def test_pairwise_mahalanobis_distances(self):
""" pairwise_mahalanobis_distances is a Sparsifier function, but a use
case here made me suspect that it's wrong. To confirm this I'm putting
a test here first. Will need to make a new one (and probably ammend
existing ones that are currently passing but shouldn't be) in that
test suite once I am convinced it's the culprit. """
cov_type = 'spherical'
rs = np.random.RandomState(10)
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=2,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
random_state=rs)
gmm.fit_sparsifier(X=self.td.X)
means = rs.rand(gmm.n_components, gmm.num_feat_full)
covariances = rs.rand(gmm.n_components)
mahadist_test = gmm.pairwise_mahalanobis_distances(
means, covariances, cov_type)**2
#undo the rescaling due to compression
mahadist_test *= gmm.num_feat_comp / gmm.num_feat_full
mahadist_true = np.zeros_like(mahadist_test)
for data_ind in range(gmm.num_samp):
for comp_ind in range(gmm.n_components):
mahadist_true[data_ind, comp_ind] = 1/covariances[comp_ind] * \
np.linalg.norm(gmm.RHDX[data_ind] -
means[comp_ind][gmm.mask[data_ind]])**2
self.assertArrayEqual(mahadist_test, mahadist_true)
def test__estimate_gaussian_means_and_covariances_diagonal_no_compression(
self):
""" Test _estimate_gaussian_means_and_covariances against hard-coded
example. Should be redundant with test__estimate_gaussian_parameters_*
tests above, which test against sklearn's results. """
X = np.array([[0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 1, 2]],
dtype=np.float64)
gmm = GaussianMixture(n_components=2,
num_feat_full=4,
num_feat_comp=4,
num_feat_shared=4,
num_samp=3,
transform=None,
D_indices=None,
mask=None,
reg_covar=0)
gmm.fit_sparsifier(X=X)
# note: columns should sum to 1, but don't have to because the weighted
# means computation has to renormalize anyway to account for the mask
resp = np.array([[.6, .3], [.4, .2], [0, .5]], dtype=np.float64)
means, covariances = gmm._estimate_gaussian_means_and_covariances(
resp, 'diag')
correct_means = np.array([[.4, .6, .0, .0], [.2, .3, .5, 1.]],
dtype=np.float64)
correct_covariances = np.array([[.24, .24, 0, 0], [.16, .21, .25, 1]],
dtype=np.float64)
self.assertArrayEqual(correct_means, means)
self.assertArrayEqual(correct_covariances, covariances)
def test__compute_log_prob_spherical_shared_compression(self):
""" Compare the log_prob computation to that of sklearn with
shared compression. Spherical covariances. """
cov_type = 'spherical'
rs = np.random.RandomState(10)
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=3,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
random_state=rs)
gmm.fit_sparsifier(X=self.td.X)
means = rs.rand(gmm.n_components, gmm.num_feat_full)
covariances = rs.rand(gmm.n_components)
log_prob_test = gmm._compute_log_prob(means, covariances, cov_type)
log_prob_true = np.zeros((gmm.num_samp, gmm.n_components))
for data_ind in range(gmm.num_samp):
for comp_ind in range(gmm.n_components):
true_const = gmm.num_feat_comp * np.log(2 * np.pi)
true_logdet = gmm.num_feat_comp * np.log(covariances[comp_ind])
true_mahadist = 1/covariances[comp_ind] * \
np.linalg.norm(gmm.RHDX[data_ind] -
means[comp_ind][gmm.mask[data_ind]])**2
log_prob_true[data_ind, comp_ind] = -.5*(true_const + \
true_logdet + true_mahadist)
self.assertArrayEqual(log_prob_test, log_prob_true)
def test__estimate_gaussian_parameters_diagonal_no_compression(self):
""" Test _estiamte_gaussian_parameters against sklearn's
implementation. Diagonal covariances, no compression.
"""
cov_type = 'diag'
reg_covar = 1e-6
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=5,
num_feat_shared=5,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
reg_covar=reg_covar)
gmm.fit_sparsifier(X=self.td.X)
resp = np.random.rand(gmm.num_samp, gmm.n_components)
weights_test, means_test, covariances_test = gmm._estimate_gaussian_parameters(
resp, cov_type)
# skl
counts_true, means_true, covariances_true = _estimate_gaussian_parameters(
self.td.X, resp, reg_covar, cov_type)
# skl returns counts instead of weights.
weights_true = counts_true / gmm.num_samp
self.assertArrayEqual(weights_test, weights_true)
self.assertArrayEqual(means_test, means_true)
self.assertArrayEqual(covariances_test, covariances_true)
def test__init_resp_from_means(self):
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=1,
num_samp=4,
transform='dct',
D_indices=self.td.D_indices,
mask=self.td.mask)
gmm.fit_sparsifier(X=self.td.X)
resp_test = gmm._init_resp_from_means(self.td.U)
resp_correct = np.array([[0, 1, 0], [1, 0, 0], [0, 1, 0], [0, 1, 0]],
dtype=int)
def test_fit_sparsifier(self):
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=1,
num_samp=4,
transform='dct',
D_indices=self.td.D_indices,
mask=self.td.mask)
gmm.fit_sparsifier(X=self.td.X)
self.assertArrayEqual(self.td.RHDX, gmm.RHDX)
self.assertArrayEqual(self.td.mask, gmm.mask)
self.assertEqual(self.td.N, gmm.num_samp)
self.assertEqual(self.td.Q, gmm.num_feat_comp)
self.assertEqual(self.td.P, gmm.num_feat_full)
def test__compute_logdet_array(self):
""" Test spherical and diagonal on hard-coded results. """
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=1,
num_samp=4,
transform='dct',
D_indices=self.td.D_indices,
mask=self.td.mask)
logdet_spherical = gmm._compute_logdet_array(
self.td.spherical_covariances, 'spherical')
logdet_diag = gmm._compute_logdet_array(self.td.diagonal_covariances,
'diag')
self.assertArrayEqual(self.td.correct_logdet_spherical,
logdet_spherical)
self.assertArrayEqual(self.td.correct_logdet_diag, logdet_diag)
def test__initialize_weights_case3(self):
""" multi-init
"""
random_state = np.random.RandomState(12)
n_init = 3
means_init_true = random_state.rand(n_init, self.td.K, self.td.P)
weights_init_true = random_state.rand(n_init, self.td.K)
weights_init_true /= weights_init_true.sum(axis=1)[:, np.newaxis]
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
weights_init=weights_init_true,
n_init=n_init,
covariance_type='diag',
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
# init means twice to cycle covariances
_ = gmm._initialize_means()
means_init = gmm._initialize_means()
weights_init_test = gmm._initialize_weights(means_init)
self.assertArrayEqual(weights_init_test, weights_init_true[1])
def test__initialize_covariances_case4(self):
""" diagonal covariance, multi-init.
"""
random_state = np.random.RandomState(12)
n_init = 3
means_init_true = random_state.rand(n_init, self.td.K, self.td.P)
covariances_init_true = random_state.rand(n_init, self.td.K, self.td.P)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
covariances_init=covariances_init_true,
covariance_type='diag',
n_init=n_init,
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
# init means twice to cycle covariances
_ = gmm._initialize_means()
means_init = gmm._initialize_means()
covariances_init_test = gmm._initialize_covariances(means_init)
self.assertArrayEqual(covariances_init_test, covariances_init_true[1])
def test__initialize_means_case1(self):
""" means_init is a 2D array.
"""
random_state = np.random.RandomState(12)
means_init_true = random_state.rand(self.td.K, self.td.P)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
means_init_test = gmm._initialize_means()
self.assertArrayEqual(means_init_test, means_init_true)
def test_hand_computation_of_log_prob_vs_sklearn(self):
""" Something seems wrong with my mahadist computation. Before digging
further into the C library to find the error, I want to make sure that
the results I think it should give are right. One way to gather
evidence in favor of this conclusion is to use the result in the
computation of the log probability (this is what led me here in the
first place). This test does so, and consequently doesn't actually
test any of the code in gmm.py. For this to work the mask must be
entirely shared. """
cov_type = 'spherical'
rs = np.random.RandomState(10)
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=3,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
random_state=rs)
gmm.fit_sparsifier(X=self.td.X)
means = rs.rand(gmm.n_components, gmm.num_feat_full)
covariances = rs.rand(gmm.n_components)
precisions = _compute_precision_cholesky(covariances, cov_type)
# this is where we need the mask to be shared, so that all mask rows
# equal mask[0]
masked_means = means[:, gmm.mask[0]]
log_prob_true = _estimate_log_gaussian_prob(gmm.RHDX, masked_means,
precisions, cov_type)
log_prob_test = np.zeros((gmm.num_samp, gmm.n_components))
for data_ind in range(gmm.num_samp):
for comp_ind in range(gmm.n_components):
test_const = gmm.num_feat_comp * np.log(2 * np.pi)
test_logdet = gmm.num_feat_comp * np.log(covariances[comp_ind])
test_mahadist = 1/covariances[comp_ind] * \
np.linalg.norm(gmm.RHDX[data_ind] -
means[comp_ind][gmm.mask[data_ind]])**2
log_prob_test[data_ind, comp_ind] = -.5*(test_const + \
test_logdet + test_mahadist)
self.assertArrayEqual(log_prob_test, log_prob_true)
def test__initialize_means_case4(self):
""" means_init is None, init_params is 'random'.
Only checks that the initialized means are of the correct shape.
"""
random_state = np.random.RandomState(12)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=None,
init_params='random',
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
means_init_shape_test = gmm._initialize_means().shape
means_init_shape_true = np.array([self.td.K, self.td.P])
self.assertArrayEqual(means_init_shape_test, means_init_shape_true)
def instantiate_standard_gmm(self, random_state):
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
random_state=random_state)
return gmm
def test__estimate_log_prob_resp_spherical_shared_compression(self):
rs = np.random.RandomState(11)
cov_type = 'spherical'
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=3,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
random_state=rs)
gmm.fit_sparsifier(X=self.td.X)
means = rs.rand(gmm.n_components, gmm.num_feat_full)
covariances = rs.rand(gmm.n_components)
weights = rs.rand(gmm.n_components)
weights /= weights.sum()
log_prob_test, log_resp_test, log_prob_norm_test = gmm._estimate_log_prob_resp(
weights, means, covariances, cov_type)
# find skl's values, pretty ugly to do.
precisions = _compute_precision_cholesky(covariances, cov_type)
gmm_skl = GMSKL(n_components=3, covariance_type=cov_type)
# we need the mask to be shared so that we can use mask[0] on all means
gmm_skl.means_ = means[:, gmm.mask[0]]
gmm_skl.precisions_cholesky_ = precisions
gmm_skl.weights_ = weights
gmm_skl.covariance_type_ = cov_type
log_prob_norm_true, log_resp_true = gmm_skl._estimate_log_prob_resp(
gmm.RHDX)
# if anything is bad later this overwrite with mean seems suspect:
log_prob_norm_true = log_prob_norm_true.mean()
# now get the log_prob from another function
log_prob_true = _estimate_log_gaussian_prob(gmm.RHDX, gmm_skl.means_,
precisions, cov_type)
# run the tests
self.assertArrayEqual(log_prob_test, log_prob_true)
self.assertArrayEqual(log_prob_norm_true, log_prob_norm_test)
self.assertArrayEqual(log_resp_true, log_resp_test)
def test__compute_log_prob_diagonal_no_compression(self):
""" Compare the log_prob computation to that of sklearn with no
compression. Implemented as a precursor to testing it with
compression, to follow. Diagonal covariances. """
cov_type = 'diag'
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=5,
num_feat_shared=5,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type)
gmm.fit_sparsifier(X=self.td.X)
means = np.random.rand(gmm.n_components, gmm.num_feat_comp)
covariances = np.random.rand(gmm.n_components, gmm.num_feat_comp)
log_prob_test = gmm._compute_log_prob(means, covariances, cov_type)
precisions = _compute_precision_cholesky(covariances, cov_type)
log_prob_true = _estimate_log_gaussian_prob(self.td.X, means,
precisions, cov_type)
self.assertArrayEqual(log_prob_test, log_prob_true)
def test__estimate_log_prob_resp_diagonal_no_compression(self):
cov_type = 'diag'
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=5,
num_feat_shared=5,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type)
gmm.fit_sparsifier(X=self.td.X)
means = np.random.rand(gmm.n_components, gmm.num_feat_comp)
covariances = np.random.rand(gmm.n_components, gmm.num_feat_comp)
weights = np.random.rand(gmm.n_components)
weights /= weights.sum()
log_prob_test, log_resp_test, log_prob_norm_test = gmm._estimate_log_prob_resp(
weights, means, covariances, cov_type)
# find skl's values, pretty ugly to do.
precisions = _compute_precision_cholesky(covariances, cov_type)
gmm_skl = GMSKL(n_components=3, covariance_type=cov_type)
gmm_skl.means_ = means
gmm_skl.precisions_cholesky_ = precisions
gmm_skl.weights_ = weights
gmm_skl.covariance_type_ = cov_type
log_prob_norm_true, log_resp_true = gmm_skl._estimate_log_prob_resp(
self.td.X)
# if anything is bad later this overwrite with mean seems suspect:
log_prob_norm_true = log_prob_norm_true.mean()
# now get the log_prob from another function
log_prob_true = _estimate_log_gaussian_prob(self.td.X, means,
precisions, cov_type)
# run the tests
self.assertArrayEqual(log_prob_test, log_prob_true)
self.assertArrayEqual(log_prob_norm_true, log_prob_norm_test)
self.assertArrayEqual(log_resp_true, log_resp_test)
def test__compute_logdet_array_spherical(self):
""" Test spherical logdet under compression on an example
computed here. Redundant with test__compute_logdet_array below but was
implemented to confirm that test is correct. """
cov_type = 'spherical'
rs = np.random.RandomState(10)
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=2,
num_samp=4,
transform=None,
mask=None,
D_indices=None,
covariance_type=cov_type,
random_state=rs)
gmm.fit_sparsifier(X=self.td.X)
means = rs.rand(gmm.n_components, gmm.num_feat_full)
covariances = rs.rand(gmm.n_components)
logdet_test = gmm._compute_logdet_array(covariances, 'spherical')
logdet_true = gmm.num_feat_comp * np.log(covariances)
logdet_true = np.tile(logdet_true, (gmm.num_samp, 1))
self.assertArrayEqual(logdet_test, logdet_true)
def test_fit(self):
""" Catches a case where covariance goes to 0."""
reg_covar = 1e-6
np.random.seed(0)
X = np.array([[0, 1, 0, 0], [1, 0, 0, 0], [0, 0, 1, 2]],
dtype=np.float64)
gmm = GaussianMixture(n_components=2,
covariance_type='diag',
num_feat_full=4,
num_feat_comp=2,
num_feat_shared=1,
num_samp=3,
transform=None,
D_indices=None,
mask=None,
reg_covar=reg_covar,
init_params='random',
max_iter=5)
gmm.fit(X=X)
correct_means = np.array([[0, 0, 1, 0], [1, 0, 0, 0]],
dtype=np.float64)
correct_covariances = np.ones_like(correct_means) * reg_covar
self.assertArrayEqual(gmm.means_, correct_means)
self.assertArrayEqual(gmm.covariances_, correct_covariances)
def test__initialize_parameters(self):
""" Only tests if it runs. """
init_params = 'random'
means_init = None
gmm = GaussianMixture(n_components=3,
num_feat_full=5,
num_feat_comp=3,
num_feat_shared=1,
num_samp=4,
transform='dct',
D_indices=self.td.D_indices,
mask=self.td.mask,
init_params=init_params,
means_init=means_init)
gmm.fit_sparsifier(HDX=self.td.HDX)
gmm._initialize_parameters()
def test__initialize_covariances_case1(self):
""" spherical covariance, 1 init.
"""
random_state = np.random.RandomState(12)
means_init_true = random_state.rand(self.td.K, self.td.P)
covariances_init_true = random_state.rand(self.td.K)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
covariances_init=covariances_init_true,
covariance_type='spherical',
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
means_init = gmm._initialize_means()
covariances_init_test = gmm._initialize_covariances(means_init)
self.assertArrayEqual(covariances_init_test, covariances_init_true)
def test__initialize_covariances_case3(self):
""" No covariances given, just check shape.
"""
random_state = np.random.RandomState(12)
means_init_true = random_state.rand(self.td.K, self.td.P)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
covariances_init=None,
covariance_type='diag',
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
means_init = gmm._initialize_means()
covariances_init_test = gmm._initialize_covariances(means_init)
true_shape = np.array((self.td.K, self.td.P))
self.assertArrayEqual(covariances_init_test.shape, true_shape)
def test__initialize_means_case2(self):
""" means_init is a 3D array.
"""
random_state = np.random.RandomState(12)
n_init = 3
means_init_true = random_state.rand(n_init, self.td.K, self.td.P)
gmm = GaussianMixture(n_components=self.td.K,
num_feat_full=self.td.P,
num_feat_comp=self.td.Q,
num_feat_shared=self.td.Qs,
num_samp=self.td.N,
transform=self.td.transform,
D_indices=self.td.D_indices,
mask=self.td.mask,
means_init=means_init_true,
n_init=n_init,
random_state=random_state)
gmm.fit_sparsifier(X=self.td.X)
# first one is discarded for this test
_ = gmm._initialize_means()
# this should recover the second one
means_init_test = gmm._initialize_means()
self.assertArrayEqual(means_init_test, means_init_true[1])