| |
| """Validate the bundled BEND-BCI Space tables and their paper provenance. |
| |
| The local checks run in the standalone Hugging Face Space. Passing |
| ``--canonical-root`` additionally compares every manuscript-facing summary |
| against ``paper/results`` in the main benchmark repository. |
| """ |
|
|
| from __future__ import annotations |
|
|
| import argparse |
| import hashlib |
| import json |
| from pathlib import Path |
| from typing import Iterable |
|
|
| import numpy as np |
| import pandas as pd |
|
|
|
|
| DATASETS = { |
| "monkey", |
| "allen_neuropixels", |
| "speech", |
| "mc_pacman", |
| "ratinabox", |
| } |
| CONSISTENCY_DATASETS = DATASETS - {"mc_pacman"} |
| LATENT_COORDINATE_SPACE = "per_session_whitened_reference_aligned_3d" |
| FIGURE5_TARGET_SESSION = "sub-C_ses-CO-20150716_behavior+ecephys" |
|
|
| |
| EXPECTED_COVERAGE = { |
| "clean_prediction_summary.csv": (115, 112), |
| "robustness_summary.csv": (115, 112), |
| "scalability_summary.csv": (115, 112), |
| "consistency_summary.csv": (54, 46), |
| "neuron_shap_summary.csv": (105, 105), |
| "trial_shapley_summary.csv": (81, 81), |
| "trial_shapley_retrain_summary.csv": (99, 99), |
| } |
|
|
| REQUIRED_COLUMNS = { |
| "clean_prediction_summary.csv": { |
| "model", "dataset", "status", "metric", "score", "decoder", |
| }, |
| "robustness_summary.csv": { |
| "model", "dataset", "status", "metric", "noise_levels", "scores", |
| "raw_auc", |
| }, |
| "scalability_summary.csv": { |
| "model", "dataset", "status", "training_time_sec", |
| "inference_time_sec", "peak_ram_gb", "peak_vram_gb", |
| }, |
| "consistency_summary.csv": { |
| "model", "dataset", "is_active_model", "mean_r2", "n_sessions", |
| "sessions", "latent_dim", "scoring_modes", "normalizations", |
| }, |
| "neuron_shap_summary.csv": { |
| "model", "dataset", "is_active_model", "auc", "spearman_corr", |
| "shap_mean_value", "shap_min_value", "shap_max_value", |
| "shap_fraction_positive", "shap_fraction_negative", |
| }, |
| "trial_shapley_summary.csv": { |
| "model", "dataset", "is_active_model", "analysis", "perturbation_auc", |
| "rotation_angle_deg", "rotation_subspace_dim_spec", |
| "trial_selection_mode", "converged", "shapley_mean_value", |
| "shapley_min_value", "shapley_max_value", |
| "shapley_fraction_positive", "shapley_fraction_negative", |
| }, |
| "trial_shapley_retrain_summary.csv": { |
| "analysis", "model", "is_active_model", "condition", "metric", "score", |
| }, |
| "trial_historical_trajectories.csv": { |
| "model", "target_session", "trial_index", "trial_id", |
| "direction_index", "direction_label", "time_index", "target_x", |
| "target_y", "current_only_x", "current_only_y", |
| "historical_selected_x", "historical_selected_y", "current_only_r2", |
| "historical_selected_r2", |
| }, |
| "latent_samples.csv": { |
| "model", "dataset", "session", "session_label", "x", "y", "z", |
| "condition", "trial_index", "time_index", "eval_time_index", |
| "coordinate_space", "reference_session", "alignment", "landmark_type", |
| "n_alignment_landmarks", "is_reference", "session_order", |
| }, |
| "latent_trajectories.csv": { |
| "model", "dataset", "session", "session_label", "x", "y", "z", |
| "condition", "time_index", "eval_time_index", "n_points", |
| "coordinate_space", "reference_session", "alignment", "landmark_type", |
| "n_alignment_landmarks", "is_reference", "session_order", |
| }, |
| } |
|
|
| UNIQUE_KEYS = { |
| "clean_prediction_summary.csv": ["model", "dataset"], |
| "robustness_summary.csv": ["model", "dataset"], |
| "scalability_summary.csv": ["model", "dataset"], |
| "consistency_summary.csv": ["model", "dataset"], |
| "neuron_shap_summary.csv": ["model", "dataset"], |
| "trial_shapley_summary.csv": ["model", "dataset"], |
| "trial_shapley_retrain_summary.csv": ["analysis", "model", "condition"], |
| } |
|
|
| CANONICAL_NAMES = { |
| "clean_prediction_summary.csv": "metrics_summary.csv", |
| "robustness_summary.csv": "robustness_summary.csv", |
| "scalability_summary.csv": "scalability_summary.csv", |
| "consistency_summary.csv": "consistency_summary.csv", |
| "neuron_shap_summary.csv": "neuron_shap_summary.csv", |
| "trial_shapley_summary.csv": "trial_shapley_summary.csv", |
| "trial_shapley_retrain_summary.csv": "trial_shapley_retrain_summary.csv", |
| } |
|
|
|
|
| class ValidationError(RuntimeError): |
| """Raised when Space data violates its manuscript-facing contract.""" |
|
|
|
|
| def _sha256(path: Path) -> str: |
| digest = hashlib.sha256() |
| with path.open("rb") as handle: |
| for chunk in iter(lambda: handle.read(1024 * 1024), b""): |
| digest.update(chunk) |
| return digest.hexdigest() |
|
|
|
|
| def _active_mask(frame: pd.DataFrame) -> pd.Series: |
| if "status" in frame.columns: |
| return frame["status"].fillna("").eq("present") |
| if "is_active_model" in frame.columns: |
| return frame["is_active_model"].astype(str).str.lower().eq("true") |
| return pd.Series(True, index=frame.index) |
|
|
|
|
| def _require(condition: bool, message: str, errors: list[str]) -> None: |
| if not condition: |
| errors.append(message) |
|
|
|
|
| def _same_values(left: pd.DataFrame, right: pd.DataFrame) -> None: |
| pd.testing.assert_frame_equal( |
| left.reset_index(drop=True), |
| right.reset_index(drop=True), |
| check_dtype=False, |
| check_exact=True, |
| check_categorical=False, |
| ) |
|
|
|
|
| def _validate_latent_cell( |
| frame: pd.DataFrame, |
| *, |
| table_label: str, |
| model: str, |
| dataset: str, |
| sessions: list[str], |
| landmark_type: str, |
| errors: list[str], |
| ) -> None: |
| """Validate reference/alignment metadata for one method-dataset cell.""" |
| cell = frame[ |
| frame["model"].astype(str).eq(model) |
| & frame["dataset"].astype(str).eq(dataset) |
| ] |
| for session_order, session in enumerate(sessions): |
| session_rows = cell[cell["session"].astype(str).eq(session)] |
| if session_rows.empty: |
| errors.append(f"{table_label}: missing {model}/{dataset}/{session}") |
| continue |
|
|
| expected_reference = "true" if session_order == 0 else "false" |
| observed_reference = set( |
| session_rows["is_reference"].dropna().astype(str).str.lower() |
| ) |
| _require( |
| observed_reference == {expected_reference}, |
| f"{table_label}: {model}/{dataset}/{session} is_reference " |
| f"values {sorted(observed_reference)}", |
| errors, |
| ) |
| expected_alignment = "identity" if session_order == 0 else "proper_similarity_procrustes" |
| observed_alignment = set(session_rows["alignment"].dropna().astype(str)) |
| _require( |
| observed_alignment == {expected_alignment}, |
| f"{table_label}: {model}/{dataset}/{session} alignment " |
| f"values {sorted(observed_alignment)}", |
| errors, |
| ) |
| observed_reference_sessions = set( |
| session_rows["reference_session"].dropna().astype(str) |
| ) |
| _require( |
| observed_reference_sessions == {sessions[0]}, |
| f"{table_label}: {model}/{dataset}/{session} reference metadata " |
| f"{sorted(observed_reference_sessions)}", |
| errors, |
| ) |
| observed_landmarks = set(session_rows["landmark_type"].dropna().astype(str)) |
| _require( |
| observed_landmarks == {landmark_type}, |
| f"{table_label}: {model}/{dataset}/{session} landmarks " |
| f"{sorted(observed_landmarks)}", |
| errors, |
| ) |
| orders = pd.to_numeric(session_rows["session_order"], errors="coerce") |
| _require( |
| orders.notna().all() |
| and np.isfinite(orders.to_numpy()).all() |
| and orders.eq(session_order).all(), |
| f"{table_label}: {model}/{dataset}/{session} has invalid session_order", |
| errors, |
| ) |
| landmark_counts = pd.to_numeric( |
| session_rows["n_alignment_landmarks"], errors="coerce" |
| ) |
| _require( |
| landmark_counts.notna().all() |
| and np.isfinite(landmark_counts.to_numpy()).all() |
| and landmark_counts.ge(3).all(), |
| f"{table_label}: {model}/{dataset}/{session} has invalid landmark count", |
| errors, |
| ) |
|
|
|
|
| def validate_local(data_dir: Path) -> dict[str, pd.DataFrame]: |
| """Validate schemas, coverage, uniqueness, and fixed analysis conventions.""" |
|
|
| frames: dict[str, pd.DataFrame] = {} |
| errors: list[str] = [] |
|
|
| for name, columns in REQUIRED_COLUMNS.items(): |
| path = data_dir / name |
| if not path.exists(): |
| errors.append(f"missing required table: {path}") |
| continue |
| frame = pd.read_csv(path) |
| missing = sorted(columns - set(frame.columns)) |
| _require(not missing, f"{name}: missing columns {missing}", errors) |
| if missing: |
| continue |
| frames[name] = frame |
|
|
| manifest_path = data_dir / "release_manifest.json" |
| if not manifest_path.exists(): |
| errors.append(f"missing release manifest: {manifest_path}") |
| else: |
| try: |
| manifest = json.loads(manifest_path.read_text(encoding="utf-8")) |
| except (json.JSONDecodeError, OSError) as exc: |
| errors.append(f"invalid release manifest: {exc}") |
| manifest = {} |
| if not isinstance(manifest, dict): |
| errors.append("invalid release manifest: top-level value must be an object") |
| manifest = {} |
| raw_manifest_spaces = manifest.get("latent_coordinate_spaces", []) |
| if not isinstance(raw_manifest_spaces, list): |
| errors.append("release manifest: latent_coordinate_spaces must be a list") |
| raw_manifest_spaces = [] |
| elif not all(isinstance(value, str) for value in raw_manifest_spaces): |
| errors.append("release manifest: coordinate-space values must be strings") |
| raw_manifest_spaces = [] |
| manifest_spaces = set(raw_manifest_spaces) |
| _require( |
| manifest_spaces == {LATENT_COORDINATE_SPACE}, |
| f"release manifest: coordinate spaces {sorted(manifest_spaces)}", |
| errors, |
| ) |
| manifest_tables = manifest.get("tables", {}) |
| if not isinstance(manifest_tables, dict): |
| errors.append("release manifest: tables must be an object") |
| manifest_tables = {} |
| for name in REQUIRED_COLUMNS: |
| entry = manifest_tables.get(name) |
| if not isinstance(entry, dict): |
| errors.append(f"release manifest: missing table entry {name}") |
| continue |
| path = data_dir / name |
| if not path.exists(): |
| continue |
| expected_hash = entry.get("sha256") |
| actual_hash = _sha256(path) |
| _require( |
| expected_hash == actual_hash, |
| f"release manifest: SHA-256 mismatch for {name}", |
| errors, |
| ) |
| if name in frames: |
| _require( |
| entry.get("rows") == len(frames[name]), |
| f"release manifest: row-count mismatch for {name}", |
| errors, |
| ) |
|
|
| for name, (n_rows, n_active) in EXPECTED_COVERAGE.items(): |
| if name not in frames: |
| continue |
| frame = frames[name] |
| _require(len(frame) == n_rows, f"{name}: expected {n_rows} rows, found {len(frame)}", errors) |
| active = int(_active_mask(frame).sum()) |
| _require(active == n_active, f"{name}: expected {n_active} available rows, found {active}", errors) |
|
|
| for name, keys in UNIQUE_KEYS.items(): |
| if name not in frames or not set(keys).issubset(frames[name].columns): |
| continue |
| duplicates = frames[name].duplicated(keys, keep=False) |
| _require(not duplicates.any(), f"{name}: duplicate keys for {keys}", errors) |
|
|
| for name in ("clean_prediction_summary.csv", "robustness_summary.csv", "scalability_summary.csv"): |
| if name in frames: |
| observed = set(frames[name]["dataset"].dropna().astype(str)) |
| _require(observed == DATASETS, f"{name}: dataset set is {sorted(observed)}", errors) |
|
|
| if "clean_prediction_summary.csv" in frames: |
| prediction = frames["clean_prediction_summary.csv"] |
| _require(prediction["model"].nunique() == 23, "prediction: expected 23 methods", errors) |
| metrics = set(prediction.loc[_active_mask(prediction), "metric"].dropna()) |
| _require(metrics == {"accuracy", "r2"}, f"prediction: unexpected metrics {sorted(metrics)}", errors) |
|
|
| if "consistency_summary.csv" in frames: |
| consistency = frames["consistency_summary.csv"] |
| active = consistency.loc[_active_mask(consistency)] |
| observed = set(active["dataset"].dropna().astype(str)) |
| _require(observed == CONSISTENCY_DATASETS, f"consistency: dataset set is {sorted(observed)}", errors) |
| norms = set(active["normalizations"].dropna().astype(str)) |
| _require(norms == {"per_session_whitening"}, f"consistency: unexpected normalization {sorted(norms)}", errors) |
|
|
| if "neuron_shap_summary.csv" in frames: |
| feature = frames["neuron_shap_summary.csv"] |
| allen = feature[feature["dataset"].eq("allen_neuropixels")] |
| _require(not allen.empty and allen["spearman_corr"].notna().all(), "feature attribution: Allen Spearman values missing", errors) |
| other = feature[~feature["dataset"].eq("allen_neuropixels")] |
| _require(other["auc"].notna().all(), "feature attribution: ROC-AUC values missing", errors) |
| _require(feature["shap_min_value"].lt(0).any(), "feature attribution: signed negative values absent", errors) |
|
|
| if "trial_shapley_summary.csv" in frames: |
| trial = frames["trial_shapley_summary.csv"] |
| _require(set(trial["analysis"].dropna()) == {"subspace_rotation"}, "trial valuation: noncanonical analysis", errors) |
| angles = set(pd.to_numeric(trial["rotation_angle_deg"], errors="coerce").dropna()) |
| _require(angles == {75.0}, f"trial valuation: rotation angles {sorted(angles)}", errors) |
| dims = set(trial["rotation_subspace_dim_spec"].dropna().astype(str)) |
| _require(dims == {"full"}, f"trial valuation: subspace specs {sorted(dims)}", errors) |
| modes = set(trial["trial_selection_mode"].dropna().astype(str)) |
| _require(modes == {"random"}, f"trial valuation: selection modes {sorted(modes)}", errors) |
| _require(trial["perturbation_auc"].notna().all(), "trial valuation: detection AUC missing", errors) |
| _require(trial["shapley_min_value"].lt(0).any(), "trial valuation: signed negative values absent", errors) |
|
|
| if "trial_shapley_retrain_summary.csv" in frames: |
| retrain = frames["trial_shapley_retrain_summary.csv"] |
| expected = { |
| "within_session_cleaning": {"mixed_full", "data_shapley", "oracle"}, |
| "cross_session_old_trial_selection": { |
| "target_only", "all_sessions", "oldonly_dshap_negative_removal", |
| }, |
| } |
| observed = { |
| analysis: set(group["condition"].dropna().astype(str)) |
| for analysis, group in retrain.groupby("analysis") |
| } |
| _require(observed == expected, f"trial retraining: conditions {observed}", errors) |
|
|
| if "trial_historical_trajectories.csv" in frames: |
| historical = frames["trial_historical_trajectories.csv"] |
| _require( |
| len(historical) == 135 * 35, |
| "historical trajectories: expected 135 trials × 35 time bins", |
| errors, |
| ) |
| keys = ["trial_index", "time_index"] |
| _require( |
| not historical.duplicated(keys, keep=False).any(), |
| f"historical trajectories: duplicate keys for {keys}", |
| errors, |
| ) |
| _require( |
| set(historical["model"].dropna().astype(str)) == {"rnn"}, |
| "historical trajectories: expected the Figure 5e RNN example", |
| errors, |
| ) |
| _require( |
| set(historical["target_session"].dropna().astype(str)) |
| == {FIGURE5_TARGET_SESSION}, |
| "historical trajectories: unexpected target session", |
| errors, |
| ) |
| _require( |
| historical["trial_index"].nunique() == 135 |
| and historical["trial_id"].nunique() == 135, |
| "historical trajectories: expected 135 held-out trials and trial IDs", |
| errors, |
| ) |
| time_counts = historical.groupby("trial_index")["time_index"].nunique() |
| _require( |
| len(time_counts) == 135 and time_counts.eq(35).all(), |
| "historical trajectories: every trial must contain 35 time bins", |
| errors, |
| ) |
| direction_indices = pd.to_numeric( |
| historical["direction_index"], errors="coerce" |
| ) |
| _require( |
| direction_indices.notna().all() |
| and set(direction_indices.astype(int)) == set(range(8)), |
| "historical trajectories: expected all eight reach directions", |
| errors, |
| ) |
| for column in ( |
| "target_x", |
| "target_y", |
| "current_only_x", |
| "current_only_y", |
| "historical_selected_x", |
| "historical_selected_y", |
| "current_only_r2", |
| "historical_selected_r2", |
| ): |
| values = pd.to_numeric(historical[column], errors="coerce") |
| _require( |
| values.notna().all() and np.isfinite(values.to_numpy()).all(), |
| f"historical trajectories: non-finite {column} values", |
| errors, |
| ) |
| _require( |
| historical["current_only_r2"].nunique() == 1 |
| and historical["historical_selected_r2"].nunique() == 1, |
| "historical trajectories: expected one R² value per condition", |
| errors, |
| ) |
|
|
| for name in ("latent_samples.csv", "latent_trajectories.csv"): |
| if name not in frames: |
| continue |
| latent = frames[name] |
| observed = set(latent["dataset"].dropna().astype(str)) |
| _require(observed.issubset(CONSISTENCY_DATASETS), f"{name}: unsupported datasets {sorted(observed - CONSISTENCY_DATASETS)}", errors) |
| for column in ("x", "y", "z"): |
| values = pd.to_numeric(latent[column], errors="coerce") |
| _require( |
| values.notna().all() and np.isfinite(values.to_numpy()).all(), |
| f"{name}: non-finite {column} values", |
| errors, |
| ) |
| for column in ( |
| "coordinate_space", |
| "reference_session", |
| "alignment", |
| "landmark_type", |
| "n_alignment_landmarks", |
| "is_reference", |
| "session_order", |
| ): |
| _require( |
| latent[column].notna().all(), |
| f"{name}: missing {column} values", |
| errors, |
| ) |
| spaces = set(latent["coordinate_space"].dropna().astype(str)) |
| _require( |
| spaces == {LATENT_COORDINATE_SPACE}, |
| f"{name}: coordinate spaces {sorted(spaces)}", |
| errors, |
| ) |
|
|
| if { |
| "consistency_summary.csv", "latent_samples.csv", "latent_trajectories.csv" |
| }.issubset(frames): |
| consistency = frames["consistency_summary.csv"] |
| consistency = consistency.loc[_active_mask(consistency)].copy() |
| samples = frames["latent_samples.csv"] |
| trajectories = frames["latent_trajectories.csv"] |
| expected_sample_sessions: set[tuple[str, str, str]] = set() |
| expected_trajectory_sessions: set[tuple[str, str, str]] = set() |
| for row in consistency.itertuples(index=False): |
| sessions = ( |
| [] |
| if pd.isna(row.sessions) |
| else [item.strip() for item in str(row.sessions).split(";") if item.strip()] |
| ) |
| if not sessions: |
| errors.append(f"consistency: {row.model}/{row.dataset} has no sessions") |
| continue |
| try: |
| expected_n_sessions = int(row.n_sessions) |
| except (TypeError, ValueError): |
| expected_n_sessions = -1 |
| _require( |
| len(sessions) == expected_n_sessions, |
| f"consistency: {row.model}/{row.dataset} lists {len(sessions)} " |
| f"sessions but n_sessions={row.n_sessions}", |
| errors, |
| ) |
| expected_sample_sessions.update( |
| (str(row.model), str(row.dataset), session) for session in sessions |
| ) |
| if str(row.dataset) != "ratinabox": |
| expected_trajectory_sessions.update( |
| (str(row.model), str(row.dataset), session) for session in sessions |
| ) |
| _validate_latent_cell( |
| samples, |
| table_label="latent samples", |
| model=str(row.model), |
| dataset=str(row.dataset), |
| sessions=sessions, |
| landmark_type=str(row.scoring_modes), |
| errors=errors, |
| ) |
| if str(row.dataset) != "ratinabox": |
| _validate_latent_cell( |
| trajectories, |
| table_label="latent trajectories", |
| model=str(row.model), |
| dataset=str(row.dataset), |
| sessions=sessions, |
| landmark_type=str(row.scoring_modes), |
| errors=errors, |
| ) |
|
|
| observed_sample_sessions = set( |
| samples[["model", "dataset", "session"]].astype(str).itertuples(index=False, name=None) |
| ) |
| observed_trajectory_sessions = set( |
| trajectories[["model", "dataset", "session"]].astype(str).itertuples(index=False, name=None) |
| ) |
| _require( |
| observed_sample_sessions == expected_sample_sessions, |
| "latent samples: active consistency session coverage differs", |
| errors, |
| ) |
| _require( |
| observed_trajectory_sessions == expected_trajectory_sessions, |
| "latent trajectories: applicable consistency session coverage differs", |
| errors, |
| ) |
| _require( |
| len(observed_sample_sessions) == 173, |
| f"latent samples: expected 173 sessions, found {len(observed_sample_sessions)}", |
| errors, |
| ) |
|
|
| if errors: |
| raise ValidationError("\n".join(f"- {item}" for item in errors)) |
| return frames |
|
|
|
|
| def validate_canonical(data_dir: Path, canonical_root: Path) -> None: |
| """Require Space summaries to equal the current paper result tables.""" |
|
|
| results_dir = canonical_root / "paper" / "results" |
| errors: list[str] = [] |
| for dashboard_name, paper_name in CANONICAL_NAMES.items(): |
| dashboard_path = data_dir / dashboard_name |
| paper_path = results_dir / paper_name |
| if not dashboard_path.exists(): |
| errors.append(f"missing dashboard table: {dashboard_path}") |
| continue |
| if not paper_path.exists(): |
| errors.append(f"missing canonical table: {paper_path}") |
| continue |
| try: |
| _same_values(pd.read_csv(dashboard_path), pd.read_csv(paper_path)) |
| except AssertionError as exc: |
| first_line = str(exc).splitlines()[0] if str(exc) else "values differ" |
| errors.append(f"{dashboard_name} != {paper_name}: {first_line}") |
| if errors: |
| raise ValidationError("\n".join(f"- {item}" for item in errors)) |
|
|
|
|
| def build_parser() -> argparse.ArgumentParser: |
| parser = argparse.ArgumentParser(description=__doc__) |
| parser.add_argument("--data-dir", type=Path, default=Path(__file__).resolve().parent / "data") |
| parser.add_argument( |
| "--canonical-root", |
| type=Path, |
| help="Main benchmark repository root; enables exact paper/results comparisons.", |
| ) |
| return parser |
|
|
|
|
| def main(argv: Iterable[str] | None = None) -> int: |
| args = build_parser().parse_args(argv) |
| frames = validate_local(args.data_dir) |
| if args.canonical_root is not None: |
| validate_canonical(args.data_dir, args.canonical_root.resolve()) |
| print(f"Validated {len(frames)} BEND-BCI Space tables in {args.data_dir}") |
| if args.canonical_root is not None: |
| print("Canonical paper/results comparison passed") |
| return 0 |
|
|
|
|
| if __name__ == "__main__": |
| raise SystemExit(main()) |
|
|
