def test_integration_adaptive_graph_lasso(self, params_in):
'''
Just tests inputs/outputs (not validity of result).
'''
n_features = 20
n_samples = 25
cov, prec, adj = ClusterGraph(
n_blocks=1,
chain_blocks=False,
seed=1,
).create(n_features, 0.8)
prng = np.random.RandomState(2)
X = prng.multivariate_normal(np.zeros(n_features), cov, size=n_samples)
model = AdaptiveGraphLasso(**params_in)
model.fit(X)
assert model.estimator_ is not None
assert model.lam_ is not None
assert np.sum(model.lam_[np.diag_indices(n_features)]) == 0
if params_in['method'] == 'binary':
uvals = set(model.lam_.flat)
assert len(uvals) == 2
assert 0 in uvals
assert 1 in uvals
elif params_in['method'] == 'inverse' or\
params_in['method'] == 'inverse_squared':
uvals = set(model.lam_.flat[model.lam_.flat != 0])
assert len(uvals) > 0
def adaptive_graph_lasso(X, model_selector, method):
'''Run QuicGraphLassoCV or QuicGraphLassoEBIC as a two step adaptive fit
with method of choice (currently: 'binary', 'inverse', 'inverse_squared').
Compare the support and values to the model-selection estimator.
'''
metric = 'log_likelihood'
print 'Adaptive {} with:'.format(model_selector)
print ' adaptive-method: {}'.format(method)
if model_selector == 'QuicGraphLassoCV':
print ' metric: {}'.format(metric)
model = AdaptiveGraphLasso(
estimator=QuicGraphLassoCV(
cv=2, # cant deal w more folds at small size
n_refinements=6,
init_method='cov',
score_metric=metric),
method=method,
)
elif model_selector == 'QuicGraphLassoEBIC':
model = AdaptiveGraphLasso(
estimator=QuicGraphLassoEBIC(),
method=method,
)
model.fit(X)
lam_norm_ = np.linalg.norm(model.estimator_.lam_)
print ' ||lam_||_2: {}'.format(lam_norm_)
return model.estimator_.covariance_, model.estimator_.precision_, lam_norm_
def adaptive_model_average(X, penalization, method):
'''Run ModelAverage in default mode (QuicGraphLassoCV) to obtain proportion
matrix.
NOTE: Only method = 'binary' really makes sense in this case.
'''
n_trials = 100
print('Adaptive ModelAverage with:')
print(' estimator: QuicGraphLasso (default)')
print(' n_trials: {}'.format(n_trials))
print(' penalization: {}'.format(penalization))
print(' adaptive-method: {}'.format(method))
# if penalization is random, first find a decent scalar lam_ to build
# random perturbation matrix around. lam doesn't matter for fully-random.
lam = 0.5
if penalization == 'random':
cv_model = QuicGraphLassoCV(
cv=2,
n_refinements=6,
sc=spark.sparkContext, # NOQA
init_method='cov',
score_metric=metric)
cv_model.fit(X)
lam = cv_model.lam_
print(' lam: {}'.format(lam))
model = AdaptiveGraphLasso(
estimator=ModelAverage(n_trials=n_trials,
penalization=penalization,
lam=lam,
sc=spark.sparkContext), # NOQA
method=method,
)
model.fit(X)
lam_norm_ = np.linalg.norm(model.estimator_.lam_)
print(' ||lam_||_2: {}'.format(lam_norm_))
return model.estimator_.covariance_, model.estimator_.precision_, lam_norm_
def test_integration_adaptive_graph_lasso(self, params_in):
'''
Just tests inputs/outputs (not validity of result).
'''
X = datasets.load_diabetes().data
n_examples, n_features = X.shape
model = AdaptiveGraphLasso(**params_in)
model.fit(X)
assert model.estimator_ is not None
assert model.lam_ is not None
assert np.sum(model.lam_[np.diag_indices(n_features)]) == 0
if params_in['method'] == 'binary':
uvals = set(model.lam_.flat)
assert len(uvals) == 2
assert 0 in uvals
assert 1 in uvals
elif params_in['method'] == 'inverse' or\
params_in['method'] == 'inverse_squared':
uvals = set(model.lam_.flat[model.lam_.flat != 0])
assert len(uvals) > 0
def get_conn_matrix(time_series, conn_model):
import warnings
warnings.simplefilter("ignore")
from nilearn.connectome import ConnectivityMeasure
from sklearn.covariance import GraphLassoCV
try:
from brainiak.fcma.util import compute_correlation
except ImportError:
pass
if conn_model == 'corr':
# credit: nilearn
print('\nComputing correlation matrix...\n')
conn_measure = ConnectivityMeasure(kind='correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
elif conn_model == 'corr_fast':
# credit: brainiak
try:
print('\nComputing accelerated fcma correlation matrix...\n')
conn_matrix = compute_correlation(time_series, time_series)
except RuntimeError:
print(
'Cannot run accelerated correlation computation due to a missing dependency. You need brainiak installed!'
)
elif conn_model == 'partcorr':
# credit: nilearn
print('\nComputing partial correlation matrix...\n')
conn_measure = ConnectivityMeasure(kind='partial correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
elif conn_model == 'tangent':
# credit: nilearn
print('\nComputing tangent matrix...\n')
conn_measure = ConnectivityMeasure(kind='tangent')
conn_matrix = conn_measure.fit_transform([time_series])[0]
elif conn_model == 'cov' or conn_model == 'sps':
##Fit estimator to matrix to get sparse matrix
estimator = GraphLassoCV()
try:
print('\nComputing covariance...\n')
estimator.fit(time_series)
except:
try:
print(
'Unstable Lasso estimation--Attempting to re-run by first applying shrinkage...'
)
from sklearn.covariance import GraphLasso, empirical_covariance, shrunk_covariance
emp_cov = empirical_covariance(time_series)
for i in np.arange(0.8, 0.99, 0.01):
shrunk_cov = shrunk_covariance(emp_cov, shrinkage=i)
alphaRange = 10.0**np.arange(-8, 0)
for alpha in alphaRange:
try:
estimator_shrunk = GraphLasso(alpha)
estimator_shrunk.fit(shrunk_cov)
print(
"Calculated graph-lasso covariance matrix for alpha=%s"
% alpha)
break
except FloatingPointError:
print("Failed at alpha=%s" % alpha)
if estimator_shrunk == None:
pass
else:
break
except:
raise ValueError(
'Unstable Lasso estimation! Shrinkage failed.')
if conn_model == 'sps':
try:
print(
'\nFetching precision matrix from covariance estimator...\n'
)
conn_matrix = -estimator.precision_
except:
print(
'\nFetching shrunk precision matrix from covariance estimator...\n'
)
conn_matrix = -estimator_shrunk.precision_
elif conn_model == 'cov':
try:
print(
'\nFetching covariance matrix from covariance estimator...\n'
)
conn_matrix = estimator.covariance_
except:
conn_matrix = estimator_shrunk.covariance_
elif conn_model == 'QuicGraphLasso':
from inverse_covariance import QuicGraphLasso
# Compute the sparse inverse covariance via QuicGraphLasso
# credit: skggm
model = QuicGraphLasso(init_method='cov',
lam=0.5,
mode='default',
verbose=1)
print('\nCalculating QuicGraphLasso precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'QuicGraphLassoCV':
from inverse_covariance import QuicGraphLassoCV
# Compute the sparse inverse covariance via QuicGraphLassoCV
# credit: skggm
model = QuicGraphLassoCV(init_method='cov', verbose=1)
print(
'\nCalculating QuicGraphLassoCV precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'QuicGraphLassoEBIC':
from inverse_covariance import QuicGraphLassoEBIC
# Compute the sparse inverse covariance via QuicGraphLassoEBIC
# credit: skggm
model = QuicGraphLassoEBIC(init_method='cov', verbose=1)
print(
'\nCalculating QuicGraphLassoEBIC precision matrix using skggm...\n'
)
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'AdaptiveQuicGraphLasso':
from inverse_covariance import AdaptiveGraphLasso, QuicGraphLassoEBIC
# Compute the sparse inverse covariance via
# AdaptiveGraphLasso + QuicGraphLassoEBIC + method='binary'
# credit: skggm
model = AdaptiveGraphLasso(
estimator=QuicGraphLassoEBIC(init_method='cov', ),
method='binary',
)
print(
'\nCalculating AdaptiveQuicGraphLasso precision matrix using skggm...\n'
)
model.fit(time_series)
conn_matrix = -model.estimator_.precision_
return (conn_matrix)
def get_conn_matrix(time_series, conn_model):
from nilearn.connectome import ConnectivityMeasure
from sklearn.covariance import GraphLassoCV
conn_matrix = None
if conn_model == 'corr':
# credit: nilearn
print('\nComputing correlation matrix...\n')
conn_measure = ConnectivityMeasure(kind='correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
elif conn_model == 'partcorr':
# credit: nilearn
print('\nComputing partial correlation matrix...\n')
conn_measure = ConnectivityMeasure(kind='partial correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
elif conn_model == 'cov' or conn_model == 'sps':
# Fit estimator to matrix to get sparse matrix
estimator_shrunk = None
estimator = GraphLassoCV()
try:
print('\nComputing covariance...\n')
estimator.fit(time_series)
except RuntimeWarning:
print('Unstable Lasso estimation--Attempting to re-run by first applying shrinkage...')
try:
from sklearn.covariance import GraphLasso, empirical_covariance, shrunk_covariance
emp_cov = empirical_covariance(time_series)
for i in np.arange(0.8, 0.99, 0.01):
shrunk_cov = shrunk_covariance(emp_cov, shrinkage=i)
alphaRange = 10.0 ** np.arange(-8, 0)
for alpha in alphaRange:
try:
estimator_shrunk = GraphLasso(alpha)
estimator_shrunk.fit(shrunk_cov)
print("Retrying covariance matrix estimate with alpha=%s" % alpha)
if estimator_shrunk is None:
pass
else:
break
except RuntimeWarning:
print("Covariance estimation failed with shrinkage at alpha=%s" % alpha)
continue
except ValueError:
print('Unstable Lasso estimation! Shrinkage failed. A different connectivity model may be needed.')
if estimator is None and estimator_shrunk is None:
raise RuntimeError('ERROR: Covariance estimation failed.')
if conn_model == 'sps':
if estimator_shrunk is None:
print('\nFetching precision matrix from covariance estimator...\n')
conn_matrix = -estimator.precision_
else:
print('\nFetching shrunk precision matrix from covariance estimator...\n')
conn_matrix = -estimator_shrunk.precision_
elif conn_model == 'cov':
if estimator_shrunk is None:
print('\nFetching covariance matrix from covariance estimator...\n')
conn_matrix = estimator.covariance_
else:
conn_matrix = estimator_shrunk.covariance_
elif conn_model == 'QuicGraphLasso':
from inverse_covariance import QuicGraphLasso
# Compute the sparse inverse covariance via QuicGraphLasso
# credit: skggm
model = QuicGraphLasso(
init_method='cov',
lam=0.5,
mode='default',
verbose=1)
print('\nCalculating QuicGraphLasso precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'QuicGraphLassoCV':
from inverse_covariance import QuicGraphLassoCV
# Compute the sparse inverse covariance via QuicGraphLassoCV
# credit: skggm
model = QuicGraphLassoCV(
init_method='cov',
verbose=1)
print('\nCalculating QuicGraphLassoCV precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'QuicGraphLassoEBIC':
from inverse_covariance import QuicGraphLassoEBIC
# Compute the sparse inverse covariance via QuicGraphLassoEBIC
# credit: skggm
model = QuicGraphLassoEBIC(
init_method='cov',
verbose=1)
print('\nCalculating QuicGraphLassoEBIC precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.precision_
elif conn_model == 'AdaptiveQuicGraphLasso':
from inverse_covariance import AdaptiveGraphLasso, QuicGraphLassoEBIC
# Compute the sparse inverse covariance via
# AdaptiveGraphLasso + QuicGraphLassoEBIC + method='binary'
# credit: skggm
model = AdaptiveGraphLasso(
estimator=QuicGraphLassoEBIC(
init_method='cov',
),
method='binary',
)
print('\nCalculating AdaptiveQuicGraphLasso precision matrix using skggm...\n')
model.fit(time_series)
conn_matrix = -model.estimator_.precision_
return conn_matrix
def fit(self, X=None, y=None):
n_alpha_grid_points = 4
self.results_ = np.zeros((n_alpha_grid_points, self.n_grid_points))
self.grid_ = np.logspace(0, np.log10(200), self.n_grid_points)
if self.adj_type=='erdos-renyi':
self.alphas_ = np.logspace(-2.3,np.log10(.025), n_alpha_grid_points)[::1]
else:
self.alphas_ = np.logspace(np.log(.1),np.log10(.3), n_alpha_grid_points)[::1]
self.ks_ = []
for aidx, alpha in enumerate(self.alphas_):
if self.verbose:
print ('at alpha {} ({}/{})'.format(
alpha,
aidx,
n_alpha_grid_points,
))
# draw a new fixed graph for alpha
cov, prec, adj = new_graph(self.n_features, alpha, adj_type=self.adj_type,random_sign=False,seed=1)
n_nonzero_prec = np.count_nonzero(np.triu(adj,1).flat)
self.ks_.append(n_nonzero_prec)
mcmc_prng = np.random.RandomState(2)
if self.verbose:
print (' Graph has {} nonzero entries'.format(n_nonzero_prec))
for sidx, sample_grid in enumerate(self.grid_):
n_samples = int(sample_grid * self.n_features)
# Debugging
# print alpha, n_samples
# model selection (once)
X = mvn(n_samples, self.n_features, cov,random_state=mcmc_prng)
ms_estimator = clone(self.model_selection_estimator)
ms_estimator.fit(X)
lam = getattr(ms_estimator, self.penalty_)
if self.verbose:
display_lam = lam
if isinstance(lam, np.ndarray):
display_lam = np.linalg.norm(lam)
print (' ({}/{}), n_samples = {}, selected lambda = {}'.format(
sidx,
self.n_grid_points,
n_samples,
display_lam))
# setup default trial estimator
if self.trial_estimator is None:
trial_estimator = QuicGraphLasso(lam=lam,
mode='default',
init_method='corrcoef')
elif self.trial_estimator == 'Adaptive':
trial_estimator = AdaptiveGraphLasso(estimator = QuicGraphLasso(lam=lam,mode='default',init_method='corrcoef'),
method='inverse_squared')
else:
trial_estimator = self.trial_estimator
# patch trial estimator with this lambda
if self.trial_estimator == 'Adaptive':
trial_estimator.estimator_.set_params(**{
self.penalty: lam,
})
else:
trial_estimator.set_params(**{
self.penalty: lam,
})
# estimate statistical power
exact_support_counts = Parallel(
n_jobs=self.n_jobs,
verbose=False,
backend='threading',
#max_nbytes=None,
#batch_size=1,
)(
delayed(sp_trial)(
trial_estimator, n_samples, self.n_features, cov, adj, mcmc_prng
)
for nn in range(self.n_trials))
self.results_[aidx, sidx] = 1. * np.sum(exact_support_counts) / self.n_trials
if self.verbose:
print ('Results at this row: {}'.format(self.results_[aidx, :]))
self.is_fitted = True
return self
def compare_init_adaptive(X,n_samples,n_features,covariance,precision,adjacency,figures):
f, (ax1, ax2, ax3) = figures
# Initial Estimator
initial_estimator = QuicGraphLassoCV(init_method='corrcoef')
initial_estimator.fit(X)
prec_hat = initial_estimator.precision_
# Generate a custom diverging colormap
cmap = sns.diverging_palette(220, 10, as_cmap=True)
prec_vmax = np.max(np.triu(prec_hat,1))
sns.heatmap(initial_estimator.precision_,cmap=cmap, vmax=prec_vmax,
square=True, xticklabels=5, yticklabels=5,
linewidths=.5, cbar_kws={"shrink": .5},ax=ax1)
ax1.set_title('Precision Matrix, Initial Estimator')
# Check Average Power
err_frob, err_supp, err_fp, err_fn, err_inf = ae_trial(
trial_estimator=initial_estimator,
n_samples=n_samples,
n_features=n_features,
cov=covariance,
adj=adjacency,
random_state=np.random.RandomState(2),X=X)
print ('Difference in sparsity: {},{}'.format(
np.sum(np.not_equal(precision,0)),
np.sum(np.not_equal(initial_estimator.precision_,0))
))
print ('Frob Norm: {} ({}), Support Error: {}, False Pos: {}, False Neg: {}'.format(
err_frob, err_inf,
err_supp,
err_fp,
err_fn
) )
# Adaptive Estimator
twostage = AdaptiveGraphLasso(estimator=initial_estimator,method='inverse')
twostage.fit(X)
weighted_estimator = twostage.estimator_
prec_hat = weighted_estimator.precision_
prec_vmax = np.max(np.triu(prec_hat,1))
sns.heatmap(weighted_estimator.precision_,cmap=cmap, vmax=prec_vmax,
square=True, xticklabels=5, yticklabels=5,
linewidths=.5, cbar_kws={"shrink": .5},ax=ax2)
ax2.set_title('Precision Matrix, Adaptive Estimator')
print ('Difference in sparsity: {},{}'.format(
np.sum(np.not_equal(precision,0)),
np.sum(np.not_equal(weighted_estimator.precision_,0))
))
# Check Average Power
err_frob, err_supp, err_fp, err_fn, err_inf = ae_trial(
trial_estimator=weighted_estimator,
n_samples=n_samples,
n_features=n_features,
cov=covariance,
adj=adjacency,
random_state=np.random.RandomState(2), X = X)
print ('Frob Norm: {} ({}), Support Error: {}, False Pos: {}, False Neg: {}'.format(
err_frob,err_inf,
err_supp,
err_fp,
err_fn
))
print()
prec_vmax = np.max(np.triu(precision,1))
sns.heatmap(adjacency,cmap=cmap, vmax=prec_vmax,
square=True, xticklabels=5, yticklabels=5,
linewidths=.5, cbar_kws={"shrink": .5},ax=ax3)
ax3.set_title('True Precision')
elif estimator_type == 'QuicGraphLassoCV':
# Compute the sparse inverse covariance via QuicGraphLassoCV
estimator = QuicGraphLassoCV(init_method='cov', verbose=1)
estimator.fit(timeseries)
elif estimator_type == 'QuicGraphLassoEBIC':
# Compute the sparse inverse covariance via QuicGraphLassoEBIC
estimator = QuicGraphLassoEBIC(init_method='cov', verbose=1)
estimator.fit(timeseries)
elif estimator_type == 'AdaptiveQuicGraphLasso':
# Compute the sparse inverse covariance via
# AdaptiveGraphLasso + QuicGraphLassoEBIC + method='binary'
model = AdaptiveGraphLasso(
estimator=QuicGraphLassoEBIC(init_method='cov', ),
method='binary',
)
model.fit(timeseries)
estimator = model.estimator_
# Display the sparse inverse covariance
plt.figure(figsize=(7.5, 7.5))
plt.imshow(np.triu(-estimator.precision_, 1),
interpolation="nearest",
cmap=plt.cm.RdBu_r)
plt.title('Precision (Sparse Inverse Covariance) matrix')
plt.colorbar()
# And now display the corresponding graph
plotting.plot_connectome(
-estimator.precision_,