Fixes bug in greedy selector when scores are degenerate (#265)

* Fix general bug in GreedySelector that would pick the same point if there are degeneracies
* Write failing tests for when there are non-unique selections for zero score
* Only select idxs that have been previously selected
* CUR feature selection test

---------

Co-authored-by: Joseph Abbott <[email protected]>

Author: ceriottm

src/skmatter/_selection.py

@@ -228,8 +228,6 @@ def fit(self, X, y=None, warm_start=False):
         n_to_select_from = X.shape[self._axis]
         self.n_samples_in_, self.n_features_in_ = X.shape
 
-        self.n_samples_in_, self.n_features_in_ = X.shape
-
         error_msg = (
             "n_to_select must be either None, an "
             f"integer in [1, n_{self.selection_type}s] "
@@ -428,6 +426,8 @@ def _continue_greedy_search(self, X, y, n_to_select):
     def _get_best_new_selection(self, scorer, X, y):
         scores = scorer(X, y)
 
+        # Get the score argmax, but only for idxs not already selected
+        scores[self.selected_idx_[: self.n_selected_]] = -np.inf
         max_score_idx = np.argmax(scores)
         if self.score_threshold is not None:
             if self.first_score_ is None:

tests/test_feature_pcov_cur.py

@@ -33,7 +33,6 @@ def test_non_it(self):
         self.idx = [2, 8, 3, 6, 7, 9, 1, 0, 5]
         selector = PCovCUR(n_to_select=9, recompute_every=0)
         selector.fit(self.X, self.y)
-
         self.assertTrue(np.allclose(selector.selected_idx_, self.idx))
 
 

tests/test_feature_simple_cur.py

@@ -41,6 +41,22 @@ def test_non_it(self):
 
         self.assertTrue(np.allclose(selector.selected_idx_, ref_idx))
 
+    def test_unique_selected_idx_zero_score(self):
+        """
+        Tests that the selected idxs are unique, which may not be the
+        case when the score is numerically zero
+        """
+        np.random.seed(0)
+        n_samples = 10
+        n_features = 15
+        X = np.random.rand(n_samples, n_features)
+        X[:, 1] = X[:, 0]
+        X[:, 2] = X[:, 0]
+        selector_problem = CUR(n_to_select=len(X.T)).fit(X)
+        assert len(selector_problem.selected_idx_) == len(
+            set(selector_problem.selected_idx_)
+        )
+
 
 if __name__ == "__main__":
     unittest.main(verbosity=2)

tests/test_feature_simple_fps.py

@@ -84,6 +84,22 @@ def test_get_distances(self):
             selector = FPS(n_to_select=7)
             _ = selector.get_select_distance()
 
+    def test_unique_selected_idx_zero_score(self):
+        """
+        Tests that the selected idxs are unique, which may not be the
+        case when the score is numerically zero
+        """
+        np.random.seed(0)
+        n_samples = 10
+        n_features = 15
+        X = np.random.rand(n_samples, n_features)
+        X[:, 1] = X[:, 0]
+        X[:, 2] = X[:, 0]
+        selector_problem = FPS(n_to_select=len(X.T)).fit(X)
+        assert len(selector_problem.selected_idx_) == len(
+            set(selector_problem.selected_idx_)
+        )
+
 
 if __name__ == "__main__":
     unittest.main(verbosity=2)

tests/test_sample_simple_cur.py

@@ -52,6 +52,23 @@ def test_non_it(self):
 
         self.assertTrue(np.allclose(selector.selected_idx_, ref_idx))
 
+    def test_unique_selected_idx_zero_score(self):
+        """
+        Tests that the selected idxs are unique, which may not be the
+        case when the score is numerically zero.
+        """
+        np.random.seed(0)
+        n_samples = 10
+        n_features = 15
+        X = np.random.rand(n_samples, n_features)
+        X[1] = X[0]
+        X[2] = X[0]
+        X[3] = X[0]
+        selector_problem = CUR(n_to_select=len(X)).fit(X)
+        assert len(selector_problem.selected_idx_) == len(
+            set(selector_problem.selected_idx_)
+        )
+
 
 if __name__ == "__main__":
     unittest.main(verbosity=2)

tests/test_sample_simple_fps.py

@@ -99,6 +99,23 @@ def test_threshold(self):
         self.assertEqual(len(selector.selected_idx_), 5)
         self.assertEqual(selector.selected_idx_.tolist(), self.idx[:5])
 
+    def test_unique_selected_idx_zero_score(self):
+        """
+        Tests that the selected idxs are unique, which may not be the
+        case when the score is numerically zero.
+        """
+        np.random.seed(0)
+        n_samples = 10
+        n_features = 15
+        X = np.random.rand(n_samples, n_features)
+        X[1] = X[0]
+        X[2] = X[0]
+        X[3] = X[0]
+        selector_problem = FPS(n_to_select=len(X)).fit(X)
+        assert len(selector_problem.selected_idx_) == len(
+            set(selector_problem.selected_idx_)
+        )
+
 
 if __name__ == "__main__":
     unittest.main(verbosity=2)

tests/test_voronoi_fps.py

@@ -165,6 +165,22 @@ def test_score(self):
             )
         )
 
+    def test_unique_selected_idx_zero_score(self):
+        """
+        Tests that the selected idxs are unique, which may not be the
+        case when the score is numerically zero
+        """
+        np.random.seed(0)
+        n_samples = 10
+        n_features = 15
+        X = np.random.rand(n_samples, n_features)
+        X[1] = X[0]
+        X[2] = X[0]
+        selector_problem = VoronoiFPS(n_to_select=n_samples, initialize=3).fit(X)
+        assert len(selector_problem.selected_idx_) == len(
+            set(selector_problem.selected_idx_)
+        )
+
 
 if __name__ == "__main__":
     unittest.main(verbosity=2)