def create_feat_eng_data(self, train_file, dev_file, test_file, train_out_file, dev_out_file, test_out_file): ''' Feature engineered data creation using TF-IDF train_file: file containing (training) input features dev_file: file containing (dev) input features test_file: file containing (test) input features train_out_file: output file for engineered (training) features dev_out_file: output file for engineered (dev) features test_out_file: output file for engineered (test) features ''' #create training features #x_mat = self.load_sparse_csr(feature_file).transpose().todense() #feature matrix #x_mat = self.load_sparse_csr(train_file).transpose().toarray() #feature matrix x_mat = self.load_sparse_csr(train_file).tocsc() #feature matrix x_mat = x_mat[:,1:] #removing the first (all 1) feature #dict_terms = ast.literal_eval(open(dict_file, 'r').read()) N = x_mat.shape[0] idf_arr = [math.log((N*1.0)/max(1., x_mat[:,i].nnz)) for i in range(x_mat.shape[1])] idf = np.asarray(idf_arr) x_mat = x_mat.tocsr() for i in range(0, N, 50000): j = min(i + 50000, N) x_mat_temp = csr(x_mat[i:j,:].multiply(idf)) if i==0: x_mat_new = x_mat_temp else: x_mat_new = vstack([x_mat_new, x_mat_temp]) print i all1_row = csr(np.asarray([1] * x_mat.shape[0])).transpose() x_mat_new = hstack([all1_row, x_mat_new]) self.save_sparse_csr(train_out_file, csr(x_mat_new)) #create dev features if dev_file != None: x_mat = self.load_sparse_csr(dev_file).transpose().toarray() #feature matrix x_mat = x_mat[1:,:] #removing the first (all 1) feature x_mat = np.multiply(x_mat.transpose(), idf) all1_row = np.asarray([1] * x_mat.shape[0]).transpose() self.save_sparse_csr(dev_out_file, csr(np.column_stack((all1_row, x_mat)))) #create test features if test_file != None: x_mat = self.load_sparse_csr(test_file).transpose().toarray() #feature matrix x_mat = x_mat[1:,:] #removing the first (all 1) feature x_mat = np.multiply(x_mat.transpose(), idf) all1_row = np.asarray([1] * x_mat.shape[0]).transpose() self.save_sparse_csr(test_out_file, csr(np.column_stack((all1_row, x_mat))))
def test_eval_sparse_dense(tmpdir, device_id):
from cntk import Axis
from cntk.io import MinibatchSource, CTFDeserializer, StreamDef, StreamDefs
from cntk.ops import times
input_vocab_dim = label_vocab_dim = 69
ctf_data = '''\
0 |S0 3:1 |# <s> |S1 3:1 |# <s>
0 |S0 4:1 |# A |S1 32:1 |# ~AH
0 |S0 5:1 |# B |S1 36:1 |# ~B
0 |S0 4:1 |# A |S1 31:1 |# ~AE
0 |S0 7:1 |# D |S1 38:1 |# ~D
0 |S0 12:1 |# I |S1 47:1 |# ~IY
0 |S0 1:1 |# </s> |S1 1:1 |# </s>
2 |S0 60:1 |# <s> |S1 3:1 |# <s>
2 |S0 61:1 |# A |S1 32:1 |# ~AH
'''
ctf_file = str(tmpdir / '2seqtest.txt')
with open(ctf_file, 'w') as f:
f.write(ctf_data)
mbs = MinibatchSource(CTFDeserializer(
ctf_file,
StreamDefs(features=StreamDef(field='S0',
shape=input_vocab_dim,
is_sparse=True),
labels=StreamDef(field='S1',
shape=label_vocab_dim,
is_sparse=True))),
randomize=False,
max_samples=2)
raw_input = sequence.input_variable(shape=input_vocab_dim,
sequence_axis=Axis('inputAxis'),
name='raw_input',
is_sparse=True)
mb_valid = mbs.next_minibatch(minibatch_size_in_samples=100,
input_map={raw_input: mbs.streams.features},
device=cntk_device(device_id))
z = times(raw_input, np.eye(input_vocab_dim))
e_reader = z.eval(mb_valid, device=cntk_device(device_id))
# CSR with the raw_input encoding in ctf_data
one_hot_data = [[3, 4, 5, 4, 7, 12, 1], [60, 61]]
data = [
csr(np.eye(input_vocab_dim, dtype=np.float32)[d]) for d in one_hot_data
]
e_csr = z.eval({raw_input: data}, device=cntk_device(device_id))
assert np.all([np.allclose(a, b) for a, b in zip(e_reader, e_csr)])
# One-hot with the raw_input encoding in ctf_data
data = Value.one_hot(one_hot_data,
num_classes=input_vocab_dim,
device=cntk_device(device_id))
e_hot = z.eval({raw_input: data}, device=cntk_device(device_id))
assert np.all([np.allclose(a, b) for a, b in zip(e_reader, e_hot)])
def train(self, start_section, end_section):
print 'Fitting the hyperplane...'
#Applying 'csr' to the vectors makes a sparse matrix.
X_matrix = csr(self.getfeaturevectors(start_section, end_section))
y_vector = np.array(self.getgsdata(start_section, end_section))
self.hyperplane.fit(X_matrix, y_vector)
def _get_kl(n, dx):
rows2 = [i for i in range(n)]
lower1rows = [i + 1 for i in range(n - 1)]
rows = rows2 + rows2[:-1] + lower1rows
cols = rows2 + lower1rows + rows2[:-1]
vals = np.array([2.] * n + [-1.] * (n - 1) * 2) / dx**2
k = csr((vals, (rows, cols)))
vals = (np.array([2.] * n + [-1.] * (n - 1) * 2) * -1 / dx**2).tolist()
iden = [1.] * n
rowsid = (np.array(rows2) + n).tolist()
i = csr((iden, (rows2, rows2)))
l = csr(
(vals + iden, ((np.array(rows) + n).tolist() + rows2, cols + rowsid)))
return i, k, l
def train(self, start_section, end_section):
print 'Fitting the hyperplane...'
#Applying 'csr' to the vectors makes a sparse matrix.
X_matrix = csr(self.getfeaturevectors(start_section, end_section))
y_vector = np.array(self.getgsdata(start_section, end_section))
self.hyperplane.fit(X_matrix, y_vector)
def root_function_first_derivative_numerical(self,beta):
num = beta.shape[0]
idx = list(range(num))
idx_diag_ends = np.array([0,num-1])
Amatrix = csr((num,num))
Amatrix += csr((np.ones(num-1),(idx[:-1],idx[1:])),shape=(num,num))
Amatrix -= csr((np.ones(num-1),(idx[1:],idx[:-1])),shape=(num,num))
Amatrix += csr((np.array([-1,1]),(idx_diag_ends,idx_diag_ends)),shape=(num,num))
y_prime = Amatrix*root_function(beta,self.RR)
x_prime = Amatrix*beta
return y_prime/x_prime
def test_eval_sparse_dense(tmpdir, device_id):
from cntk import Axis
from cntk.io import MinibatchSource, CTFDeserializer, StreamDef, StreamDefs
from cntk.ops import input_variable, times
input_vocab_dim = label_vocab_dim = 69
ctf_data = '''\
0 |S0 3:1 |# <s> |S1 3:1 |# <s>
0 |S0 4:1 |# A |S1 32:1 |# ~AH
0 |S0 5:1 |# B |S1 36:1 |# ~B
0 |S0 4:1 |# A |S1 31:1 |# ~AE
0 |S0 7:1 |# D |S1 38:1 |# ~D
0 |S0 12:1 |# I |S1 47:1 |# ~IY
0 |S0 1:1 |# </s> |S1 1:1 |# </s>
2 |S0 60:1 |# <s> |S1 3:1 |# <s>
2 |S0 61:1 |# A |S1 32:1 |# ~AH
'''
ctf_file = str(tmpdir/'2seqtest.txt')
with open(ctf_file, 'w') as f:
f.write(ctf_data)
mbs = MinibatchSource(CTFDeserializer(ctf_file, StreamDefs(
features = StreamDef(field='S0', shape=input_vocab_dim, is_sparse=True),
labels = StreamDef(field='S1', shape=label_vocab_dim, is_sparse=True)
)), randomize=False, epoch_size = 2)
batch_axis = Axis.default_batch_axis()
input_seq_axis = Axis('inputAxis')
label_seq_axis = Axis('labelAxis')
input_dynamic_axes = [batch_axis, input_seq_axis]
raw_input = input_variable(
shape=input_vocab_dim, dynamic_axes=input_dynamic_axes,
name='raw_input', is_sparse=True)
mb_valid = mbs.next_minibatch(minibatch_size_in_samples=100,
input_map={raw_input : mbs.streams.features},
device=cntk_device(device_id))
z = times(raw_input, np.eye(input_vocab_dim))
e_reader = z.eval(mb_valid, device=cntk_device(device_id))
# CSR with the raw_input encoding in ctf_data
one_hot_data = [
[3, 4, 5, 4, 7, 12, 1],
[60, 61]
]
data = [csr(np.eye(input_vocab_dim, dtype=np.float32)[d]) for d in
one_hot_data]
e_csr = z.eval({raw_input: data}, device=cntk_device(device_id))
assert np.all([np.allclose(a, b) for a,b in zip(e_reader, e_csr)])
# One-hot with the raw_input encoding in ctf_data
data = Value.one_hot(one_hot_data, num_classes=input_vocab_dim, device=cntk_device(device_id))
e_hot = z.eval({raw_input: data}, device=cntk_device(device_id))
assert np.all([np.allclose(a, b) for a,b in zip(e_reader, e_hot)])
def devtest(self, start_section, end_section, verbose=False):
print 'Predicting...'
#Applying 'csr' to the vectors makes a sparse matrix.
predictions = self.hyperplane.predict(
csr(self.getfeaturevectors(start_section, end_section)))
self.compare(self.getgsdata(start_section, end_section),
predictions,
start_section,
verbose=verbose)
def predict_class(self, from_file, w_file, test_file, pred_file, x_crossval, w_crossval):
'''
Predicts the classes for the dev or test set
Parameters:
from_file: boolean value to check if data is to be read from file
w_file: file containing the w learned from the training data for each class
test_file: file containing the dev or test data (in csr)
pred_file: prediction output file
x_crossval: the testing can be done on a small cross validation set (test_file should be None)
w_crossval: weights for cross validation
'''
if from_file:
x = self.load_sparse_csr(test_file) #157010 x 1001
x = csr(x[:,1:]) #removing the first (all 1) feature
w = self.load_sparse_csr(w_file) #5 x 1001, and without the first feature, 5 x 1000
else:
x = x_crossval
w = w_crossval
w_dot_x = x.dot(w.transpose()) #157010 x 5
hard_pred = w_dot_x.toarray().argmax(axis=1) + 1
w_dot_x_arr = w_dot_x.toarray()
w_dot_x_arr[w_dot_x_arr>20] = 20
w_dot_x_arr[w_dot_x_arr<-20] = -20
w_dot_x = csr(w_dot_x_arr)
w_dot_x_exp = csr(np.exp(w_dot_x.toarray())) #157010 x 5
w_dot_x_sum = w_dot_x_exp.sum(axis=1) #row sum (157010 x 1)
x_div_mat = csr(w_dot_x_exp.toarray()/w_dot_x_sum) #157010 x 5
num_vectors = 5
rating_arr = np.array([1,2,3,4,5]).transpose()
soft_pred = x_div_mat.toarray().dot(rating_arr)
if from_file:
w = open(pred_file, 'w')
for index in range(len(hard_pred)):
w.write(str(hard_pred[index]))
w.write(' ')
w.write(str(soft_pred[index]))
w.write('\n')
w.close
return hard_pred, soft_pred
def term_transitions(replace, DIST='damerau'):
index2term = list(
set([item for item in replace.keys()])
| set([item for item in replace.values()]))
term2index = {index2term[i]: i
for i in range(len(index2term))}
rows, cols = zip(*[[term2index[item[0]], term2index[item[1]]]
for item in replace.items()])
R = csr((np.ones(2 * len(rows)), (rows + cols, cols + rows)),
dtype=bool,
shape=(len(index2term), len(index2term)))
labels = connected_components(R)[1]
sorting = np.argsort(labels)
labels_s = labels[sorting]
_, starts = np.unique(labels_s, return_index=True)
sizes = np.diff(starts)
groups = [
group for group in np.split(sorting, starts[1:]) if group.size > 1
]
transition = dict()
for group in groups:
sum_group = float(sum([d[(index2term[index], )] for index in group]))
max_index = None
max_freq = 0
for index in group:
predict_term = index2term[index]
predict_freq = d[(predict_term, )]
if predict_freq > max_freq:
max_freq = predict_freq
max_index = index
for index1 in group:
given_term = index2term[index1]
len_1 = len(given_term)
transition[given_term] = dict()
for index2 in [index1, max_index]:
predict_term = index2term[index2]
len_2 = len(predict_term)
sim_prefix = prefix_normed(given_term, predict_term, len_1,
len_2)
sim_similar = similarity_normed(given_term, predict_term,
len_1, len_2, DIST)
transition[given_term][predict_term] = (d[
(predict_term, )] / sum_group) * sim_similar
#(sim_similar+sim_prefix)/2;
sum_sim = sum([
transition[given_term][predict_term]
for predict_term in transition[given_term]
])
for predict_term in transition[given_term]:
transition[given_term][predict_term] /= sum_sim
for index2 in [index1, max_index]:
print(given_term, '-->', index2term[index2],
transition[given_term][index2term[index2]])
return transition
def test_eval_sparse_no_seq(batch_index_data, device_id):
dim = 10
multiplier = 2
for var_is_sparse in [True, False]:
in1 = sequence.input(shape=(dim, ), is_sparse=var_is_sparse)
z = times(in1, multiplier * np.eye(dim))
batch = np.eye(dim)[batch_index_data]
expected = batch * multiplier
sparse_val = csr(batch.astype('f'))
result = z.eval({in1: [sparse_val]}, device=cntk_device(device_id))
assert np.allclose(result, [expected])
def test_eval_sparse_no_seq(batch_index_data, device_id):
dim = 10
multiplier = 2
in1 = input_variable(shape=(dim, ), is_sparse=True)
z = times(in1, np.eye(dim).astype(np.float32))
z *= multiplier
batch = (np.eye(dim)[batch_index_data]).astype(np.float32)
expected = batch * multiplier
sparse_val = csr(batch)
result = z.eval({in1: sparse_val}, device=cntk_device(device_id))
assert np.allclose(result, [expected])
def test_eval_sparse_no_seq(batch_index_data, device_id):
dim = 10
multiplier = 2
for var_is_sparse in [True, False]:
in1 = input_variable(shape=(dim,), is_sparse=var_is_sparse)
z = times(in1, multiplier*np.eye(dim))
batch = np.eye(dim)[batch_index_data]
expected = batch * multiplier
sparse_val = csr(batch.astype('f'))
result = z.eval({in1: [sparse_val]}, device=cntk_device(device_id))
assert np.allclose(result, [expected])
def adjust_n_max(new_n_max):
global n_max
n_max = new_n_max
global n_phonon
n_phonon = np.array([i for i in range(n_max + 1)], dtype=np.float64)
global sqrt_n
sqrt_n = np.array([sqrt(i) for i in range(1, n_max + 1)])
global annihilation, creation
annihilation = csr(np.diag(sqrt_n, k=1))
creation = csr(np.diag(sqrt_n, k=-1))
annihilation.prune()
creation.prune()
global x_hat, p_hat ### we assume \hbar = m * \omega = 1
x_hat = sqrt(1 / 2) * (creation + annihilation)
p_hat = 1.j * sqrt(1 / 2) * (creation - annihilation)
x_hat.prune()
p_hat.prune()
global x_hat_2, p_hat_2, xp_px_hat
x_hat_2 = x_hat.dot(x_hat)
p_hat_2 = np.real(p_hat.dot(p_hat))
xp_px_hat = x_hat.dot(p_hat) + p_hat.dot(x_hat)
x_hat_2.prune()
p_hat_2.prune()
xp_px_hat.prune()
global harmonic_Hamil
harmonic_Hamil = omega * np.diag(1 / 2 + n_phonon)
harmonic_Hamil = csr(harmonic_Hamil)
harmonic_Hamil.prune()
if __name__ == '__main__':
print('n_max adjusted to {}'.format(new_n_max))
global eigen_states
eigen_states = []
for i in range(new_n_max + 1):
eigen_states.append(
common_factor_of_1Dharmonics(i) *
np.polynomial.hermite.hermval(
x.astype(np.float128, order='C'),
np.array([0.
for j in range(i)] + [1.], dtype=np.float128)))
eigen_states = np.array(eigen_states).transpose().astype(np.float64,
order='C')
def construct_graph(indices, costs, N):
""" Creates a compressed sparse row matrix of the travel costs associated with each
node connection. The SciPy sparse row matrix function takes the following input arguments:
:param indices: indices of the connected nodes. Each index is split into start nodes and end
nodes for each connection. This is equivalent to the transposed indices matrix.
:param costs: the costs associated with each node connection
:param N: is the size of the sparse graph
:return: a SciPy compressed sparse row matrix describing the costs associated with each node connection.
"""
s_graph = csr((costs, (indices[:, 0], indices[:, 1])), shape=(N, N))
return s_graph
def test_validate():
csr = sparse.csr_matrix
sym = DiscreteSymmetry(
projectors=[csr(np.array([[1], [0]])),
csr(np.array([[0], [1]]))])
assert sym.validate(csr(np.array([[0], [1]]))) == 'Conservation law'
assert sym.validate(np.array([[1], [0]])) is None
assert sym.validate(np.eye(2)) is None
assert sym.validate(1 - np.eye(2)) == 'Conservation law'
sym = DiscreteSymmetry(particle_hole=sparse.identity(2))
assert sym.validate(1j * sparse.identity(2)) is None
assert sym.validate(sparse.identity(2)) == 'Particle-hole'
sym = DiscreteSymmetry(time_reversal=sparse.identity(2))
assert sym.validate(sparse.identity(2)) is None
assert sym.validate(1j * sparse.identity(2)) == 'Time reversal'
sym = DiscreteSymmetry(chiral=csr(np.diag((1, -1))))
assert sym.validate(np.eye(2)) == 'Chiral'
assert sym.validate(1 - np.eye(2)) is None
def intra_u(img, tmap, X):
##yet to add symmetricity
N = X.shape[0]
kuu = 5
X[:, 3:5] = X[:, 3:5] / 20
alpha = tmap.ravel()
ind = np.arange(X.shape[0])
unk = X[(alpha > 0.1) & (alpha < 0.9)]
unkind = ind[(alpha > 0.1) & (alpha < 0.9)]
#nearest unknown pixels to unknown
kdt = KDTree(unk, leaf_size=30, metric='euclidean')
nu = kdt.query(unk, k=kuu, return_distance=False)
unk_nbr_true_ind = unkind[nu]
unk_nu_ind = np.asarray(
[int(i / kuu) for i in range(nu.shape[0] * nu.shape[1])])
unk_nu_true_ind = unkind[unk_nu_ind]
nbr = unk[nu]
nbr = np.swapaxes(nbr, 1, 2)
unk = unk.reshape((unk.shape[0], unk.shape[1], 1))
x = nbr - unk
x = np.abs(x)
print(x.shape)
y = 1 - np.sum(x, axis=1)
y[y < 0] = 0
# print(y.shape)
row = unk_nu_true_ind
col = unk_nbr_true_ind.ravel()
data = y.ravel()
z = csr((data, (col, row)), shape=(N, N))
w = csr((data, (row, col)), shape=(N, N))
# z = csr((data,(col,row)),shape=(h*w,h*w))
w = w + z
return w
def input_to_features(self, feature_list, unhashed_features, hashed_features, unhashed_csr_file, hashed_csr_file, num_features):
'''
Converts the parsed input file to features and returns a scipy csr matrix
Parameters:
feature_list: list of features in order of input
unhashed_features: top n features
hashed_features: top m features (hashed)
unhashed_csr_file: file where csr matrix is to be stored (unhashed)
hashed_csr_file: file where csr matrix is to be stored (hashed)
num_features: number of features
'''
row_arr = []
col_arr_unhashed = []
col_arr_hashed = []
data_arr = []
row = 0
for text_arr in feature_list:
#add 1 corresponding to x_0 and w_0
row_arr.append(row)
col_arr_unhashed.append(0)
col_arr_hashed.append(0)
data_arr.append(1)
for term in text_arr:
term = term.encode('ascii', 'ignore')
try:
col_unhashed = unhashed_features[term]
col_hashed = hashed_features[term]
row_arr.append(row)
col_arr_unhashed.append(col_unhashed+1)
col_arr_hashed.append(col_hashed+1)
data_arr.append(1)
except KeyError:
pass
row += 1
if row%5000==0:
print row
mat = csr((data_arr, (row_arr, col_arr_unhashed)), shape=(row, num_features+1))
self.save_sparse_csr(unhashed_csr_file, mat)
mat = csr((data_arr, (row_arr, col_arr_hashed)), shape=(row, num_features+1))
self.save_sparse_csr(hashed_csr_file, mat)
def __init__(self, factorList=None, copy=True, isLog=False):
"""Take in a list of factors and convert & store them in the internal format
Can also accept a matrix of Ising parameters
"""
if factorList is None:
self.h = np.zeros(0)
self.L = csr((0, 0))
return
if not isinstance(factorList[0],
Factor): # not a factor list => matrix?
L = coo(factorList)
LL = csr(factorList)
n = L.shape[0]
self.h = np.array([LL[i, i] for i in range(n)])
# extract diagonal
self.dims = np.array([2 for i in range(n)], dtype=int)
# all variables binary
keep = (L.row != L.col)
data, row, col = L.data[keep], L.row[keep], L.col[keep]
#for j in np.where(L.row > L.col): row[j],col[j] = col[j],row[j]
self.L = csr((data, (row, col)),
shape=(n, n)) # keep in csr format
self.L = .5 * (
self.L + self.L.T
) # force symmetric if not (TODO: detect zeros & overwrite?)
else:
n = np.max(
[np.max(f.vars.labels) for f in factorList if len(f.vars)]) + 1
assert np.max([np.max(f.vars.dims()) for f in factorList
]) <= 2, "Variables must be binary"
assert np.max([f.nvar for f in factorList
]) <= 2, "Factors must be pairwise"
self.dims = np.zeros((n, ), dtype=int)
for f in factorList:
for v in f.vars:
self.dims[v] = v.states
self.h = np.zeros(n)
self.L = csr(([], ([], [])), shape=(n, n))
self.addFactors(factorList, isLog=isLog)
def get_banded(a: np.ndarray, p, q):
"""
Converts the matrix a into a banded scipy.sparse.csr_matrix object with
lower and upper bandwidths p and q, respectively. Returns a CSR matrix
of the same shape and banded entries as a.
"""
for i in range(a.shape[0]):
for j in range(a.shape[1]):
if i > j + p or j > i + q:
a[i, j] = 0.
return csr(a)
def LBP(ising, maxIter=100, verbose=False):
"""Run loopy belief propagation (specialized for Ising models)
lnZ, bel = LBP(ising, maxIter, verbose)
lnZ : float, estimate of the log partition function
bel : vector, bel[i] = estimated marginal probability that Xi = +1
"""
# TODO: pass requested beliefs (like JT?), or "single", "factors", etc.
assert isinstance(ising,Ising), "Model must be an Ising model for this version to work"
R = ising.L.tocoo(); row = R.row; col = R.col;
mu = csr(([],([],[])),shape=ising.L.shape)
L_tanh = ising.L.tanh();
for it in range(maxIter):
mu_sum = arr(mu.sum(0)).reshape(-1);
#R = csr( (ising.h[row]+mu_sum[row], (row,col)), shape=ising.L.shape) - mu.T
R = csr( (ising.h[row]+mu_sum[row]-arr(mu[col,row]).reshape(-1), (row,col)), shape=ising.L.shape);
mu = (L_tanh.multiply(R.tanh())).arctanh()
if verbose: print("Iter "+str(it)+": "+str(__Bethe(ising,R,mu)));
R = csr( (ising.h[row]+mu_sum[row]-arr(mu[col,row]).reshape(-1), (row,col)), shape=ising.L.shape);
bel = 1./(1+np.exp(-2.*(arr(mu.sum(0)).reshape(-1)+ising.h)))
lnZ = __Bethe(ising,R,mu,bel)
return lnZ, bel
def writeSparseMatrix(nDays):
for i in range(nDays):
fil="day"+"%d"%i+"PoissonParametersNonHom.txt"
A=np.loadtxt(os.path.join("NonHomegeneousPP",fil))
fil2="daySparse"+"%d"%i+"PoissonParametersNonHom.txt"
f=open(os.path.join("NonHomogeneousPP2",fil2),'w')
A=csr(A)
temp=A.nonzero()
temp2=np.array([A.data,temp[0],temp[1]])
np.savetxt(f,temp2)
f.close()
fil="day"+"%d"%i+"ExponentialTimesNonHom.txt"
A=np.loadtxt(os.path.join("NonHomegeneousPP",fil))
fil2="daySparse"+"%d"%i+"ExponentialTimesNonHom.txt"
f=open(os.path.join("NonHomogeneousPP2",fil2),'w')
A=csr(A)
temp=A.nonzero()
temp2=np.array([A.data,temp[0],temp[1]])
np.savetxt(f,temp2)
f.close()
def writeSparseMatrix(nDays):
for i in range(nDays):
fil = "day" + "%d" % i + "PoissonParametersNonHom.txt"
A = np.loadtxt(os.path.join("NonHomogeneousPP2", fil))
fil2 = "daySparse" + "%d" % i + "PoissonParametersNonHom.txt"
f = open(os.path.join("SparseNonHomogeneousPP2", fil2), 'w')
A = csr(A)
temp = A.nonzero()
temp2 = np.array([A.data, temp[0], temp[1]])
np.savetxt(f, temp2)
f.close()
fil = "day" + "%d" % i + "ExponentialTimesNonHom.txt"
A = np.loadtxt(os.path.join("NonHomogeneousPP2", fil))
fil2 = "daySparse" + "%d" % i + "ExponentialTimesNonHom.txt"
f = open(os.path.join("SparseNonHomogeneousPP2", fil2), 'w')
A = csr(A)
temp = A.nonzero()
temp2 = np.array([A.data, temp[0], temp[1]])
np.savetxt(f, temp2)
f.close()
def row_agg(self, mat, mapping, rowK): ''' Aggregates the row (document) vectors Params: mat: original matrix mapping: the row mapping (to cluster centroids) rowK: number of document clusters ''' agg_mat = np.zeros(shape=(rowK, mat.shape[1])) i = 0 for key in mapping: agg_mat[key].__iadd__(mat[i,:]) i += 1 return csr(agg_mat)
def test_validate_commutator():
symm_class = ['AI', 'AII', 'D', 'C', 'AIII', 'BDI']
sym_dict = {
'AI': ['Time reversal'],
'AII': ['Time reversal'],
'D': ['Particle-hole'],
'C': ['Particle-hole'],
'AIII': ['Chiral'],
'BDI': ['Time reversal', 'Particle-hole', 'Chiral']
}
n = 10
rng = 10
for sym in symm_class:
# Random matrix in symmetry class
h = kwant.rmt.gaussian(n, sym, rng=rng)
if kwant.rmt.p(sym):
p_mat = np.array(kwant.rmt.h_p_matrix[sym])
p_mat = csr(np.kron(np.identity(n // len(p_mat)), p_mat))
else:
p_mat = None
if kwant.rmt.t(sym):
t_mat = np.array(kwant.rmt.h_t_matrix[sym])
t_mat = csr(np.kron(np.identity(n // len(t_mat)), t_mat))
else:
t_mat = None
if kwant.rmt.c(sym):
c_mat = csr(np.kron(np.identity(n // 2), np.diag([1, -1])))
else:
c_mat = None
disc_symm = DiscreteSymmetry(particle_hole=p_mat,
time_reversal=t_mat,
chiral=c_mat)
assert disc_symm.validate(h) == []
a = random_onsite_hop(n, rng=rng)[1]
for symmetry in disc_symm.validate(a):
assert symmetry in sym_dict[sym]
def test_eval_sparse_seq_0(batch_index_data, device_id):
if cntk_device(device_id) != cpu(): # FIXME
pytest.skip("sparse is not yet supported on GPU")
dim = 10
multiplier = 2
in1 = input_variable(shape=(dim, ), is_sparse=True)
z = times(in1, np.eye(dim).astype(np.float32))
z *= multiplier
batch = [(np.eye(dim)[seq_index_data]).astype(np.float32)
for seq_index_data in batch_index_data]
expected = batch * multiplier
sparse_val = [csr(seq) for seq in batch]
result = z.eval({in1: sparse_val}, device=cntk_device(device_id))
assert np.all(np.allclose(a,b) \
for a,b in zip(result, expected))
def set_diagonal(
matrix, new
): #WARNING: new is expected to be sparse csr matrix (as opposed to what is expected in set_new)
matrix.eliminate_zeros()
new.eliminate_zeros()
rows, cols = matrix.nonzero()
data = matrix.data
old = rows != cols
rows_old, cols_old = rows[old], cols[old]
data_old = data[old]
rows_cols_new = new.nonzero()[0]
data_new = new.data
cols_, rows_ = np.concatenate([cols_old, rows_cols_new],
0), np.concatenate([rows_old, rows_cols_new],
0)
data_ = np.concatenate([data_old, data_new], 0)
return csr((data_, (rows_, cols_)), shape=matrix.shape)
def normalize_rows(self, mat, mapping): ''' Normalizes the row clusters Parameters: mat: matrix mapping: mapping of row to cluster ''' cluster_sum = [0] * mat.shape[0] for key in mapping: cluster_sum[key] += 1. for row_no in range(mat.shape[0]): if cluster_sum[row_no] == 0: cluster_sum[row_no] = 1. cluster_sum = np.array(cluster_sum) return csr((mat.T.toarray().__mul__(1/cluster_sum)).T)
def kron_s(A, B, sec): fp = A.fparity ss = A.sym_sum sym = A.sym dim = sym * A.dim * B.dim ret = csr((dim, dim), dtype=np.complex) for row1 in range(sym): for col1 in range(sym): row2 = ss(sec, -row1) col2 = ss(sec, -col1) if not A._empty_(row1, col1) and not B._empty_(row2, col2): sign = 1 - 2*( fp[col1] * fp[ss(col2, -row2)] ) temp = coo( sparse.kron(A.val[row1][col1], B.val[row2][col2]) * sign ) block = A.dim * B.dim add = coo((temp.data, (temp.row + row1*block, temp.col + col1*block)),(dim, dim), dtype=np.complex) ret += add return ret
def __init__(self, sym=2, dim=1, datatype=np.float, fparity=None, sym_sum=None): def sym_sum_n(a, b): return (a+b+sym)%sym self.sym = sym # number of total symmetry sectors self.dim = dim # dimension of each symmetry sector self.datatype = datatype if fparity is None: self.fparity = np.zeros(sym, dtype=np.int) # fermion parity else: self.fparity = fparity if sym_sum is None: self.sym_sum = sym_sum_n # the rule to sum the symmetries else: self.sym_sum = sym_sum self.val = [[csr((dim,dim), dtype=datatype) for x in range(sym)] for y in range(sym)] self.basis = None self.L = 1
def normalize_cols(self, mat, mapping): ''' Normalizes the column clusters Parameters: mat: matrix mapping: mapping of column to cluster ''' cluster_sum = [0] * mat.shape[1] for key in mapping: cluster_sum[key] += 1. for col_no in range(mat.shape[1]): if cluster_sum[col_no] == 0: cluster_sum[col_no] = 1. cluster_sum = np.array(cluster_sum) return csr(mat.toarray().__mul__(1/cluster_sum))
def fp_fv_mod(x,y,time,m_tmp,a1_tmp,a2_tmp,D11,D22,D12,dt,dx): I = x.size J = y.size eye = sparse.identity((I*J),format='lil') #get function values [f1_array, f2_array] = iF.f_global(time,x,y,a1_tmp,a2_tmp) D11 = iF.Sigma_D11_test(time,x,y,a1_tmp,a2_tmp,m_tmp) D12 = iF.Sigma_D12_test(time,x,y,a1_tmp,a2_tmp,m_tmp) D22 = iF.Sigma_D22_test(time,x,y,a1_tmp,a2_tmp,m_tmp) #make matrices LHS = mg.add_diffusion_flux_Ometh(eye,D11,D22,D12,I,J,dx,dt) LHS = sparse.csr(LHS) RHS = mg.fp_fv_convection(time,x,a_tmp,m_tmp,dt,dx) #print LHS #print RHS #print ss #LHS = sparse.csr(sparse.eye(I)-mg.fp_fv_diffusion(time,x,a_tmp,m_tmp,dt,dx)) #RHS = sparse.csr(sparse.eye(I)+mg.fp_fv_convection(time,x,a_tmp,m_tmp,dt,dx)) return sparse.linalg.spsolve(LHS,RHS*m_tmp)
def addFactors(self, flist, copy=True, isLog=False):
"""Add a list of (binary, pairwise) factors to the model; factors are converted to Ising parameters"""
row = np.zeros(2*len(flist),dtype=int)-1; col=row.copy(); data=np.zeros(2*len(flist));
for k,f in enumerate(flist):
if not isLog:
if np.any(f.t<=0): f = f+1e-10; # TODO: log nonzero tol
f = f.log()
if f.nvar == 1:
Xi = f.vars[0]
self.h[Xi] += .5*(f[1]-f[0])
self.c += .5*(f[1]+f[0])
else:
Xi,Xj = f.vars[0],f.vars[1]
row[2*k],col[2*k],data[2*k] = int(Xi),int(Xj), .25*(f[1,1]+f[0,0]-f[0,1]-f[1,0])
row[2*k+1],col[2*k+1],data[2*k+1] = col[2*k],row[2*k],data[2*k]
#L[Xi,Xj] += .25*(f[1,1]+f[0,0]-f[0,1]-f[1,0])
self.h[Xi] += .5*(f[1,0]-f[0,0])+data[2*k] #L[Xi,Xj]
self.h[Xj] += .5*(f[0,1]-f[0,0])+data[2*k] #L[Xi,Xj]
self.c += .25*(f[1,1]+f[1,0]+f[0,1]+f[0,0])
self.L += csr((data[row>=0],(row[row>=0],col[row>=0])),shape=(self.nvar,self.nvar));
def file_to_csr(self, file_name):
'''
Converts file to list of maps where each map represents a doc vector
'''
f = open(file_name, 'r')
count = 0
row_arr = []
col_arr = []
val_arr = []
max_col = 0
for line in iter(lambda: f.readline().rstrip(), ''):
for x in line.split(' '):
col = int(x.split(':')[0])
if col>max_col:
max_col = col
col_arr.append(col)
val_arr.append(int(x.split(':')[1]))
row_arr.append(count)
count += 1
return csr((val_arr, (row_arr, col_arr)), shape=(count, max_col+1)).tocsc()
def __init__(self,
coor_x,
coor_y,
val,
max_rat,
min_rat,
user_num,
movie_num,
U=None,
V=None,
alpha=2.0,
mu0=0.0,
D=30,
T=100):
"""
coor和val是表示稀疏的评分矩阵
coor是一个列表，每一项为一个列表，此列表第一项为用户，第二项为电影
val是一个列表，每一项为coor中对应的评分
"""
self.alpha = alpha
self.mu0 = mu0
self.D = D
self.v0 = D
self.beta0 = 2.0
self.val = val
self.N = user_num
self.M = movie_num
self.max_rat = max_rat
self.min_rat = min_rat
self.T = T
self.R = csr((val, (coor_x, coor_y)), shape=(self.N, self.M))
self.U = np.random.normal(size=(self.N, self.D))
self.V = np.random.normal(size=(self.M, self.D))
self.W0_user = np.eye(self.D)
self.W0_item = np.eye(self.D)
self.rmses = []
def bandedLU(M: csr, ml, mu):
"""
Computes standard LU decomposition of a class 'scipy.sparse.csr.csr_matrix'
banded square matrix M with lower and upper bandwidths ml and mu, respectively.
Returns L and U as sparse CSR matrices.
"""
m = M.shape[0]
u = M.copy() # can remove to act directly on M
# Allocating memory to store nnzl number of non-zero entries of L
nnzl = int(m * (ml + 1) - ml * (ml + 1) / 2)
l_row = np.zeros(nnzl).astype(np.int_)
l_val = np.ones(nnzl).astype(M.dtype)
for i in range(m):
l_row[i] = i
l_col = l_row.copy()
count = i + 1 # counter for the next entry of L
for k in range(m - 1):
column_entries_ind = u.indptr[k] + (
u.indices[u.indptr[k]:u.indptr[min(k + ml + 1, m)]]
== k).nonzero()[0]
for i, ind in enumerate(column_entries_ind[1:]):
l = u.data[ind] / u.data[column_entries_ind[0]]
l_val[count] = l
l_col[count] = k
l_row[count] = int(k + i + 1)
count += 1
b = min(mu + 1, m - k)
u.data[ind + 1:ind + b] -= l * u.data[column_entries_ind[0] +
1:column_entries_ind[0] + b]
u.data[ind] = 0.
u.eliminate_zeros()
l = csr((l_val, (l_row, l_col)))
return l, u
def fractionalflow(self):
self.fw = (self.krw * self.muo) / (self.krw * self.muo +
self.kro * self.muw)
N = self.fw.size
one = np.ones(N - 1)
idx = np.array(list(range(N)))
row = np.concatenate(((idx[0], idx[-1]), idx[:-1], idx[1:]))
col = np.concatenate(((idx[0], idx[-1]), idx[1:], idx[:-1]))
val = np.concatenate(((-1, 1), one, -one))
G = csr((val, (row, col)), shape=(N, N))
fw_diff = G * self.fw
Sw_diff = G * self.Sw
self.fw_der = fw_diff / Sw_diff
def generate_matrix(df, r, g_item1, g_item2):
at1 = pd.to_numeric(df[g_item1[0]])
op1 = g_item1[1]
at2 = pd.to_numeric(df[g_item2[0]])
op2 = g_item2[1]
N = len(at1)
matrix = np.zeros((N, N)) # Length is the number of transactions...
if op1 == '>' and op2 == '>':
for i in range(N):
for j in range(N):
if i != j:
matrix[i,j] = Concordance_degree([at1[i], at1[j]],[at2[i], at2[j]],r)
if op1 == '>' and op2 == '<':
for i in range(N):
for j in range(N):
if i != j:
matrix[i,j] = Concordance_degree([at1[i], at1[j]],[at2[j], at2[i]],r)
return csr(matrix)
def kron_s(A, B, sec):
fp = A.fparity
ss = A.sym_sum
sym = A.sym
dim = sym * A.dim * B.dim
ret = csr((dim, dim), dtype=np.complex)
for row1 in range(sym):
for col1 in range(sym):
row2 = ss(sec, -row1)
col2 = ss(sec, -col1)
if not A._empty_(row1, col1) and not B._empty_(row2, col2):
sign = 1 - 2 * (fp[col1] * fp[ss(col2, -row2)])
temp = coo(
sparse.kron(A.val[row1][col1], B.val[row2][col2]) *
sign)
block = A.dim * B.dim
add = coo(
(temp.data,
(temp.row + row1 * block, temp.col + col1 * block)),
(dim, dim),
dtype=np.complex)
ret += add
return ret
def load_data(input_file, test_percentage):
data = np.loadtxt(input_file)
rating = data[:, 2] #1-5
number_ratings = len(rating)
user_ids = data[:, 0].astype(int)
user_ids -= 1 #convert to 0 based indexing
movie_ids = data[:, 1].astype(int)
movie_ids -= 1 #convert to 0 based indexing
reviews = csr((rating, (user_ids, movie_ids)), shape = (max(user_ids) + 1, max(movie_ids) + 1))
reviews = reviews.toarray()
test_idxs = np.array(random.sample(range(number_ratings), number_ratings/test_percentage))
train_reviews = np.array(reviews)
for idx in test_idxs:
train_reviews[user_ids[idx]][movie_ids[idx]] = 0
test_reviews = np.zeros_like(reviews)
for idx in test_idxs:
test_reviews[user_ids[idx]][movie_ids[idx]] = reviews[user_ids[idx]][movie_ids[idx]]
return train_reviews, test_reviews
def __init__(self, mesh, **kwargs):
LinearSimulation.__init__(self, mesh, **kwargs)
# Find non-zero cells
if getattr(self, "actInd", None) is not None:
if self.actInd.dtype == "bool":
indices = np.where(self.actInd)[0]
else:
indices = self.actInd
else:
indices = np.asarray(range(self.mesh.nC))
self.nC = len(indices)
# Create active cell projector
projection = csr(
(np.ones(self.nC), (indices, range(self.nC))), shape=(self.mesh.nC, self.nC)
)
# Create vectors of nodal location for the lower and upper corners
bsw = self.mesh.gridCC - self.mesh.h_gridded / 2.0
tne = self.mesh.gridCC + self.mesh.h_gridded / 2.0
xn1, xn2 = bsw[:, 0], tne[:, 0]
yn1, yn2 = bsw[:, 1], tne[:, 1]
self.Yn = projection.T * np.c_[mkvc(yn1), mkvc(yn2)]
self.Xn = projection.T * np.c_[mkvc(xn1), mkvc(xn2)]
# Allows for 2D mesh where Zn is defined by user
if self.mesh.dim > 2:
zn1, zn2 = bsw[:, 2], tne[:, 2]
self.Zn = projection.T * np.c_[mkvc(zn1), mkvc(zn2)]
def split_data(X, test_percentage=10):
X = csr(X)
number_ratings = len(X.indices)
user_ids = []
indptr = X.indptr
for i in range(len(indptr) - 1):
t1 = indptr[i + 1] - indptr[i]
for j in range(t1):
user_ids.append(i)
movie_ids = X.indices
test_idxs = np.array(
random.sample(range(number_ratings), number_ratings / test_percentage))
X = X.toarray()
train_reviews = np.array(X)
for idx in test_idxs:
train_reviews[user_ids[idx]][movie_ids[idx]] = 0
test_reviews = np.zeros_like(X)
for idx in test_idxs:
test_reviews[user_ids[idx]][movie_ids[idx]] = X[user_ids[idx]][
movie_ids[idx]]
return train_reviews, test_reviews
def ls_featuresign_sub(A,y, AtA, Aty, gamma, xinit=None): L, M = A.shape rankA = min(A.shape[0]-10, A.shape[0]-10) # Step 1: initialize usexinit=False if xinit is None: xinit = [] x = ssp.csr(np.zeros((M,1))) theta = ssp.csr(np.zeros((M,1))) act = ssp.csr(np.zeros((M,1))) allowZero = False else x = ssp.csr(xinit) theta = ssp.csr(x) act = ssp.csr(np.abs(theta)) usexinit = True allowZero = True #[TO BE INSERTED] debug file fobj = 0 ITERMAX=1000 optimality1=False for iter in range(ITERMAX): act_indx0 = np.where(act==0) grad = np.dot(AtA,ssp.csr(x)) - Aty theta = np.sign(x) optimality0 = False #step 2 mx, indx = max(np.abs(grad[act_indx0])) if mx is None and mx >= gamma and (iter > 1 or not usexinit): act[act_indx0[idx]] = 1 theta[act_indx0[idx]] = -np.sign(grad[act_indx0[idx]]) usexinit = False else optimality0 =True if optimality1: break act_indx1 = np.where(act == 1) if len(act_indx1) > rankA: print "warning: sparsity penality is too small: too many coefficients are activated!" return if act_indx1.size == 0: if allowZero: allowZero = False continue return k=0 while 1: k +=1 if k > ITERMAX print "Maximum number of iterations reached. The solution may not be optimal" return if act_indx1.size == 0: if allowZero: allowZero = False break return #step 3 x, theta, act, act_indx1, optimality1, lsearch, fobj = compute_FS_step(x,A,y,AtA,Aty,theta, act, act_indx1, gamma) #step 4 if optimality1: break; if lsearch>0: continue; if iter >= ITERMAX: print "maximum number of iterations reached. The solution may not be optimal" #[add later] if 0 #check optimality fobj = fobj_featersign(x,A,y,AtA, Aty, gamma) return x, fobj
def devtest(self, start_section, end_section, verbose=False):
print 'Predicting...'
#Applying 'csr' to the vectors makes a sparse matrix.
predictions = self.hyperplane.predict(csr(self.getfeaturevectors(start_section, end_section)))
self.compare(self.getgsdata(start_section, end_section), predictions, start_section, verbose=verbose)
[0,1,6],
])
def test_eval_sparse_no_seq(batch_index_data, device_id):
dim = 10
multiplier = 2
for var_is_sparse in [True, False]:
in1 = input_variable(shape=(dim,), is_sparse=var_is_sparse)
z = times(in1, multiplier*np.eye(dim))
batch = np.eye(dim)[batch_index_data]
expected = batch * multiplier
sparse_val = csr(batch.astype('f'))
result = z.eval({in1: [sparse_val]}, device=cntk_device(device_id))
assert np.allclose(result, [expected])
@pytest.mark.parametrize("batch", [
[csr([0,1,2,0])],
[
csr([[0, 2, 0, 7], [10, 20, 0, 0]]),
csr([0, 0, 0, 3])
]
])
def test_eval_sparse_seq_1(batch, device_id):
dim = 4
multiplier = 2
for var_is_sparse in [True, False]:
in1 = input_variable(shape=(dim,), is_sparse=var_is_sparse)
z = times(in1, multiplier*np.eye(dim))
if isinstance(batch[0], list):
expected = [np.vstack([m.todense() * multiplier for m in seq]) for seq in
batch]
else:
def batched_gradient_descent(self, feature_file, y_file, w_final_file, num_features, alpha, batch_size, lambda_var, cv_percentage): ''' Batched gradient descent function Parameters: feature_file: file containing features in sparse scipy format y_file: file containing ratings in same order as feature_file w_final_file: file storing final w as csr matrix num_features: number of features alpha: value of alpha for gradient descent batch_size: size of each batch lambda_var: value of lambda cv_percentage: percentage of dataset to be used for cross validation ''' x_mat = obj.load_sparse_csr(feature_file) #feature matrix x_mat = csr(x_mat[:,1:]) #removing the first (all 1) feature min_rating = 1000 max_rating = 0 y_arr = [] #y values corr to feature matrix f = open(y_file, 'r') stars_list = ast.literal_eval(f.read()) for rating in stars_list: if rating>max_rating: max_rating = rating if rating<min_rating: min_rating = rating y_arr.append(rating) f.close() y_mat = np.zeros((max_rating-min_rating+1, len(y_arr))) #5 x num_input_examples #y_mat = csr((y_arr,(row_arr, col_arr)), shape=(1, len(col_arr))) col = 0 for rating in y_arr: y_mat[rating-1][col] = 1 col += 1 #init max_rating-min_rating+1 number of feature vectors; init with all weights as 1/n num_vectors = max_rating-min_rating+1 #w_mat = csr(np.random.rand(num_vectors, num_features)) w_mat = np.zeros(shape = (num_vectors, num_features)) w_mat[:] = 1./num_features w_mat = csr(w_mat) #parameters m = batch_size #batch size total_x = len(y_arr) #determine cross validation dataset cv_size = int((cv_percentage*0.01*total_x)%m) * m max_start = int(total_x/m) * m - m - cv_size cv_start = 0 while True: rand_start = random.randint(0, max_start) cv_start = int(rand_start/m) * m if cv_start <= max_start: break #iterate i = 0 j = 0 old_hard_accuracy = 0. old_soft_accuracy = 0. iter_no = 1 #gold_y = y_arr[cv_start:(cv_start+cv_size)] #x_crossval = x_mat[cv_start:(cv_start+cv_size),:] temp_alpha = alpha while True: if i==cv_start: i = cv_start + cv_size if i>=total_x: #check stopping condition: cross validation error #NOTE: soft_accuracy = rmse gold_y = y_arr[cv_start:(cv_start+cv_size)] x_crossval = x_mat[cv_start:(cv_start+cv_size),:] hard_pred, soft_pred = self.predict_class(False, None, None, None, x_crossval, w_mat) hard_accuracy, soft_accuracy = self.compute_cv_error(hard_pred, soft_pred, gold_y) print hard_accuracy, soft_accuracy if math.fabs(hard_accuracy-old_hard_accuracy)<0.01 and iter_no>10: print 'FINAL TRAINING ACCURACY:' hard_pred, soft_pred = self.predict_class(False, None, None, None, x_mat, w_mat) hard_accuracy, rmse = self.compute_cv_error(hard_pred, soft_pred, y_arr) print hard_accuracy, rmse print '--------------------------' break ''' w_sq = ((w_mat-w_mat_prev).toarray())**2 print np.sqrt(np.sum(w_sq)) if np.sqrt(np.sum(w_sq)) < 0.01: break ''' i = 0 old_hard_accuracy = hard_accuracy old_soft_accuracy = soft_accuracy #get a new set of examples to be used for cross validation: random cross-validation cv_start = 0 while True: rand_start = random.randint(0, max_start) cv_start = int(rand_start/m) * m if cv_start <= max_start: break iter_no += 1 #alpha /= (iter_no**2) alpha /= (2**iter_no) #alpha = temp_alpha / (iter_no**2) #alpha *= 0.8 continue j = min(i+m-1, total_x-1) #total m examples in a batch x_batch_mat = csr(x_mat[i:j+1,:]) #m x num_features w_dot_x = w_mat.dot(x_batch_mat.transpose()).transpose() #m x 5 w_dot_x_arr = w_dot_x.toarray() w_dot_x_arr[w_dot_x_arr>20] = 20 w_dot_x_arr[w_dot_x_arr<-20] = -20 w_dot_x = csr(w_dot_x_arr) w_dot_x_exp = csr(np.exp(w_dot_x.toarray())) #m x 5 w_dot_x_sum = w_dot_x_exp.sum(axis=1) #row sum (m x 1) x_div_mat = csr(w_dot_x_exp.toarray()/w_dot_x_sum) #m x 5 y_batch_mat = csr(y_mat[:,i:j+1].transpose()) #m x 5 sub_mat = csr(y_batch_mat.toarray() - x_div_mat.toarray()) #m x 5 sum_by_m_mat = csr(sub_mat.transpose().dot(x_batch_mat)/m) #5 x num_features w_mat_prev = w_mat w_mat = w_mat + alpha * (sum_by_m_mat - lambda_var * w_mat) i = j + 1 self.save_sparse_csr(w_final_file, w_mat)
[0, 1, 6],
])
def test_eval_sparse_no_seq(batch_index_data, device_id):
dim = 10
multiplier = 2
for var_is_sparse in [True, False]:
in1 = sequence.input(shape=(dim, ), is_sparse=var_is_sparse)
z = times(in1, multiplier * np.eye(dim))
batch = np.eye(dim)[batch_index_data]
expected = batch * multiplier
sparse_val = csr(batch.astype('f'))
result = z.eval({in1: [sparse_val]}, device=cntk_device(device_id))
assert np.allclose(result, [expected])
@pytest.mark.parametrize("batch", [[csr(
[0, 1, 2, 0])], [csr([[0, 2, 0, 7], [10, 20, 0, 0]]),
csr([0, 0, 0, 3])]])
def test_eval_sparse_seq_1(batch, device_id):
dim = 4
multiplier = 2
for var_is_sparse in [True, False]:
in1 = sequence.input(shape=(dim, ), is_sparse=var_is_sparse)
z = times(in1, multiplier * np.eye(dim))
if isinstance(batch[0], list):
expected = [
np.vstack([m.todense() * multiplier for m in seq])
for seq in batch
]
else:
expected = [seq.todense() * multiplier for seq in batch]
result = z.eval({in1: batch}, device=cntk_device(device_id))
def load_sparse_csr(self, filename): ''' Loads a sparse matrix ''' loader = np.load(filename) return csr((loader['data'], loader['indices'], loader['indptr']), shape=loader['shape'])