speed up cpi.predict

mind-inria · Nov 14, 2024 · dc63c98 · dc63c98
1 parent 3ca0a79
commit dc63c98
Showing 1 changed file with 36 additions and 12 deletions.
diff --git a/hidimstat/cpi.py b/hidimstat/cpi.py
@@ -169,18 +169,42 @@ def _joblib_predict_one_group(imputation_model, X, j):
             X_j_hat = imputation_model.predict(X_minus_j).reshape(X_j.shape)
             residual_j = X_j - X_j_hat
 
-            for _ in range(self.n_permutations):
-                X_j_perm = X_j_hat + self.rng.permutation(residual_j)
-                X_perm = np.empty_like(X)
-                X_perm[:, non_group_ids] = X_minus_j
-                X_perm[:, group_ids] = X_j_perm
-                if isinstance(X, pd.DataFrame):
-                    X_perm = pd.DataFrame(X_perm, columns=X.columns)
-
-                y_pred_perm = getattr(self.estimator, self.method)(X_perm)
-                list_y_pred_perm.append(y_pred_perm)
-
-            return np.array(list_y_pred_perm)
+            X_perm_all = np.empty((self.n_permutations, X.shape[0], X.shape[1]))
+            X_perm_all[:, :, non_group_ids] = X_minus_j
+            # n_permutations x n_samples x n_features_j
+            residual_j_perm = np.array(
+                [self.rng.permutation(residual_j) for _ in range(self.n_permutations)]
+            )
+            X_perm_all[:, :, group_ids] = X_j_hat[np.newaxis, :, :] + residual_j_perm
+
+            X_perm_batch = X_perm_all.reshape(-1, X.shape[1])
+            if isinstance(X, pd.DataFrame):
+                X_perm_batch = pd.DataFrame(
+                    X_perm_batch.reshape(-1, X.shape[1]), columns=X.columns
+                )
+            y_pred_perm = getattr(self.estimator, self.method)(X_perm_batch)
+
+            # In case of classification, the output is a 2D array. Reshape accordingly
+            if y_pred_perm.ndim == 1:
+                y_pred_perm = y_pred_perm.reshape(self.n_permutations, X.shape[0])
+            else:
+                y_pred_perm = y_pred_perm.reshape(
+                    self.n_permutations, X.shape[0], y_pred_perm.shape[1]
+                )
+            return y_pred_perm
+
+            # for _ in range(self.n_permutations):
+            #     X_j_perm = X_j_hat + self.rng.permutation(residual_j)
+            #     X_perm = np.empty_like(X)
+            #     X_perm[:, non_group_ids] = X_minus_j
+            #     X_perm[:, group_ids] = X_j_perm
+            #     if isinstance(X, pd.DataFrame):
+            #         X_perm = pd.DataFrame(X_perm, columns=X.columns)
+
+            #     y_pred_perm = getattr(self.estimator, self.method)(X_perm)
+            #     list_y_pred_perm.append(y_pred_perm)
+
+            # return np.array(list_y_pred_perm)
 
         # Parallelize the computation of the importance scores for each group
         out_list = Parallel(n_jobs=self.n_jobs)(