class TestMarkovModelCreation(unittest.TestCase):
def setUp(self):
self.graph = MarkovModel()
def test_class_init_without_data(self):
self.assertIsInstance(self.graph, MarkovModel)
def test_class_init_with_data_string(self):
self.g = MarkovModel([('a', 'b'), ('b', 'c')])
self.assertListEqual(sorted(self.g.nodes()), ['a', 'b', 'c'])
self.assertListEqual(hf.recursive_sorted(self.g.edges()),
[['a', 'b'], ['b', 'c']])
def test_class_init_with_data_nonstring(self):
self.g = MarkovModel([(1, 2), (2, 3)])
def test_add_node_string(self):
self.graph.add_node('a')
self.assertListEqual(self.graph.nodes(), ['a'])
def test_add_node_nonstring(self):
self.graph.add_node(1)
def test_add_nodes_from_string(self):
self.graph.add_nodes_from(['a', 'b', 'c', 'd'])
self.assertListEqual(sorted(self.graph.nodes()), ['a', 'b', 'c', 'd'])
def test_add_nodes_from_non_string(self):
self.graph.add_nodes_from([1, 2, 3, 4])
def test_add_edge_string(self):
self.graph.add_edge('d', 'e')
self.assertListEqual(sorted(self.graph.nodes()), ['d', 'e'])
self.assertListEqual(hf.recursive_sorted(self.graph.edges()),
[['d', 'e']])
self.graph.add_nodes_from(['a', 'b', 'c'])
self.graph.add_edge('a', 'b')
self.assertListEqual(hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['d', 'e']])
def test_add_edge_nonstring(self):
self.graph.add_edge(1, 2)
def test_add_edge_selfloop(self):
self.assertRaises(ValueError, self.graph.add_edge, 'a', 'a')
def test_add_edges_from_string(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c')])
self.assertListEqual(sorted(self.graph.nodes()), ['a', 'b', 'c'])
self.assertListEqual(hf.recursive_sorted(self.graph.edges()),
[['a', 'b'], ['b', 'c']])
self.graph.add_nodes_from(['d', 'e', 'f'])
self.graph.add_edges_from([('d', 'e'), ('e', 'f')])
self.assertListEqual(sorted(self.graph.nodes()),
['a', 'b', 'c', 'd', 'e', 'f'])
self.assertListEqual(
hf.recursive_sorted(self.graph.edges()),
hf.recursive_sorted([('a', 'b'), ('b', 'c'), ('d', 'e'),
('e', 'f')]))
def test_add_edges_from_nonstring(self):
self.graph.add_edges_from([(1, 2), (2, 3)])
def test_add_edges_from_self_loop(self):
self.assertRaises(ValueError, self.graph.add_edges_from, [('a', 'a')])
def test_number_of_neighbors(self):
self.graph.add_edges_from([('a', 'b'), ('b', 'c')])
self.assertEqual(len(self.graph.neighbors('b')), 2)
def tearDown(self):
del self.graph
class TestGibbsSampling(unittest.TestCase):
def setUp(self):
# A test Bayesian model
diff_cpd = TabularCPD('diff', 2, [[0.6], [0.4]])
intel_cpd = TabularCPD('intel', 2, [[0.7], [0.3]])
grade_cpd = TabularCPD('grade',
3,
[[0.3, 0.05, 0.9, 0.5], [0.4, 0.25, 0.08, 0.3],
[0.3, 0.7, 0.02, 0.2]],
evidence=['diff', 'intel'],
evidence_card=[2, 2])
self.bayesian_model = BayesianModel()
self.bayesian_model.add_nodes_from(['diff', 'intel', 'grade'])
self.bayesian_model.add_edges_from([('diff', 'grade'),
('intel', 'grade')])
self.bayesian_model.add_cpds(diff_cpd, intel_cpd, grade_cpd)
# A test Markov model
self.markov_model = MarkovModel([('A', 'B'), ('C', 'B'), ('B', 'D')])
factor_ab = DiscreteFactor(['A', 'B'], [2, 3], [1, 2, 3, 4, 5, 6])
factor_cb = DiscreteFactor(['C', 'B'], [4, 3],
[3, 1, 4, 5, 7, 8, 1, 3, 10, 4, 5, 6])
factor_bd = DiscreteFactor(['B', 'D'], [3, 2], [5, 7, 2, 1, 9, 3])
self.markov_model.add_factors(factor_ab, factor_cb, factor_bd)
self.gibbs = GibbsSampling(self.bayesian_model)
def tearDown(self):
del self.bayesian_model
del self.markov_model
@patch('pgm.sampling.GibbsSampling._get_kernel_from_bayesian_model',
autospec=True)
@patch('pgm.models.MarkovChain.__init__', autospec=True)
def test_init_bayesian_model(self, init, get_kernel):
model = MagicMock(spec_set=BayesianModel)
gibbs = GibbsSampling(model)
init.assert_called_once_with(gibbs)
get_kernel.assert_called_once_with(gibbs, model)
@patch('pgm.sampling.GibbsSampling._get_kernel_from_markov_model',
autospec=True)
def test_init_markov_model(self, get_kernel):
model = MagicMock(spec_set=MarkovModel)
gibbs = GibbsSampling(model)
get_kernel.assert_called_once_with(gibbs, model)
def test_get_kernel_from_bayesian_model(self):
gibbs = GibbsSampling()
gibbs._get_kernel_from_bayesian_model(self.bayesian_model)
self.assertListEqual(list(gibbs.variables),
self.bayesian_model.nodes())
self.assertDictEqual(gibbs.cardinalities, {
'diff': 2,
'intel': 2,
'grade': 3
})
def test_get_kernel_from_markov_model(self):
gibbs = GibbsSampling()
gibbs._get_kernel_from_markov_model(self.markov_model)
self.assertListEqual(list(gibbs.variables), self.markov_model.nodes())
self.assertDictEqual(gibbs.cardinalities, {
'A': 2,
'B': 3,
'C': 4,
'D': 2
})
def test_sample(self):
start_state = [State('diff', 0), State('intel', 0), State('grade', 0)]
sample = self.gibbs.sample(start_state, 2)
self.assertEquals(len(sample), 2)
self.assertEquals(len(sample.columns), 3)
self.assertIn('diff', sample.columns)
self.assertIn('intel', sample.columns)
self.assertIn('grade', sample.columns)
self.assertTrue(set(sample['diff']).issubset({0, 1}))
self.assertTrue(set(sample['intel']).issubset({0, 1}))
self.assertTrue(set(sample['grade']).issubset({0, 1, 2}))
@patch("pgm.sampling.GibbsSampling.random_state", autospec=True)
def test_sample_less_arg(self, random_state):
self.gibbs.state = None
random_state.return_value = [
State('diff', 0),
State('intel', 0),
State('grade', 0)
]
sample = self.gibbs.sample(size=2)
random_state.assert_called_once_with(self.gibbs)
self.assertEqual(len(sample), 2)
def test_generate_sample(self):
start_state = [State('diff', 0), State('intel', 0), State('grade', 0)]
gen = self.gibbs.generate_sample(start_state, 2)
samples = [sample for sample in gen]
self.assertEqual(len(samples), 2)
self.assertEqual(
{samples[0][0].var, samples[0][1].var, samples[0][2].var},
{'diff', 'intel', 'grade'})
self.assertEqual(
{samples[1][0].var, samples[1][1].var, samples[1][2].var},
{'diff', 'intel', 'grade'})
@patch("pgm.sampling.GibbsSampling.random_state", autospec=True)
def test_generate_sample_less_arg(self, random_state):
self.gibbs.state = None
gen = self.gibbs.generate_sample(size=2)
samples = [sample for sample in gen]
random_state.assert_called_once_with(self.gibbs)
self.assertEqual(len(samples), 2)