def run_nmf(V):
"""
Run standard nonnegative matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
# Euclidean
rank = 10
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "nmf",
max_iter = 12,
initialize_only = True,
update = 'euclidean',
objective = 'fro')
fit = mf.mf_run(model)
print_info(fit)
# divergence
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "nmf",
max_iter = 12,
initialize_only = True,
update = 'divergence',
objective = 'div')
fit = mf.mf_run(model)
print_info(fit)
def factorize(V):
"""
Perform LSNMF factorization on the ORL faces data matrix.
Return basis and mixture matrices of the fitted factorization model.
:param V: The ORL faces data matrix.
:type V: `numpy.matrix`
"""
print "Performing LSNMF factorization ..."
model = mf.mf(V,
seed = "random_vcol",
rank = 25,
method = "lsnmf",
max_iter = 50,
initialize_only = True,
sub_iter = 10,
inner_sub_iter = 10,
beta = 0.1,
min_residuals = 1e-8)
fit = mf.mf_run(model)
print " ... Finished"
print """Stats:
- iterations: %d
- final projected gradients norm: %5.3f
- Euclidean distance: %5.3f""" % (fit.fit.n_iter, fit.distance(), fit.distance(metric = 'euclidean'))
return fit.basis(), fit.coef()
def run_snmnmf(V, V1):
"""
Run sparse network-regularized multiple NMF.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(target = (V, V1),
seed = "random_c",
rank = rank,
method = "snmnmf",
max_iter = 12,
initialize_only = True,
A = abs(sp.rand(V1.shape[1], V1.shape[1], density = 0.7, format = 'csr')),
B = abs(sp.rand(V.shape[1], V1.shape[1], density = 0.7, format = 'csr')),
gamma = 0.01,
gamma_1 = 0.01,
lamb = 0.01,
lamb_1 = 0.01)
fit = mf.mf_run(model)
# print all quality measures concerning first target and mixture matrix in multiple NMF
print_info(fit, idx = 0)
# print all quality measures concerning second target and mixture matrix in multiple NMF
print_info(fit, idx = 1)
def run_bd(V):
"""
Run Bayesian decomposition.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(V,
seed = "random_c",
rank = rank,
method = "bd",
max_iter = 12,
initialize_only = True,
alpha = np.mat(np.zeros((V.shape[0], rank))),
beta = np.mat(np.zeros((rank, V.shape[1]))),
theta = .0,
k = .0,
sigma = 1.,
skip = 100,
stride = 1,
n_w = np.mat(np.zeros((rank, 1))),
n_h = np.mat(np.zeros((rank, 1))),
n_sigma = False)
fit = mf.mf_run(model)
print_info(fit)
def factorize(V):
"""
Perform NMF - Divergence factorization on the sparse Medlars data matrix.
Return basis and mixture matrices of the fitted factorization model.
:param V: The Medlars data matrix.
:type V: `scipy.sparse.csr_matrix`
"""
print "Performing NMF - Divergence factorization ..."
model = mf.mf(V,
seed = "random_vcol",
rank = 12,
method = "nmf",
max_iter = 15,
initialize_only = True,
update = 'divergence',
objective = 'div')
fit = mf.mf_run(model)
print "... Finished"
sparse_w, sparse_h = fit.fit.sparseness()
print """Stats:
- iterations: %d
- KL Divergence: %5.3f
- Euclidean distance: %5.3f
- Sparseness basis: %5.3f, mixture: %5.3f""" % (fit.fit.n_iter, fit.distance(), fit.distance(metric = 'euclidean'), sparse_w, sparse_h)
return fit.basis(), fit.coef()
def run_snmf(V):
"""
Run sparse nonnegative matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
# SNMF/R
rank = 10
model = mf.mf(V,
seed = "random_c",
rank = rank,
method = "snmf",
max_iter = 12,
initialize_only = True,
version = 'r',
eta = 1.,
beta = 1e-4,
i_conv = 10,
w_min_change = 0)
fit = mf.mf_run(model)
print_info(fit)
# SNMF/L
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "snmf",
max_iter = 12,
initialize_only = True,
version = 'l',
eta = 1.,
beta = 1e-4,
i_conv = 10,
w_min_change = 0)
fit = mf.mf_run(model)
print_info(fit)
def run_pmf(V):
"""
Run probabilistic matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "pmf",
max_iter = 12,
initialize_only = True,
rel_error = 1e-5)
fit = mf.mf_run(model)
print_info(fit)
def run_nsnmf(V):
"""
Run nonsmooth nonnegative matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(V,
seed = "random",
rank = rank,
method = "nsnmf",
max_iter = 12,
initialize_only = True,
theta = 0.5)
fit = mf.mf_run(model)
print_info(fit)
def run_psmf(V):
"""
Run probabilistic sparse matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
prng = np.random.RandomState()
model = mf.mf(V,
seed = None,
rank = rank,
method = "psmf",
max_iter = 12,
initialize_only = True,
prior = prng.uniform(low = 0., high = 1., size = 10))
fit = mf.mf_run(model)
print_info(fit)
def run_bmf(V):
"""
Run binary matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "bmf",
max_iter = 12,
initialize_only = True,
lambda_w = 1.1,
lambda_h = 1.1)
fit = mf.mf_run(model)
print_info(fit)
def run_lsnmf(V):
"""
Run least squares nonnegative matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
model = mf.mf(V,
seed = "random_vcol",
rank = rank,
method = "lsnmf",
max_iter = 12,
initialize_only = True,
sub_iter = 10,
inner_sub_iter = 10,
beta = 0.1,
min_residuals = 1e-5)
fit = mf.mf_run(model)
print_info(fit)
def run_lfnmf(V):
"""
Run local fisher nonnegative matrix factorization.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
pnrg = np.random.RandomState()
model = mf.mf(V,
seed = None,
W = abs(pnrg.randn(V.shape[0], rank)),
H = abs(pnrg.randn(rank, V.shape[1])),
rank = rank,
method = "lfnmf",
max_iter = 12,
initialize_only = True,
alpha = 0.01)
fit = mf.mf_run(model)
print_info(fit)
def run_one(V, rank):
"""
Run standard NMF on leukemia data set. 50 runs of Standard NMF are performed and obtained consensus matrix
averages all 50 connectivity matrices.
:param V: Target matrix with gene expression data.
:type V: `numpy.matrix` (of course it could be any format of scipy.sparse, but we will use numpy here)
:param rank: Factorization rank.
:type rank: `int`
"""
print "================= Rank = %d =================" % rank
consensus = np.mat(np.zeros((V.shape[1], V.shape[1])))
for i in xrange(50):
# Standard NMF with Euclidean update equations is used. For initialization random Vcol method is used.
# Objective function is the number of consecutive iterations in which the connectivity matrix has not changed.
# We demand that factorization does not terminate before 30 consecutive iterations in which connectivity matrix
# does not change. For a backup we also specify the maximum number of iterations. Note that the satisfiability
# of one stopping criteria terminates the run (there is no chance for divergence).
model = mf.mf(V,
method = "nmf",
rank = rank,
seed = "random_vcol",
max_iter = 200,
update = 'euclidean',
objective = 'conn',
conn_change = 40,
initialize_only = True)
fit = mf.mf_run(model)
print "%2d / 50 :: %s - init: %s ran with ... %3d / 200 iters ..." % (i + 1, fit.fit, fit.fit.seed, fit.fit.n_iter)
# Compute connectivity matrix of factorization.
# Again, we could use multiple runs support of the MF library, track factorization model across 50 runs and then
# just call fit.consensus()
consensus += fit.fit.connectivity()
# averaging connectivity matrices
consensus /= 50.
# reorder consensus matrix
p_consensus = reorder(consensus)
# plot reordered consensus matrix
plot(p_consensus, rank)
def run_icm(V):
"""
Run iterated conditional modes.
:param V: Target matrix to estimate.
:type V: :class:`numpy.matrix`
"""
rank = 10
pnrg = np.random.RandomState()
model = mf.mf(V,
seed = "nndsvd",
rank = rank,
method = "icm",
max_iter = 12,
initialize_only = True,
iiter = 20,
alpha = pnrg.randn(V.shape[0], rank),
beta = pnrg.randn(rank, V.shape[1]),
theta = 0.,
k = 0.,
sigma = 1.)
fit = mf.mf_run(model)
print_info(fit)