[Tests] Check if Gram matrices are semi-definite.

gklearn/tests/test_graph_kernels.py

@@ -102,6 +102,16 @@ def assert_equality(compute_fun, **kwargs):
 			assert np.array_equal(lst[i], lst[i + 1])
 
 
+def assert_semidefinite(gram_matrix):
+	"""Check if a matrix is positive semi-definite.
+	"""
+	eigvals = np.linalg.eigvals(gram_matrix)
+	assert np.all(eigvals >= 10e-9), "Gram matrix is not positive semi-definite."
+
+
+##############################################################################
+
+
 @pytest.mark.parametrize('ds_name', ['Alkane_unlabeled', 'AIDS'])
 @pytest.mark.parametrize('weight,compute_method', [(0.01, 'geo'), (1, 'exp')])
 # @pytest.mark.parametrize('parallel', ['imap_unordered', None])
@@ -143,6 +153,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -198,6 +210,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -249,6 +263,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -319,6 +335,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -388,6 +406,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -441,6 +461,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -558,6 +580,8 @@ def compute(parallel=None, fcsp=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -633,6 +657,8 @@ def compute(parallel=None, fcsp=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -691,6 +717,8 @@ def compute(parallel=None, compute_method=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -742,6 +770,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception
@@ -798,6 +828,8 @@ def compute(parallel=None):
 				verbose=True
 			)
 
+			assert_semidefinite(gram_matrix)
+
 		except Exception as exception:
 			print(repr(exception))
 			assert False, exception