Set diagonal of precomputed matrix to zero in silhoutte_samples (#12258)

Author: sjtrny

doc/whats_new/v0.22.rst

@@ -224,8 +224,15 @@ Changelog
   to return root mean squared error.
   :pr:`13467` by :user:`Urvang Patel <urvang96>`.
 
+:mod:`sklearn.metrics`
+......................
+
+- |Fix| Raise a ValueError in :func:`metrics.silhouette_score` when a
+  precomputed distance matrix contains non-zero diagonal entries.
+  :pr:`12258` by :user:`Stephen Tierney <sjtrny>`.
+
 :mod:`sklearn.model_selection`
-...............................
+..............................
 
 - |Enhancement| :class:`model_selection.learning_curve` now accepts parameter
   ``return_times`` which can be used to retrieve computation times in order to

sklearn/metrics/cluster/tests/test_unsupervised.py

@@ -168,6 +168,22 @@ def test_non_numpy_labels():
         silhouette_score(list(X), list(y)) == silhouette_score(X, y))
 
 
+def test_silhouette_nonzero_diag():
+    # Construct a zero-diagonal matrix
+    dists = pairwise_distances(
+        np.array([[0.2, 0.1, 0.12, 1.34, 1.11, 1.6]]).transpose())
+
+    # Construct a nonzero-diagonal distance matrix
+    diag_dists = dists.copy()
+    np.fill_diagonal(diag_dists, 1)
+
+    labels = [0, 0, 0, 1, 1, 1]
+
+    assert_raise_message(ValueError, "distance matrix contains non-zero",
+                         silhouette_samples,
+                         diag_dists, labels, metric='precomputed')
+
+
 def assert_raises_on_only_one_label(func):
     """Assert message when there is only one label"""
     rng = np.random.RandomState(seed=0)

sklearn/metrics/cluster/unsupervised.py

@@ -185,7 +185,8 @@ def silhouette_samples(X, labels, metric='euclidean', **kwds):
         The metric to use when calculating distance between instances in a
         feature array. If metric is a string, it must be one of the options
         allowed by :func:`sklearn.metrics.pairwise.pairwise_distances`. If X is
-        the distance array itself, use "precomputed" as the metric.
+        the distance array itself, use "precomputed" as the metric. Precomputed
+        distance matrices must have 0 along the diagonal.
 
     `**kwds` : optional keyword parameters
         Any further parameters are passed directly to the distance function.
@@ -210,6 +211,15 @@ def silhouette_samples(X, labels, metric='euclidean', **kwds):
 
     """
     X, labels = check_X_y(X, labels, accept_sparse=['csc', 'csr'])
+
+    # Check for diagonal entries in precomputed distance matrix
+    if metric == 'precomputed':
+        if np.any(np.diagonal(X)):
+            raise ValueError(
+                'The precomputed distance matrix contains non-zero '
+                'elements on the diagonal. Use np.fill_diagonal(X, 0).'
+            )
+
     le = LabelEncoder()
     labels = le.fit_transform(labels)
     n_samples = len(labels)