Merge pull request #50 from microsoft/din-dout-fix

Use degree in and degree out instead of just degree out for Laplacian…

docs/release_notes.md

@@ -1,4 +1,6 @@
 # Release Notes
+## 0.1.4
+- Fixed a bug during Laplacian matrix construction for directed graphs
 ## 0.1.3
 - Added `modularity` and `modularity_components` functions, and deprecated `q_score`.
 ## 0.1.2

tests/embedding/test_laplacian_spectral_embedding.py

@@ -15,11 +15,13 @@
 class TestLaplacianSpectralEmbedding(unittest.TestCase):
     def test_laplacian_embedding(self):
         graph = nx.Graph([('a', 'b', {'weight': 1.0}), ('b', 'c', {'weight': 2.0})])
+
         result = laplacian_embedding(
             graph,
             elbow_cut=1,
             svd_seed=1234
         )
+
         self.assertIsNotNone(result)
         (matrix, labels) = result
         self.assertIsInstance(matrix, np.ndarray)
@@ -32,6 +34,27 @@ def test_laplacian_embedding(self):
         np.testing.assert_allclose(expected_matrix, matrix, rtol=1e-5)
         self.assertListEqual(expected_label, labels)
 
+    def test_laplacian_embedding_digraph(self):
+        graph = nx.DiGraph([('a', 'b', {'weight': 1.0}), ('b', 'c', {'weight': 2.0})])
+
+        result = laplacian_embedding(
+            graph,
+            elbow_cut=1,
+            svd_seed=1234
+        )
+
+        self.assertIsNotNone(result)
+        (matrix, labels) = result
+        self.assertIsInstance(matrix, np.ndarray)
+        self.assertIsInstance(labels, list)
+        self.assertEqual(2, matrix.ndim)
+        expected_matrix = np.array([[0.527046, 0.235702],
+                                    [0.781736, 0.62361 ],
+                                    [0.333333, 0.745356]])
+        expected_label = ['a', 'b', 'c']
+        np.testing.assert_allclose(expected_matrix, matrix, rtol=1e-5)
+        self.assertListEqual(expected_label, labels)
+
     @unittest.skipIf(
         sys.platform.startswith('darwin') and os.getenv("SKIP_TEST_35", "false") == "true",
         "Test not supported on MacOS Github Actions, see: https://github.com/microsoft/topologic/issues/35"

topologic/embedding/laplacian_spectral_embedding.py

@@ -72,10 +72,16 @@ def laplacian_embedding(
     minimum_matrix_dimension = min(graph_matrix.shape)
 
     # make Laplacian matrix (DAD)
-    degree = graph_matrix.sum(axis=1).T.astype(float)
-    degree_array = np.squeeze(np.asarray(degree))
-    diagonal = sp.sparse.diags(degree_array ** (-0.5))
-    lse_matrix = diagonal.dot(graph_matrix).dot(diagonal)
+    in_degree = graph_matrix.sum(axis=0).astype(float)
+    out_degree = graph_matrix.sum(axis=1).T.astype(float)
+
+    in_degree_array = np.squeeze(np.asarray(in_degree))
+    out_degree_array = np.squeeze(np.asarray(out_degree))
+
+    in_diagonal = sp.sparse.diags(in_degree_array ** (-0.5))
+    out_diagonal = sp.sparse.diags(out_degree_array ** (-0.5))
+
+    lse_matrix = out_diagonal.dot(graph_matrix).dot(in_diagonal)
 
     embedding = _generate_embedding(
         elbow_cut,

topologic/embedding/omnibus_embedding.py

@@ -207,11 +207,16 @@ def _get_laplacian_matrices(graphs):
 
 
 def _get_lse_matrix(adjacency_matrix: np.ndarray):
-    degree = adjacency_matrix.sum(axis=1).T.astype(float)
-    degree_array = np.squeeze(np.asarray(degree))
-    diagonal = sp.sparse.diags(degree_array ** -.5)
+    in_degree = adjacency_matrix.sum(axis=0).astype(float)
+    out_degree = adjacency_matrix.sum(axis=1).T.astype(float)
 
-    lse_matrix = diagonal.dot(adjacency_matrix).dot(diagonal)
+    in_degree_array = np.squeeze(np.asarray(in_degree))
+    out_degree_array = np.squeeze(np.asarray(out_degree))
+
+    in_diagonal = sp.sparse.diags(in_degree_array ** (-0.5))
+    out_diagonal = sp.sparse.diags(out_degree_array ** (-0.5))
+
+    lse_matrix = out_diagonal.dot(adjacency_matrix).dot(in_diagonal)
 
     return lse_matrix
 

topologic/version/version.py

@@ -10,7 +10,7 @@
 name = "topologic"
 
 # manually updated
-__semver = "0.1.3"
+__semver = "0.1.4"
 #  full version (may be same as __semver on release)
 __version_file = "version.txt"
 

topologic/version/version.txt

@@ -0,0 +1 @@
+