def compute_duality_gap_lasso(X, y, w, lbd):
"""Compute duality gap for Lasso.
"""
# part of the code is designed for sparse matrix.
if type(lbd) is not np.array:
lbd = np.ones(X.shape[1]) * lbd
rho = y - X.dot(w)
if not isspmatrix(X):
normrho2 = np.linalg.norm(rho, axis=0, ord=2)**2
primalcost = 0.5 * normrho2 + np.sum(np.abs(w) * lbd)
else:
normrho2 = spnorm(rho, axis=0)**2
primalcost = 0.5 * normrho2 + (abs(w * lbd).sum())
correl = X.T.dot(rho)
# nu is a feasible approximation of nu
max_viol = np.max(np.abs(correl) / lbd)
if max_viol > 1:
nu = rho / max_viol
else:
nu = rho
if not isspmatrix(X):
dualcost = -0.5 * np.sum(nu * nu) + np.sum(nu * y)
else:
dualcost = -0.5 * spnorm(nu)**2 + (nu.multiply(y)).sum()
gap = primalcost - dualcost
return gap, rho, correl, nu
def compute_duality_gap_prox_lasso(X, y, w, lbd, w_0, alpha):
"""Compute duality gap for prox_Lasso."""
if type(lbd) is not np.array:
lbd = np.ones(X.shape[1]) * lbd
rho = y - X.dot(w)
if not isspmatrix(X):
normrho2 = np.linalg.norm(rho, axis=0, ord=2)**2
primalcost = 0.5 * normrho2 + np.sum(np.abs(w) * lbd) + \
0.5 / alpha * np.sum((w - w_0)**2)
else:
normrho2 = spnorm(rho, axis=0)**2
primalcost = 0.5 * normrho2 + (abs(w * lbd).sum())
v = (w - w_0) / alpha
correl = X.T.dot(rho)
max_viol = np.max(np.abs(correl - v) / lbd)
if max_viol > 1:
nu = rho / max_viol
v = v / max_viol
else:
nu = rho
if not isspmatrix(X):
dualcost = - 0.5 * np.sum(nu * nu) + np.sum(nu * y) - \
v.T.dot(w_0) - alpha / 2 * np.sum(v**2)
else:
dualcost = -0.5 * spnorm(nu)**2 + (nu.multiply(y)).sum() - \
v.T.dot(w_0) - alpha / 2 * np.sum(v**2)
gap = primalcost - dualcost
return gap, rho, correl, nu, v
def test_sparse_vector_norms(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
for axis in (0, 1, -1, -2, (0,), (1,), (-1,), (-2,)):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
for ord in None, 2, np.inf, -np.inf, 1, 0.5, 0.42:
assert_allclose(spnorm(S, ord, axis=axis), npnorm(M, ord, axis=axis))
def test_vector_norm(self):
v = [4.5825756949558398, 4.2426406871192848, 4.5825756949558398]
for m, a in (self.b, 0), (self.b.T, 1):
for axis in a, (a, ), a - 2, (a - 2, ):
assert_allclose(spnorm(m, 1, axis=axis), [7, 6, 7])
assert_allclose(spnorm(m, np.inf, axis=axis), [4, 3, 4])
assert_allclose(spnorm(m, axis=axis), v)
assert_allclose(spnorm(m, ord=2, axis=axis), v)
assert_allclose(spnorm(m, ord=None, axis=axis), v)
def test_sparse_vector_norms(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
for axis in (0, 1, -1, -2, (0, ), (1, ), (-1, ), (-2, )):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
for ord in None, 2, np.inf, -np.inf, 1, 0.5, 0.42:
assert_allclose(spnorm(S, ord, axis=axis),
npnorm(M, ord, axis=axis))
def test_vector_norm(self):
v = [4.5825756949558398, 4.2426406871192848, 4.5825756949558398]
for m, a in (self.b, 0), (self.b.T, 1):
for axis in a, (a, ), a-2, (a-2, ):
assert_allclose(spnorm(m, 1, axis=axis), [7, 6, 7])
assert_allclose(spnorm(m, np.inf, axis=axis), [4, 3, 4])
assert_allclose(spnorm(m, axis=axis), v)
assert_allclose(spnorm(m, ord=2, axis=axis), v)
assert_allclose(spnorm(m, ord=None, axis=axis), v)
def test_sparray_norm():
row = np.array([0, 0, 1, 1])
col = np.array([0, 1, 2, 3])
data = np.array([4, 5, 7, 9])
test_arr = scipy.sparse.coo_array((data, (row, col)), shape=(2, 4))
test_mat = scipy.sparse.coo_matrix((data, (row, col)), shape=(2, 4))
assert_equal(spnorm(test_arr, ord=1, axis=0), np.array([4, 5, 7, 9]))
assert_equal(spnorm(test_mat, ord=1, axis=0), np.array([4, 5, 7, 9]))
assert_equal(spnorm(test_arr, ord=1, axis=1), np.array([9, 16]))
assert_equal(spnorm(test_mat, ord=1, axis=1), np.array([9, 16]))
def test_sparse_matrix_norms_with_axis(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
for axis in None, (0, 1), (1, 0):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
for ord in "fro", np.inf, -np.inf, 1, -1:
assert_allclose(spnorm(S, ord, axis=axis), npnorm(M, ord, axis=axis))
# Some numpy matrix norms are allergic to negative axes.
for axis in (-2, -1), (-1, -2), (1, -2):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
assert_allclose(spnorm(S, "f", axis=axis), npnorm(M, "f", axis=axis))
assert_allclose(spnorm(S, "fro", axis=axis), npnorm(M, "fro", axis=axis))
def is_hermitian(operator):
"""
Check if matrix or operator is hermitian.
:param (numpy.ndarray|qutip.Qobj) operator: The operator or matrix to be tested.
:return: True if the operator is hermitian.
:rtype: bool
"""
if isinstance(operator, qt.Qobj):
return (operator.dag() -
operator).norm(FROBENIUS) / operator.norm(FROBENIUS) < EPS
if isinstance(operator, np.ndarray):
return np.linalg.norm(operator.T.conj() -
operator) / np.linalg.norm(operator) < EPS
return spnorm(operator.H - operator) / spnorm(operator) < EPS
def test_sparse_matrix_norms_with_axis(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
for axis in None, (0, 1), (1, 0):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
for ord in 'fro', np.inf, -np.inf, 1, -1:
assert_allclose(spnorm(S, ord, axis=axis),
npnorm(M, ord, axis=axis))
# Some numpy matrix norms are allergic to negative axes.
for axis in (-2, -1), (-1, -2), (1, -2):
assert_allclose(spnorm(S, axis=axis), npnorm(M, axis=axis))
assert_allclose(spnorm(S, 'f', axis=axis),
npnorm(M, 'f', axis=axis))
assert_allclose(spnorm(S, 'fro', axis=axis),
npnorm(M, 'fro', axis=axis))
def rescale_matrix(matrix,
scaling,
axis,
binary=True,
return_scaling_values=False):
'''Function to scale either rows or columns of the sparse rating matrix'''
result = None
scaling_values = None
if scaling == 1: # no scaling (standard SVD case)
result = matrix
if binary:
norm = np.sqrt(matrix.getnnz(
axis=axis)) # compute Euclidean norm as if values are binary
else:
norm = spnorm(matrix, axis=axis, ord=2) # compute Euclidean norm
scaling_values = power(norm, scaling - 1, where=norm != 0)
scaling_matrix = diags(scaling_values)
if axis == 0: # scale columns
result = matrix.dot(scaling_matrix)
if axis == 1: # scale rows
result = scaling_matrix.dot(matrix)
if return_scaling_values:
result = (result, scaling_values)
return result
def test_matrix_norm_axis(self):
for m, axis in ((self.b, None), (self.b, (0, 1)), (self.b.T, (1, 0))):
assert_allclose(spnorm(m, axis=axis), 7.745966692414834)
assert_allclose(spnorm(m, 'fro', axis=axis), 7.745966692414834)
assert_allclose(spnorm(m, np.inf, axis=axis), 9)
assert_allclose(spnorm(m, -np.inf, axis=axis), 2)
assert_allclose(spnorm(m, 1, axis=axis), 7)
assert_allclose(spnorm(m, -1, axis=axis), 6)
def test_matrix_norm_axis(self):
for m, axis in ((self.b, None), (self.b, (0, 1)), (self.b.T, (1, 0))):
assert_allclose(spnorm(m, axis=axis), 7.745966692414834)
assert_allclose(spnorm(m, 'fro', axis=axis), 7.745966692414834)
assert_allclose(spnorm(m, np.inf, axis=axis), 9)
assert_allclose(spnorm(m, -np.inf, axis=axis), 2)
assert_allclose(spnorm(m, 1, axis=axis), 7)
assert_allclose(spnorm(m, -1, axis=axis), 6)
def test_sparse_matrix_norms(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
assert_allclose(spnorm(S), npnorm(M))
assert_allclose(spnorm(S, 'fro'), npnorm(M, 'fro'))
assert_allclose(spnorm(S, np.inf), npnorm(M, np.inf))
assert_allclose(spnorm(S, -np.inf), npnorm(M, -np.inf))
assert_allclose(spnorm(S, 1), npnorm(M, 1))
assert_allclose(spnorm(S, -1), npnorm(M, -1))
def test_sparse_matrix_norms(self):
for sparse_type in self._sparse_types:
for M in self._test_matrices:
S = sparse_type(M)
assert_allclose(spnorm(S), npnorm(M))
assert_allclose(spnorm(S, 'fro'), npnorm(M, 'fro'))
assert_allclose(spnorm(S, np.inf), npnorm(M, np.inf))
assert_allclose(spnorm(S, -np.inf), npnorm(M, -np.inf))
assert_allclose(spnorm(S, 1), npnorm(M, 1))
assert_allclose(spnorm(S, -1), npnorm(M, -1))
def baseline_add():
adj_new = randomly_delete_edges(adj_orig, k=FLAGS.k)
testacc_clean, valid_acc_clean = GCN.run(FLAGS.dataset,
adj_orig,
name="clean")
testacc, valid_acc = GCN.run(FLAGS.dataset, adj_new, name="original")
cos = features_csr.dot(features_csr.transpose())
norm = spnorm(features_csr, axis=1)
norm = norm[:, np.newaxis]
norm_mat = norm.dot(norm.T)
cos = cos / norm_mat
normalize_cos = 0.5 + 0.5 * cos
normalize_cos = np.array(normalize_cos)
zero_mat = np.zeros([num_nodes, num_nodes])
adj_new_dense = adj_new.todense()
flag_adj = np.triu(np.ones([num_nodes, num_nodes]), k=1) - np.triu(
adj_new_dense, k=1)
zero_mat[flag_adj > 0] = normalize_cos[flag_adj > 0]
one_mat = zero_mat.flatten()
one_mat[np.isnan(one_mat)] = 0
add_idx = np.argsort(one_mat)
add_idx = add_idx[-FLAGS.k:]
row_idx = add_idx % num_nodes
col_idx = add_idx // num_nodes
for idx in range(len(row_idx)):
adj_new[row_idx, col_idx] = 1
adj_new[col_idx, row_idx] = 1
testacc_new, valid_acc_new = GCN.run(FLAGS.dataset, adj_new, name="new1")
testacc_new2, valid_acc_new = GCN.run(FLAGS.dataset, adj_new, name="new2")
testacc_new3, valid_acc_new = GCN.run(FLAGS.dataset, adj_new, name="new3")
print("**#" * 10)
print("clean one")
print(testacc_clean)
print("**#" * 10)
print("original one")
print(testacc)
print("new one")
print(testacc_new)
print("new two")
print(testacc_new2)
print("new three")
print(testacc_new3)
print("**#" * 10)
return testacc_clean, testacc, testacc_new, testacc_new2, testacc_new3
def test_matrix_norm(self):
# Frobenius norm is the default
assert_allclose(spnorm(self.b), 7.745966692414834)
assert_allclose(spnorm(self.b, 'fro'), 7.745966692414834)
assert_allclose(spnorm(self.b, np.inf), 9)
assert_allclose(spnorm(self.b, -np.inf), 2)
assert_allclose(spnorm(self.b, 1), 7)
assert_allclose(spnorm(self.b, -1), 6)
# _multi_svd_norm is not implemented for sparse matrix
assert_raises(NotImplementedError, spnorm, self.b, 2)
assert_raises(NotImplementedError, spnorm, self.b, -2)
def test_matrix_norm(self):
# Frobenius norm is the default
assert_allclose(spnorm(self.b), 7.745966692414834)
assert_allclose(spnorm(self.b, 'fro'), 7.745966692414834)
assert_allclose(spnorm(self.b, np.inf), 9)
assert_allclose(spnorm(self.b, -np.inf), 2)
assert_allclose(spnorm(self.b, 1), 7)
assert_allclose(spnorm(self.b, -1), 6)
# _multi_svd_norm is not implemented for sparse matrix
assert_raises(NotImplementedError, spnorm, self.b, 2)
assert_raises(NotImplementedError, spnorm, self.b, -2)
def test_norm(self):
a = np.arange(9) - 4
b = a.reshape((3, 3))
b = scipy.sparse.csr_matrix(b)
#Frobenius norm is the default
assert_equal(spnorm(b), 7.745966692414834)
assert_equal(spnorm(b, 'fro'), 7.745966692414834)
assert_equal(spnorm(b, np.inf), 9)
assert_equal(spnorm(b, -np.inf), 2)
assert_equal(spnorm(b, 1), 7)
assert_equal(spnorm(b, -1), 6)
#_multi_svd_norm is not implemented for sparse matrix
assert_raises(NotImplementedError, spnorm, b, 2)
assert_raises(NotImplementedError, spnorm, b, -2)
def test_norm(self):
a = np.arange(9) - 4
b = a.reshape((3, 3))
b = scipy.sparse.csr_matrix(b)
#Frobenius norm is the default
assert_equal(spnorm(b), 7.745966692414834)
assert_equal(spnorm(b, 'fro'), 7.745966692414834)
assert_equal(spnorm(b, np.inf), 9)
assert_equal(spnorm(b, -np.inf), 2)
assert_equal(spnorm(b, 1), 7)
assert_equal(spnorm(b, -1), 6)
#_multi_svd_norm is not implemented for sparse matrix
assert_raises(NotImplementedError, spnorm, b, 2)
assert_raises(NotImplementedError, spnorm, b, -2)
def max_Li_logistic(X, reg):
# import pdb; pdb.set_trace()
if issparse(X):
return 0.25 * spnorm(X.power(2), np.inf) + reg
else:
return 0.25 * np.max(np.sum(X**2, axis=1)) + reg
def compute_sparse_norm(sparse_data):
sparse_norm = spnorm(sparse_data, axis=1)
return sparse_norm.astype(np.float32)
#tmp1=np.dot(L_21, score2)
#print tmp1.shape
score1 = (1 - args.w) * score1 + args.w * np.dot(L_11, np.dot(L_21, score2))
score2 = (1 - args.w) * score2 + args.w * np.dot(L_22, np.dot(L_12, score1))
#print "score1 shape"
#print np.shape(score1)
#print "prevs1 shape"
#print np.shape(prevs1)
#print prevs1-score1
#difs1=np.sum(np.absolute(prevs1-score1),0)
#difs1=np.sum(np.absolute(prevs1-score1),0)
score1=score1/(np.sum(np.sum(score1.todense())))
score2=score2/(np.sum(np.sum(score2.todense())))
#difs1=LA.norm((prevs1-score1).todense().getA(),ord=2)
#difs2=LA.norm((prevs2-score2).todense().getA(),ord=2)
difs1=spnorm(prevs1-score1,'fro')
difs2=spnorm(prevs2-score2,'fro')
print str(i)+"th iter : dif1 is "+str(difs1)+" dif2 is "+str(difs2)
#score1 = abs(v[:, 0])/sum(abs(v[:, 0]))
#score2 = (1 - args.w) * S2 + args.w * np.dot(L_22, np.dot(L_21, S1))
if args.outfile1 != None:
output_file(args.outfile1, score1.todense())
else:
sys.stdout.write("Scores for layer1: ")
for i in range(0, num1):
sys.stdout.write("%f " %score1[i])
sys.stdout.write("\n")
if args.outfile2 != None:
output_file(args.outfile2, score2.todense())
def weighted_prox_lasso_bcd_screening(X,
y,
lbd,
w_0=np.array([]),
alpha=1e9,
nbitermax=10000,
winit=np.array([]),
screen_init=np.array([]),
screen_frq=3,
dual_gap_tol=1e-6,
do_screen=True):
"""
solve min_w 0.5 *|| y - Xw ||^2 + 1/2\alpha ||w - w_0||^2 + \sum_i \lbda_i |w_i|
using coordinatewise descent + screening
"""
n_features = X.shape[1]
bool_sparse = isspmatrix(X)
if not bool_sparse:
normX = np.linalg.norm(X, axis=0, ord=2)
if len(winit) == 0:
w = np.zeros(n_features)
else:
w = np.copy(winit)
else:
normX = spnorm(X, axis=0)
winit = csr_matrix(winit)
if winit.nnz == 0:
w = csr_matrix(np.zeros(n_features))
else:
w = winit.copy()
if len(screen_init) == 0:
screened = np.zeros(n_features)
else:
screened = np.copy(screen_init)
nb_screened = np.zeros(nbitermax)
if len(w_0) == 0:
w_0 = np.zeros(n_features)
i = 0
gap = float("inf")
if bool_sparse:
w = csr_matrix(w.reshape(-1, 1))
rho = y - X.dot(w)
while i < nbitermax and gap > dual_gap_tol:
for k in range(n_features):
if not screened[k]:
# Updating the variable
# computing the partial residual through update of the residual
xk = X[:, k]
s = rho + (xk * w[k])
Xts = (xk.T.dot(s) + w_0[k] / alpha)
wp = prox_l1(Xts, lbd[k]) / (normX[k]**2 + 1 / alpha)
rho = rho - xk * (wp - w[k])
w[k] = wp
gap, rho, correl, nu, v = compute_duality_gap_prox_lasso(
X, y, w, lbd, w_0, alpha)
if i % screen_frq == 0 and do_screen:
# Updating screeening
for k in range(n_features):
if not screened[k]:
bound = (normX[k] + 1 / alpha) * np.sqrt(2 * gap)
if not bool_sparse:
rhotxk = np.sum(nu * X[:, k])
else:
rhotxk = nu.multiply(X[:, k]).sum()
screened[k] = ((abs(rhotxk - v[k]) + bound) < lbd[k])
nb_screened[i] = (sum(screened == 1))
else:
nb_screened[i] = nb_screened[i - 1]
#print(i,gap,nb_screened[i])
i += 1
return w, nb_screened[:i], screened, rho, correl
def weighted_lasso_bcd_screening(X,
y,
lbd,
nbitermax=10000,
winit=np.array([]),
screen_init=np.array([]),
screen_frq=3,
dual_gap_tol=1e-6):
"""
solve min_w 0.5 *|| y - Xw ||^2 + \sum_i \lbda_i |w_i|
using coordinatewise descent + screening
"""
n_features = X.shape[1]
bool_sparse = isspmatrix(X)
if not bool_sparse:
normX = np.linalg.norm(X, axis=0, ord=2)
if len(winit) == 0:
w = np.zeros(n_features)
else:
w = np.copy(winit)
else:
normX = spnorm(X, axis=0)
winit = csr_matrix(winit)
if winit.nnz == 0:
w = csr_matrix(np.zeros(n_features))
else:
w = winit.copy()
if len(screen_init) == 0:
screened = np.zeros(n_features)
else:
screened = np.copy(screen_init)
nb_screened = np.zeros(nbitermax)
i = 0
gap = float("inf")
if bool_sparse:
w = csr_matrix(w.reshape(-1, 1))
rho = y - X.dot(w)
for i in range(nbitermax):
for k in range(n_features):
if not screened[k]:
# computing the partial residual through update of the res
xk = X[:, k]
s = rho + (xk * w[k])
Xts = xk.T.dot(s)
if not bool_sparse:
# w[k] = np.sign(Xts)* np.maximum((np.abs(Xts) - lbd[k]),0)
wp = prox_l1(Xts, lbd[k]) / (
normX[k]**2
) #np.sign(Xts) * np.maximum((np.abs(Xts) - lbd), 0) / (normX[k]**2)
rho = rho - xk * (wp - w[k])
w[k] = wp
else: # sparse
Xts = Xts[0, 0]
wp = prox_l1(Xts, lbd[k]) / (
normX[k]**2
) #np.sign(Xts) * np.maximum((np.abs(Xts) - lbd), 0) / (normX[k]**2)
# wp = np.sign(Xts) * np.maximum((np.abs(Xts) - lbd[k]), 0) / (normX[k]**2)
rho = rho - xk * (csr_matrix(wp) - w[k])
gap, rho, correl, nu = compute_duality_gap_lasso(X, y, w, lbd)
if i % screen_frq == 0:
# Updating screeening
for k in range(n_features):
if not screened[k]:
bound = normX[k] * np.sqrt(2 * gap)
if not bool_sparse:
rhotxk = np.sum(nu * X[:, k])
else:
rhotxk = nu.multiply(X[:, k]).sum()
screened[k] = ((abs(rhotxk) + bound) < lbd[k])
nb_screened[i] = (sum(screened == 1))
else:
nb_screened[i] = nb_screened[i - 1]
gap = float("inf")
i += 1
#print('L', i, gap, 's', nb_screened[i - 1])
if gap < dual_gap_tol:
# print('L Sorti', gap)
break
return w, nb_screened[:i], screened, rho, correl
def expmv(t, A, v, tol=1e-7, krylov_dim=30):
"""
Evaluates exp(t * A) @ v efficiently using Krylov subspace projection
techniques and matrix-vector product operations.
This function implements the expv function of the Expokit library
(https://www.maths.uq.edu.au/expokit). It is in particular suitable for
large sparse matrices.
Args:
t (float): real or complex time-like parameter
A (array or sparse): an numpy.array or scipy.sparse square matrix
v (array): a vector with size compatible with A
tol (real): the required tolerance (default 1e-7)
krylov_dim (int): dimension of the Krylov subspace
(typically a number between 15 and 50, default 30)
Returns:
The array w(t) = exp(t * A) @ v.
"""
assert A.shape[1] == A.shape[0], "A must be square"
assert A.shape[1] == v.shape[0], "v and A must have compatible shapes"
n = A.shape[0]
m = min(krylov_dim, n)
anorm = spnorm(A, ord=np.inf)
out_type = np.result_type(type(t), A.dtype, v.dtype)
# safety factors
gamma = 0.9
delta = 1.2
btol = 1e-7 # tolerance for "happy-breakdown"
maxiter = 10 # max number of time-step refinements
rndoff = anorm * np.spacing(1)
# estimate first time-step and round to two significant digits
beta = norm(v)
r = 1 / m
fact = (((m + 1) / np.exp(1.0))**(m + 1)) * np.sqrt(2.0 * np.pi * (m + 1))
tau = (1.0 / anorm) * ((fact * tol) / (4.0 * beta * anorm))**r
outvec = np.zeros(v.shape, dtype=out_type)
# storage for Krylov subspace vectors
v_m = np.zeros((m + 1, len(v)), dtype=out_type)
# for i in range(1, m + 2):
# vm.append(np.empty_like(outvec))
h_m = np.zeros((m + 2, m + 2), dtype=outvec.dtype)
t_f = np.abs(t)
# For some reason numpy.sign has a different definition than Julia or MATLAB
if isinstance(t, complex):
tsgn = t / np.abs(t)
else:
tsgn = np.sign(t)
t_k = 0. * t_f
w = np.array(v, dtype=out_type)
p = np.empty_like(w)
m_x = m
while t_k < t_f:
tau = min(t_f - t_k, tau)
# Arnoldi procedure
v_m[0] = w / beta
m_x = m
for j in range(m):
p = A.dot(v_m[j])
h_m[:j + 1, j] = v_m[:j + 1, :].conj() @ p
tmp = h_m[:j + 1, j][:, np.newaxis] * v_m[:j + 1]
p -= np.sum(tmp, axis=0)
s = norm(p)
if s < btol: # happy-breakdown
tau = t_f - t_k
err_loc = btol
f_m = expm(tsgn * tau * h_m[:j + 1, :j + 1])
tmp = beta * f_m[:j + 1, 0][:, np.newaxis] * v_m[:j + 1, :]
w = np.sum(tmp, axis=0)
m_x = j
break
h_m[j + 1, j] = s
v_m[j + 1] = p / s
h_m[m + 1, m] = 1.
if m_x == m:
avnorm = norm(A @ v_m[m])
# propagate using adaptive step size
i = 1
while i < maxiter and m_x == m:
f_m = expm(tsgn * tau * h_m)
err1 = abs(beta * f_m[m, 0])
err2 = abs(beta * f_m[m + 1, 0] * avnorm)
if err1 > 10 * err2: # err1 >> err2
err_loc = err2
r = 1 / m
elif err1 > err2:
err_loc = (err1 * err2) / (err1 - err2)
r = 1 / m
else:
err_loc = err1
r = 1 / (m - 1)
# is time step sufficient?
if err_loc <= delta * tau * (tau * tol / err_loc)**r:
tmp = beta * f_m[:m + 1, 0][:, np.newaxis] * v_m[:m + 1, :]
w = np.sum(tmp, axis=0)
break
# estimate new time-step
tau = gamma * tau * (tau * tol / err_loc)**r
i += 1
if i == maxiter:
raise (RuntimeError("Number of iteration exceeded maxiter. "
"Requested tolerance might be too high."))
beta = norm(w)
t_k += tau
tau = gamma * tau * (tau * tol / err_loc)**r # estimate new time-step
err_loc = max(err_loc, rndoff)
h_m.fill(0.)
return w
def PSNR(clean_adj, modified_adj):
# mse = spnorm(clean_adj - modified_adj, ord = 1) / (clean_adj.shape[0]*(clean_adj.shape[1] - 1))
# mse = max(spnorm(clean_adj - modified_adj, ord = 1),1.0) / (clean_adj.shape[0]*(clean_adj.shape[1] - 1))
mse = max(spnorm(clean_adj - modified_adj, ord = 1),0.1) / (clean_adj.shape[0]*(clean_adj.shape[1] - 1))
PSNR = 10 * np.log(1/ mse)
return PSNR
def PSNR_with_features(clean_adj, clean_fea, modified_adj, modified_fea):
mse = spnorm(clean_adj - modified_adj, ord = 1) / (clean_adj.shape[0]*(clean_adj.shape[1] - 1))
mse = mse + sp.linalg.norm(clean_fea - modified_fea, ord = 1) / (clean_fea.shape[0]* modified_fea.shape[1])
PSNR = 10 * np.log(1/ mse)
return PSNR
def train():
# train GCN first
adj_norm_sparse_csr = adj_norm_sparse.tocsr()
# sizes = [FLAGS.gcn_hidden1, FLAGS.gcn_hidden2, n_class]
# surrogate_model = GCN.GCN(sizes, adj_norm_sparse_csr, features_csr, with_relu=True, name="surrogate", gpu_id=gpu_id)
# surrogate_model.train(adj_norm_sparse_csr, split_train, split_val, node_labels)
# ori_acc = surrogate_model.test(split_unlabeled, node_labels, adj_norm_sparse_csr)
testacc, valid_acc = GCN.run(FLAGS.dataset, adj_orig, name="original")
cos = sp.dot(features_csr.transpose(), features_csr)
norm = spnorm(features_csr, axis=1)
norm_mat = norm.dot(norm.transpose())
if_drop_edge = True
## set the checkpoint path
checkpoints_dir_base = "./checkpoints"
current_time = datetime.datetime.now().strftime("%y%m%d%H%M%S")
checkpoints_dir = os.path.join(checkpoints_dir_base, current_time,
current_time)
############
global_steps = tf.get_variable('global_step',
trainable=False,
initializer=0)
new_learning_rate = tf.train.exponential_decay(FLAGS.learn_rate_init,
global_step=global_steps,
decay_steps=10000,
decay_rate=0.98)
new_learn_rate_value = FLAGS.learn_rate_init
## set the placeholders
placeholders = {
'features': tf.sparse_placeholder(tf.float32, name="ph_features"),
'adj': tf.sparse_placeholder(tf.float32, name="ph_adj"),
'adj_orig': tf.sparse_placeholder(tf.float32, name="ph_orig"),
'dropout': tf.placeholder_with_default(0., shape=(),
name="ph_dropout"),
# 'node_labels': tf.placeholder(tf.float32, name = "ph_node_labels"),
# 'node_ids' : tf.placeholder(tf.float32, name = "ph_node_ids")
}
# build models
model = None
if model_str == "gae_gan":
model = gaegan(placeholders, num_features, num_nodes, features_nonzero,
new_learning_rate)
model.build_model()
pos_weight = float(adj.shape[0] * adj.shape[0] - adj.sum()) / adj.sum()
norm = adj.shape[0] * adj.shape[0] / float(
(adj.shape[0] * adj.shape[0] - adj.sum()) * 2)
opt = 0
# Optimizer
with tf.name_scope('optimizer'):
if model_str == 'gae_gan':
opt = Optimizergaegan(
preds=tf.reshape(model.x_tilde, [-1]),
labels=tf.reshape(
tf.sparse_tensor_to_dense(placeholders['adj_orig'],
validate_indices=False), [-1]),
#comm_label=placeholders["comm_label"],
model=model,
num_nodes=num_nodes,
pos_weight=pos_weight,
norm=norm,
global_step=global_steps,
new_learning_rate=new_learning_rate)
# init the sess
sess = tf.Session()
sess.run(tf.global_variables_initializer())
saver = ""
var_list = tf.global_variables()
var_list = [
var for var in var_list
if ("encoder" in var.name) or ('generate' in var.name)
]
saver = tf.train.Saver(var_list, max_to_keep=10)
if if_save_model:
os.mkdir(os.path.join(checkpoints_dir_base, current_time))
saver.save(sess, checkpoints_dir) # save the graph
if restore_trained_our:
checkpoints_dir_our = "./checkpoints"
checkpoints_dir_our = os.path.join(checkpoints_dir_our,
FLAGS.trained_our_path)
# checkpoints_dir_meta = os.path.join(checkpoints_dir_base, FLAGS.trained_our_path,
# FLAGS.trained_our_path + ".meta")
#saver.restore(sess,tf.train.latest_checkpoint(checkpoints_dir_our))
saver.restore(
sess,
os.path.join("./checkpoints", "191215231708", "191215231708-1601"))
print("model_load_successfully")
# else: # if not restore the original then restore the base dis one.
# checkpoints_dir_base = os.path.join("./checkpoints/base", FLAGS.trained_base_path)
# saver.restore(sess, tf.train.latest_checkpoint(checkpoints_dir_base))
feed_dict = construct_feed_dict(adj_norm, adj_label, features,
placeholders)
feed_dict.update({placeholders['dropout']: FLAGS.dropout})
# pred_dis_res = model.vaeD_tilde.eval(session=sess, feed_dict=feed_dict)
#### save new_adj without norm#############
if restore_trained_our:
modified_adj = get_new_adj(feed_dict, sess, model)
modified_adj = sp.csr_matrix(modified_adj)
sp.save_npz("transfer_new/transfer_1216_1/qq_5000_gaegan_new.npz",
modified_adj)
sp.save_npz("transfer_new/transfer_1216_1/qq_5000_gaegan_ori.npz",
adj_orig)
print("save the loaded adj")
# print("before training generator")
#####################################################
#####################################################
G_loss_min = 1000
for epoch in range(FLAGS.epochs):
t = time.time()
# run Encoder's optimizer
#sess.run(opt.encoder_min_op, feed_dict=feed_dict)
# run G optimizer on trained model
if restore_trained_our:
sess.run(opt.G_min_op, feed_dict=feed_dict)
else: # it is the new model
if epoch < FLAGS.epochs:
sess.run(opt.G_min_op, feed_dict=feed_dict)
#
##
##
if epoch % 50 == 0:
print("Epoch:", '%04d' % (epoch + 1), "time=",
"{:.5f}".format(time.time() - t))
G_loss, laplacian_para, new_learn_rate_value = sess.run(
[opt.G_comm_loss, opt.reg, new_learning_rate],
feed_dict=feed_dict)
#new_adj = get_new_adj(feed_dict, sess, model)
new_adj = model.new_adj_output.eval(session=sess,
feed_dict=feed_dict)
temp_pred = new_adj.reshape(-1)
#temp_ori = adj_norm_sparse.todense().A.reshape(-1)
temp_ori = adj_label_sparse.todense().A.reshape(-1)
mutual_info = normalized_mutual_info_score(temp_pred, temp_ori)
print(
"Step: %d,G: loss=%.7f ,Lap_para: %f ,info_score = %.6f, LR=%.7f"
% (epoch, G_loss, laplacian_para, mutual_info,
new_learn_rate_value))
## here is the debug part of the model#################################
laplacian_mat, reg_trace, reg_log, reward_ratio = sess.run(
[
opt.reg_mat, opt.reg_trace, opt.reg_log,
opt.new_percent_softmax
],
feed_dict=feed_dict)
print("lap_mat is:")
print(np.diag(laplacian_mat))
print("reg_trace is:")
print(reg_trace)
print("reg_log is:")
print(reg_log)
print("reward_percentage")
print(reward_ratio)
##########################################
#';# check the D_loss_min
if (G_loss < G_loss_min) and (epoch > 1000) and (if_save_model):
saver.save(sess,
checkpoints_dir,
global_step=epoch,
write_meta_graph=False)
print("min G_loss new")
if G_loss < G_loss_min:
G_loss_min = G_loss
if (epoch % 200 == 1) and if_save_model:
saver.save(sess,
checkpoints_dir,
global_step=epoch,
write_meta_graph=False)
print("Epoch:", '%04d' % (epoch + 1), "time=",
"{:.5f}".format(time.time() - t))
saver.save(sess,
checkpoints_dir,
global_step=FLAGS.epochs,
write_meta_graph=True)
print("Optimization Finished!")
feed_dict.update({placeholders['dropout']: 0})
new_adj = get_new_adj(feed_dict, sess, model)
new_adj = new_adj - np.diag(np.diag(new_adj))
new_adj_sparse = sp.csr_matrix(new_adj)
print((abs(new_adj_sparse - new_adj_sparse.T) > 1e-10).nnz == 0)
# new_adj_norm, new_adj_norm_sparse = preprocess_graph(new_adj)
# new_adj_norm_sparse_csr = new_adj_norm_sparse.tocsr()
# modified_model = GCN.GCN(sizes, new_adj_norm_sparse_csr, features_csr, with_relu=True, name="surrogate", gpu_id=gpu_id)
# modified_model.train(new_adj_norm_sparse_csr, split_train, split_val, node_labels)
# modified_acc = modified_model.test(split_unlabeled, node_labels, new_adj_norm_sparse_csr)
testacc_new, valid_acc_new = GCN.run(FLAGS.dataset,
new_adj_sparse,
name="modified")
new_adj = get_new_adj(feed_dict, sess, model)
new_adj = new_adj - np.diag(np.diag(new_adj))
new_adj_sparse = sp.csr_matrix(new_adj)
testacc_new2, valid_acc_new = GCN.run(FLAGS.dataset,
new_adj_sparse,
name="modified")
new_adj = get_new_adj(feed_dict, sess, model)
new_adj = new_adj - np.diag(np.diag(new_adj))
new_adj_sparse = sp.csr_matrix(new_adj)
testacc_new3, valid_acc_new = GCN.run(FLAGS.dataset,
new_adj_sparse,
name="modified")
#np.save("./data/hinton/hinton_new_adj_48_0815.npy", new_adj)
#roc_score, ap_score = get_roc_score(test_edges, test_edges_false,feed_dict, sess, model)
##### The final results ####
print("*" * 30)
print("the final results:\n")
print("The original acc is: ")
print(testacc)
print("*#" * 15)
print("The modified acc is : ")
print(testacc_new)
print("*#" * 15)
print("The modified acc is : ")
print(testacc_new2)
print("*#" * 15)
print("The modified acc is : ")
print(testacc_new3)
return new_adj, testacc, testacc_new, testacc_new2, testacc_new3