def compareRandom(num_trials, tensor_dimensions, matrix_data, cluster_dimensions,
maxit_ebc, jitter_max_ebc, objective_tolerance):
deltas = []
iterations_M = []
iterations_Mr = []
noconverge_M = 0
noconverge_Mr = 0
for j in range(num_trials):
print "Trial ", j
M = SparseMatrix(tensor_dimensions)
M.read_data(matrix_data)
Mr = M.shuffle() # could also be M.shuffle_old()
M.normalize()
ebc_M = EBC(M, cluster_dimensions, maxit_ebc, jitter_max_ebc, objective_tolerance)
cXY_M, objective_M, it_M = ebc_M.run()
if it_M == maxit_ebc:
noconverge_M += 1
else:
iterations_M.append(it_M)
Mr.normalize()
ebc_Mr = EBC(Mr, cluster_dimensions, maxit_ebc, jitter_max_ebc, objective_tolerance)
cXY_Mr, objective_Mr, it_Mr = ebc_Mr.run()
if it_Mr == maxit_ebc:
noconverge_Mr += 1
else:
iterations_Mr.append(it_Mr)
deltas.append(objective_M - objective_Mr)
return deltas, iterations_M, iterations_Mr, noconverge_M, noconverge_Mr
class TestMatrix(unittest.TestCase):
def setUp(self):
self.data = [l.split('\t') for l in open('tests/sample-matrix-file.txt', 'r').readlines()]
self.matrix = SparseMatrix([2, 4, 9])
self.matrix.read_data(self.data)
def testMatrixInit(self):
self.assertEquals(self.matrix.nonzero_elements[(1, 3, 7)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(0, 0, 0)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(0, 0, 2)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 1, 5)], 7.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 1, 3)], 3.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 3, 6)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 3, 8)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(0, 0, 1)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 1, 4)], 2.0)
self.assertEquals(self.matrix.nonzero_elements[(1, 2, 5)], 2.0)
self.assertEquals(len(self.matrix.nonzero_elements), 10)
self.assertEquals(self.matrix.feature_ids[0], {'mice': 1, 'patient': 0})
self.assertEquals(self.matrix.feature_ids[1], {'R92Q': 1, 'R91W': 2, 'Val30Met': 0, 'R90W': 3})
self.assertEquals(self.matrix.feature_ids[2], {'START_ENTITY|nmod|END_ENTITY': 1,
'START_ENTITY|nummod|END_ENTITY': 5,
'FAP|compound|END_ENTITY': 2,
'expression|nmod|END_ENTITY': 8,
'+|compound|END_ENTITY': 7,
'mice|nummod|END_ENTITY': 3,
'homozygous|nsubj|START_ENTITY': 6,
'mutation|appos|END_ENTITY': 4,
'START_ENTITY|nmod|FAP': 0})
def testShuffle(self):
shuffled_matrix = self.matrix.shuffle()
self.assertEquals(len(shuffled_matrix.nonzero_elements), len(self.matrix.nonzero_elements))
self.assertEquals(set(shuffled_matrix.nonzero_elements.values()), set(self.matrix.nonzero_elements.values()))
print("shuffled matrix elements: ", shuffled_matrix.nonzero_elements)
