def split_af(_af, _inds):
"""
splits the input matrix into diagonal and off-diagonal portions, with the split being determined by _inds
:param _af:
:param _inds:
:return:
"""
_af = _af.tocoo()
_r = _af.row
_c = _af.col
_d = _af.data
_d_non = []
_d_scc = []
_shape = _af.shape
for i in range(len(_d)):
if _r[i] in _inds and _c[i] in _inds:
_d_non.append(0)
_d_scc.append(_d[i])
else:
_d_non.append(_d[i])
_d_scc.append(0)
_af_non = csc_matrix((_d_non, (_r, _c)), shape=_shape)
_af_scc = csc_matrix((_d_scc, (_r, _c)), shape=_shape)
assert (_af_non + _af_scc - _af).nnz == 0
return _af_non, _af_scc
def test_bfs(self):
a = igl.adjacency_matrix(self.f1)
p, d = igl.bfs(a, 0)
self.assertEqual(p.shape, (self.v1.shape[0],))
self.assertEqual(p.shape, (self.v1.shape[0],))
try:
p, d, = igl.bfs(a, -1)
self.assertTrue(False)
except IndexError as e:
pass
a = csc.csc_matrix(np.zeros([0, 0], dtype=np.int32))
try:
p, d, = igl.bfs(a, 0)
self.assertTrue(False)
except ValueError as e:
pass
a = csc.csc_matrix(np.zeros([10, 11], dtype=np.int32))
try:
p, d, = igl.bfs(a, 0)
self.assertTrue(False)
except ValueError as e:
pass
a = csc.csc_matrix(np.zeros([10, 10], dtype=np.int32))
p, d, = igl.bfs(a, 0)
self.assertEqual(p.shape, ())
self.assertTrue(np.array_equal(d, -np.ones(10)))
self.assertTrue(p.flags.c_contiguous)
def __init__(self,
positions,
masses,
springs,
fixed,
method,
profiling_rate=0):
"""
method: 'Newton' | 'FMS' | 'Jacobi'
profiling_rate: the step rate at which the performance will be graphed
"""
# General state setup
self.profiling_rate = profiling_rate
self.method = method
self.g = -9.8
self.m = len(positions)
self.s = len(springs)
self.q0 = np.array(positions).reshape(self.ndim * self.m, 1)
self.q = copy(self.q0)
# Store initial state
self.state0 = copy(self.q)
self.fixed = fixed
self.qFixed = copy(self.q0)
self.M = kron(diags(masses), np.eye(self.ndim), format='csc')
self.Minv = kron(diags(
list(map(lambda x: 0 if x == 0 else 1.0 / x, masses))),
np.eye(self.ndim),
format='csc')
self.springs = np.array(springs, dtype=spring_type)
self.d = np.empty((self.ndim * self.s, 1))
# Matrices L and J setup
self.L = csc_matrix((self.m, self.m))
self.J = csc_matrix((self.m, self.s))
for idx, s in enumerate(self.springs):
Ai = None
if idx in self.fixed:
Ai = csc_matrix(([1], ([s['p1']], [0])), shape=(self.m, 1))
else:
Ai = csc_matrix(([1, -1], ([s['p1'], s['p2']], [0, 0])),
shape=(self.m, 1))
self.L += s['k'] * Ai * Ai.transpose()
self.J += s['k'] * Ai * csc_matrix(
([1.0], ([idx], [0])), shape=(self.s, 1)).transpose()
self.L = kron(self.L, np.eye(self.ndim), format='csc')
self.J = kron(self.J, np.eye(self.ndim), format='csc')
# Matrix A precomputation (Global step)
self.A = self.M + self.dt2 * self.L
self.Ch = cho_factor(self.A.toarray())
# Implemented methods
self.implemented = {
'FMS': self.step_LocalGlobal,
'Jacobi': self.step_Jacobi,
'Newton': self.step_Newton,
'Anderson': self.step_Anderson
}
def load_dataset(fname):
z = np.load(open(fname,'rb'))
X_train = z['arr_0']
X_test = z['arr_1']
y_train = z['arr_2']
y_test = z['arr_3']
X_train = csc.csc_matrix(X_train.tolist())
X_test = csc.csc_matrix(X_test.tolist())
return X_train, X_test, y_train, y_test
def load_lda_dataset_small(uid, neg_to_pos_rate):
fname = 'ldads_small%d_%d' % (neg_to_pos_rate, uid)
fname = join(DATASETS_FOLDER, '%s.npz' % fname)
z = np.load(open(fname,'rb'))
X_train_lda = z['arr_0']
X_test_lda = z['arr_1']
y_train = z['arr_2']
y_test = z['arr_3']
X_train_lda = csc.csc_matrix(X_train_lda.tolist())
X_test_lda = csc.csc_matrix(X_test_lda.tolist())
return X_train_lda, X_test_lda, y_train, y_test
def load_lda_dataset_big(uid, train_size):
fname = 'ldads_%d' % uid
if train_size:
fname += '_tr%d' % train_size
fname = join(DATASETS_FOLDER, '%s.npz' % fname)
z = np.load(open(fname,'rb'))
X_train_lda = z['arr_0']
X_test_lda = z['arr_1']
y_train = z['arr_2']
y_test = z['arr_3']
X_train_lda = csc.csc_matrix(X_train_lda.tolist())
X_test_lda = csc.csc_matrix(X_test_lda.tolist())
return X_train_lda, X_test_lda, y_train, y_test
def positive_mass_stiffness_smooth(triangles,
vertices,
nb_iter=1,
diffusion_step=1.0,
flow_file=None,
gaussian_threshold=0.2,
angle_threshold=1.0):
vertices_csc = csc_matrix(vertices)
curvature_normal_mtx = mean_curvature_normal_matrix(triangles,
vertices,
area_weighted=False)
# mass_mtx = mass_matrix(triangles, vertices_csc)
if isinstance(diffusion_step, (int, long, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
if flow_file is not None:
mem_map = np.memmap(flow_file,
dtype=G_DTYPE,
mode='w+',
shape=(nb_iter, vertices.shape[0],
vertices.shape[1]))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices_csc.todense()
# third try
mass_mtx = mass_matrix(triangles, vertices_csc)
pos_curv = vertices_cotan_curvature(triangles, vertices_csc,
False) > -G_ATOL
if gaussian_threshold is not None:
# Gaussian threshold: maximum value PI, cube corner = PI/2 # = 0.8
deg_vts = np.abs(
vertices_gaussian_curvature(triangles, vertices_csc,
False)) > gaussian_threshold
pos_curv = np.logical_or(pos_curv, deg_vts)
if angle_threshold is not None:
# angle_threshold: PI, cube corner = PI/2 # = 1.7
deg_seg = edge_triangle_normal_angle(
triangles,
vertices_csc).max(1).toarray().squeeze() > angle_threshold
pos_curv = np.logical_or(pos_curv, deg_seg)
possitive_diffusion_step = pos_curv * diffusion_step
# (D - d*L)*y = D*x = b
A_matrix = mass_mtx - \
(diags(possitive_diffusion_step, 0).dot(curvature_normal_mtx))
b_matrix = mass_mtx.dot(vertices_csc)
vertices_csc = spsolve(A_matrix, b_matrix)
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
return vertices_csc.toarray()
def log_det_estimate_shogun(Q):
logging.debug("Entering")
op = RealSparseMatrixOperator(csc_matrix(Q))
engine = SerialComputationEngine()
linear_solver = CGMShiftedFamilySolver()
accuracy = 1e-3
eigen_solver = LanczosEigenSolver(op)
eigen_solver.set_min_eigenvalue(OzonePosterior.ridge)
op_func = LogRationalApproximationCGM(op, engine, eigen_solver, linear_solver, accuracy)
# limit computation time
linear_solver.set_iteration_limit(1000)
eigen_solver.set_max_iteration_limit(1000)
logging.info("Computing Eigenvalues (only largest)")
eigen_solver.compute()
trace_sampler = ProbingSampler(op)
log_det_estimator = LogDetEstimator(trace_sampler, op_func, engine)
n_estimates = 1
logging.info("Sampling log-determinant with probing vectors and rational approximation")
estimates = log_det_estimator.sample(n_estimates)
logging.debug("Leaving")
return mean(estimates)
def curvature_normal_smooth(triangles, vertices, nb_iter=1,
diffusion_step=1.0, area_weighted=False,
backward_step=False, flow_file=None):
if flow_file is not None:
mem_map = np.memmap(flow_file, dtype=G_DTYPE, mode='w+',
shape=(nb_iter, vertices.shape[0], vertices.shape[1]))
vertices_csc = csc_matrix(vertices)
if isinstance(diffusion_step, (int, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices_csc.toarray()
# get curvature_normal_matrix
curvature_normal_mtx = mean_curvature_normal_matrix(
triangles, vertices_csc, area_weighted=area_weighted)
next_vertices_csc = euler_step(
curvature_normal_mtx, vertices_csc, diffusion_step, backward_step)
vertices_csc = next_vertices_csc
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
# return next_vertices_csc
return vertices_csc.toarray()
def volume_curvature_normal_smooth(triangles, vertices, nb_iter=1,
diffusion_step=1.0, area_weighted=False,
backward_step=False, flow_file=None):
if isinstance(diffusion_step, (int, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
if flow_file is not None:
mem_map = np.memmap(flow_file, dtype=G_DTYPE, mode='w+',
shape=(nb_iter, vertices.shape[0], vertices.shape[1]))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices
# get curvature_normal_matrix
# todo not optimal, because operation done twice etc
curvature_normal_mtx = mean_curvature_normal_matrix(
triangles, vertices, area_weighted=area_weighted)
# do the first step
next_vertices = euler_step(curvature_normal_mtx, csc_matrix(
vertices), diffusion_step, backward_step).toarray()
# test if direction is positive
direction = next_vertices - vertices
normal_dir = vertices_cotan_normal(triangles, vertices, normalize=True)
dotv = dot(normalize_vectors(direction), normal_dir, keepdims=True)
vertices += direction * np.maximum(0.0, -dotv)
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
return vertices
def dtm_to_gensim_corpus(dtm):
"""
Convert a (sparse) DTM to a Gensim Corpus object.
.. seealso:: :func:`~tmtoolkit.bow.dtm.gensim_corpus_to_dtm` for the reverse function or
:func:`~tmtoolkit.bow.dtm.dtm_and_vocab_to_gensim_corpus_and_dict` which additionally creates a Gensim
:class:`~gensim.corpora.dictionary.Dictionary`.
:param dtm: (sparse) document-term-matrix of size NxM (N docs, M is vocab size) with raw terms counts
:return: a Gensim :class:`gensim.matutils.Sparse2Corpus` object
"""
import gensim
# DTM with documents to words sparse matrix in COO format has to be converted to transposed sparse matrix in CSC
# format
dtm_t = dtm.transpose()
if issparse(dtm_t):
if dtm_t.format != 'csc':
dtm_sparse = dtm_t.tocsc()
else:
dtm_sparse = dtm_t
else:
from scipy.sparse.csc import csc_matrix
dtm_sparse = csc_matrix(dtm_t)
return gensim.matutils.Sparse2Corpus(dtm_sparse)
def log_det_estimate_shogun(Q):
logging.debug("Entering")
op = RealSparseMatrixOperator(csc_matrix(Q))
engine = SerialComputationEngine()
linear_solver = CGMShiftedFamilySolver()
accuracy = 1e-3
eigen_solver = LanczosEigenSolver(op)
eigen_solver.set_min_eigenvalue(OzonePosterior.ridge)
op_func = LogRationalApproximationCGM(op, engine, eigen_solver,
linear_solver, accuracy)
# limit computation time
linear_solver.set_iteration_limit(1000)
eigen_solver.set_max_iteration_limit(1000)
logging.info("Computing Eigenvalues (only largest)")
eigen_solver.compute()
trace_sampler = ProbingSampler(op)
log_det_estimator = LogDetEstimator(trace_sampler, op_func, engine)
n_estimates = 1
logging.info(
"Sampling log-determinant with probing vectors and rational approximation"
)
estimates = log_det_estimator.sample(n_estimates)
logging.debug("Leaving")
return mean(estimates)
def solve_sparse_linear_system_shogun(A, b):
logging.debug("Entering")
solver = DirectSparseLinearSolver()
operator = RealSparseMatrixOperator(csc_matrix(A))
result = solver.solve(operator, b)
logging.debug("Leaving")
return result
def test_from_csc1():
from siconos.numerics import SBM_from_csparse, SBM_get_value
from scipy.sparse.csc import csc_matrix
M = csc_matrix([[1,2,3],
[4,5,6],
[7,8,9]])
# print(M.indices)
# print(M.indptr)
# print(M.data)
blocksize =3
r,SBM = SBM_from_csparse(blocksize,M)
assert SBM_get_value(SBM,0,0) == 1
assert SBM_get_value(SBM,0,1) == 2
assert SBM_get_value(SBM,0,2) == 3
assert SBM_get_value(SBM,1,0) == 4
assert SBM_get_value(SBM,1,1) == 5
assert SBM_get_value(SBM,1,2) == 6
assert SBM_get_value(SBM,2,0) == 7
assert SBM_get_value(SBM,2,1) == 8
assert SBM_get_value(SBM,2,2) == 9
def load_results(f_results):
"""
Load results from CNMF on various FOVs and merge them after some preprocessing
"""
# load data
i = 0
A_s = []
C_s = []
YrA_s = []
Cn_s = []
shape = None
b_s = []
f_s = []
for f_res in f_results:
print f_res
i += 1
with np.load(f_res) as ld:
A_s.append(csc.csc_matrix(ld['A2']))
C_s.append(ld['C2'])
YrA_s.append(ld['YrA'])
Cn_s.append(ld['Cn'])
b_s.append(ld['b2'])
f_s.append(ld['f2'])
if shape is not None:
shape_new = (ld['d1'], ld['d2'])
if shape_new != shape:
raise Exception('Shapes of FOVs not matching')
else:
shape = shape_new
else:
shape = (ld['d1'], ld['d2'])
return A_s, C_s, YrA_s, Cn_s, b_s, f_s, shape
def solve_sparse_linear_system_shogun(A, b):
logging.debug("Entering")
solver = DirectSparseLinearSolver()
operator = RealSparseMatrixOperator(csc_matrix(A))
result = solver.solve(operator, b)
logging.debug("Leaving")
return result
def load_results(f_results):
"""
Load results from CNMF on various FOVs and merge them after some preprocessing
"""
# load data
i=0
A_s=[]
C_s=[]
YrA_s=[]
Cn_s=[]
shape = None
b_s=[]
f_s=[]
for f_res in f_results:
print(f_res)
i+=1
with np.load(f_res) as ld:
A_s.append(csc.csc_matrix(ld['A2']))
C_s.append(ld['C2'])
YrA_s.append(ld['YrA'])
Cn_s.append(ld['Cn'])
b_s.append(ld['b2'])
f_s.append(ld['f2'])
if shape is not None:
shape_new=(ld['d1'],ld['d2'])
if shape_new != shape:
raise Exception('Shapes of FOVs not matching')
else:
shape = shape_new
else:
shape=(ld['d1'],ld['d2'])
return A_s,C_s,YrA_s, Cn_s, b_s, f_s, shape
def mass_stiffness_smooth(triangles, vertices, nb_iter=1,
diffusion_step=1.0, flow_file=None):
vertices_csc = csc_matrix(vertices)
curvature_normal_mtx = mean_curvature_normal_matrix(
triangles, vertices_csc, area_weighted=False)
# mass_mtx = mass_matrix(triangles, vertices_csc).astype(np.float)
if isinstance(diffusion_step, (int, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
if flow_file is not None:
mem_map = np.memmap(flow_file, dtype=G_DTYPE, mode='w+',
shape=(nb_iter, vertices.shape[0], vertices.shape[1]))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices_csc.toarray()
# get curvature_normal_matrix
mass_mtx = mass_matrix(triangles, vertices_csc).astype(np.float)
# (D - d*L)*y = D*x = b
A_matrix = mass_mtx - \
(diags(diffusion_step, 0).dot(curvature_normal_mtx))
b_matrix = mass_mtx.dot(vertices_csc)
vertices_csc = spsolve(A_matrix, b_matrix)
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
# return next_vertices_csc
return vertices_csc.toarray()
def CSCfromCompactRepresentation(diag_vals, upper_rows, upper_cols, upper_vals): n = len(diag_vals) rows = np.concatenate((np.arange(n), upper_rows, upper_cols)) cols = np.concatenate((np.arange(n), upper_cols, upper_rows)) ij = np.vstack((rows, cols)) vals = np.concatenate((diag_vals, upper_vals, upper_vals)) return csc_matrix((vals, ij), shape=(n, n))
def positive_curvature_normal_smooth(triangles, vertices, nb_iter=1,
diffusion_step=1.0, area_weighted=False,
backward_step=False, flow_file=None):
if flow_file is not None:
mem_map = np.memmap(flow_file, dtype=G_DTYPE, mode='w+',
shape=(nb_iter, vertices.shape[0], vertices.shape[1]))
if isinstance(diffusion_step, (int, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
curvature_normal_mtx = mean_curvature_normal_matrix(
triangles, vertices, area_weighted=area_weighted)
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices
# do the first step
next_vertices = euler_step(curvature_normal_mtx, csc_matrix(
vertices), diffusion_step, backward_step).toarray()
# test if direction is positive
direction = next_vertices - vertices
normal_dir = vertices_normal(triangles, next_vertices, normalize=False)
pos_curv = dot(direction, normal_dir, keepdims=True) < 0
vertices += direction * pos_curv
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
return vertices
def volume_mass_stiffness_smooth(triangles,
vertices,
nb_iter=1,
diffusion_step=1.0,
flow_file=None):
vertices_csc = csc_matrix(vertices)
curvature_normal_mtx = mean_curvature_normal_matrix(triangles,
vertices,
area_weighted=False)
if isinstance(diffusion_step, (int, long, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
if flow_file is not None:
mem_map = np.memmap(flow_file,
dtype=G_DTYPE,
mode='w+',
shape=(nb_iter, vertices.shape[0],
vertices.shape[1]))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices_csc.toarray()
# get curvature_normal_matrix
mass_mtx = mass_matrix(triangles, vertices)
raise NotImplementedError()
# (D - d*L)*y = D*x = b
A_matrix = mass_mtx - \
diags(diffusion_step, 0).dot(curvature_normal_mtx)
b_matrix = mass_mtx.dot(csc_matrix(vertices_csc))
next_vertices = spsolve(A_matrix, b_matrix)
# test if direction is positive
direction = next_vertices.toarray() - vertices_csc
normal_dir = vertices_cotan_normal(triangles,
next_vertices,
normalize=True)
dotv = normalize_vectors(direction).multiply(normal_dir)
vertices_csc += direction * np.maximum(0.0, -dotv)
# vertices_csc += direction * sigmoid(-np.arctan(dotv)*np.pi - np.pi)
# vertices_csc += direction * softplus(-dotv)
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
return vertices_csc.toarray()
def test_tocsc(self):
cscm = self.basic_m.tocsc()
m = self.basic_m
scipym = csc_matrix((m.data, (m.row, m.col)), shape=(4, 4))
self.assertListEqual(cscm.indices.tolist(), scipym.indices.tolist())
self.assertListEqual(cscm.indptr.tolist(), scipym.indptr.tolist())
self.assertListEqual(cscm.data.tolist(), scipym.data.tolist())
self.assertEqual(cscm.shape, scipym.shape)
self.assertIsInstance(cscm, SparseBase)
def build_sparse(R,U,rows,cols): """ Returns an equivalent matrix in CSC format. """ n = len(R) all_rows = np.concatenate((np.arange(n),rows,cols)) all_cols = np.concatenate((np.arange(n),cols,rows)) ij = np.vstack((all_rows,all_cols)) vals = np.concatenate((R,U,U)) return csc_matrix((vals,ij),shape=(n,n))
def subtract_dtm_frequencies(dtm_1, terms_1, dtm_2, terms_2):
"""
:param dtm_1: DTM to subtract frequencies from
:param terms_1: Terms (column names) for dtm_1
:param dtm_2: DTM to subtract frequencies to dtm_1
:param terms_2: Terms (column names) for dtm_2
:return: DTM with a unique row with the difference of frequencies from terms_1 minus terms_2
"""
arr_freq_1 = dtm_1.sum(axis=0).getA1()
arr_freq_2 = dtm_2.sum(axis=0).getA1()
return csc_matrix(subtract_term_frequencies(terms_1, arr_freq_1, terms_2, arr_freq_2))
def transpose(self, axes=None, copy=False):
if axes is not None:
raise ValueError(("Sparse matrices do not support "
"an 'axes' parameter because swapping "
"dimensions is the only logical permutation."))
M, N = self.shape
from scipy.sparse.csc import csc_matrix
return csc_matrix((self.data, self.indices, self.indptr),
shape=(N, M),
copy=copy)
def laplacian_smooth(triangles,
vertices,
nb_iter=1,
diffusion_step=1.0,
l2_dist_weighted=False,
area_weighted=False,
backward_step=False,
flow_file=None):
if flow_file is not None:
mem_map = np.memmap(flow_file,
dtype=G_DTYPE,
mode='w+',
shape=(nb_iter, vertices.shape[0],
vertices.shape[1]))
vertices_csc = csc_matrix(vertices)
if isinstance(diffusion_step, (int, long, float)):
diffusion_step = diffusion_step * np.ones(len(vertices))
for i in range(nb_iter):
stdout.write("\r step %d on %d done" % (i, nb_iter))
stdout.flush()
if flow_file is not None:
mem_map[i] = vertices_csc.toarray()
if l2_dist_weighted:
# if l2_dist_weighted, we need to compute laplacian_matrix
# each iteration (because ||e_ij|| change)
# A_ij_l2_dist_weighted = A_ij / ||e_ij||
adjacency_matrix = edge_length(triangles, vertices_csc)
###################################################################
# adjacency_matrix.data **= -1
# laplacian_matrix = laplacian(adjacency_matrix, diag_of_1=False)
###################################################################
adjacency_matrix.data **= 1 # 1
laplacian_matrix = laplacian(adjacency_matrix, diag_of_1=True)
else:
adjacency_matrix = edge_adjacency(triangles, vertices_csc)
laplacian_matrix = laplacian(adjacency_matrix, diag_of_1=True)
if area_weighted:
vts_mix_area = vertices_mix_area(triangles, vertices_csc)
laplacian_matrix = diags(vts_mix_area**-1, 0).dot(laplacian_matrix)
next_vertices_csc = euler_step(laplacian_matrix, vertices_csc,
diffusion_step, backward_step)
vertices_csc = next_vertices_csc
stdout.write("\r step %d on %d done \n" % (nb_iter, nb_iter))
# return next_vertices_csc
return next_vertices_csc.toarray()
def exhaustive_set(G, query_nodes, target_nodes, n_edges, start_dist):
"""Exaustively searches all the combinations of k links between
a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(G, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if G.has_edge(candidates[i][0], candidates[i][1]) == False]
ac_scores = [row_sums]
exhaustive_links = []
for L in range(1, n_edges+1):
print '\t Number of edges {}'.format(L)
round_min = -1
best_combination = []
for subset in combinations(eligible, L):
H = G.copy()
F_modified = F.copy()
for links_to_add in subset:
F_updated = update_fundamental_mat(F_modified, H, map_query_to_org, links_to_add[0])
H.add_edge(links_to_add[0], links_to_add[1])
F_modified = F_updated
abs_cen = start_dist.dot( F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
best_combination = subset
round_min = abs_cen
exhaustive_links.append(best_combination)
ac_scores.append(round_min)
return exhaustive_links, ac_scores
def dtm_to_gensim_corpus(dtm):
import gensim
# DTM with documents to words sparse matrix in COO format has to be converted to transposed sparse matrix in CSC
# format
dtm_t = dtm.transpose()
if hasattr(dtm_t, 'tocsc'):
dtm_sparse = dtm_t.tocsc()
else:
from scipy.sparse.csc import csc_matrix
dtm_sparse = csc_matrix(dtm_t)
return gensim.matutils.Sparse2Corpus(dtm_sparse)
def test_get_dtm_frequency_diff(self):
texts_2 = [
"Más texto con la letra eñe", "Este texto también contiene la eñe"
]
dtm_1 = vec.fit_transform(TEXTS)
terms_1 = np.array(vec.get_feature_names())
dtm_2 = vec.fit_transform(texts_2)
terms_2 = np.array(vec.get_feature_names())
result = dtm.subtract_dtm_frequencies(dtm_1, terms_1, dtm_2, terms_2)
expected = csc_matrix([0, 2, 1, 1, -1, -1, 0, 1, 2, 1])
self.assertTrue(dtm.equal(expected, result))
def test():
"""
Test function ran with -t flag
"""
print "Running 5 node test ...."
g = csc_matrix([[0, 1, 0, 0, 1], [1, 0, 1, 1, 0], [0, 1, 0, 1, 0],
[0, 1, 1, 0, 0], [1, 0, 0, 0, 1]])
print "Input csc: \n", g.todense()
print "Python igraph ...\n", csc_to_igraph(g).get_adjacency()
from r_utils import r_igraph_get_adjacency
print "R igraph ...\n", r_igraph_get_adjacency(csc_to_r_igraph(g))
def tocsc(self, copy=False):
idx_dtype = get_index_dtype((self.indptr, self.indices),
maxval=max(self.nnz, self.shape[0]))
indptr = np.empty(self.shape[1] + 1, dtype=idx_dtype)
indices = np.empty(self.nnz, dtype=idx_dtype)
data = np.empty(self.nnz, dtype=upcast(self.dtype))
csr_tocsc(self.shape[0], self.shape[1], self.indptr.astype(idx_dtype),
self.indices.astype(idx_dtype), self.data, indptr, indices,
data)
from scipy.sparse.csc import csc_matrix
A = csc_matrix((data, indices, indptr), shape=self.shape)
A.has_sorted_indices = True
return A
def test_jaccard():
implicit_matrix = np.array([[1, 1, 1, 1], [1, 1, 0, 0], [0, 0, 1, 0]])
assert implicit_matrix.shape == (3, 4)
implicit_matrix = csc_matrix(implicit_matrix)
n2i = {"huey": 0, "dewey": 1, "louie": 2, "chewy": 3}
t2i = {"Batman": 0, "Mystery Men": 1, "Taxi Driver": 2}
i2n = {v: k for k, v in n2i.items()}
i2t = {v: k for k, v in t2i.items()}
jrec = JaccardRecommender(implicit_matrix,
p2i=None,
t2i=t2i,
i2t=i2t,
i2p=None)
print(jrec.item_to_item(N=10, title="Batman"))
def tf_idf(df, voc, idf=None, mode='train'):
vectorizer_tit = CountVectorizer(token_pattern='\w+', vocabulary=voc)
vectorizer_des = CountVectorizer(token_pattern='\w+', vocabulary=voc)
vectorizer_com = CountVectorizer(token_pattern='\w+', vocabulary=voc)
# fit vectorizer on data(text:srting) -> vector of features
vec_fit_tit = vectorizer_tit.fit_transform(df['title'])
vec_fit_des = vectorizer_des.fit_transform(df['description'])
vec_fit_com = vectorizer_com.fit_transform(df['combined'])
# count each word
counts_tit = np.array(vec_fit_tit.sum(axis=0)).flatten().tolist()
counts_des = np.array(vec_fit_des.sum(axis=0)).flatten().tolist()
counts_com = np.array(vec_fit_com.sum(axis=0)).flatten().tolist()
# get each uniq word in data
words_tit = vectorizer_tit.get_feature_names()
words_des = vectorizer_des.get_feature_names()
words_com = vectorizer_com.get_feature_names()
# dictionary of word and collection frequency
df_tit = pd.Series(counts_tit, index=words_tit).to_dict()
df_des = pd.Series(counts_des, index=words_des).to_dict()
df_com = pd.Series(counts_com, index=words_com).to_dict()
if (mode == 'train'):
# calculate idf vector
N = df.shape[0]
idf = {}
for term in df_com.keys():
idf[term] = np.log(N) - np.log(
df_com[term] + 0.000001
) # calculate idf based on combined 'title'+'description'.
idf = csc.csc_matrix(list(
idf.values())) # convert idf values to sparse matrix
# calculate tfidf vectors
tfidf_tit_csc = idf.multiply(vec_fit_tit)
tfidf_des_csc = idf.multiply(vec_fit_des)
tfidf_com_csc = idf.multiply(vec_fit_com)
for index, row in df.iterrows():
df.at[index, 'title'] = tfidf_tit_csc[index]
df.at[index, 'description'] = tfidf_des_csc[index]
df.at[index, 'combined'] = tfidf_com_csc[index]
return (df, idf)
def test_mul_sparse_matrix(self):
#from pyomo.contrib.pynumero.sparse.block_matrix import BlockMatrix
# test unsymmetric times unsymmetric
m = self.basic_m
dense_m = m.toarray()
res = m * m
dense_res = np.matmul(dense_m, dense_m)
self.assertFalse(res.is_symmetric)
self.assertTrue(np.allclose(res.toarray(), dense_res))
# test symmetric result
m = self.basic_m
dense_m = m.toarray()
res = m.transpose() * m
dense_res = np.matmul(dense_m.transpose(), dense_m)
self.assertTrue(res.is_symmetric)
self.assertTrue(np.allclose(res.toarray(), dense_res))
# test unsymmetric with rectangular
m = self.basic_m
dense_m2 = np.array([[1.0, 2.0], [3.0, 4.0], [5.0, 6.0], [7.0, 8.0]])
m2 = CSCMatrix(dense_m2)
res = m * m2
dense_res = np.matmul(m.toarray(), dense_m2)
self.assertFalse(res.is_symmetric)
self.assertTrue(np.allclose(res.toarray(), dense_res))
# test unsymmetric with rectangular scipycsr
m = self.basic_m
dense_m2 = np.array([[1.0, 2.0], [3.0, 4.0], [5.0, 6.0], [7.0, 8.0]])
m2 = csc_matrix(dense_m2)
with self.assertRaises(Exception) as context:
res = m * m2
# test product with symmetric matrix
m = self.basic_m
dense_m = m.todense()
m2 = self.basic_sym_m
dense_m2 = m2.todense()
res = m * m2
res_dense = np.matmul(dense_m, dense_m2)
self.assertTrue(np.allclose(res.todense(), res_dense))
"""
def lpDot(mat, arr):
"""
CSC matrix-vector or CSC matrix-matrix dot product (A x b)
:param mat: CSC sparse matrix (A)
:param arr: dense vector or matrix of object type (b)
:return: vector or matrix result of the product
"""
n_rows, n_cols = mat.shape
# check dimensional compatibility
assert (n_cols == arr.shape[0])
# check that the sparse matrix is indeed of CSC format
if mat.format == 'csc':
mat_2 = mat
else:
# convert the matrix to CSC sparse
mat_2 = csc_matrix(mat)
if len(arr.shape) == 1:
"""
Uni-dimensional sparse matrix - vector product
"""
res = np.zeros(n_rows, dtype=arr.dtype)
for i in range(n_cols):
for ii in range(mat_2.indptr[i], mat_2.indptr[i + 1]):
j = mat_2.indices[ii] # row index
res[j] += mat_2.data[ii] * arr[
i] # C.data[ii] is equivalent to C[i, j]
else:
"""
Multi-dimensional sparse matrix - matrix product
"""
cols_vec = arr.shape[1]
res = np.zeros((n_rows, cols_vec), dtype=arr.dtype)
for k in range(
cols_vec
): # for each column of the matrix "vec", do the matrix vector product
for i in range(n_cols):
for ii in range(mat_2.indptr[i], mat_2.indptr[i + 1]):
j = mat_2.indices[ii] # row index
res[j, k] += mat_2.data[ii] * arr[
i, k] # C.data[ii] is equivalent to C[i, j]
return res
def test():
"""
Test function ran with -t flag
"""
print "Running 5 node test ...."
g = csc_matrix([
[0, 1, 0, 0, 1],
[1, 0, 1, 1, 0],
[0, 1, 0, 1, 0],
[0, 1, 1, 0, 0],
[1, 0, 0, 0, 1]
])
print "Input csc: \n", g.todense()
print "Python igraph ...\n", csc_to_igraph(g).get_adjacency()
from r_utils import r_igraph_get_adjacency
print "R igraph ...\n", r_igraph_get_adjacency(csc_to_r_igraph(g))
def random_links(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a random set of links between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(G, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if G.has_edge(candidates[i][0], candidates[i][1]) == False]
links_to_add = sample(eligible, n_edges)
ac_scores = []
ac_scores.append(row_sums)
i = 0
while i < n_edges:
F_updated = update_fundamental_mat(F, G, map_query_to_org, links_to_add[i][0])
G.add_edge(links_to_add[i][0], links_to_add[i][1])
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
F = F_updated
ac_scores.append(abs_cen)
i += 1
return links_to_add, ac_scores
def doFeatureEncoding(self, features):
""" do feature encoding to original features"""
encodedFeatures = None
whitenedFeatures = whiten(features)
if self._featureEncodingMethod == 'vector-quantization':
# Vector quantization
# each row is a feature vector
index, _ = vq(whitenedFeatures, self._codebook)
row, _ = features.shape
col = config.codebookSize
encodedFeatures = np.zeros((row, col))
for i in xrange(len(index)):
encodedFeatures[i, index[i]] = 1
elif self._featureEncodingMethod == 'sparse-coding':
# Sparse coding
# each column is a feature vector
X = np.asfortranarray(whitenedFeatures.transpose())
X = np.asfortranarray(X / np.tile(np.sqrt((X*X).sum(axis=0)),
(X.shape[0],1)),
dtype= X.dtype)
D = np.asfortranarray(self._codebook.transpose())
D = np.asfortranarray(D / np.tile(np.sqrt((D*D).sum(axis=0)),
(D.shape[0],1)),
dtype = D.dtype)
# Parameters of the optimization are chosen
param = {
'lambda1': 0.15,
'numThreads': -1,
'mode': 0
}
alpha = spams.lasso(X, D, **param) # alpha is sparse matrix
alphaShape = (D.shape[1], X.shape[1])
denseMatrix = csc_matrix(alpha, shape = alphaShape).todense()
encodedFeatures = np.asarray(denseMatrix).transpose()
return encodedFeatures
def kmeans(X, K, maxiters, M=None, eps=1e-3):
"""Standard k-means.
_X_ is data rowwise. _K_ is the number of
clusters. _M_ is the set of centers.
Implementation tries to save some computation cycles.
"""
N, d = X.shape
if M is None:
tmp = np.random.permutation(N)
M = X[tmp[:K]].copy()
costs = []
last = np.inf
X_sq_sum = np.sum(X**2)
for i in xrange(maxiters):
# see metric.py, but here: don't need squares from
# X, because _minimal_ cost over K is independent from it.
cost = -2*np.dot(X, M.T) + np.sum(M**2, axis=1)
idx = np.argmin(cost, axis=1)
cost = cost[xrange(N), idx]
costs.append(X_sq_sum + np.sum(cost))
if (last - costs[-1]) < eps:
break
last = costs[-1]
# Determine new centers
# Sparseification from Jakob Verbeek's kmeans code,
# http://lear.inrialpes.fr/~verbeek/software.php
ind = csc.csc_matrix( (np.ones(N), (idx, xrange(N))), shape=(K, N))
M = ind.dot(X)
weights = np.array(ind.sum(axis=1))
# Handle problem: no points assigned to a cluster
zeros_idx = (weights.ravel()==0)
zeros = np.sum(zeros_idx)
tmp = np.random.permutation(N)
M[zeros_idx, :] = X[tmp[:zeros]].copy()
weights[zeros_idx] = 1
M /= weights
return M, costs
def kmeans(X, K, maxiters, M=None, eps=1e-3):
"""Standard k-means.
_X_ is data rowwise. _K_ is the number of
clusters. _M_ is the set of centers.
Implementation tries to save some computation cycles.
"""
N, d = X.shape
if M is None:
tmp = np.random.permutation(N)
M = X[tmp[:K]].copy()
costs = []
last = np.inf
X_sq_sum = np.sum(X**2)
for i in xrange(maxiters):
# see metric.py, but here: don't need squares from
# X, because _minimal_ cost over K is independent from it.
cost = -2 * np.dot(X, M.T) + np.sum(M**2, axis=1)
idx = np.argmin(cost, axis=1)
cost = cost[xrange(N), idx]
costs.append(X_sq_sum + np.sum(cost))
if (last - costs[-1]) < eps:
break
last = costs[-1]
# Determine new centers
# Sparseification from Jakob Verbeek's kmeans code,
# http://lear.inrialpes.fr/~verbeek/software.php
ind = csc.csc_matrix((np.ones(N), (idx, xrange(N))), shape=(K, N))
M = ind.dot(X)
weights = np.array(ind.sum(axis=1))
# Handle problem: no points assigned to a cluster
zeros_idx = (weights.ravel() == 0)
zeros = np.sum(zeros_idx)
tmp = np.random.permutation(N)
M[zeros_idx, :] = X[tmp[:zeros]].copy()
weights[zeros_idx] = 1
M /= weights
return M, costs
def kmeans_np(X, lmbda, M=None):
"""Non-parametric kmeans.
_X_ is input data, rowwise. _lmbda_ controls
tradeoff between standard kmeans and cluster
penalty term.
See http://www.cs.berkeley.edu/~jordan/papers/kulis-jordan-icml12.pdf
"""
N, d = X.shape
if M is None:
M = np.mean(X, axis=0).reshape(1, d)
k = M.shape[0] - 1
X_sq_sum = np.sum(X**2, axis=1)
ind = np.zeros(N)
old_ind = ind.copy()
tmp = 0
iters = 1
while True:
print "Iteration ", iters
iters = iters + 1
for i in xrange(N):
tmp = -2 * np.dot(X[i], M.T) + np.sum(M**2, axis=1)
idx = np.argmin(tmp)
if (X_sq_sum[i] + tmp[idx]) > lmbda:
k = k + 1
M = np.append(M, X[i].copy().reshape(1, d), axis=0)
ind[i] = k
print "Adding cluster for ", i, k
else:
ind[i] = idx
if np.all(old_ind == ind):
break
# see kmeans above
ind_all = csc.csc_matrix((np.ones(N), (ind, xrange(N))),
shape=(k + 1, N))
M = ind_all.dot(X)
M /= np.array(ind_all.sum(axis=1))
old_ind = ind
ind = np.zeros(N)
return M, np.array(ind_all.sum(axis=1)).ravel()
def writetest(desikan):
"""
Write Test function ran with -t flag
Positional Args:
===============
desikan - use the desikan mapping?
"""
from scipy.sparse.csc import csc_matrix
print "Running 5 node test ...."
g = csc_matrix([
[0, 1, 0, 0, 5],
[1, 0, 3, 1, 0],
[0, 3, 0, 1, 0],
[0, 1, 1, 0, 0],
[5, 0, 0, 0, 0]
])
src = csc_to_graphml(g, test=True, desikan=desikan)
print "Test complete ..."
print src
def kmeans_np(X, lmbda, M=None):
"""Non-parametric kmeans.
_X_ is input data, rowwise. _lmbda_ controls
tradeoff between standard kmeans and cluster
penalty term.
See http://www.cs.berkeley.edu/~jordan/papers/kulis-jordan-icml12.pdf
"""
N, d = X.shape
if M is None:
M = np.mean(X, axis=0).reshape(1, d)
k = M.shape[0] - 1
X_sq_sum = np.sum(X**2, axis=1)
ind = np.zeros(N)
old_ind = ind.copy()
tmp = 0
iters = 1
while True:
print "Iteration ", iters
iters = iters + 1
for i in xrange(N):
tmp = -2*np.dot(X[i], M.T) + np.sum(M**2, axis=1)
idx = np.argmin(tmp)
if (X_sq_sum[i] + tmp[idx]) > lmbda:
k = k + 1
M = np.append(M, X[i].copy().reshape(1, d), axis=0)
ind[i] = k
print "Adding cluster for ", i, k
else:
ind[i] = idx
if np.all(old_ind == ind):
break
# see kmeans above
ind_all = csc.csc_matrix((np.ones(N), (ind, xrange(N))), shape=(k+1, N))
M = ind_all.dot(X)
M /= np.array(ind_all.sum(axis=1))
old_ind = ind
ind = np.zeros(N)
return M, np.array(ind_all.sum(axis=1)).ravel()
def igraph_to_csc(g, save=False, fn="csc_matlab"):
"""
Convert an igraph to scipy.sparse.csc.csc_matrix
Positional arguments:
=====================
g - the igraph graph
Optional arguments:
===================
save - save file to disk
fn - the file name to be used when writing (appendmat = True by default)
"""
assert isinstance(g, igraph.Graph), "Arg1 'g' must be an igraph graph"
print "Creating CSC from igraph object ..."
gs = csc_matrix(g.get_adjacency().data) # Equiv of calling to_dense so may case MemError
print "CSC creation complete ..."
if save:
print "Saving to MAT file ..."
sio.savemat(fn, {"data":gs}, True) # save as MAT format only. No other options!
return gs
def doFeatureEncoding(self, features):
""" do feature encoding to original features"""
encodedFeatures = None
whitenedFeatures = whiten(features)
if self._featureEncodingMethod == 'vector-quantization':
# Vector quantization
# each row is a feature vector
index, _ = vq(whitenedFeatures, self._codebook)
row, _ = features.shape
col = config.codebookSize
encodedFeatures = np.zeros((row, col))
for i in xrange(len(index)):
encodedFeatures[i, index[i]] = 1
elif self._featureEncodingMethod == 'sparse-coding':
# Sparse coding
# each column is a feature vector
X = np.asfortranarray(whitenedFeatures.transpose())
X = np.asfortranarray(X / np.tile(np.sqrt((X * X).sum(axis=0)),
(X.shape[0], 1)),
dtype=X.dtype)
D = np.asfortranarray(self._codebook.transpose())
D = np.asfortranarray(D / np.tile(np.sqrt((D * D).sum(axis=0)),
(D.shape[0], 1)),
dtype=D.dtype)
# Parameters of the optimization are chosen
param = {'lambda1': 0.15, 'numThreads': -1, 'mode': 0}
alpha = spams.lasso(X, D, **param) # alpha is sparse matrix
alphaShape = (D.shape[1], X.shape[1])
denseMatrix = csc_matrix(alpha, shape=alphaShape).todense()
encodedFeatures = np.asarray(denseMatrix).transpose()
return encodedFeatures
def test_from_csc1():
from siconos.numerics import SBM_from_csparse, SBM_get_value
from scipy.sparse.csc import csc_matrix
M = csc_matrix([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
# print(M.indices)
# print(M.indptr)
# print(M.data)
blocksize = 3
r, SBM = SBM_from_csparse(blocksize, M)
assert SBM_get_value(SBM, 0, 0) == 1
assert SBM_get_value(SBM, 0, 1) == 2
assert SBM_get_value(SBM, 0, 2) == 3
assert SBM_get_value(SBM, 1, 0) == 4
assert SBM_get_value(SBM, 1, 1) == 5
assert SBM_get_value(SBM, 1, 2) == 6
assert SBM_get_value(SBM, 2, 0) == 7
assert SBM_get_value(SBM, 2, 1) == 8
assert SBM_get_value(SBM, 2, 2) == 9
# ================================================================================
import numpy as np
from scipy.sparse.csc import csc_matrix
import pyGPs
from pyGPs.Validation import valid
from pyGPs.GraphExtensions import graphUtil, graphKernels
location = "graphData/"
data = np.load(location + "MUTAG.npz")
# n = num of nodes
# N = num of graphs
# p = num of labels
A = csc_matrix(
(data["adj_data"], data["adj_indice"], data["adj_indptr"]), shape=data["adj_shape"]
) # n x n adjancy array (sparse matrix)
gr_id = data["graph_ind"] # n x 1 graph id array
node_label = data["responses"] # n x 1 node label array
graph_label = data["labels"] # N x 1 graph label array
N = graph_label.shape[0] # number of graphs)
graph_label = np.int8(graph_label)
for i in xrange(N):
if graph_label[i, 0] == 0:
graph_label[i, 0] -= 1
# ===========================================================================
# COMPUTE PROPAGATION KERNELS
# ===========================================================================
num_Iteration = 10
# Marion Neumann, Daniel Marthaler, Shan Huang & Kristian Kersting, 18/02/2014
#================================================================================
import numpy as np
from scipy.sparse.csc import csc_matrix
import pyGPs
from pyGPs.Validation import valid
from pyGPs.GraphExtensions import graphUtil,graphKernels
location = 'graphData/'
data = np.load(location+'MUTAG.npz')
# n = num of nodes
# N = num of graphs
# p = num of labels
A = csc_matrix( (data['adj_data'], data['adj_indice'], \
data['adj_indptr']), shape=data['adj_shape']) # n x n adjancy array (sparse matrix)
gr_id = data['graph_ind'] # n x 1 graph id array
node_label = data['responses'] # n x 1 node label array
graph_label = data['labels'] # N x 1 graph label array
N = graph_label.shape[0] # number of graphs)
graph_label = np.int8(graph_label)
for i in range(N):
if graph_label[i,0] == 0:
graph_label[i,0] -= 1
#===========================================================================
# COMPUTE PROPAGATION KERNELS
#===========================================================================
num_Iteration = 10
w = 1e-4
def get_approx_boundary(G, query_nodes, target_nodes, n_edges, start_dist):
"""
Used to calculate an approximation guarantee for greedy algorithm
"""
H = G.copy() # GET A COPY OF THE GRAPH
query_set_size = len(query_nodes)
target_set_size = len(target_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
candidates = list(product(query_nodes, target_nodes))
# ALL minus exitsting in G
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
# CALCULATE MARGINAL GAIN TO EMPTY SET FOR ALL NODES IN STEEPNESS FUNCTION
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums_empty = start_dist.dot(F.sum(axis=1))[0,0] # F(\emptyset)
# candidates = list(product(query_nodes, target_nodes))
ac_marginal_empty = []
ac_marginal_full = []
source_idx_empty = []
node_processed = -1
for out_edge in eligible:
abs_cen = -1
source_node = out_edge[0]
if(node_processed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_processed = source_node
F_updated = update_fundamental_mat(F, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
ac_marginal_empty.append(abs_cen)
source_idx_empty.append(source_node)
sorted_indexes_empty = [i[0] for i in sorted(enumerate(source_idx_empty), key=lambda x:x[1])]
ac_marginal_empty = [ac_marginal_empty[i] for i in sorted_indexes_empty]
# CALCULATE MARGINAL GAIN FOR FULL SET
H.add_edges_from(eligible)
P_all = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs_all = P_all[list(query_nodes),:][:,list(query_nodes)]
F_all = compute_fundamental(P_abs_all)
row_sums_all = start_dist.dot(F_all.sum(axis=1))[0,0]
node_prcessed = -1
source_idx = []
for out_edge in eligible:
abs_cen = -1
source_node = out_edge[0]
if(node_prcessed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_prcessed = source_node
F_all_updated = update_rev_fundamental_mat(F_all, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_all_updated.sum(axis = 1))[0,0]
ac_marginal_full.append(abs_cen)
source_idx.append(source_node)
sorted_indexes = [i[0] for i in sorted(enumerate(source_idx), key=lambda x:x[1])]
ac_marginal_full = [ac_marginal_full[i] for i in sorted_indexes]
assert sorted_indexes == sorted_indexes_empty , "Something is wrong with the way scores are appended"
all_steepness = (asarray(ac_marginal_full) - row_sums_all) / (row_sums_empty-asarray(ac_marginal_empty))
s = min(all_steepness)
node_max = argmin(all_steepness)
return 1-s, sorted_indexes[node_max]
def greedy_navigation(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a set of links with a greedy descent algorithm that reduce the
absorbing RW centrality between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset. The query and target set
must be a 'viable' partition of the graph.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
P : Scipy matrix
The transition matrix of the graph G
F : Scipy matrix
The fundamental matrix for the graph G with the given set of absorbing
random walk nodes
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
"""
H = G.copy()
prng = RandomState()
query_set_size = len(query_nodes)
target_set_size = len(target_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum(axis=1))[0,0]
best_F = zeros(F.shape)
optimal_set = []
ac_scores = []
ac_scores.append(row_sums)
while n_edges > 0:
round_min = -1
best_node = -1
for i in query_nodes:
abs_neighbours = [l for l in H.neighbors(i) if l in target_nodes]
if len(abs_neighbours) == target_set_size:
continue
F_updated = update_fundamental_mat(F, H, map_query_to_org, i)
abs_cen = start_dist.dot( F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
best_node = i
round_min = abs_cen
best_F = F_updated
F = best_F
ac_scores.append(round_min)
optimal_candidate_edges = [(best_node, k, round_min)
for k in target_nodes
if H.has_edge(best_node, k) == False ]
try:
edge_idx = prng.randint(0, len(optimal_candidate_edges))
except ValueError:
print(H.neighbors(best_node))
print([l for l in H.neighbors(best_node) if l in target_nodes])
print(best_node)
print(optimal_candidate_edges)
print(target_nodes)
H.add_edge(optimal_candidate_edges[edge_idx][0],
optimal_candidate_edges[edge_idx][1])
optimal_set.append(optimal_candidate_edges[edge_idx])
n_edges -= 1
return optimal_set, ac_scores
def reverse_greedy(G, query_nodes, target_nodes, n_edges, start_dist):
"""Selects a set of links with a reverse greedy descent algorithm that reduce the
absorbing RW centrality between a set of query nodes Q and a set of absorbing
target nodes C such that Q \cap C = \emptyset. The query and target set
must be a 'viable' partition of the graph.
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
P : Scipy matrix
The transition matrix of the graph G
F : Scipy matrix
The fundamental matrix for the graph G with the given set of absorbing
random walk nodes
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
"""
H = G.copy()
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
H.add_edges_from(eligible)
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum(axis=1))[0,0]
# candidates = list(product(query_nodes, target_nodes))
worst_F = zeros(F.shape)
worst_set = []
optimal_set = []
ac_scores = []
# ac_scores.append(row_sums)
while len(eligible) > 0:
round_min = -1
worst_link = (-1,-1)
node_prcessed = -1
for out_edge in eligible:
source_node = out_edge[0]
if(node_prcessed == source_node):
# skip updating matrix because this updates the F matrix in the same way
continue
node_prcessed = source_node
F_updated = update_rev_fundamental_mat(F, H, map_query_to_org, source_node)
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
if abs_cen < round_min or round_min == -1:
worst_link = out_edge
round_min = abs_cen
worst_F = F_updated
F = worst_F
H.remove_edge(*worst_link)
worst_set.append(worst_link)
eligible.remove(worst_link)
if (len(eligible) <= n_edges):
ac_scores.append(round_min)
optimal_set.append(worst_link)
return list(reversed(optimal_set)), list(reversed(ac_scores))
def link_prediction(G, query_nodes, target_nodes, n_edges, start_dist, alg = "ra"):
"""Selects a random set of links between based on the scores calculated by
a standard link-prediction algorithm from networkx library
Parameters
----------
G : Networkx graph
The graph from which the team will be selected.
query : list
The set of nodes from which random walker starts.
target : list
The set of nodes from where the random walker ends.
n_edges : integer
the number of links to be added
start_dist: list
The starting distribution over the query set
alg: string
A string describing the link-prediction algorithm to be used
Returns
-------
links : list
The set of links that reduce the absorbing RW centrality
ac_scores: list
The set of scores of adding the links
"""
assert alg in ["ra", "pa", "jaccard", "aa"], "alg must be one of [\"ra\", \"pa\", \"jaccard\", \"aa\"]."
H = G.copy()
query_set_size = len(query_nodes)
map_query_to_org = dict(zip(query_nodes, range(query_set_size)))
P = csc_matrix(nx.google_matrix(H, alpha=1))
P_abs = P[list(query_nodes),:][:,list(query_nodes)]
F = compute_fundamental(P_abs)
row_sums = start_dist.dot(F.sum())[0,0]
candidates = list(product(query_nodes, target_nodes))
eligible = [candidates[i] for i in range(len(candidates))
if H.has_edge(candidates[i][0], candidates[i][1]) == False]
links_to_add = []
if alg == 'ra':
preds = nx.resource_allocation_index(H, eligible)
elif alg == 'jaccard':
preds = nx.jaccard_coefficient(H, eligible)
elif alg == 'aa':
preds = nx.adamic_adar_index(H, eligible)
elif alg == 'pa':
preds = nx.preferential_attachment(H, eligible)
for u,v,p in preds:
links_to_add.append((u,v,p))
links_to_add.sort(key=lambda x: x[2], reverse = True)
ac_scores = []
ac_scores.append(row_sums)
i = 0
while i < n_edges:
F_updated = update_fundamental_mat(F, H, map_query_to_org, links_to_add[i][0])
H.add_edge(links_to_add[i][0], links_to_add[i][1])
abs_cen = start_dist.dot(F_updated.sum(axis = 1))[0,0]
F = F_updated
ac_scores.append(abs_cen)
i += 1
return links_to_add, ac_scores
def threshold_components(A_s,shape,min_size=5,max_size=np.inf,max_perc=.5,remove_unconnected_components=True):
"""
Threshold components output of a CNMF algorithm (A matrices)
Parameters:
----------
A_s: list
list of A matrice output from CNMF
min_size: int
min size of the component in pixels
max_size: int
max size of the component in pixels
max_perc: float
fraction of the maximum of each component used to threshold
remove_unconnected_components: boolean
whether to remove components that are fragmented in space
Returns:
-------
B_s: list of the thresholded components
lab_imgs: image representing the components in ndimage format
cm_s: center of masses of each components
"""
B_s=[]
lab_imgs=[]
cm_s=[]
for A_ in A_s:
print('*')
max_comps=A_.max(0).todense().T
tmp=[]
cm=[]
lim=np.zeros(shape)
for idx,a in enumerate(A_.T):
#create mask by thresholding to 50% of the max
mask=np.reshape(a.todense()>(max_comps[idx]*max_perc),shape)
label_im, nb_labels = ndimage.label(mask)
sizes = ndimage.sum(mask, label_im, list(range(nb_labels + 1)))
if remove_unconnected_components:
l_largest=(label_im==np.argmax(sizes))
cm.append(scipy.ndimage.measurements.center_of_mass(l_largest,l_largest))
lim[l_largest] = (idx+1)
# #remove connected components that are too small
mask_size=np.logical_or(sizes<min_size,sizes>max_size)
if np.sum(mask_size[1:])>1:
print(('removing ' + str( np.sum(mask_size[1:])-1) + ' components'))
remove_pixel=mask_size[label_im]
label_im[remove_pixel] = 0
label_im=(label_im>0)*1
tmp.append(label_im.flatten())
cm_s.append(cm)
lab_imgs.append(lim)
B_s.append(csc.csc_matrix(np.array(tmp)).T)
return B_s, lab_imgs, cm_s
def log_det_shogun_exact(Q):
logging.debug("Entering")
logdet = Statistics.log_det(csc_matrix(Q))
logging.debug("Leaving")
return logdet
def log_det_shogun_exact_plus_noise(Q):
logging.debug("Entering")
logdet = Statistics.log_det(csc_matrix(Q)) + randn()
logging.debug("Leaving")
return logdet
def log_det_scikits(Q):
d = cholesky(csc_matrix(Q)).L().diagonal()
return 2 * sum(log(d))
raise Exception("cholmod not installed")
fh.seek(pos)
print "Getting edges ..."
line = ""
while True:
line += fh.readline().replace(" ", "").strip() # remove if inefficient
if line.endswith("</edge>"):
edge = get_edge(line)
g[edge[0], edge[1]] = edge[2] # Naive i.e slow. TODO: Optimize
line = ""
elif line.endswith("</graphml>"):
break
return csc_matrix(g) # Convert to CSC first
def get_edge(st):
"""
Given a string I need to extract src, dest, weight (if available)
No other edge attributes are representable
Positional Args:
===============
st - the string
"""
global __weight__
src = int(re.search("(?<=source=[\"']n)\d+", st).group())
dest = int(re.search("(?<=target=[\"']n)\d+", st).group())
if __weight__:
def csc_to_graphml(g, is_weighted=True, desikan=False, is_directed=False, save_fn="default_name.graphml", is_tri=False, test=False):
"""
Convert a csc graph to graphml format for writing to disk
Positional arguments:
====================
g - the csc graph
Optional arguments:
===================
is_weighted - is the graph weighted. Type: boolean.
desikan - use the desikan mapping to label nodes. Type: boolean
is_directed - is g symmetric ? Type: boolean
save_fn - file name to use when saving. Type: boolean
is_tri - is the adjacency mat upper or lower triangular. Type: boolean
test - are we running a test. Type: boolean
"""
print "Beginning graphml construction .."
if test: test_str = ""
tabs = 2 # How many tabs on affix to the front
src = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<!-- Created by script: %s -->\n""" % __file__
# Do we have desikan labels ?
if desikan:
from mrcap import desikan
src += " "*2+"<key id=\"v_region\" for=\"node\" attr.name=\"region\" attr.type=\"string\"/>\n" # Desikan vertex attr called v_region
tabs = 3
# Is our graph weighted ?
if is_weighted:
src += " "*2+"<key id=\"e_weight\" for=\"edge\" attr.name=\"weight\" attr.type=\"double\"/>\n" # Desikan vertex attr called v_region
tabs = 3
# Directed graph ?
if is_directed:
src += "\n <graph id=\"G\" edgedefault=\"undirected\">"
# Undirected graph?
else: # not directed so just use upper tri
if not is_tri:
print "Converting to upper triangular ..."
from scipy.sparse.csc import csc_matrix
from scipy.sparse import triu
g = g = csc_matrix(triu(g, k=0))
src += "\n <graph id=\"G\" edgedefault=\"undirected\">\n"
NUM_NODES = g.shape[0]
if not test: f = open(save_fn if os.path.splitext(save_fn)[1] == ".graphml" else save_fn+".graphml", "wb")
# Can be #pragma for
for node in xrange(NUM_NODES): # Cycle through all nodes
s = "<node id=\"n%d\">\n" % node
if desikan:
s += " "*(tabs+1)+"<data key=\"v_region\">\"%s\"</data>\n" % (desikan.des_map.get(node, "Undefined"))
s += " "*tabs+"</node>\n"
src += " "*tabs+s
if node % 50000 == 0:
print "Processing node %d / %d ..." % (node, NUM_NODES)
if test: test_str += src
else: f.write(src)
src = ""
del s # free mem
print "Adding edges to graph ..."
# Get all edge data
nodes_from, nodes_to = g.nonzero()
data = g.data
del g # free some mem
# Can be #pragma for
NUM_EDGES = nodes_from.shape[0]
for idx in xrange(NUM_EDGES): # Only the edges that exist
src += " "*tabs+"<edge source=\"n%d\" target=\"n%d\">\n" % (nodes_from[idx], nodes_to[idx])
if is_weighted:
src += " "*(tabs+1)+"<data key=\"e_weight\">%d</data>\n" % data[idx]
src += " "*tabs+"</edge>\n"
if idx % 100000 == 0:
print "Processing edge %d / %d ..." % (idx, NUM_EDGES)
if test: test_str += src
else: f.write(src)
src = ""
src += " </graph>\n</graphml>"
if test:
test_str += src
return test_str
f.write(src)
f.close