bella-companion 0.0.47__py3-none-any.whl → 0.1.1__py3-none-any.whl

bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv

@@ -1,6 +0,0 @@
-0.019125683060110532
-0.057377049180331596
-0.0983606557379062
-0.12295081967226906
-0.1420765027323796
-0.18306010928972682

bella_companion/simulations/features.py

@@ -1,7 +0,0 @@
-from dataclasses import dataclass
-
-
-@dataclass
-class Feature:
-    is_binary: bool
-    is_relevant: bool

bella_companion/simulations/figures/explain/__init__.py

@@ -1,6 +0,0 @@
-from bella_companion.simulations.figures.explain.pdp import plot_partial_dependencies
-from bella_companion.simulations.figures.explain.shap import (
-    plot_shap_features_importance,
-)
-
-__all__ = ["plot_partial_dependencies", "plot_shap_features_importance"]

bella_companion/simulations/figures/explain/shap.py

@@ -1,62 +0,0 @@
-from functools import partial
-from itertools import product
-from pathlib import Path
-from typing import Callable
-
-import matplotlib.pyplot as plt
-import numpy as np
-import seaborn as sns
-from joblib import Parallel, delayed
-from lumiere.typing import ActivationFunction, Weights
-from tqdm import tqdm
-
-from bella_companion.simulations.features import Feature
-from bella_companion.utils import get_median_shap_features_importance
-
-
-def plot_shap_features_importance(
-    weights: list[list[Weights]],  # shape: (n_runs, n_weights_samples, ...)
-    features: dict[str, Feature],
-    output_file: Path,
-    hidden_activation: ActivationFunction,
-    output_activation: ActivationFunction,
-):
-    continuous_grid: list[float] = np.linspace(0, 1, 10).tolist()
-    features_grid: list[list[float]] = [
-        [0, 1] if feature.is_binary else continuous_grid
-        for feature in features.values()
-    ]
-    inputs = list(product(*features_grid))
-
-    jobs = Parallel(n_jobs=-1, return_as="generator_unordered")(
-        delayed(
-            partial(
-                get_median_shap_features_importance,
-                inputs=inputs,
-                hidden_activation=hidden_activation,
-                output_activation=output_activation,
-            )
-        )(w)
-        for w in weights
-    )
-    features_importances = np.array(
-        [job for job in tqdm(jobs, total=len(weights), desc="Evaluating SHAPs")]
-    )  # shape: (n_runs, n_features)
-    features_importances /= features_importances.sum(axis=1, keepdims=True)
-
-    def _plot_violins(group_check: Callable[[Feature], bool]):
-        for i, (feature_name, feature) in enumerate(features.items()):
-            if group_check(feature):
-                sns.violinplot(
-                    y=features_importances[:, i],
-                    x=[feature_name] * len(features_importances),
-                    cut=0,
-                    color="#E74C3C" if feature.is_relevant else "gray",
-                )
-
-    _plot_violins(lambda f: not f.is_binary)
-    _plot_violins(lambda f: f.is_binary)
-    plt.xlabel("Feature")  # pyright: ignore
-    plt.ylabel("Importance")  # pyright: ignore
-    plt.savefig(output_file)  # pyright: ignore
-    plt.close()

bella_companion/utils/explain.py

@@ -1,45 +0,0 @@
-import numpy as np
-from lumiere import get_partial_dependence_values, get_shap_features_importance
-from lumiere.typing import ActivationFunction, Weights
-from numpy.typing import ArrayLike
-
-
-def get_median_partial_dependence_values(
-    weights: list[Weights],  # shape: (n_weight_samples, ...)
-    features_grid: list[list[float]],
-    hidden_activation: ActivationFunction,
-    output_activation: ActivationFunction,
-) -> list[list[float]]:  # shape: (n_features, n_grid_points)
-    pdvalues = [
-        get_partial_dependence_values(
-            weights=w,
-            features_grid=features_grid,
-            hidden_activation=hidden_activation,
-            output_activation=output_activation,
-        )
-        for w in weights
-    ]
-    return [
-        np.median([pd[feature_idx] for pd in pdvalues], axis=0).tolist()
-        for feature_idx in range(len(features_grid))
-    ]
-
-
-def get_median_shap_features_importance(
-    weights: list[Weights],
-    inputs: ArrayLike,
-    hidden_activation: ActivationFunction,
-    output_activation: ActivationFunction,
-) -> list[float]:  # length: n_features
-    features_importance = np.array(
-        [
-            get_shap_features_importance(
-                weights=w,
-                inputs=inputs,
-                hidden_activation=hidden_activation,
-                output_activation=output_activation,
-            )
-            for w in weights
-        ]
-    )
-    return np.median(features_importance, axis=0).tolist()

bella_companion-0.0.47.dist-info/RECORD

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