True) |
| parser.add_argument("--reference-mode", default="sampled", choices=["sampled", "none"]) |
| parser.add_argument("--reference-sample-size", type=int, default=1000) |
| parser.add_argument("--reference-sample-seed", type=int, default=42) |
| parser.add_argument("--fidelity-levels", default="5,10,15,30,50") |
| parser.add_argument("--cost-budget-runs", type=int, default=3000) |
| parser.add_argument("--calibration-size", type=int, default=500) |
| parser.add_argument("--fidelity-validation-size", type=int, default=150) |
| parser.add_argument("--seeds", default="1,2,3") |
| parser.add_argument("--jobs", default="10") |
| parser.add_argument("--chunk-size", type=int, default=20) |
| parser.add_argument("--cpu-fraction", type=float, default=0.85) |
| parser.add_argument("--out", required=True) |
| parser.add_argument("--resume", action="store_true") |
| parser.add_argument("--force", action="store_true") |
| parser.add_argument("--rdock-timeout-seconds", type=int, default=14400) |
| parser.add_argument( |
| "--rdock-safe-jobs", |
| action="store_true", |
| default=True, |
| help="Clamp rDock jobs to ligand/stage size for tiny stages to avoid hangs on final batches.", |
| ) |
| parser.add_argument("--triage-target-recall", type=float, default=0.98) |
| parser.add_argument("--triage-retain-fraction", type=float, default=0.02) |
| parser.add_argument("--triage-model", default="classifier") |
| parser.add_argument("--classifier-top-percentile", type=float, default=0.05) |
| parser.add_argument("--classifier-threshold-mode", default="recall_target") |
| parser.add_argument("--classifier-min-positives", type=int, default=10) |
| parser.add_argument("--classifier-holdout-fraction", type=float, default=0.25) |
| parser.add_argument("--classifier-fallback", default="cluster_only") |
| parser.add_argument("--promotion-policy", default="balanced") |
| parser.add_argument("--adaptive-policy", default="classifier_only") |
| parser.add_argument("--regressor-contribution-mode", default="gate", choices=["none", "linear", "gate", "rescue"]) |
| parser.add_argument("--classifier-weight", type=float, default=1.0) |
| parser.add_argument("--regressor-weight", type=float, default=0.35) |
| parser.add_argument("--cluster-quality-weight", type=float, default=0.5) |
| parser.add_argument("--uncertainty-weight", type=float, default=0.35) |
| parser.add_argument("--diversity-weight", type=float, default=0.75) |
| parser.add_argument("--outlier-risk-weight", type=float, default=2.0) |
| parser.add_argument("--fixed-score-regressor-name", default="fixed_score_regressor_v1") |
| parser.add_argument("--fixed-score-regressor-target", default="component_sane_affinity_like") |
| parser.add_argument("--regressor-model-type", default="extra_trees", choices=["extra_trees", "random_forest", "hist_gradient_boosting", "ridge"]) |
| parser.add_argument("--model-validation-split", default="cluster", choices=["random", "cluster"]) |
| parser.add_argument("--variants", default=",".join(ABALATION_VARIANTS)) |
| return parser |
|
|
|
|
| def run_from_args(args: argparse.Namespace) -> dict[str, Any]: |
| return benchmark_regressor_ablation(args) |
|
|
|
|
| def main() -> int: |
| print(json.dumps(run_from_args(build_arg_parser().parse_args()), indent=2)) |
| return 0 |
|
|
|
|
| if __name__ == "__main__": |
| raise SystemExit(main()) |
|
|