Inference

neureptrace.inference

sign_flip_time_inference(csv_paths, *, metric='accuracy', chance=0.5, n_permutations=10000, random_state=13, cluster_alpha=0.05, decoder=None, emission_mode=None, observation_csv_paths=None, observation_subject_column=None, ece_bins=DEFAULT_ECE_BINS, metric_direction='auto')

Run one-sided subject-level sign-flip inference over time.

The test uses fold-size-weighted subject time courses as independent samples. Pointwise p-values test whether the metric is better than the reference value chance. Higher-is-better metrics use metric - chance; lower-is-better metrics use chance - metric. Cluster p-values use a max-cluster-mass correction over contiguous positive-effect time points.

Source code in src/neureptrace/inference.py

def sign_flip_time_inference(
    csv_paths: list[Path],
    *,
    metric: str = "accuracy",
    chance: float = 0.5,
    n_permutations: int = 10_000,
    random_state: int = 13,
    cluster_alpha: float = 0.05,
    decoder: str | None = None,
    emission_mode: str | None = None,
    observation_csv_paths: list[Path] | None = None,
    observation_subject_column: str | None = None,
    ece_bins: int = DEFAULT_ECE_BINS,
    metric_direction: str = "auto",
) -> tuple[pd.DataFrame, pd.DataFrame]:
    """Run one-sided subject-level sign-flip inference over time.

    The test uses fold-size-weighted subject time courses as independent
    samples. Pointwise p-values test whether the metric is better than the
    reference value ``chance``. Higher-is-better metrics use ``metric - chance``;
    lower-is-better metrics use ``chance - metric``. Cluster p-values use a
    max-cluster-mass correction over contiguous positive-effect time points.
    """
    if not 0 < cluster_alpha < 1:
        raise ValueError("cluster_alpha must be between 0 and 1.")

    effects, condition_values, resolved_direction = _subject_time_effects_and_conditions(
        csv_paths,
        metric=metric,
        chance=chance,
        decoder=decoder,
        emission_mode=emission_mode,
        observation_csv_paths=observation_csv_paths,
        observation_subject_column=observation_subject_column,
        ece_bins=ece_bins,
        metric_direction=metric_direction,
    )
    effect_values = effects.to_numpy(dtype=float)
    times = effects.columns.to_numpy(dtype=float)
    n_subjects = effect_values.shape[0]

    observed_statistic = _t_statistic(effect_values)
    observed_effect = effect_values.mean(axis=0)
    null_statistics = _sign_flip_t_statistics(effect_values, n_permutations=n_permutations, random_state=random_state)

    pointwise_p = (1.0 + (null_statistics >= observed_statistic[None, :]).sum(axis=0)) / (n_permutations + 1.0)
    cluster_threshold = np.quantile(null_statistics, 1.0 - cluster_alpha, axis=0)

    observed_clusters = _contiguous_clusters(observed_statistic >= cluster_threshold)
    max_null_masses = np.zeros(n_permutations)
    for idx, null_statistic in enumerate(null_statistics):
        masses = _cluster_masses(null_statistic, cluster_threshold)
        max_null_masses[idx] = max(masses) if masses else 0.0

    cluster_ids = np.full(len(times), -1, dtype=int)
    cluster_p_values = np.full(len(times), np.nan, dtype=float)
    cluster_rows = []
    for cluster_id, (start, stop) in enumerate(observed_clusters, start=1):
        cluster_statistic = observed_statistic[start:stop]
        cluster_mass = float(cluster_statistic.sum())
        cluster_p = float((1.0 + np.sum(max_null_masses >= cluster_mass)) / (n_permutations + 1.0))
        peak_offset = int(np.argmax(cluster_statistic))
        cluster_ids[start:stop] = cluster_id
        cluster_p_values[start:stop] = cluster_p
        cluster_rows.append(
            {
                "cluster_id": cluster_id,
                "start_time": float(times[start]),
                "stop_time": float(times[stop - 1]),
                "peak_time": float(times[start + peak_offset]),
                "n_timepoints": stop - start,
                "cluster_mass": cluster_mass,
                "peak_statistic": float(cluster_statistic[peak_offset]),
                "cluster_p": cluster_p,
            }
        )

    time_table = pd.DataFrame(
        {
            "time": times,
            "n_subjects": n_subjects,
            "metric_direction": resolved_direction,
            "reference_value": chance,
            f"{metric}_mean": observed_effect + chance if resolved_direction == "higher" else chance - observed_effect,
            "effect_mean": observed_effect,
            "statistic": observed_statistic,
            "pointwise_p": pointwise_p,
            "cluster_threshold": cluster_threshold,
            "cluster_id": cluster_ids,
            "cluster_p": cluster_p_values,
        }
    )
    cluster_table = pd.DataFrame(
        cluster_rows,
        columns=[
            "cluster_id",
            "start_time",
            "stop_time",
            "peak_time",
            "n_timepoints",
            "cluster_mass",
            "peak_statistic",
            "cluster_p",
        ],
    )
    cluster_table["metric_direction"] = resolved_direction
    cluster_table["reference_value"] = chance
    return _prepend_condition_columns(time_table, condition_values), _prepend_condition_columns(cluster_table, condition_values)

subject_time_effects(csv_paths, *, metric='accuracy', chance=0.5, decoder=None, emission_mode=None, observation_csv_paths=None, observation_subject_column=None, ece_bins=DEFAULT_ECE_BINS, metric_direction='auto')

Return a subject-by-time matrix of signed effects against a reference value.

The sign is chosen so positive values mean better than the reference: higher-is-better metrics use metric minus reference, while lower-is-better metrics use reference minus metric. ECE inference uses pooled held-out probability observations. Pass observation_csv_paths when metric='ece'; fold-averaged ECE is not used for inferential tests.

Source code in src/neureptrace/inference.py

def subject_time_effects(
    csv_paths: list[Path],
    *,
    metric: str = "accuracy",
    chance: float = 0.5,
    decoder: str | None = None,
    emission_mode: str | None = None,
    observation_csv_paths: list[Path] | None = None,
    observation_subject_column: str | None = None,
    ece_bins: int = DEFAULT_ECE_BINS,
    metric_direction: str = "auto",
) -> pd.DataFrame:
    """Return a subject-by-time matrix of signed effects against a reference value.

    The sign is chosen so positive values mean better than the reference:
    higher-is-better metrics use metric minus reference, while lower-is-better
    metrics use reference minus metric. ECE inference uses pooled held-out
    probability observations. Pass observation_csv_paths when metric='ece';
    fold-averaged ECE is not used for inferential tests.
    """
    effects, _, _ = _subject_time_effects_and_conditions(
        csv_paths,
        metric=metric,
        chance=chance,
        decoder=decoder,
        emission_mode=emission_mode,
        observation_csv_paths=observation_csv_paths,
        observation_subject_column=observation_subject_column,
        ece_bins=ece_bins,
        metric_direction=metric_direction,
    )
    return effects