def _fit(self, V0):
Ph0 = np.zeros((self.n_hiddens, ) + self.h_shape)
H0 = np.zeros((self.n_hiddens, ) + self.h_shape)
Grad0 = np.zeros((self.n_hiddens, ) + (self.w_size, self.w_size))
for k in xrange(self.n_hiddens):
Ph0[k] = logistic_sigmoid(
convolve(V0, self.weights[k]) + self.h_intercepts[k])
Grad0[k] = convolve(V0, Ph0[k])
H0[k][self.rng.uniform(size=self.h_shape) < Ph0[k]] = 1
h_convolved = self.v_intercept
for k in xrange(self.n_hiddens):
h_convolved += convolve(H0[k],
np.flipud(np.fliplr(self.weights[k])))
V1m = logistic_sigmoid(h_convolved)
V1 = V0.copy()
middle_offset = self.w_size - 1
V1[middle_offset:-middle_offset, middle_offset:-middle_offset] = V1m
Ph1 = np.zeros((self.n_hiddens, ) + self.h_shape)
Grad1 = np.zeros((self.n_hiddens, ) + (self.w_size, self.w_size))
for k in xrange(self.n_hiddens):
Ph1[k] = logistic_sigmoid(
convolve(V1, self.weights[k]) + self.h_intercepts[k])
Grad1[k] = convolve(V1, Ph1[k])
self.weights += self.lr * (Grad0[k] - Grad1[k])
return self._net_probability(V0)
def _fit(self, V0):
Ph0 = np.zeros((self.n_hiddens,) + self.h_shape)
H0 = np.zeros((self.n_hiddens,) + self.h_shape)
Grad0 = np.zeros((self.n_hiddens,) + (self.w_size, self.w_size))
for k in xrange(self.n_hiddens):
Ph0[k] = logistic_sigmoid(convolve(V0, self.weights[k])
+ self.h_intercepts[k])
Grad0[k] = convolve(V0, Ph0[k])
H0[k][self.rng.uniform(size=self.h_shape) < Ph0[k]] = 1
h_convolved = self.v_intercept
for k in xrange(self.n_hiddens):
h_convolved += convolve(H0[k], np.flipud(np.fliplr(self.weights[k])))
V1m = logistic_sigmoid(h_convolved)
V1 = V0.copy()
middle_offset = self.w_size - 1
V1[middle_offset:-middle_offset, middle_offset:-middle_offset] = V1m
Ph1 = np.zeros((self.n_hiddens,) + self.h_shape)
Grad1 = np.zeros((self.n_hiddens,) + (self.w_size, self.w_size))
for k in xrange(self.n_hiddens):
Ph1[k] = logistic_sigmoid(convolve(V1, self.weights[k])
+ self.h_intercepts[k])
Grad1[k] = convolve(V1, Ph1[k])
self.weights += self.lr * (Grad0[k] - Grad1[k])
return self._net_probability(V0)
def score_samples(self, v):
"""Compute the pseudo-likelihood of v.
Parameters
----------
v : {array-like, sparse matrix} shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
pseudo_likelihood : array-like, shape (n_samples,)
Value of the pseudo-likelihood (proxy to likelihood).
print update"""
rng = check_random_state(self.random_state)
fe = self._free_energy(v)
if issparse(v):
v_ = v.toarray()
else:
v_ = v.copy()
i_ = rng.randint(0, v.shape[1], v.shape[0])
v_[np.arange(v.shape[0]), i_] = 1 - v_[np.arange(v.shape[0]), i_]
fe_ = self._free_energy(v_)
#print fe_
#print fe
return v.shape[1] * logistic_sigmoid(fe_ - fe, log=True)
def _mean_visibles_theano(self,h,v):
"""
Computes the probabilities P(v=1|h).
Parameters
----------
h : array-like, shape (n_samples, n_groups, n_components)
values of the hidden layer.
v : The input original Visible Nodes
Returns
-------
v: array-like,shape (n_samples, n_features)
"""
activations = np.array([convTheano(h[:,i,:],self.components_[i],border='full') + self.intercept_visible_ for i in range(self.n_groups)]).sum(axis = 0)
visibles = np.array(v)
windowSize = self.window_size
visualSize = int(sqrt(v.shape[1]))
innerSize = visualSize - 2 * windowSize + 2
n_sample = v.shape[0]
innerV = logistic_sigmoid(activations)
innerV = innerV.reshape(n_sample,visualSize, visualSize)[:,windowSize - 1:visualSize - windowSize + 1, windowSize - 1: visualSize - windowSize + 1]
visibles = visibles.reshape(n_sample,visualSize,visualSize)
visibles[:,windowSize - 1: visualSize - windowSize + 1,windowSize - 1: visualSize - windowSize + 1] = innerV
visibles = visibles.reshape(n_sample, -1)
return visibles
def cnnConvolve(self, X, W, b):
n_images = X.shape[0]
dim_images = X.shape[1]
dim_conv = dim_images - self.dim_filter + 1
convolved_features = np.zeros(
(n_images, self.n_filters, dim_conv, dim_conv))
for image_num in range(n_images):
for filter_num in range(self.n_filters):
convolved_image = np.zeros((dim_conv, dim_conv))
filter_ = W[filter_num]
b_ = b[filter_num]
filter_ = np.rot90(np.squeeze(filter_), 2)
im = np.squeeze(X[image_num])
convolved_image = convolve2d(im, filter_, 'valid')
convolved_image = logistic_sigmoid(convolved_image + b_)
convolved_features[image_num, filter_num] = convolved_image
return convolved_features
def predict(self, X):
"""Predict using the multi-layer perceptron model
Parameters
----------
X : {array-like, sparse matrix}, shape (n_samples, n_features)
Returns
-------
array, shape (n_samples)
Predicted target values per element in X.
"""
X = atleast2d_or_csr(X)
scores = self.decision_function(X)
if len(scores.shape) == 1 or self.multi_label is True:
scores = logistic_sigmoid(scores)
results = (scores > 0.5).astype(np.int)
if self.multi_label:
return self._lbin.inverse_transform(results)
else:
scores = _softmax(scores)
results = scores.argmax(axis=1)
return self.classes_[results]
def predict(self, X):
"""Predict using the multi-layer perceptron model
Parameters
----------
X : {array-like, sparse matrix}, shape (n_samples, n_features)
Returns
-------
array, shape (n_samples)
Predicted target values per element in X.
"""
X = atleast2d_or_csr(X)
scores = self.decision_function(X)
if len(scores.shape) == 1 or self.multi_label is True:
scores = logistic_sigmoid(scores)
results = (scores > 0.5).astype(np.int)
if self.multi_label:
return self._lbin.inverse_transform(results)
else:
scores = _softmax(scores)
results = scores.argmax(axis=1)
return self.classes_[results]
def _mean_hiddens_theano(self, v):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_groups, n_components)
Corresponding mean field values for the hidden layer.
"""
activationsWithoutIntercept = convTheano(v, self.components_)
activations = np.array([
activationsWithoutIntercept[:, i, :] + self.intercept_hidden_[i]
for i in range(self.n_groups)
])
n_samples = v.shape[0]
return logistic_sigmoid(
activations.reshape(n_samples * self.n_groups,
self.n_components)).reshape(
n_samples, self.n_groups,
self.n_components)
def _mean_visibles_theano(self, h, v):
"""
Computes the probabilities P(v=1|h).
Parameters
----------
h : array-like, shape (n_samples, n_groups, n_components)
values of the hidden layer.
v : The input original Visible Nodes
Returns
-------
v: array-like,shape (n_samples, n_features)
"""
activations = np.array([
convTheano(h[:, i, :], self.components_[i], border='full') +
self.intercept_visible_ for i in range(self.n_groups)
]).sum(axis=0)
visibles = np.array(v)
windowSize = self.window_size
visualSize = int(sqrt(v.shape[1]))
innerSize = visualSize - 2 * windowSize + 2
n_sample = v.shape[0]
innerV = logistic_sigmoid(activations)
innerV = innerV.reshape(
n_sample, visualSize,
visualSize)[:, windowSize - 1:visualSize - windowSize + 1,
windowSize - 1:visualSize - windowSize + 1]
visibles = visibles.reshape(n_sample, visualSize, visualSize)
visibles[:, windowSize - 1:visualSize - windowSize + 1,
windowSize - 1:visualSize - windowSize + 1] = innerV
visibles = visibles.reshape(n_sample, -1)
return visibles
def score_samples(self, v):
"""Compute the pseudo-likelihood of v.
Parameters
----------
v : {array-like, sparse matrix} shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
pseudo_likelihood : array-like, shape (n_samples,)
Value of the pseudo-likelihood (proxy to likelihood).
print update"""
rng = check_random_state(self.random_state)
fe = self._free_energy(v)
if issparse(v):
v_ = v.toarray()
else:
v_ = v.copy()
i_ = rng.randint(0, v.shape[1], v.shape[0])
v_[np.arange(v.shape[0]), i_] = 1 - v_[np.arange(v.shape[0]), i_]
fe_ = self._free_energy(v_)
#print fe_
#print fe
return v.shape[1] * logistic_sigmoid(fe_ - fe, log=True)
def sample(self, rng, act = None, assign = False):
act = self.value if act is None else act
h = act + rng.normal(0,1,act.shape)*np.sqrt(logistic_sigmoid(act))
h[h<0] = 0
if assign:
self.value = h
return h
def predict_proba(self, X):
scores = self.decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
return np.vstack([1 - scores, scores]).T
else:
return _softmax(scores)
def predict_proba(self, X):
scores = self.decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
return np.vstack([1 - scores, scores]).T
else:
return _softmax(scores)
def _get_hidden_activations(self, X):
A = safe_sparse_dot(X, self.coef_hidden_)
A += self.intercept_hidden_
Z = logistic_sigmoid(A)
return Z
def _get_hidden_activations(self, X):
A = safe_sparse_dot(X, self.coef_hidden_)
A += self.intercept_hidden_
Z = logistic_sigmoid(A)
return Z
def test_logistic_sigmoid():
"""Check correctness and robustness of logistic sigmoid implementation"""
naive_logistic = lambda x: 1 / (1 + np.exp(-x))
naive_log_logistic = lambda x: np.log(naive_logistic(x))
x = np.linspace(-2, 2, 50)
with warnings.catch_warnings(record=True):
assert_array_almost_equal(logistic_sigmoid(x), naive_logistic(x))
assert_array_almost_equal(log_logistic(x), naive_log_logistic(x))
extreme_x = np.array([-100., 100.])
assert_array_almost_equal(log_logistic(extreme_x), [-100, 0])
def test_logistic_sigmoid():
"""Check correctness and robustness of logistic sigmoid implementation"""
naive_logistic = lambda x: 1 / (1 + np.exp(-x))
naive_log_logistic = lambda x: np.log(naive_logistic(x))
x = np.linspace(-2, 2, 50)
with warnings.catch_warnings(record=True):
assert_array_almost_equal(logistic_sigmoid(x), naive_logistic(x))
assert_array_almost_equal(log_logistic(x), naive_log_logistic(x))
extreme_x = np.array([-100., 100.])
assert_array_almost_equal(log_logistic(extreme_x), [-100, 0])
def test_logistic_sigmoid():
"""Check correctness and robustness of logistic sigmoid implementation"""
naive_logsig = lambda x: 1 / (1 + np.exp(-x))
naive_log_logsig = lambda x: np.log(naive_logsig(x))
# Simulate the previous Cython implementations of logistic_sigmoid based on
#http://fa.bianp.net/blog/2013/numerical-optimizers-for-logistic-regression
def stable_logsig(x):
out = np.zeros_like(x)
positive = x > 0
negative = x <= 0
out[positive] = 1. / (1 + np.exp(-x[positive]))
out[negative] = np.exp(x[negative]) / (1. + np.exp(x[negative]))
return out
x = np.linspace(-2, 2, 50)
assert_array_almost_equal(logistic_sigmoid(x), naive_logsig(x))
assert_array_almost_equal(logistic_sigmoid(x, log=True),
naive_log_logsig(x))
assert_array_almost_equal(logistic_sigmoid(x), stable_logsig(x),
decimal=16)
extreme_x = np.array([-100, 100], dtype=np.float)
assert_array_almost_equal(logistic_sigmoid(extreme_x), [0, 1])
assert_array_almost_equal(logistic_sigmoid(extreme_x, log=True), [-100, 0])
assert_array_almost_equal(logistic_sigmoid(extreme_x),
stable_logsig(extreme_x),
decimal=16)
def test_logistic_sigmoid():
"""Check correctness and robustness of logistic sigmoid implementation"""
naive_logsig = lambda x: 1 / (1 + np.exp(-x))
naive_log_logsig = lambda x: np.log(naive_logsig(x))
# Simulate the previous Cython implementations of logistic_sigmoid based on
#http://fa.bianp.net/blog/2013/numerical-optimizers-for-logistic-regression
def stable_logsig(x):
out = np.zeros_like(x)
positive = x > 0
negative = x <= 0
out[positive] = 1. / (1 + np.exp(-x[positive]))
out[negative] = np.exp(x[negative]) / (1. + np.exp(x[negative]))
return out
x = np.linspace(-2, 2, 50)
assert_array_almost_equal(logistic_sigmoid(x), naive_logsig(x))
assert_array_almost_equal(logistic_sigmoid(x, log=True),
naive_log_logsig(x))
assert_array_almost_equal(logistic_sigmoid(x), stable_logsig(x),
decimal=16)
extreme_x = np.array([-100, 100], dtype=np.float)
assert_array_almost_equal(logistic_sigmoid(extreme_x), [0, 1])
assert_array_almost_equal(logistic_sigmoid(extreme_x, log=True), [-100, 0])
assert_array_almost_equal(logistic_sigmoid(extreme_x),
stable_logsig(extreme_x),
decimal=16)
def _mean_hiddens(self, v):
"""Computes the probabilities P(h=1|v), i.e. mean-field values of the hidden layer
Parameters
v: array of shape (input_size, ) (considered 1 X input_size in dot product below )
Returns:
h: array of shape (hidden_size,)
Corresponding mean field values for the hidden layer
"""
return logistic_sigmoid(np.dot(v, self.W) + self.b)
def _net_probability(self, V):
"""
Computes pseudo probability of the current network
"""
v_energy = 0
for k in xrange(self.n_hiddens):
v_energy -= (self.hiddens[k] * convolve(V, self.weights[k])).sum()
h_int_energy = 0
for k in xrange(self.n_hiddens):
h_int_energy -= self.h_intercepts[k].sum() * self.hiddens[k].sum()
v_int_energy = - self.v_intercept.sum() * V.sum()
energy = v_energy + h_int_energy + v_int_energy
print(energy)
return logistic_sigmoid(- energy)
def _net_probability(self, V):
"""
Computes pseudo probability of the current network
"""
v_energy = 0
for k in xrange(self.n_hiddens):
v_energy -= (self.hiddens[k] * convolve(V, self.weights[k])).sum()
h_int_energy = 0
for k in xrange(self.n_hiddens):
h_int_energy -= self.h_intercepts[k].sum() * self.hiddens[k].sum()
v_int_energy = -self.v_intercept.sum() * V.sum()
energy = v_energy + h_int_energy + v_int_energy
print(energy)
return logistic_sigmoid(-energy)
def _sample_visibles(self, h, rng):
"""Sample from the distribution P(v|h).
rng: Random Number generator to be used.
Parameters :
h : array of shape (hidden_size,) (considered 1 X hidden_size in dot product below)
Returns:
v : array of shape (input_size,)
Values of the visible layer
"""
p = logistic_sigmoid(np.dot(h, self.W.T) + self.c)
p[rng.uniform(size=p.shape) < p] = 1.
return np.floor(p, p)
def _mean_hiddens(self, v):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_components)
Corresponding mean field values for the hidden layer.
"""
return logistic_sigmoid(safe_sparse_dot(v, self.components_.T)
+ self.intercept_hidden_)
def _mean_hiddens(self, v):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_components)
Corresponding mean field values for the hidden layer.
"""
return logistic_sigmoid(
safe_sparse_dot(v, self.components_.T) + self.intercept_hidden_)
def _mean_visibles(self, h):
"""
Computes the probabilities P(v=1|h).
Parameters
----------
h : array-like, shape (n_samples, n_groups, n_components)
values of the hidden layer.
Returns
-------
v: array-like,shape (n_samples, n_features)
"""
n_samples = h.shape[0]
activations = np.array([convExpendGroup(h[i],self.components_) + self.intercept_visible_ for i in range(n_samples)])
return logistic_sigmoid(activations)
def _mean_hiddens(self, v,k):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_components)
Corresponding mean field values for the hidden layer.
"""
n_samples = v.shape[0]
activations = np.array([conv(v[i,:],self.components_[k]) + self.intercept_hidden_[k] for i in range(n_samples)])
return logistic_sigmoid(activations)
def score_samples(self,v):
"""Computer the pseudo-likelihood of v
returns
--------
pseudo_likelihood : array-like shape (n_samples,)
"""
v = np.hstack(v)
fe = self.free_energy(v)
v_ = v.copy()
rng = check_random_state(self.random_state)
i_ = rng.randint(0,v.shape[1],v.shape[0])
v_[np.arange(v.shape[0]),i_] = 1 - v_[np.arange(v.shape[0]), i_]
fe_ = self.free_energy(v_)
return v.shape[1] * logistic_sigmoid(fe_ - fe, log=True)
def _mean_hiddens_theano(self,v):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_groups, n_components)
Corresponding mean field values for the hidden layer.
"""
activationsWithoutIntercept = convTheano(v,self.components_)
activations = np.array([activationsWithoutIntercept[:,i,:] + self.intercept_hidden_[i] for i in range(self.n_groups)])
n_samples = v.shape[0]
return logistic_sigmoid(activations.reshape(n_samples * self.n_groups, self.n_components)).reshape(n_samples,self.n_groups,self.n_components)
def _mean_hiddens(self, v, k):
"""Computes the probabilities P(h=1|v).
Parameters
----------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
Returns
-------
h : array-like, shape (n_samples, n_components)
Corresponding mean field values for the hidden layer.
"""
n_samples = v.shape[0]
activations = np.array([
conv(v[i, :], self.components_[k]) + self.intercept_hidden_[k]
for i in range(n_samples)
])
return logistic_sigmoid(activations)
def predict_proba(self, X):
"""Probability estimates.
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Returns
-------
array, shape = [n_samples, n_outputs]
Returns the probability of the sample for each class in the model,
where classes are ordered as they are in `self.classes_`.
"""
scores = super(DBNClassifier, self).decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
return np.vstack([1 - scores, scores]).T
else:
return _softmax(scores)
def predict_proba(self, X):
"""Probability estimates.
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Returns
-------
array, shape = [n_samples, n_outputs]
Returns the probability of the sample for each class in the model,
where classes are ordered as they are in `self.classes_`.
"""
scores = super(DBNClassifier, self).decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
return np.vstack([1 - scores, scores]).T
else:
return _softmax(scores)
def _mean_visibles(self, h):
"""
Computes the probabilities P(v=1|h).
Parameters
----------
h : array-like, shape (n_samples, n_groups, n_components)
values of the hidden layer.
Returns
-------
v: array-like,shape (n_samples, n_features)
"""
n_samples = h.shape[0]
activations = np.array([
convExpendGroup(h[i], self.components_) + self.intercept_visible_
for i in range(n_samples)
])
return logistic_sigmoid(activations)
def _sample_visibles(self, h, rng):
"""Sample from the distribution P(v|h).
Parameters
----------
h : array-like, shape (n_samples, n_components)
Values of the hidden layer to sample from.
rng : RandomState
Random number generator to use.
Returns
-------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
"""
p = logistic_sigmoid(np.dot(h, self.components_)
+ self.intercept_visible_)
p[rng.uniform(size=p.shape) < p] = 1.
return np.floor(p, p)
def _sample_visibles(self, h, rng):
"""Sample from the distribution P(v|h).
Parameters
----------
h : array-like, shape (n_samples, n_components)
Values of the hidden layer to sample from.
rng : RandomState
Random number generator to use.
Returns
-------
v : array-like, shape (n_samples, n_features)
Values of the visible layer.
"""
p = logistic_sigmoid(
np.dot(h, self.components_) + self.intercept_visible_)
p[rng.uniform(size=p.shape) < p] = 1.
return np.floor(p, p)
def predict(self, X):
"""Predict using the multi-layer perceptron model
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Returns
-------
array, shape = [n_samples]
Predicted target values per element in X.
"""
X = atleast2d_or_csr(X)
scores = super(DBNClassifier, self).decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
indices = (scores > 0.5).astype(np.int)
else:
scores = _softmax(scores)
indices = scores.argmax(axis=1)
return self._lbin.classes_[indices]
def predict(self, X):
"""Predict using the multi-layer perceptron model
Parameters
----------
X : {array-like, sparse matrix}, shape = [n_samples, n_features]
Returns
-------
array, shape = [n_samples]
Predicted target values per element in X.
"""
X = atleast2d_or_csr(X)
scores = super(DBNClassifier, self).decision_function(X)
if len(scores.shape) == 1:
scores = logistic_sigmoid(scores)
indices = (scores > 0.5).astype(np.int)
else:
scores = _softmax(scores)
indices = scores.argmax(axis=1)
return self._lbin.classes_[indices]
def _mean_visible(self, h):
v = np.zeros(self.v_shape)
for k in xrange(self.n_hiddens):
v += conv2(h[k], self.W[k], 'full')
return logistic_sigmoid(v + self.b)
def _mean_visible(self, h):
v = np.zeros(self.v_shape)
for k in xrange(self.n_hiddens):
v += conv2(h[k], self.W[k], 'full')
return logistic_sigmoid(v + self.b)