class TestUndirectedGraphTriangulation(unittest.TestCase):
def setUp(self):
self.graph = MarkovModel()
def test_check_clique(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'a')])
self.assertTrue(self.graph.check_clique(['a', 'b', 'c']))
def test_is_triangulated(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'a')])
self.assertTrue(self.graph.is_triangulated())
def test_triangulation_h1_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H1', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'c'], ['a', 'd'], ['b', 'c'], ['c', 'd']])
def test_triangulation_h2_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H2', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'c'], ['a', 'd'], ['b', 'c'], ['c', 'd']])
def test_triangulation_h3_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H3', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h4_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H4', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h5_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H4', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h6_inplace(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
self.graph.triangulate(heuristic='H4', inplace=True)
self.assertTrue(self.graph.is_triangulated())
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_cardinality_mismatch_raises_error(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
factor_list = [
DiscreteFactor(edge, [2, 2], np.random.rand(4))
for edge in self.graph.edges()
]
self.graph.add_factors(*factor_list)
self.graph.add_factors(
DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6)))
self.assertRaises(ValueError, self.graph.triangulate)
def test_triangulation_h1_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H1', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'c'], ['a', 'd'], ['b', 'c'], ['c', 'd']])
def test_triangulation_h2_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H2', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'c'], ['a', 'd'], ['b', 'c'], ['c', 'd']])
def test_triangulation_h3_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H3', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h4_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H4', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h5_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H5', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_triangulation_h6_create_new(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c'), ('c', 'd'),
('d', 'a')])
phi1 = DiscreteFactor(['a', 'b'], [2, 3], np.random.rand(6))
phi2 = DiscreteFactor(['b', 'c'], [3, 4], np.random.rand(12))
phi3 = DiscreteFactor(['c', 'd'], [4, 5], np.random.rand(20))
phi4 = DiscreteFactor(['d', 'a'], [5, 2], np.random.random(10))
self.graph.add_factors(phi1, phi2, phi3, phi4)
H = self.graph.triangulate(heuristic='H6', inplace=True)
self.assertListEqual(
hf.recursive_sorted(H.edges()),
[['a', 'b'], ['a', 'd'], ['b', 'c'], ['b', 'd'], ['c', 'd']])
def test_copy(self):
# Setup the original graph
self.graph.add_nodes_from(['a', 'b'])
self.graph.add_edges_from([('a', 'b')])
# Generate the copy
copy = self.graph.copy()
# Ensure the copied model is correct
self.assertTrue(copy.check_model())
# Basic sanity checks to ensure the graph was copied correctly
self.assertEqual(len(copy.nodes()), 2)
self.assertListEqual(copy.neighbors('a'), ['b'])
self.assertListEqual(copy.neighbors('b'), ['a'])
# Modify the original graph ...
self.graph.add_nodes_from(['c'])
self.graph.add_edges_from([('c', 'b')])
# ... and ensure none of those changes get propagated
self.assertEqual(len(copy.nodes()), 2)
self.assertListEqual(copy.neighbors('a'), ['b'])
self.assertListEqual(copy.neighbors('b'), ['a'])
with self.assertRaises(nx.NetworkXError):
copy.neighbors('c')
# Ensure the copy has no factors at this point
self.assertEqual(len(copy.get_factors()), 0)
# Add factors to the original graph
phi1 = DiscreteFactor(['a', 'b'], [2, 2], [[0.3, 0.7], [0.9, 0.1]])
self.graph.add_factors(phi1)
# The factors should not get copied over
with self.assertRaises(AssertionError):
self.assertListEqual(copy.get_factors(), self.graph.get_factors())
# Create a fresh copy
del copy
copy = self.graph.copy()
self.assertListEqual(copy.get_factors(), self.graph.get_factors())
# If we change factors in the original, it should not be passed to the clone
phi1.values = np.array([[0.5, 0.5], [0.5, 0.5]])
self.assertNotEqual(self.graph.get_factors(), copy.get_factors())
# Start with a fresh copy
del copy
self.graph.add_nodes_from(['d'])
copy = self.graph.copy()
# Ensure an unconnected node gets copied over as well
self.assertEqual(len(copy.nodes()), 4)
self.assertListEqual(self.graph.neighbors('a'), ['b'])
self.assertTrue('a' in self.graph.neighbors('b'))
self.assertTrue('c' in self.graph.neighbors('b'))
self.assertListEqual(self.graph.neighbors('c'), ['b'])
self.assertListEqual(self.graph.neighbors('d'), [])
# Verify that changing the copied model should not update the original
copy.add_nodes_from(['e'])
self.assertListEqual(copy.neighbors('e'), [])
with self.assertRaises(nx.NetworkXError):
self.graph.neighbors('e')
# Verify that changing edges in the copy doesn't create edges in the original
copy.add_edges_from([('d', 'b')])
self.assertTrue('a' in copy.neighbors('b'))
self.assertTrue('c' in copy.neighbors('b'))
self.assertTrue('d' in copy.neighbors('b'))
self.assertTrue('a' in self.graph.neighbors('b'))
self.assertTrue('c' in self.graph.neighbors('b'))
self.assertFalse('d' in self.graph.neighbors('b'))
# If we remove factors from the copied model, it should not reflect in the original
copy.remove_factors(phi1)
self.assertEqual(len(self.graph.get_factors()), 1)
self.assertEqual(len(copy.get_factors()), 0)
def tearDown(self):
del self.graph
class TestUndirectedGraphFactorOperations(unittest.TestCase):
def setUp(self):
self.graph = MarkovModel()
def test_add_factor_raises_error(self):
self.graph.add_edges_from([('Alice', 'Bob'), ('Bob', 'Charles'),
('Charles', 'Debbie'), ('Debbie', 'Alice')])
factor = DiscreteFactor(['Alice', 'Bob', 'John'], [2, 2, 2],
np.random.rand(8))
self.assertRaises(ValueError, self.graph.add_factors, factor)
def test_add_single_factor(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi = DiscreteFactor(['a', 'b'], [2, 2], range(4))
self.graph.add_factors(phi)
six.assertCountEqual(self, self.graph.factors, [phi])
def test_add_multiple_factors(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
self.graph.add_factors(phi1, phi2)
six.assertCountEqual(self, self.graph.factors, [phi1, phi2])
def test_get_factors(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
six.assertCountEqual(self, self.graph.get_factors(), [])
self.graph.add_factors(phi1, phi2)
six.assertCountEqual(self, self.graph.get_factors(), [phi1, phi2])
def test_remove_single_factor(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
self.graph.add_factors(phi1, phi2)
self.graph.remove_factors(phi1)
six.assertCountEqual(self, self.graph.factors, [phi2])
def test_remove_multiple_factors(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
self.graph.add_factors(phi1, phi2)
self.graph.remove_factors(phi1, phi2)
six.assertCountEqual(self, self.graph.factors, [])
def test_partition_function(self):
self.graph.add_nodes_from(['a', 'b', 'c'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
self.graph.add_factors(phi1, phi2)
self.graph.add_edges_from([('a', 'b'), ('b', 'c')])
self.assertEqual(self.graph.get_partition_function(), 22.0)
def test_partition_function_raises_error(self):
self.graph.add_nodes_from(['a', 'b', 'c', 'd'])
phi1 = DiscreteFactor(['a', 'b'], [2, 2], range(4))
phi2 = DiscreteFactor(['b', 'c'], [2, 2], range(4))
self.graph.add_factors(phi1, phi2)
self.assertRaises(ValueError, self.graph.get_partition_function)
def tearDown(self):
del self.graph