def test_calc_mutual_info(self):
all_entrezs = np.array([1,2,3,4])
labels = np.array([1,1,1,0,0,0])
expr_data = np.array([[1,1,1,0,0,0],
[1,1,1,0,0,0],
[0,0,1,1,0,1],
[0,1,0,0,1,0]])
expression = Expression(expr_data, all_entrezs, labels, binarize=False)
state = State([1,2], [1,0], expression)
self.assertEqual(state.calc_mutual_info(), 1.0)
class TestState(unittest.TestCase):
def setUp(self):
all_entrezs = np.array([1,2,3,4])
self.labels = np.array([1,1,1,0,0,0])
self.expr_data = np.array([[1,0,1,1,0,1],
[0,1,0,1,0,1],
[0,1,1,1,0,0],
[0,0,0,0,1,1]])
self.expression = Expression(self.expr_data, all_entrezs, self.labels, binarize=False)
self.entrezs = [1,2]
self.expr_ptn = [1,0]
self.state = State(self.entrezs, self.expr_ptn, self.expression)
def tearDown(self):
pass
def test_iter_gene(self):
genes = list(self.state.iter_gene())
np.testing.assert_array_equal(genes, self.entrezs)
def test_calc_info(self):
self.assertAlmostEqual(self.state.calc_info(), 1. / 3 * np.log(2))
def test_calc_info_omit(self):
self.assertEqual(self.state.calc_info_omit(2), 0)
self.assertAlmostEqual(self.state.calc_info_omit(1),
3. / 6 * (2. / 3 * np.log(2. / 3 * 2) + 1. / 3 * np.log(2. / 3)))
self.assertGreater(self.state.calc_info(), self.state.calc_info_omit(1))
self.assertGreater(self.state.calc_info(), self.state.calc_info_omit(2))
self.assertEqual(self.state.calc_info_omit(self.entrezs[1]),
State([self.entrezs[0]], [self.expr_ptn[0]], self.expression).calc_info())
self.assertEqual(self.state.calc_info_omit(self.entrezs[0]),
State([self.entrezs[1]], [self.expr_ptn[1]], self.expression).calc_info())
def test_calc_info_bound(self):
self.assertAlmostEqual(self.state.calc_info_bound(), 1. / 3 * np.log(2))
def test_len(self):
self.assertEqual(len(self.state), len(self.entrezs))
def test_calc_mutual_info(self):
all_entrezs = np.array([1,2,3,4])
labels = np.array([1,1,1,0,0,0])
expr_data = np.array([[1,1,1,0,0,0],
[1,1,1,0,0,0],
[0,0,1,1,0,1],
[0,1,0,0,1,0]])
expression = Expression(expr_data, all_entrezs, labels, binarize=False)
state = State([1,2], [1,0], expression)
self.assertEqual(state.calc_mutual_info(), 1.0)
def setUp(self):
all_entrezs = np.array([1,2,3,4])
self.labels = np.array([1,1,1,0,0,0])
self.expr_data = np.array([[1,0,1,1,0,1],
[0,1,0,1,0,1],
[0,1,1,1,0,0],
[0,0,0,0,1,1]])
self.expression = Expression(self.expr_data, all_entrezs, self.labels, binarize=False)
self.entrezs = [1,2]
self.expr_ptn = [1,0]
self.state = State(self.entrezs, self.expr_ptn, self.expression)
