def get_cost_updates(self, x, W, W_prime, b, b_prime, corruption_level, learning_rate, l2reg=0., l1reg=0.):
""" This function computes the cost and the updates for one trainng
step of the dA """
self.x = x
self.W = W
self.W_prime = W_prime
self.b = b
self.b_prime = b_prime
self.params = [self.W, self.W_prime, self.b, self.b_prime]
if corruption_level == None:
tilde_x = self.x
else:
tilde_x = self.get_corrupted_input(self.x, corruption_level)
y = self.get_hidden_values( tilde_x)
z = self.get_reconstructed_input(y)
# note : we sum over the size of a datapoint; if we are using minibatches,
# L will be a vector, with one entry per example in minibatch
XE = self.x * T.log(z) + (1 - self.x) * T.log(1-z)
cost = -T.mean(T.sum(XE, axis=1),axis=0)
if l2reg != 0.:
cost += l2reg * (T.mean(T.sum(self.W*self.W,1),0) + T.mean(T.sum(self.W_prime*self.W_prime,1),0))
if l1reg != 0.:
cost += l1reg * (T.mean(T.sum(T.abs_(y),1),0) + T.mean(T.sum(T.abs_(y),1),0))
# compute the gradients of the cost of the `dA` with respect
# to its parameters
gparams = T.grad(cost, self.params)
# # generate the list of updates
# updates = {}
# for param, gparam in zip(self.params, gparams):
# updates[param] = param - learning_rate*gparam
updates = [-learning_rate*gparam for gparam in gparams]
return (cost, updates)
def sample(self, Y):
""" Given samples from the upper layer Y, sample values from X
and return then together with their log probability.
Parameters
----------
Y: T.tensor
samples from the upper layer
Returns
-------
X: T.tensor
samples from the lower layer
log_p: T.tensor
log-posterior for the samples returned in X
"""
n_X, = self.get_hyper_params(['n_X'])
W, b = self.get_model_params(['W', 'b'])
n_samples = Y.shape[0]
# sample X given Y
prob_X = self.sigmoid(T.dot(Y, W) + b)
U = theano_rng.uniform((n_samples, n_X), nstreams=512)
X = T.cast(U <= prob_X, dtype=floatX)
log_prob = X*T.log(prob_X) + (1-X)*T.log(1-prob_X)
log_prob = log_prob.sum(axis=1)
return X, log_prob
def get_cost_updates(self, corruption_level, learning_rate):
""" This function computes the cost and the updates for one trainng
step of the dA """
tilde_x = self.get_corrupted_input(self.x, corruption_level)
y = self.get_hidden_values(tilde_x)
z = self.get_reconstructed_input(y)
# note : we sum over the size of a datapoint; if we are using
# minibatches, L will be a vector, with one entry per
# example in minibatch
L = - T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z), axis=1)
# note : L is now a vector, where each element is the
# cross-entropy cost of the reconstruction of the
# corresponding example of the minibatch. We need to
# compute the average of all these to get the cost of
# the minibatch
cost = T.mean(L)
# compute the gradients of the cost of the `dA` with respect
# to its parameters
gparams = T.grad(cost, self.params)
# generate the list of updates
updates = [
(param, param - learning_rate * gparam)
for param, gparam in zip(self.params, gparams)
]
return (cost, updates)
def cross_entropy(self, y):
#return (-(y * T.log(self.y) + (1.0 - y) * T.log(1.0 - self.y))).mean()
#return T.nnet.binary_crossentropy(self.y, y).mean()
y_used = self.y
y_used = T.clip(self.y, 0.0000001, 0.999999999)
return T.mean(-y * T.log(y_used) - (1 - y) * T.log(1 - y_used))
def get_reconstruction_cost(self, updates, pre_sigmoid_nv):
""" Approximation to the recontruction error
Note that this function requires the pre-sigmoid actiavtion as input. To
undertstand why this is so you need to understand a bit about how Theano works.
Whenever you compile a Theano function, the computational graph that you pass as input
gets optimized for speed and stability. This is done by changing several parts of
the subgraphs with others. One such optimization expresses terms of softplus. We need this
optimizations for the cross-entropy since sigmoid of numbers larger than 30. (or even less
then that) return to 1. and numbers of smaller than -30, turn to 0 which ini terms will force
theano to compute log(0) and thereforce we will get either -inf or NaN as cost. If the value is
expressed in terms of softplus we do not get this undersirable behaviour. This optimiation usually
works fine, but here we have a special case. The sigmoid is applied inside the scan op, while
the log is outisde. Therefore Theano will only see log(scan(...)) instead of log(sigmoid(..))
and will not apply the wanted optimization. We can not go and replace the sigmoid in scan
with something else alse, because this only needs to be done on the last step. Therefore the
easiest adn more efficient way is to get also teh pre-sigmoid activation as an output of
scan, and apply both the log and sigmoid outside scan sunch that Theano can catch and optimize
the expression.
"""
cross_entropy = T.mean(
T.sum(
self.input * T.log(T.nnet.sigmoid(pre_sigmoid_nv)) +
( 1 - self.input) * T.log(1 - T.nnet.sigmoid(pre_sigmoid_nv)),
axis=1
)
)
return cross_entropy
def _build_marginal_likelihood_logp(self, y, X, Xu, sigma):
sigma2 = tt.square(sigma)
Kuu = self.cov_func(Xu)
Kuf = self.cov_func(Xu, X)
Luu = cholesky(stabilize(Kuu))
A = solve_lower(Luu, Kuf)
Qffd = tt.sum(A * A, 0)
if self.approx == "FITC":
Kffd = self.cov_func(X, diag=True)
Lamd = tt.clip(Kffd - Qffd, 0.0, np.inf) + sigma2
trace = 0.0
elif self.approx == "VFE":
Lamd = tt.ones_like(Qffd) * sigma2
trace = ((1.0 / (2.0 * sigma2)) *
(tt.sum(self.cov_func(X, diag=True)) -
tt.sum(tt.sum(A * A, 0))))
else: # DTC
Lamd = tt.ones_like(Qffd) * sigma2
trace = 0.0
A_l = A / Lamd
L_B = cholesky(tt.eye(Xu.shape[0]) + tt.dot(A_l, tt.transpose(A)))
r = y - self.mean_func(X)
r_l = r / Lamd
c = solve_lower(L_B, tt.dot(A, r_l))
constant = 0.5 * X.shape[0] * tt.log(2.0 * np.pi)
logdet = 0.5 * tt.sum(tt.log(Lamd)) + tt.sum(tt.log(tt.diag(L_B)))
quadratic = 0.5 * (tt.dot(r, r_l) - tt.dot(c, c))
return -1.0 * (constant + logdet + quadratic + trace)
def compileFunctions(self, x_image_global, examples, ib, B, K, corrupt):
if x_image_global == None:
x_image_global = self.x
if corrupt == 0.0:
self.x_c = self.x
else:
self.x_c = self.theano_rng.binomial(
size=self.x.shape, n=1, p=1-corrupt,
dtype=theano.config.floatX) * self.x
self.h = self.g(T.dot(self.x_c, self.W_hl) + self.b_hl)
self.x_r = self.o(T.dot(self.h, self.W_ol) + self.b_ol)
self.params = [self.W_hl, self.b_hl, self.b_ol]
self.cost = \
(- T.sum(
self.x * T.log(self.x_r) + (1 - self.x) * T.log(1 - self.x_r),
axis=(0,1)))
gparams = T.grad(self.cost, self.params)
updates = [
(param, param - K * gparam)
for param, gparam in zip(self.params, gparams)
]
fun_train = theano.function(
inputs=[ib],
outputs=(self.cost, self.x_r, self.x_c),
updates=updates,
givens={
x_image_global: examples[ib*B: (ib+1)*B]
}
)
return fun_train
def binomial_lpdf(node, x, kw):
random_state, size, n, p = node.inputs
# for the n > 1 the "choose" operation is required
# TODO assert n == 1
return tensor.switch(tensor.eq(x, 1.0), tensor.log(p), tensor.log(1.0 - p))
def _elbo_t(logp, uw, inarray, n_mcsamples, random_seed):
"""Create Theano tensor of approximate ELBO by Monte Carlo sampling.
"""
l = (uw.size / 2)
l_int = l.astype('int64')
u = uw[:l_int]
w = uw[l_int:]
# Callable tensor
def logp_(input):
return theano.clone(logp, {inarray: input}, strict=False)
# Naive Monte-Carlo
if random_seed is None:
r = MRG_RandomStreams(gen_random_state())
else:
r = MRG_RandomStreams(seed=random_seed)
if n_mcsamples == 1:
n = r.normal(size=inarray.tag.test_value.shape)
q = n * tt.exp(w) + u
elbo = logp_(q) + tt.sum(w) + 0.5 * l * (1 + tt.log(2.0 * np.pi))
else:
n = r.normal(size=(n_mcsamples, u.tag.test_value.shape[0]))
qs = n * tt.exp(w) + u
logps, _ = theano.scan(fn=lambda q: logp_(q),
outputs_info=None,
sequences=[qs])
elbo = tt.mean(logps) + tt.sum(w) + 0.5 * l * (1 + tt.log(2.0 * np.pi))
return elbo
def logp(self, value):
mu = self.mu
tau = self.tau
return bound(-0.5 * tau * (T.log(value) - mu)**2
+ 0.5 * T.log(tau/(2. * np.pi))
- T.log(value),
tau > 0)
def logp(self, value):
alpha = self.alpha
beta = self.beta
return bound(T.log(alpha) - T.log(beta)
+ (alpha - 1) * T.log(value/beta)
- (value/beta)**alpha,
value >= 0, alpha > 0, beta > 0)
def grad_init(self):
mask_ = self.mask.flatten()
rewards_ = self.rewards.flatten()
actions_ = self.actions.reshape([self.actions.shape[0]*self.actions.shape[1],-1])
#self.mov_std = theano.shared(numpy.float32(1.), 'std')
pp = self.params.values()
mean_rewards = (mask_ * rewards_).sum(-1, keepdims=True) / tensor.maximum(1., mask_.sum(-1, keepdims=True))
centered_rewards = rewards_ - self.vapprox.v[:,0] - mean_rewards
mean2_rewards = (mask_ * (rewards_ ** 2)).sum(-1, keepdims=True) / tensor.maximum(1., mask_.sum(-1, keepdims=True))
var_rewards = mean2_rewards - (mean_rewards ** 2)
scaled_rewards = centered_rewards / tensor.maximum(1., tensor.sqrt(tensor.maximum(0., var_rewards)))
#scaled_rewards = centered_rewards
logprob = 0.
reg = 0.
for oi in xrange(self.n_out):
labs = actions_[:,oi].flatten()
labs_idx = tensor.arange(labs.shape[0]) * self.out_dim + labs
logprob = logprob + (mask_ * tensor.log(self.pi[oi].flatten()+1e-6)[labs_idx])
reg = reg - (self.pi[oi] * tensor.log(self.pi[oi]+1e-6)).sum(-1).sum(0)
self.cost = -tensor.mean(scaled_rewards * logprob + self.reg_c * reg)
self.grads = tensor.grad(self.cost, wrt=pp)
def get_cost(self, p=0, sigma=1):
# the last layer
z = self.sigmoid_layers[-1].output
L = -T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z), axis=1)
p_idx = len(self.sigmoid_layers)/2 - 1 #penalty layer, the middle layer
if p == 0:
cost = T.mean(L)
# cost = T.mean(T.sqrt(T.mean(self.errors, axis=1))) #Log Spectral Distance(LSD)
elif (p != 0) and (sigma == 0):# for square penalty
square_cost = self.get_square_cost(self.sigmoid_layers[p_idx].output, p)
cost = T.mean(L) + T.mean(square_cost)
elif(p != 0) and (sigma != 0):# for Gaussian penalty
gaussian_cost = self.get_gaussian_cost(self.sigmoid_layers[p_idx].output, p, sigma)
cost = T.mean(L) + T.mean(gaussian_cost)
# elif(p == -1) and (sigma == 0):#binary
# code_val = self.sigmoid_layers[p_idx].output
# binary_val = code_val>=0.5
# self.sigmoid_layers[p_idx+1].input = binary_val
# z = self.sigmoid_layers[-1].output
# L = -T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z), axis=1)
# cost = T.mean(L)
# elif(p == -1) and (sigma != 0):#add gaussian noise
# gaussian_data = self.theano_rng.normal(size=self.sigmoid_layers[p_idx-1].output.shape, std=sigma,
# dtype=theano.config.floatX)
# self.sigmoid_layers[p_idx].input = self.sigmoid_layers[p_idx-1].output + gaussian_data
# z = self.sigmoid_layers[-1].output
# L = -T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z), axis=1)
# cost = T.mean(L)
else:
cost = T.mean(L)
return cost
def unet_crossentropy_loss_sampled(y_true, y_pred):
print 'unet_crossentropy_loss_sampled'
epsilon = 1.0e-4
y_pred_clipped = T.flatten(T.clip(y_pred, epsilon, 1.0-epsilon))
y_true = T.flatten(y_true)
# this seems to work
# it is super ugly though and I am sure there is a better way to do it
# but I am struggling with theano to cooperate
# filter the right indices
indPos = T.nonzero(y_true)[0] # no idea why this is a tuple
indNeg = T.nonzero(1-y_true)[0]
# shuffle
n = indPos.shape[0]
indPos = indPos[srng.permutation(n=n)]
n = indNeg.shape[0]
indNeg = indNeg[srng.permutation(n=n)]
# take equal number of samples depending on which class has less
n_samples = T.cast(T.min([T.sum(y_true), T.sum(1-y_true)]), dtype='int64')
indPos = indPos[:n_samples]
indNeg = indNeg[:n_samples]
loss_vector = -T.mean(T.log(y_pred_clipped[indPos])) - T.mean(T.log(1-y_pred_clipped[indNeg]))
average_loss = T.mean(loss_vector)
print 'average_loss:', average_loss
return average_loss
def get_model(Ws, bs, dropout=False):
v = T.matrix('input')
m = T.matrix('missing')
q = T.matrix('target')
k = T.vector('normalization factor')
# Set all missing/target values to 0.5
keep_mask = (1-m) * (1-q)
h = keep_mask * (v * 2 - 1) # Convert to +1, -1
# Normalize layer 0
h *= k.dimshuffle(0, 'x')
for l in xrange(len(Ws)):
h = T.dot(h, Ws[l]) + bs[l]
if l < len(Ws) - 1:
h = h * (h > 0) # relu
if dropout:
mask = srng.binomial(n=1, p=0.5, size=h.shape)
h = h * mask * 2
output = sigmoid(h)
LL = v * T.log(output) + (1 - v) * T.log(1 - output)
# loss = -(q * LL).sum() / q.sum()
loss = -((1 - m) * LL).sum() / (1 - m).sum()
return v, m, q, k, output, loss
def expr(self, model, data):
v = data
mid = model.get_enc(v)
rou_mid = mid.mean(axis=0)
cs294_sparse = (self.rou * T.log(self.rou / rou_mid) + (1 - self.rou) * T.log((1 - self.rou) / (1 - rou_mid))).sum()
return cs294_sparse
def GMM(y, mu, sig, coeff):
"""
Gaussian mixture model negative log-likelihood
Parameters
----------
y : TensorVariable
mu : FullyConnected (Linear)
sig : FullyConnected (Softplus)
coeff : FullyConnected (Softmax)
"""
n_dim = y.ndim
shape_y = y.shape
y = y.reshape((-1, shape_y[-1]))
y = y.dimshuffle(0, 1, "x")
mu = mu.reshape((-1, mu.shape[-1] / coeff.shape[-1], coeff.shape[-1]))
sig = sig.reshape((-1, sig.shape[-1] / coeff.shape[-1], coeff.shape[-1]))
coeff = coeff.reshape((-1, coeff.shape[-1]))
inner = -0.5 * T.sum(T.sqr(y - mu) / sig ** 2 + 2 * T.log(sig) + T.log(2 * np.pi), axis=-2)
nll = -logsumexp(T.log(coeff) + inner, axis=-1)
# Adjust dimension
new_dim = T.set_subtensor(shape_y[-1], 1)
nll = nll.reshape(new_dim, ndim=n_dim)
nll = nll.flatten(n_dim - 1)
return nll
def lp_norm(self, n, k, r, c, z):
'''
Lp = ( 1/n * sum(|x_i|^p, 1..n))^(1/p) where p = 1 + ln(1+e^P)
:param n:
:param k:
:param r:
:param c:
:param z:
:return:
'''
ds0, ds1 = self.pool_size
st0, st1 = self.stride
pad_h = self.pad[0]
pad_w = self.pad[1]
row_st = r * st0
row_end = T.minimum(row_st + ds0, self.img_rows)
row_st = T.maximum(row_st, self.pad[0])
row_end = T.minimum(row_end, self.x_m2d + pad_h)
col_st = c * st1
col_end = T.minimum(col_st + ds1, self.img_cols)
col_st = T.maximum(col_st, self.pad[1])
col_end = T.minimum(col_end, self.x_m1d + pad_w)
Lp = T.pow(
T.mean(T.pow(
T.abs_(T.flatten(self.y[n, k, row_st:row_end, col_st:col_end], 1)),
1 + T.log(1 + T.exp(self.P))
)),
1 / (1 + T.log(1 + T.exp(self.P)))
)
return T.set_subtensor(z[n, k, r, c], Lp)
def sequence_log_likelihood(y, y_hat, y_mask, y_hat_mask, blank_symbol, log_scale=True):
"""
Based on code from Shawn Tan.
Credits to Kyle Kastner as well.
This function computes the CTC log likelihood for a sequence that has
been augmented with blank labels.
"""
y_hat_mask_len = tensor.sum(y_hat_mask, axis=0, dtype="int32")
y_mask_len = tensor.sum(y_mask, axis=0, dtype="int32")
if log_scale:
log_probabs = _log_path_probabs(y, T.log(y_hat), y_mask, y_hat_mask, blank_symbol)
batch_size = log_probabs.shape[1]
# Add the probabilities of the final time steps to get the total
# sequence likelihood.
log_labels_probab = _log_add(
log_probabs[y_hat_mask_len - 1, tensor.arange(batch_size), y_mask_len - 1],
log_probabs[y_hat_mask_len - 1, tensor.arange(batch_size), y_mask_len - 2],
)
else:
probabilities = _path_probabs(y, y_hat, y_mask, y_hat_mask, blank_symbol)
batch_size = probabilities.shape[1]
labels_probab = (
probabilities[y_hat_mask_len - 1, tensor.arange(batch_size), y_mask_len - 1]
+ probabilities[y_hat_mask_len - 1, tensor.arange(batch_size), y_mask_len - 2]
)
log_labels_probab = tensor.log(labels_probab)
return log_labels_probab
def __init__(self, n_in, n_out, n_h, learning_rate=0.12):
self.x = T.matrix(dtype=theano.config.floatX) # @UndefinedVariable
self.target = T.matrix(dtype=theano.config.floatX) # @UndefinedVariable
bound_x = numpy.sqrt(6. / (n_in + n_h))
bound_h = numpy.sqrt(6. / (n_h + n_h))
self.params = []
self.w_x = theano.shared(np.array(np.random.uniform(low=-bound_x, high=bound_x, size=(n_in, n_h)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.w_x)
self.w_h = theano.shared(np.array(np.random.uniform(low=-bound_h, high=bound_h, size=(n_h, n_h)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.w_h)
self.b_h = theano.shared(np.array(np.random.uniform(low=-bound_h, high=bound_h, size=(n_h,)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.b_h)
self.w = theano.shared(np.array(np.random.uniform(low=-bound_h, high=bound_h, size=(n_h, n_out)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.w)
self.b = theano.shared(np.array(np.random.uniform(low=-bound_h, high=bound_h, size=(n_out,)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.b)
self.h0 = theano.shared(np.array(np.random.uniform(low=-bound_x, high=bound_x, size=(n_h,)), dtype=theano.config.floatX)) # @UndefinedVariable
self.params.append(self.h0)
def one_step(x, h1):
h = T.nnet.sigmoid(T.dot(x, self.w_x) + T.dot(h1, self.w_h) + self.b_h)
y = T.nnet.sigmoid(T.dot(h, self.w) + self.b)
return h, y
[hs, ys], _ = theano.scan(fn=one_step, sequences=self.x, outputs_info=[self.h0, None])
cost = -T.mean(self.target * T.log(ys) + (1 - self.target) * T.log(1 - ys))
grads = T.grad(cost, self.params)
updates = [(param, param - learning_rate * grad) for param, grad in zip(self.params, grads)]
self.train = theano.function([self.x, self.target], cost, updates=updates)
self.predict = theano.function([self.x], ys)
def get_cost_updates(self, contraction_level, learning_rate):
""" This function computes the cost and the updates for one trainng
step of the cA """
y = self.get_hidden_values(self.x)
z = self.get_reconstructed_input(y)
J = self.get_jacobian(y, self.W)
# note : we sum over the size of a datapoint; if we are using
# minibatches, L will be a vector, with one entry per
# example in minibatch
self.L_rec = - T.sum(self.x * T.log(z) +
(1 - self.x) * T.log(1 - z),
axis=1)
# Compute the jacobian and average over the number of samples/minibatch
self.L_jacob = T.sum(J ** 2) // self.n_batchsize
# note : L is now a vector, where each element is the
# cross-entropy cost of the reconstruction of the
# corresponding example of the minibatch. We need to
# compute the average of all these to get the cost of
# the minibatch
cost = T.mean(self.L_rec) + contraction_level * T.mean(self.L_jacob)
# compute the gradients of the cost of the `cA` with respect
# to its parameters
gparams = T.grad(cost, self.params)
# generate the list of updates
updates = []
for param, gparam in zip(self.params, gparams):
updates.append((param, param - learning_rate * gparam))
return (cost, updates)
def test_log1msigm_to_softplus(self):
x = T.matrix()
out = T.log(1 - sigmoid(x))
f = theano.function([x], out, mode=self.m)
topo = f.maker.fgraph.toposort()
assert len(topo) == 2
assert isinstance(topo[0].op.scalar_op,
theano.tensor.nnet.sigm.ScalarSoftplus)
assert isinstance(topo[1].op.scalar_op, theano.scalar.Neg)
f(numpy.random.rand(54, 11).astype(config.floatX))
# Same test with a flatten
out = T.log(1 - T.flatten(sigmoid(x)))
f = theano.function([x], out, mode=self.m)
topo = f.maker.fgraph.toposort()
assert len(topo) == 3
assert isinstance(topo[0].op, T.Flatten)
assert isinstance(topo[1].op.scalar_op,
theano.tensor.nnet.sigm.ScalarSoftplus)
assert isinstance(topo[2].op.scalar_op, theano.scalar.Neg)
f(numpy.random.rand(54, 11).astype(config.floatX))
# Same test with a reshape
out = T.log(1 - sigmoid(x).reshape([x.size]))
f = theano.function([x], out, mode=self.m)
topo = f.maker.fgraph.toposort()
#assert len(topo) == 3
assert any(isinstance(node.op, T.Reshape) for node in topo)
assert any(isinstance(getattr(node.op, 'scalar_op', None),
theano.tensor.nnet.sigm.ScalarSoftplus)
for node in topo)
f(numpy.random.rand(54, 11).astype(config.floatX))
def negative_log_likelihood(self, y):
""" Return the mean of the negative log-likelihood of the prediction
of this model under a given target distribution.
.. math::
\frac{1}{|\mathcal{D}|} \mathcal{L} (\theta=\{W,b\}, \mathcal{D}) =
\frac{1}{|\mathcal{D}|} \sum_{i=0}^{|\mathcal{D}|} \log(P(Y=y^{(i)}|x^{(i)}, W,b)) \\
\ell (\theta=\{W,b\}, \mathcal{D})
:type y: theano.tensor.TensorType
:param y: corresponds to a vector that gives for each example the
correct label
Note: we use the mean instead of the sum so that
the learning rate is less dependent on the batch size
"""
# y.shape[0] is (symbolically) the number of rows in y, i.e.,
# number of examples (call it n) in the minibatch
# T.arange(y.shape[0]) is a symbolic vector which will contain
# [0,1,2,... n-1] T.log(self.p_y_given_x) is a matrix of
# Log-Probabilities (call it LP) with one row per example and
# one column per class LP[T.arange(y.shape[0]),y] is a vector
# v containing [LP[0,y[0]], LP[1,y[1]], LP[2,y[2]], ...,
# LP[n-1,y[n-1]]] and T.mean(LP[T.arange(y.shape[0]),y]) is
# the mean (across minibatch examples) of the elements in v,
# i.e., the mean log-likelihood across the minibatch.
if self.is_binary:
-T.mean(T.log(self.p_y_given_x))
return -T.mean(T.log(self.p_y_given_x)[T.arange(y.shape[0]), y])
def simple_RNN(nh):
Wx = theano.shared(0.2 * numpy.random.uniform(-1.0, 1.0, (1, nh)).astype(theano.config.floatX))
Wh = theano.shared(0.2 * numpy.random.uniform(-1.0, 1.0, (nh, nh)).astype(theano.config.floatX))
Wy = theano.shared(0.2 * numpy.random.uniform(-1.0, 1.0, (nh, 1)).astype(theano.config.floatX))
bh = theano.shared(numpy.zeros(nh, dtype=theano.config.floatX))
by = theano.shared(numpy.zeros(1, dtype=theano.config.floatX))
h0 = theano.shared(numpy.zeros(nh, dtype=theano.config.floatX))
p = [Wx, Wh, Wy, bh, by, h0]
x = T.matrix()
def recurrence(x_t, h_tm1):
h_t = T.tanh(T.dot(x_t, Wx) + T.dot(h_tm1, Wh) + bh)
s_t = T.dot(h_t, Wy) + by
return [h_t, s_t]
([h, activations], updates) = theano.scan(fn=recurrence, sequences=x, outputs_info=[h0, dict()])
t = x[0, 0]
s = activations[-1, 0]
y = T.nnet.sigmoid(s)
loss = -t*T.log(y + 1e-14) - (1-t)*T.log((1-y) + 1e-14)
acc = T.neq(T.round(y), t)
return p, [x], s, [loss, acc], h
def get_cost_updates(self, contraction_level, learning_rate, cost_measure="cross_entropy"):
""" This function computes the cost and the updates for one trainng
step of the cA """
y = self.get_hidden_values(self.x)
z = self.get_reconstructed_input(y)
J = self.get_jacobian(y, self.W)
if cost_measure=="cross_entropy":
#self.L_rec = - T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z), axis=1)
self.L_rec = T.mean(- T.sum(self.x * T.log(z) + (1 - self.x) * T.log(1 - z),axis=1))
elif cost_measure=="euclidean":
self.L_rec = T.mean(T.sum((self.x-z)**2,axis=1))
# Compute the jacobian and average over the number of samples/minibatch
self.L_jacob = T.mean(T.sum(J ** 2) / self.n_batchsize)
cost = self.L_rec + contraction_level * self.L_jacob
# compute the gradients of the cost of the `cA` with respect
# to its parameters
gparams = T.grad(cost, self.params)
# generate the list of updates
updates = []
for param, gparam in zip(self.params, gparams):
updates.append((param, param - learning_rate * gparam))
return (cost, updates)
def forward_jacobian_log_det(self, x):
dy_dx, _ = th.scan(lambda x_i: th.grad(self.forward_func(x_i), x_i),
sequences=[x.flatten()])
if self.fudge != 0.:
return tt.log(dy_dx + self.fudge).sum()
else:
return tt.log(dy_dx).sum()
def forward_jacobian_log_det(self, x):
y_sum = self.forward_map(x).sum()
dy_dx = th.grad(y_sum, x)
if self.fudge != 0.:
return tt.log(dy_dx + self.fudge).sum()
else:
return tt.log(dy_dx).sum()
def get_sparsity_cost(self):
# update mean activation using exponential moving average
hack_h = self.h_given_v(self.sp_pos_v)
# define loss based on value of sp_type
if self.sp_type == 'kl':
eps = npy_floatX(1./self.batch_size)
loss = lambda targ, val: - npy_floatX(targ) * T.log(eps + val) \
- npy_floatX(1-targ) * T.log(1 - val + eps)
else:
raise NotImplementedError('Sparsity type %s is not implemented' % self.sp_type)
cost = T.zeros((), dtype=floatX)
params = []
if self.sp_weight['h']:
cost += self.sp_weight['h'] * T.sum(loss(self.sp_targ['h'], hack_h.mean(axis=0)))
params += [self.hbias]
if self.sp_type in ['kl'] and self.sp_weight['h']:
params += [self.Wv, self.alpha, self.mu]
if self.flags['split_norm']:
params += [self.scalar_norms]
return costmod.Cost(cost, params)
def forward_jacobian_log_det(self, x):
if x.ndim == 1:
return tt.log(tt.abs_(self.diag_weights)).sum()
elif x.ndim == 2:
return x.shape[0] * tt.log(tt.abs_(self.diag_weights)).sum()
else:
raise ValueError('x must be one or two dimensional.')
def get_reconstruction_cost(self, updates, pre_sigmoid_nv):
cross_entropy = T.mean(
T.sum(self.input * T.log(T.nnet.sigmoid(pre_sigmoid_nv)) +
(1 - self.input) * T.log(1 - T.nnet.sigmoid(pre_sigmoid_nv)),
axis=1))
return cross_entropy
def hinge_loss(self, y):
return -T.mean(T.log(self.p_y_given_x)[:,y]) # TODO
def forward(self, x):
return tt.switch(x < 1, tt.log(x), x - 1.0)
def log(x):
return T.log(x)
def logp(self, value):
w = self.w
return bound(logsumexp(tt.log(w) + self._comp_logp(value), axis=-1).sum(),
w >= 0, w <= 1, tt.allclose(w.sum(axis=-1), 1))
def __init__(self, dim, n_entities, batch_size=None, validation_samples=2):
self.__dict__.update(locals())
del self.self
theano_rng = RandomStreams(numpy.random.randint(2**30))
#Start by defining the graph
##Parameter setup
self.emb = theano.shared((numpy.random.uniform(
-1.0, 1.0,
(self.n_entities, self.dim))).astype(theano.config.floatX))
self.emb.tag.test_value = (numpy.random.uniform(
-1.0, 1.0,
(self.n_entities, self.dim))).astype(theano.config.floatX)
self.a = theano.shared(numpy.asarray(1.0).astype(theano.config.floatX))
self.b = theano.shared(numpy.asarray(0.0).astype(theano.config.floatX))
self.params = [self.emb, self.a, self.b]
### Input setup!
self.x1_idxs = T.ivector()
self.x2_idxs = T.ivector()
self.x1_idxs.tag.test_value = numpy.asarray([0, 1], dtype=numpy.int32)
self.x2_idxs.tag.test_value = numpy.asarray([1, 2], dtype=numpy.int32)
#generate negative samples
choice = theano_rng.binomial(size=self.x1_idxs.shape)
alternative = theano_rng.random_integers(size=self.x1_idxs.shape,
low=0,
high=n_entities - 1)
self.x1_idxs_negative = T.switch(choice, self.x1_idxs, alternative)
self.x2_idxs_negative = T.switch(choice, alternative, self.x2_idxs)
### Define graph from input to predictive loss
def get_embed(index_tensor):
return sigmoid(self.emb[index_tensor].reshape(
(index_tensor.shape[0], self.dim)))
x1_emb = get_embed(self.x1_idxs)
x2_emb = get_embed(self.x2_idxs)
x1neg_emb = get_embed(self.x1_idxs_negative)
x2neg_emb = get_embed(self.x2_idxs_negative)
def get_prob1(embed_tensor1, embed_tensor2):
return sigmoid(
self.a * T.mean(embed_tensor1 * embed_tensor2 +
(1 - embed_tensor1) * (1 - embed_tensor2),
axis=1) +
self.b) #probability of a link, 0 to 1.'
self.loss = T.mean(-T.log(get_prob1(x1_emb, x2_emb)) -
T.log(1 - get_prob1(x1neg_emb, x2neg_emb)))
###Define graph from input to sampled/validated loss
randomizationA = theano_rng.uniform(size=(self.validation_samples,
self.dim))
randomizationB = theano_rng.uniform(size=(self.validation_samples,
self.dim))
def softplus_f(v):
return T.log(1 + T.exp(v))
def hinge_loss_sum(self, y):
return -T.sum(T.log(self.p_y_given_x)[:,y])
def tlogit(x):
return T.log(x / (np.float32(1) - x))
b2_init = np.zeros(output_size)
thX = T.matrix("X")
thT = T.matrix("T")
W1 = theano.shared(W1_init, "W1")
W2 = theano.shared(W2_init, "W2")
b1 = theano.shared(b1_init, "b1")
b2 = theano.shared(b2_init, "b2")
thZ = T.nnet.relu(thX.dot(W1) + b1)
thY = T.nnet.softmax(thZ.dot(W2) + b2)
prediction = T.argmax(thY, axis=1)
cost = -(thT * T.log(thY)).sum() + reg * ((W1 * W1).sum() + (b1 * b1).sum() +
(W2 * W2).sum() + (b2 * b2).sum())
update_W1 = W1 - lr * T.grad(cost, W1)
update_b1 = b1 - lr * T.grad(cost, b1)
update_W2 = W2 - lr * T.grad(cost, W2)
update_b2 = b2 - lr * T.grad(cost, b2)
train = theano.function([thX, thT],
updates=[(W1, update_W1), (W2, update_W2),
(b1, update_b1), (b2, update_b2)])
get_prediction = theano.function(inputs=[thX, thT], outputs=[cost, prediction])
costs = []
def negative_log_likelihood_sum(self, y):
return -T.sum(T.log(self.p_y_given_x)[T.arange(y.shape[0]), y])
def kld(self, mu, var):
return 0.5 * T.sum(1 + T.log(var) - mu**2 - var, axis=1)
def LME(x, axis=None, dtype=None, keepdims=False, acc_dtype=None):
return T.log(T.mean(T.exp(x), axis, dtype, keepdims, acc_dtype))
def f_softplus(x):
return T.log(T.exp(x) + 1) # - np.log(2)
def cost_nll(self, pred, label):
cost = -T.log(pred) * label
cost = T.mean(T.sum(cost, axis=1))
return cost
def __init__(self, We_initial, params):
if params.maxval:
self.nout = params.maxval - params.minval + 1
if params.traintype == "reg" or params.traintype == "rep":
p = cPickle.load(file(params.regfile, 'rb'))
print p #containes We
if params.traintype == "reg":
print "regularizing to parameters"
if params.traintype == "rep":
print "not updating embeddings"
#params
initial_We = theano.shared(np.asarray(We_initial, dtype=config.floatX))
We = theano.shared(np.asarray(We_initial, dtype=config.floatX))
if params.traintype == "reg":
initial_We = theano.shared(
np.asarray(p[0].get_value(), dtype=config.floatX))
We = theano.shared(
np.asarray(p[0].get_value(), dtype=config.floatX))
if params.traintype == "rep":
We = theano.shared(
np.asarray(p[0].get_value(), dtype=config.floatX))
g1batchindices = T.imatrix()
g2batchindices = T.imatrix()
g1mask = T.matrix()
g2mask = T.matrix()
scores = T.matrix()
l_in = lasagne.layers.InputLayer((None, None, 1))
l_mask = lasagne.layers.InputLayer(shape=(None, None))
l_emb = lasagne.layers.EmbeddingLayer(
l_in,
input_size=We.get_value().shape[0],
output_size=We.get_value().shape[1],
W=We)
l_out = lasagne_average_layer([l_emb, l_mask])
embg1 = lasagne.layers.get_output(l_out, {
l_in: g1batchindices,
l_mask: g1mask
})
embg2 = lasagne.layers.get_output(l_out, {
l_in: g2batchindices,
l_mask: g2mask
})
g1_dot_g2 = embg1 * embg2
g1_abs_g2 = abs(embg1 - embg2)
lin_dot = lasagne.layers.InputLayer((None, We.get_value().shape[1]))
lin_abs = lasagne.layers.InputLayer((None, We.get_value().shape[1]))
l_sum = lasagne.layers.ConcatLayer([lin_dot, lin_abs])
l_sigmoid = lasagne.layers.DenseLayer(
l_sum, params.memsize, nonlinearity=lasagne.nonlinearities.sigmoid)
if params.task == "sim":
l_softmax = lasagne.layers.DenseLayer(l_sigmoid,
self.nout,
nonlinearity=T.nnet.softmax)
X = lasagne.layers.get_output(l_softmax, {
lin_dot: g1_dot_g2,
lin_abs: g1_abs_g2
})
Y = T.log(X)
cost = scores * (T.log(scores) - Y)
cost = cost.sum(axis=1) / (float(self.nout))
prediction = 0.
i = params.minval
while i <= params.maxval:
prediction = prediction + i * X[:, i - 1]
i += 1
elif params.task == "ent":
l_softmax = lasagne.layers.DenseLayer(l_sigmoid,
3,
nonlinearity=T.nnet.softmax)
X = lasagne.layers.get_output(l_softmax, {
lin_dot: g1_dot_g2,
lin_abs: g1_abs_g2
})
cost = theano.tensor.nnet.categorical_crossentropy(X, scores)
prediction = T.argmax(X, axis=1)
else:
raise ValueError('Params.task not set correctly.')
# if params.l_out == '':
# lasagne.layers.set_all_param_values(l_out, s)
#
# if params.l_so
self.network_params = lasagne.layers.get_all_params(
l_out, trainable=True) + lasagne.layers.get_all_params(
l_softmax, trainable=True)
self.network_params.pop(0)
self.all_params = lasagne.layers.get_all_params(
l_out, trainable=True) + lasagne.layers.get_all_params(
l_softmax, trainable=True)
reg = self.getRegTerm(params, We, initial_We)
self.trainable = self.getTrainableParams(params)
cost = T.mean(cost) + reg
self.feedforward_function = theano.function([g1batchindices, g1mask],
embg1)
self.scoring_function = theano.function(
[g1batchindices, g2batchindices, g1mask, g2mask], prediction)
self.cost_function = theano.function(
[scores, g1batchindices, g2batchindices, g1mask, g2mask], cost)
grads = theano.gradient.grad(cost, self.trainable)
if params.clip:
grads = [
lasagne.updates.norm_constraint(grad, params.clip,
range(grad.ndim))
for grad in grads
]
updates = params.learner(grads, self.trainable, params.eta)
self.train_function = theano.function(
[scores, g1batchindices, g2batchindices, g1mask, g2mask],
cost,
updates=updates)
def multivariate_bernoulli(self, y_pred, y_true):
return T.sum(y_true * T.log(y_pred) + (1 - y_true) * T.log(1 - y_pred),
axis=1)
def _compute_losses(self, model_output):
# model_output.shape : (batch_size, seq_len, K, M, target_size)
# self.dataset.symb_targets.shape = (batch_size, seq_len+K-1, target_dims)
# mask.shape : (batch_size, seq_len) or None
mask = self.dataset.symb_mask
# mu.shape = (batch_size, seq_len, K, M, target_dims)
mu = model_output[:, :, :, :, 0:3]
# sigma.shape = (batch_size, seq_len, K, M, target_dims)
sigma = model_output[:, :, :, :, 3:6]
# Stack K targets for each input (sliding window style)
# targets.shape = (batch_size, seq_len, K, target_dims)
targets = T.stack([
self.dataset.symb_targets[:, i:(-self.model.k + i + 1) or None]
for i in range(self.model.k)
],
axis=2)
# Add new axis for sum over M
# targets.shape = (batch_size, seq_len, K, 1, target_dims)
targets = targets[:, :, :, None, :]
# For monitoring the L2 error of using $mu$ as the predicted direction (should be comparable to MICCAI's work).
normalized_mu = mu[:, :, 0, 0] / l2distance(
mu[:, :, 0, 0], keepdims=True, eps=1e-8)
normalized_targets = targets[:, :, 0, 0] / l2distance(
targets[:, :, 0, 0], keepdims=True, eps=1e-8)
self.L2_error_per_item = T.sqrt(
T.sum(((normalized_mu - normalized_targets)**2), axis=2))
if mask is not None:
self.mean_sqr_error = T.sum(self.L2_error_per_item * mask,
axis=1) / T.sum(mask, axis=1)
else:
self.mean_sqr_error = T.mean(self.L2_error_per_item, axis=1)
# Likelihood of multivariate gaussian (n dimensions) is :
# ((2 \pi)^D |\Sigma|)^{-1/2} exp(-1/2 (x - \mu)^T \Sigma^-1 (x - \mu))
# We suppose a diagonal covariance matrix, so we have :
# => |\Sigma| = \prod_n \sigma_n^2
# => (x - \mu)^T \Sigma^-1 (x - \mu) = \sum_n ((x_n - \mu_n) / \sigma_n)^2
m_log_likelihoods = -np.float32(
(self.target_dims / 2.) * np.log(2 * np.pi)) + T.sum(
-T.log(sigma) - 0.5 * T.sqr((targets - mu) / sigma), axis=4)
# k_losses_per_timestep.shape : (batch_size, seq_len, K)
self.k_losses_per_timestep = T.log(self.m) - logsumexp(
m_log_likelihoods, axis=3, keepdims=False)
# loss_per_timestep.shape : (batch_size, seq_len)
self.loss_per_time_step = T.mean(self.k_losses_per_timestep, axis=2)
# Average over sequence steps.
# k_nlls_per_seq.shape :(batch_size, K)
if mask is not None:
self.k_losses_per_seq = T.sum(
self.k_losses_per_timestep * mask[:, :, None], axis=1) / T.sum(
mask, axis=1, keepdims=True)
else:
self.k_losses_per_seq = T.mean(self.k_losses_per_timestep, axis=1)
# Average over K
# loss_per_seq.shape :(batch_size,)
self.loss_per_seq = T.mean(self.k_losses_per_seq, axis=1)
return self.loss_per_seq
def factors(self, x, z, A):
v = self.v
w = self.w
'''
z is unused
x['x'] is the data
The names of dict z[...] may be confusing here: the latent variable z is not included in the dict z[...],
but implicitely computed from epsilon and parameters in w.
z is computed with g(.) from eps and variational parameters
let logpx be the generative model density: log p(x|z) where z=g(.)
let logpz be the prior of Z plus the entropy of q(z|x): logp(z) + H_q(z|x)
So the lower bound L(x) = logpx + logpz
let logpv and logpw be the (prior) density of the parameters
'''
def f_softplus(x):
return T.log(T.exp(x) + 1) # - np.log(2)
def f_rectlin(x):
return x * (x > 0)
def f_rectlin2(x):
return x * (x > 0) + 0.01 * x
nonlinear = {
'tanh': T.tanh,
'sigmoid': T.nnet.sigmoid,
'softplus': f_softplus,
'rectlin': f_rectlin,
'rectlin2': f_rectlin2
}
nonlinear_q = nonlinear[self.nonlinear_q]
nonlinear_p = nonlinear[self.nonlinear_p]
#rng = rng_curand.CURAND_RandomStreams(0)
import theano.tensor.shared_randomstreams
rng = theano.tensor.shared_randomstreams.RandomStreams(0)
# Compute q(z|x,y)
#
# it seems that z = f(v['w0x'] * x + v['w0y'] * y + b)
#
hidden_q = [
nonlinear_q(
T.dot(v['w0x'], x['x']) + T.dot(v['w0y'], x['y']) +
T.dot(v['b0'], A))
]
for i in range(1, len(self.n_hidden_q)):
hidden_q.append(
nonlinear_q(
T.dot(v['w' + str(i)], hidden_q[-1]) +
T.dot(v['b' + str(i)], A)))
q_mean = T.dot(v['mean_w'], hidden_q[-1]) + T.dot(v['mean_b'], A)
if self.type_qz == 'gaussian' or self.type_qz == 'gaussianmarg':
q_logvar = T.dot(v['logvar_w'], hidden_q[-1]) + T.dot(
v['logvar_b'], A)
else:
raise Exception()
# function for distribution q(z|x)
theanofunc = lazytheanofunc('warn', mode='FAST_RUN')
self.dist_qz['z'] = theanofunc([x['x'], x['mean_prior'], x['y']] + [A],
[q_mean, q_logvar])
# Compute virtual sample
eps = rng.normal(size=q_mean.shape, dtype='float32')
_z = q_mean + T.exp(0.5 * q_logvar) * eps
# Compute log p(x|z)
#
# log p(x | z, y)
# It seems that x = f((w0y * y + w0z * z) + b0)
#
hidden_p = [
nonlinear_p(
T.dot(w['w0y'], x['y']) + T.dot(w['w0z'], _z) +
T.dot(w['b0'], A))
]
for i in range(1, len(self.n_hidden_p)):
hidden_p.append(
nonlinear_p(
T.dot(w['w' + str(i)], hidden_p[-1]) +
T.dot(w['b' + str(i)], A)))
if self.dropout:
hidden_p[-1] *= 2. * (rng.uniform(size=hidden_p[-1].shape,
dtype='float32') > .5)
if self.type_px == 'bernoulli':
p = T.nnet.sigmoid(
T.dot(w['out_w'], hidden_p[-1]) + T.dot(w['out_b'], A))
_logpx = -T.nnet.binary_crossentropy(p, x['x'])
self.dist_px['x'] = theanofunc([x['y'], _z] + [A], p)
elif self.type_px == 'gaussian':
x_mean = T.dot(w['out_w'], hidden_p[-1]) + T.dot(w['out_b'], A)
x_logvar = T.dot(w['out_logvar_w'], hidden_p[-1]) + T.dot(
w['out_logvar_b'], A)
_logpx = ap.logpdfs.normal2(x['x'], x_mean, x_logvar)
self.dist_px['x'] = theanofunc([x['y'], _z] + [A],
[x_mean, x_logvar])
elif self.type_px == 'laplace':
x_mean = T.dot(w['out_w'], hidden_p[-1]) + T.dot(w['out_b'], A)
x_logvar = T.dot(w['out_logvar_w'], hidden_p[-1]) + T.dot(
w['out_logvar_b'], A)
_logpx = ap.logpdfs.laplace(x['x'], x_mean, x_logvar)
self.dist_px['x'] = theanofunc([x['y'], _z] + [A],
[x_mean, x_logvar])
else:
raise Exception("")
# Note: logpx is a row vector (one element per sample)
logpx = T.dot(shared32(np.ones((1, self.n_x))),
_logpx) # logpx = log p(x|z,w)
# log p(y) (prior of y)
#_logpy = w['logpy']
#if self.uniform_y: _logpy *= 0
#py_model = T.nnet.softmax(T.dot(_logpy, A).T).T
#logpy = (- T.nnet.categorical_crossentropy(py_model.T, x['y'].T).T).reshape((1,-1))
#logpx += logpy
#self.dist_px['y'] = theanofunc([A], py_model)
# log p(z) (prior of z)
#
# E_q[log(p(z))]
#
if self.type_pz == 'gaussianmarg':
logpz = -0.5 * (np.log(2 * np.pi) + (
(q_mean - x['mean_prior'])**2 + T.exp(q_logvar))).sum(
axis=0, keepdims=True)
elif self.type_pz == 'gaussian':
logpz = ap.logpdfs.standard_normal(_z).sum(axis=0, keepdims=True)
elif self.type_pz == 'mog':
pz = 0
for i in range(self.n_mixture):
pz += T.exp(
ap.logpdfs.normal2(_z, T.dot(w['mog_mean' + str(i)], A),
T.dot(w['mog_logvar' + str(i)], A)))
logpz = T.log(pz).sum(axis=0, keepdims=True) - self.n_z * np.log(
float(self.n_mixture))
elif self.type_pz == 'laplace':
logpz = ap.logpdfs.standard_laplace(_z).sum(axis=0, keepdims=True)
elif self.type_pz == 'studentt':
logpz = ap.logpdfs.studentt(_z, T.dot(T.exp(w['logv']),
A)).sum(axis=0,
keepdims=True)
else:
raise Exception("Unknown type_pz")
# loq q(z|x) (entropy of z)
#
# E_q[-log(q)]
#
if self.type_qz == 'gaussianmarg':
logqz = -0.5 * (np.log(2 * np.pi) + 1 + q_logvar).sum(
axis=0, keepdims=True)
elif self.type_qz == 'gaussian':
logqz = ap.logpdfs.normal2(_z, q_mean, q_logvar).sum(axis=0,
keepdims=True)
else:
raise Exception()
# Note: logpv and logpw are a scalars
def f_prior(_w, prior_sd=self.prior_sd):
return ap.logpdfs.normal(_w, 0, prior_sd).sum()
logpv = 0
logpv += f_prior(v['w0x'])
logpv += f_prior(v['w0y'])
for i in range(1, len(self.n_hidden_q)):
logpv += f_prior(v['w' + str(i)])
logpv += f_prior(v['mean_w'])
if self.type_qz in ['gaussian', 'gaussianmarg']:
logpv += f_prior(v['logvar_w'])
logpw = 0
logpw += f_prior(w['w0y'])
logpw += f_prior(w['w0z'])
for i in range(1, len(self.n_hidden_p)):
logpw += f_prior(w['w' + str(i)])
logpw += f_prior(w['out_w'])
if self.type_px in ['sigmoidgaussian', 'gaussian', 'laplace']:
logpw += f_prior(w['out_logvar_w'])
if self.type_pz == 'studentt':
logpw += f_prior(w['logv'])
#return logpv, logpw, logpx, logpz, logqz
return logpx, logpz, logqz
def KL(self, y):
return T.mean(y * T.log(y / self.y_pred) +
(1 - y) * T.log((1 - y) / (1 - self.y_pred)))
x = T.dmatrix("x")
y = T.dvector("y")
learning_rate = T.dscalar("lr")
# declare the weight w and b
w = theano.shared(value=numpy.random.rand(feat), name="w")
b = theano.shared(value=0., name="b")
print("initialized weights \n")
print(w.get_value())
print(b.get_value())
# build the graph
output = 1/(1+T.exp(-T.dot(x, w)-b))
prediction = output > 0.5
cross_entropy = -y * T.log(output) - (1-y)*T.log(1-output)
loss = cross_entropy.mean() + 0.01*(w**2).sum()
gradW, gradb = T.grad(loss, [w, b])
# train function
train = theano.function(inputs=[x,y,learning_rate], outputs=[prediction, cross_entropy,loss, learning_rate], \
updates=((w,w-learning_rate*gradW), (b,b-learning_rate*gradb)))
# predict function
predict = theano.function(inputs=[x], outputs=prediction)
for i in range(training_step):
if (i < 1000):
learning_rate = 0.1
else:
learning_rate =0.01
pred, cro, l,lr = train(D[0], D[1], learning_rate)
def NLL(probs, labels) : # labels are not one-hot code
return - T.mean( T.log(probs)[T.arange(labels.shape[0]), T.cast(labels,'int32')] )
def loss(self,delta):
#return T.log(1+T.exp(euclid(self.output1,self.output2)))
#return T.log(1+T.exp(T.sqrt(T.sum(T.sqr(self.output1-self.output2)))))
#return T.log(1+T.exp(T.sqrt(T.sum(T.sqr(self.output1)))))
return T.log(1+T.exp(delta*(T.sum(T.sqr(self.output1-self.output2)))))
def trainMB(self, V_egMin, noOfEpoch, noOfMiniBatchEx):
"""
trains the current RBM object, returns nothing with parameter updates being internal
args:
V_egMin (theano.shared 2D array): call eval() to supply as argument. rows of this are input examples. V_egMin[N:M] extracts M-N examples, each of size noOfVisible units
noOfEpoch (int): total number of Epoch to simulate, each Epoch goes through V_egMin
noOfMiniBatchEx (int): number of examples to be grouped into minibatches
"""
self.miniBatchSize = noOfMiniBatchEx
print("size of input example is: " + str(V_egMin.shape))
V_egM = T.matrix(name="T_egM", dtype=theano.config.floatX)
[V_CDmAcc, H_CDmAcc, H_CDmean, V_CDmean] , scan_updates = theano.scan(self.vtovMBall, outputs_info=[V_egM, None, None, None] , n_steps=self.CD_n)
V_CDm = V_CDmAcc[-1] #these are matrixes
H_CDm = H_CDmAcc[-1] #these are matrixes
H_egM = self.vtohMB(V_egM)
energyVector_eg = self.energyFnMB(V_egM, H_egM)
energyVector_cd = self.energyFnMB(V_CDm, H_CDm)
costFn = T.mean(energyVector_eg, dtype=theano.config.floatX, acc_dtype=theano.config.floatX) - T.mean(energyVector_cd, dtype=theano.config.floatX, acc_dtype=theano.config.floatX)
Ta_grad, Tb_grad, Tz_grad, Tomg_grad = T.grad(cost=costFn,
wrt=[self.T_a, self.T_b, self.T_z, self.T_omega],
consider_constant=[V_egM, H_egM, V_CDm, H_CDm])
#regular gradient
gradFromMB = theano.function(inputs=[V_egM], outputs=[Ta_grad, Tb_grad, Tz_grad, Tomg_grad],
allow_input_downcast=True,
updates = scan_updates + [(self.T_a, self.T_a + self.aRate*Ta_grad),
(self.T_b, self.T_b + self.bRate*Tb_grad),
(self.T_z, self.T_z + self.sigmaRate*Tz_grad),
(self.T_omega, self.T_omega + self.omegaRate*Tomg_grad)],
mode='FAST_RUN')#NanGuardMode(nan_is_error=True, inf_is_error=True, big_is_error=True))
#rprop: Code not used
Ta_rpropMag = T.mul(T.abs_(self.Ta_grad_prev), T.mul(self.T_posUpdate, T.abs_(T.sgn(self.Ta_grad_prev)+T.sgn(Ta_grad))) +
T.mul(self.T_negUpdate, T.abs_(T.abs_(T.sgn(self.Ta_grad_prev)+T.sgn(Ta_grad))-np.float32(2.0))))
Ta_rprop = T.mul(T.sgn(Ta_grad),Ta_rpropMag.clip(np.float32(self.epsilon),50))
Tb_rpropMag = T.mul(T.abs_(self.Tb_grad_prev), T.mul(self.T_posUpdate, T.abs_(T.sgn(self.Tb_grad_prev)+T.sgn(Tb_grad))) +
T.mul(self.T_negUpdate, T.abs_(T.abs_(T.sgn(self.Tb_grad_prev)+T.sgn(Tb_grad))-np.float32(2.0))))
Tb_rprop = T.mul(T.sgn(Tb_grad),Tb_rpropMag.clip(np.float32(self.epsilon),50))
Tz_rpropMag = T.mul(T.abs_(self.Tz_grad_prev), T.mul(self.T_posUpdate, T.abs_(T.sgn(self.Tz_grad_prev)+T.sgn(Tz_grad))) +
T.mul(self.T_negUpdate, T.abs_(T.abs_(T.sgn(self.Tz_grad_prev)+T.sgn(Tz_grad))-np.float32(2.0))) )
Tz_rprop = T.mul(T.sgn(Tz_grad),Tz_rpropMag.clip(np.float32(self.epsilon),50))
Tomg_rpropMag = T.mul(T.abs_(self.Tomg_grad_prev), T.mul(self.T_posUpdate, T.abs_(T.sgn(self.Tomg_grad_prev)+T.sgn(Tomg_grad))) +
T.mul(self.T_negUpdate, T.abs_(T.abs_(T.sgn(self.Tomg_grad_prev)+T.sgn(Tomg_grad))-np.float32(2.0))))
Tomg_rprop = T.mul(T.sgn(Tomg_grad),Tomg_rpropMag.clip(np.float32(self.epsilon),50))
gradFromMBrprop = theano.function(inputs=[V_egM], outputs=[Ta_rprop, Tb_rprop, Tz_rprop, Tomg_rprop],
allow_input_downcast=True,
updates = scan_updates + [(self.T_a, self.T_a + Ta_rprop),
(self.T_b, self.T_b + Tb_rprop),
(self.T_z, self.T_z + Tz_rprop),
(self.T_omega, self.T_omega + Tomg_rprop),
(self.Ta_grad_prev, Ta_rprop),
(self.Tb_grad_prev, Tb_rprop),
(self.Tz_grad_prev, Tz_rprop),
(self.Tomg_grad_prev, Tomg_rprop)],
mode='FAST_RUN')#NanGuardMode(nan_is_error=True, inf_is_error=True, big_is_error=True))
#RMSprop only:
[a_grad, b_grad, z_grad, omg_grad] = gradFromMB(V_egMin[0:noOfMiniBatchEx]) #initial RMS correction
if (not(self.parameterLoaded) and not(self.parameterSaved)):
self.Ta_rms.set_value(np.float32(np.abs(a_grad))) # = theano.shared(value = np.float32(np.abs(a_grad)), name = 'Ta_rms', borrow=True, allow_downcast=True)
Tb_rms = theano.shared(value = np.float32(np.abs(b_grad)), name = 'Tb_rms', borrow=True, allow_downcast=True)
Tz_rms = theano.shared(value = np.float32(np.abs(z_grad)), name = 'Tz_rms', borrow=True, allow_downcast=True)
Tomg_rms = theano.shared(value = np.float32(np.abs(omg_grad)), name = 'Tomg_rms', borrow=True, allow_downcast=True)
gradFromMBRMSprop = theano.function(inputs=[V_egM], outputs=[Ta_grad, Tb_grad, Tz_grad, Tomg_grad],
allow_input_downcast=True,
updates = scan_updates + [(self.Ta_rms, T.sqrt(T.mul(np.float32(0.9),T.mul(self.Ta_rms,self.Ta_rms))+T.mul(np.float32(0.1),T.mul(Ta_grad,Ta_grad)))),
(Tb_rms, T.sqrt(T.mul(np.float32(0.9),T.mul(Tb_rms,Tb_rms))+T.mul(np.float32(0.1),T.mul(Tb_grad,Tb_grad)))),
(Tz_rms, T.sqrt(T.mul(np.float32(0.9),T.mul(Tz_rms,Tz_rms))+T.mul(np.float32(0.1),T.mul(Tz_grad,Tz_grad)))),
(Tomg_rms, T.sqrt(T.mul(np.float32(0.9),T.mul(Tomg_rms,Tomg_rms))+T.mul(np.float32(0.1),T.mul(Tomg_grad,Tomg_grad)))),
(self.T_a, self.T_a + self.aRate*T.mul(Ta_grad,T.maximum(np.float32(self.epsilon),self.Ta_rms)**-1)),
(self.T_b, self.T_b + self.bRate*T.mul(Tb_grad,T.maximum(np.float32(self.epsilon),Tb_rms)**-1)),
(self.T_z, self.T_z + self.sigmaRate*T.mul(Tz_grad,T.maximum(np.float32(self.epsilon),Tz_rms)**-1)),
(self.T_omega, self.T_omega + self.omegaRate*T.mul(Tomg_grad,T.maximum(np.float32(self.epsilon),Tomg_rms)**-1))],
mode='FAST_RUN')#NanGuardMode(nan_is_error=True, inf_is_error=True, big_is_error=True))
#sparse hidden units optimization + RMSprop:
#first calculate probability of hidden units firing given visible examples:
aVomg = T.dot(T.mul(T.fill(V_egM, T.exp(-self.T_z)), V_egM), self.T_omega)
aT_Hp = T.nnet.sigmoid(T.fill(aVomg, self.T_b) + aVomg)#T.nnet.ultra_fast_sigmoid() did not work for us
aT_HpMean = T.mean(aT_Hp) # mean activation over minibatch and all Hk
#cross entropy between mean hidden unit activation and target mean activation probability "self.sparseTargetp"
sparseHcost = T.mul(np.float32(-self.sparseTargetp), T.log(aT_HpMean)) - T.mul((np.float32(1.0)-self.sparseTargetp), T.log(np.float32(1.0)-aT_HpMean))
Tb_gradH, Tz_gradH, Tomg_gradH = T.grad(cost=sparseHcost,
wrt=[self.T_b, self.T_z, self.T_omega],
consider_constant=[V_egM])
sparseGradFn = theano.function(inputs = [V_egM], outputs =[Tb_gradH, Tz_gradH, Tomg_gradH], allow_input_downcast=True, mode = 'FAST_RUN')
[b_gradH, z_gradH, omg_gradH] = sparseGradFn(V_egMin[0:noOfMiniBatchEx]) #initial RMS correction
if (not(self.parameterLoaded) and not(self.parameterSaved)):
self.Tb_rmsH.set_value(np.float32(np.abs(b_grad - b_gradH)))
self.Tz_rmsH.set_value(np.float32(np.abs(z_grad - z_gradH)))
self.Tomg_rmsH.set_value(np.float32(np.abs(omg_grad - omg_gradH)))
gradSparseH = theano.function(inputs=[V_egM], outputs=[Ta_grad, Tb_grad, Tz_grad, Tomg_grad, Tb_gradH, Tz_gradH, Tomg_gradH],
allow_input_downcast=True,
updates = scan_updates + [(self.Ta_rms, T.sqrt(T.mul(np.float32(0.9),T.mul(self.Ta_rms,self.Ta_rms))+T.mul(np.float32(0.1),T.mul(Ta_grad,Ta_grad)))),
(self.Tb_rmsH, T.sqrt(T.mul(np.float32(0.9),T.mul(self.Tb_rmsH,self.Tb_rmsH))+T.mul(np.float32(0.1),T.mul(Tb_grad-Tb_gradH,Tb_grad-Tb_gradH)))),
(self.Tz_rmsH, T.sqrt(T.mul(np.float32(0.9),T.mul(self.Tz_rmsH,self.Tz_rmsH))+T.mul(np.float32(0.1),T.mul(Tz_grad-Tz_gradH,Tz_grad-Tz_gradH)))),
(self.Tomg_rmsH, T.sqrt(T.mul(np.float32(0.9),T.mul(self.Tomg_rmsH,self.Tomg_rmsH))+T.mul(np.float32(0.1),T.mul(Tomg_grad-Tomg_gradH,Tomg_grad-Tomg_gradH)))),
(self.T_a, self.T_a + self.aRate*T.mul(Ta_grad,T.maximum(np.float32(self.epsilon),self.Ta_rms)**-1)),
(self.T_b, self.T_b + self.bRate*T.mul(Tb_grad-Tb_gradH,T.maximum(np.float32(self.epsilon),self.Tb_rmsH)**-1)),
(self.T_z, self.T_z + self.sigmaRate*T.mul(Tz_grad-Tz_gradH,T.maximum(np.float32(self.epsilon),self.Tz_rmsH)**-1)),
(self.T_omega, self.T_omega + self.omegaRate*T.mul(Tomg_grad-Tomg_gradH,T.maximum(np.float32(self.epsilon),self.Tomg_rmsH)**-1))],
mode='FAST_RUN')#NanGuardMode(nan_is_error=True, inf_is_error=True, big_is_error=True))
#reconstruction errors:
[V_egM_recon, H_egM_reconStub, H_meanStubC, V_meanStubC] = self.vtovMBall(V_egM)
V_error = V_egM - V_egM_recon
V_errorSqr = T.mul(V_error, V_error)
reconError = theano.function(inputs = [V_egM], outputs = [T.mean(T.sum(V_errorSqr,axis=1, acc_dtype=theano.config.floatX), acc_dtype=theano.config.floatX)],
allow_input_downcast=True,
mode='FAST_RUN')
print("***************************************************************************************************")
print("training network with " + str(self.nv) + " real visible units and " + str(self.nh) + " binary hidden units")
print("reconstruction error before training = " + str(np.array(reconError(V_egMin))[0]))
noOfMiniBatches = np.int(len(V_egMin)/noOfMiniBatchEx)
print("number of mini-batches = " + str(noOfMiniBatches) + ", with " + str(noOfMiniBatchEx) + " examples per mini-batch")
print("number of Epochs = " + str(noOfEpoch))
print("***************************************************************************************************")
#input images already randomised with consecutive images belonging to different class, use directly as minibatch.
for j in xrange(noOfEpoch):
pretime=time.time()
for i in xrange(noOfMiniBatches):
[a_upDate, b_upDate, z_upDate, omg_upDate, b_upDateH, z_upDateH, omg_upDateH] = gradSparseH(V_egMin[i*noOfMiniBatchEx:(i+1)*noOfMiniBatchEx])
myErr = reconError(V_egMin)
self.likelihood4plot = self.likelihood4plot + [np.float32(myErr)]
print("epoch " + str(j) + ": reconstruction error = " + str(myErr[0]) + ", time taken = " + str(time.time() - pretime))
print("\n***************************************************************************************************")
print("reconstruction error after training for " + str(noOfEpoch) + " epochs = " + str(np.array(reconError(V_egMin))[0]))
self.checkNaN()
print("***************************************************************************************************")
plt.figure
plt.plot(np.arange(0.0, len(self.likelihood4plot), 1), self.likelihood4plot)
plt.show()
def CrossEntropy(self, y):
return -T.mean(y * T.log(self.y_pred))
training_epochs = 25
learning_rate = 0.1
batch_size = 128
W1 = init_weights(28 * 28, 900)
b1 = init_bias(900)
b1_prime = init_bias(28 * 28)
W1_prime = W1.transpose()
W2 = init_weights(900, 10)
b2 = init_bias(10)
tilde_x = theano_rng.binomial(
size=x.shape, n=1, p=1 - corruption_level, dtype=theano.config.floatX) * x
y1 = T.nnet.sigmoid(T.dot(tilde_x, W1) + b1)
z1 = T.nnet.sigmoid(T.dot(y1, W1_prime) + b1_prime)
cost1 = -T.mean(T.sum(x * T.log(z1) + (1 - x) * T.log(1 - z1), axis=1))
params1 = [W1, b1, b1_prime]
grads1 = T.grad(cost1, params1)
updates1 = [(param1, param1 - learning_rate * grad1)
for param1, grad1 in zip(params1, grads1)]
train_da1 = theano.function(inputs=[x],
outputs=cost1,
updates=updates1,
allow_input_downcast=True)
p_y2 = T.nnet.softmax(T.dot(y1, W2) + b2)
y2 = T.argmax(p_y2, axis=1)
cost2 = T.mean(T.nnet.categorical_crossentropy(p_y2, d))
params2 = [W1, b1, W2, b2]
def negative_log_likelihood(self, y):
return -T.mean(T.log(self.y_t)[:, y])
def get_tester(self, y):
return self.inp, T.log(self.p_y_given_x)[T.arange(y.shape[0]), y]
def build_model(alpha, beta, tparams, options):
trng = RandomStreams(SEED)
# Used for dropout.
use_noise = theano.shared(numpy_floatX(0.))
x_zheng = tensor.matrix('x_zheng', dtype='int32')
x_zheng_mask = tensor.matrix('x_zheng_mask', dtype=config.floatX)
x_ni = tensor.matrix('x_ni', dtype='int32')
x_ni_mask = tensor.matrix('x_ni_mask', dtype=config.floatX)
y = tensor.vector('y', dtype='int32')
n_timesteps = x_zheng.shape[0]
n_samples = x_zheng.shape[1]
emb_zheng = tparams['Wemb'][x_zheng.flatten()].reshape(
[n_timesteps, n_samples, options['dim_proj']])
proj1 = get_layer(options['encoder'])[1](tparams,
emb_zheng,
options,
prefix='lstm_zheng',
mask=x_zheng_mask)
if options['encoder'] == 'lstm':
proj_zheng = (proj1 * x_zheng_mask[:, :, None]).sum(axis=0)
proj_zheng = proj_zheng / x_zheng_mask.sum(axis=0)[:, None]
emb_ni = tparams['Wemb'][x_ni.flatten()].reshape(
[n_timesteps, n_samples, options['dim_proj']])
proj2 = get_layer(options['encoder'])[1](tparams,
emb_ni,
options,
prefix='lstm_ni',
mask=x_ni_mask)
if options['encoder'] == 'lstm':
proj_ni = (proj2 * x_ni_mask[:, :, None]).sum(axis=0)
proj_ni = proj_ni / x_ni_mask.sum(axis=0)[:, None]
proj = tensor.concatenate((proj_zheng, proj_ni), axis=1)
if options['use_dropout']:
proj = dropout_layer(proj, use_noise, trng)
pred = tensor.nnet.softmax(tensor.dot(proj, tparams['U']) + tparams['b'])
pred_zheng = tensor.nnet.softmax(
tensor.dot(proj_zheng, tparams['U_zheng'] + tparams['b']))
pred_ni = tensor.nnet.softmax(
tensor.dot(proj_ni, tparams['U_ni'] + tparams['b']))
f_pred_prob = theano.function([x_zheng, x_zheng_mask, x_ni, x_ni_mask],
pred,
name='f_pred_prob')
f_pred = theano.function([x_zheng, x_zheng_mask, x_ni, x_ni_mask],
pred.argmax(axis=1),
name='f_pred')
f_proj = theano.function([x_zheng, x_zheng_mask, x_ni, x_ni_mask],
proj,
name='f_proj')
off = 1e-8
if pred.dtype == 'float16':
off = 1e-6
cost1 = -tensor.log(pred[tensor.arange(n_samples), y] + off).mean()
cost2 = -tensor.log(pred_zheng[tensor.arange(n_samples), y] + off).mean()
cost3 = -tensor.log(pred_ni[tensor.arange(n_samples), y] + off).mean()
cost4 = tensor.sum(tensor.square(proj_zheng - proj_ni), axis=1).mean()
cost = alpha * (cost1 + cost2 + cost3) + beta * cost4
return use_noise, x_zheng, x_zheng_mask, x_ni, x_ni_mask, y, f_pred_prob, f_pred, cost1, cost2, cost3, cost4, cost, f_proj
def logp(self, value):
w = self.w
return bound(logsumexp(tt.log(w) + self._comp_logp(value), axis=-1),
w >= 0, w <= 1, tt.allclose(w.sum(axis=-1), 1),
broadcast_conditions=False)
def cost(self, net):
"Return the log-likelihood cost."
return -T.mean(
T.log(self.output_dropout)[T.arange(net.y.shape[0]), net.y])
