def test_score():
covar_type = 'full'
rng = np.random.RandomState(0)
rand_data = RandomData(rng, scale=7)
n_components = rand_data.n_components
X = rand_data.X[covar_type]
# Check the error message if we don't call fit
gmm1 = GaussianMixture(n_components=n_components,
n_init=1,
max_iter=1,
reg_covar=0,
random_state=rng,
covariance_type=covar_type)
assert_raise_message(
NotFittedError, "This GaussianMixture instance is not fitted "
"yet. Call 'fit' with appropriate arguments "
"before using this method.", gmm1.score, X)
# Check score value
with warnings.catch_warnings():
warnings.simplefilter("ignore", ConvergenceWarning)
gmm1.fit(X)
gmm_score = gmm1.score(X)
gmm_score_proba = gmm1.score_samples(X).mean()
assert_almost_equal(gmm_score, gmm_score_proba)
# Check if the score increase
gmm2 = GaussianMixture(n_components=n_components,
n_init=1,
reg_covar=0,
random_state=rng,
covariance_type=covar_type).fit(X)
assert_greater(gmm2.score(X), gmm1.score(X))
def test_score():
covar_type = 'full'
rng = np.random.RandomState(0)
rand_data = RandomData(rng, scale=7)
n_components = rand_data.n_components
X = rand_data.X[covar_type]
# Check the error message if we don't call fit
gmm1 = GaussianMixture(n_components=n_components, n_init=1,
max_iter=1, reg_covar=0, random_state=rng,
covariance_type=covar_type)
assert_raise_message(NotFittedError,
"This GaussianMixture instance is not fitted "
"yet. Call 'fit' with appropriate arguments "
"before using this method.", gmm1.score, X)
# Check score value
with warnings.catch_warnings():
warnings.simplefilter("ignore", ConvergenceWarning)
gmm1.fit(X)
gmm_score = gmm1.score(X)
gmm_score_proba = gmm1.score_samples(X).mean()
assert_almost_equal(gmm_score, gmm_score_proba)
# Check if the score increase
gmm2 = GaussianMixture(n_components=n_components, n_init=1, reg_covar=0,
random_state=rng,
covariance_type=covar_type).fit(X)
assert_greater(gmm2.score(X), gmm1.score(X))
def test_gaussian_mixture_fit_best_params():
rng = np.random.RandomState(0)
rand_data = RandomData(rng)
n_components = rand_data.n_components
n_init = 10
for covar_type in COVARIANCE_TYPE:
X = rand_data.X[covar_type]
g = GaussianMixture(n_components=n_components, n_init=1, reg_covar=0,
random_state=rng, covariance_type=covar_type)
ll = []
for _ in range(n_init):
g.fit(X)
ll.append(g.score(X))
ll = np.array(ll)
g_best = GaussianMixture(n_components=n_components,
n_init=n_init, reg_covar=0, random_state=rng,
covariance_type=covar_type)
g_best.fit(X)
assert_almost_equal(ll.min(), g_best.score(X))
def test_gaussian_mixture_fit_best_params():
rng = np.random.RandomState(0)
rand_data = RandomData(rng)
n_components = rand_data.n_components
n_init = 10
for covar_type in COVARIANCE_TYPE:
X = rand_data.X[covar_type]
g = GaussianMixture(n_components=n_components, n_init=1, reg_covar=0,
random_state=rng, covariance_type=covar_type)
ll = []
for _ in range(n_init):
g.fit(X)
ll.append(g.score(X))
ll = np.array(ll)
g_best = GaussianMixture(n_components=n_components,
n_init=n_init, reg_covar=0, random_state=rng,
covariance_type=covar_type)
g_best.fit(X)
assert_almost_equal(ll.min(), g_best.score(X))
class ScikitLL(LikelihoodEvaluator):
"""
Fastest Single Core Version so far!
"""
def __init__(self, Xpoints, numMixtures):
super().__init__(Xpoints, numMixtures)
self.evaluator = GaussianMixture(numMixtures, 'diag')
self.Xpoints = Xpoints
self.evaluator.fit(Xpoints)
def __str__(self):
return "SciKit's learn implementation Implementation"
def loglikelihood(self, means, diagCovs, weights):
self.evaluator.weights_ = weights
self.evaluator.covariances_ = diagCovs
self.evaluator.means_ = means
self.evaluator.precisions_cholesky_ = _compute_precision_cholesky(
diagCovs, "diag")
return self.numPoints * np.sum(self.evaluator.score(self.Xpoints))
def trainGmmEM(x,
t,
K,
cov_type='full',
n_max_iter=500,
n_restarts_random=20,
n_restarts_kmeans=20,
regularize=1e-2,
uniform_class_prior=True):
'''
Trains a GMM for each class of the given data. If EM is run for several
times, the models with the largest log-likelihood are kept.
x: The input features
t: The target values
K: List containing the number of components per class
cov_type: Which covariance type should be used ('full' or 'diag')
n_max_iter: Maximum number of iterations used for EM training
n_restarts_random: Number of random restarts with random initial values
n_restarts_kmeans: Number of random restarts where initial values are
computed with the k-means algorithm.
regularize: Regularizer for the diagonal of the covariance matrices
uniform_class_prior: If True, the class prior is set to 1/C for each class,
otherwise it is computed as the fraction of samples per class.
Returns a dictionary containing all parameters.
'''
assert n_restarts_random + n_restarts_kmeans > 0
C = int(np.max(t) + 1)
params = {}
for c in range(C):
print 'EM training for class %d/%d with %d components (N=%d, D=%d)' % (
c, C, K[c], np.sum(t == c), x.shape[1])
t_start = time()
if n_restarts_random > 0:
gmm1 = GaussianMixture(n_components=K[c],
covariance_type=cov_type,
reg_covar=regularize,
max_iter=n_max_iter,
n_init=n_restarts_random,
init_params='random',
verbose=2)
gmm1.fit(x[t == c, :])
if n_restarts_kmeans > 0:
gmm2 = GaussianMixture(n_components=K[c],
covariance_type=cov_type,
reg_covar=regularize,
max_iter=n_max_iter,
n_init=n_restarts_kmeans,
init_params='kmeans',
verbose=2)
gmm2.fit(x[t == c, :])
t_elapsed = time() - t_start
print 'EM training for class %d/%d finished in %f seconds' % (
c, C, t_elapsed)
# Select the better model of gmm1 and gmm2
# Don't use gmm.lower_bound_, it returns the last logl and not the best
score1 = gmm1.score(x[t == c, :]) if n_restarts_random > 0 else -np.Inf
score2 = gmm2.score(x[t == c, :]) if n_restarts_kmeans > 0 else -np.Inf
gmm = gmm1 if score1 > score2 else gmm2
params['alpha_%d' % (c)] = gmm.weights_
params['mu_%d' % (c)] = gmm.means_
params['Sigma_%d' % (c)] = gmm.covariances_
params['Lambda_%d' % (c)] = gmm.precisions_
if uniform_class_prior == True:
params['prior'] = np.full((C, ), 1. / C, 'float32')
else:
_, counts = np.unique(t, return_counts=True)
counts = np.asarray(counts, 'float32')
params['prior'] = counts / np.sum(counts)
return params