def get_output_for(self, inputs, **kwargs):
input = inputs[0]
hid_init = None
if self.hid_init_incoming_index > 0:
hid_init = inputs[self.hid_init_incoming_index]
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
# precompute inputs before scanning
trailing_dims = tuple(input.shape[n] for n in range(2, input.ndim))
input = T.reshape(input, (seq_len * num_batch, ) + trailing_dims)
input = helper.get_output(self.input_to_hidden, input, **kwargs)
# Reshape back to (seq_len, batch_size, trailing dimensions...)
trailing_dims = tuple(input.shape[n] for n in range(1, input.ndim))
input = T.reshape(input, (seq_len, num_batch) + trailing_dims)
# pass params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
non_seqs += helper.get_all_params(self.post_concat)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_pre = helper.get_output(self.hidden_to_hidden, hid_previous,
**kwargs)
hid_pre = T.concatenate([hid_pre, input_n], axis=1)
hid_pre = helper.get_output(self.post_concat, hid_pre, **kwargs)
if self.grad_clipping:
hid_pre = theano.gradient.grad_clip(hid_pre,
-self.grad_clipping,
self.grad_clipping)
return hid_pre
sequences = input
step_fun = step
if not isinstance(self.hid_init, Layer):
# repeats self.hid_init num_batch times in first dimension
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
hid_out = theano.scan(fn=step_fun,
sequences=sequences,
go_backwards=False,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=-1,
strict=True)[0]
# dimshuffle back to (n_batch, n_time_steps, n_features))
hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
return hid_out
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(CustomMIRecurrentLayer, self).get_params(**tags)
# Combine with all parameters from the child layers
params += helper.get_all_params(self.input_to_hidden, **tags)
params += helper.get_all_params(self.hidden_to_hidden, **tags)
return params
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(CustomRecurrentLayer, self).get_params(**tags)
# Combine with all parameters from the child layers
params += helper.get_all_params(self.input_to_hidden, **tags)
params += helper.get_all_params(self.hidden_to_hidden, **tags)
return params
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(StochsticRecurrentLayer, self).get_params(**tags)
if self.logvar_p_mlp is not None:
params += helper.get_all_params(self.logvar_p_mlp, **tags)
params += helper.get_all_params(self.q_mu_mlp, **tags)
params += helper.get_all_params(self.q_logvar_mlp, **tags)
params += helper.get_all_params(self.mu_p_mlp, **tags)
return params
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(RecurrentUnitaryLayer, self).get_params(**tags)
# Combine with all parameters from the child layers
params += helper.get_all_params(self.input_to_hidden, **tags)
params += helper.get_all_params(self.hidden_to_hidden, **tags)
if isinstance(self.nonlinearity, Layer):
params += self.nonlinearity.get_params()
return params
def get_params(self):
"""
Get all parameters of this layer.
:returns:
- params : list of theano.shared
List of all parameters
"""
params = helper.get_all_params(self.input_to_hidden) + helper.get_all_params(self.hidden_to_hidden)
if self.learn_init:
return params + self.get_init_params()
else:
return params
def get_params(self):
'''
Get all parameters of this layer.
:returns:
- params : list of theano.shared
List of all parameters
'''
params = (helper.get_all_params(self.input_to_hidden) +
helper.get_all_params(self.hidden_to_hidden))
if self.learn_init:
return params + self.get_init_params()
else:
return params
def _compile_train_func(self):
logger.info("Compiling train cost function...")
network_input = self.net.symbolic_input()
network_output = self.net.symbolic_output(deterministic=False)
target_var = ndim_tensor(name='target', ndim=network_output.ndim)
mask_var = ndim_tensor(name='mask', ndim=network_output.ndim)
loss = self.loss_func(network_output, target_var, mask_var)
all_params = get_all_params(self.net.layers[-1], trainable=True)
updates = self.updates_func(
loss, all_params, learning_rate=self._learning_rate)
train_func = theano.function(
inputs=[network_input, target_var, mask_var],
outputs=loss,
updates=updates,
on_unused_input='warn',
allow_input_downcast=True)
logger.info("Done compiling cost function.")
return train_func
def __init__(self, *args, **kwargs):
super(TrainerMixin, self).__init__(*args, **kwargs)
input_var = tensor.tensor4('inputs')
target_var = tensor.ivector('targets')
loss, _ = loss_acc(self.model,
input_var,
target_var,
deterministic=False)
layers = get_all_layers(self.model)
decay = regularize_layer_params(layers, l2) * 0.0001
loss = loss + decay
params = get_all_params(self.model, trainable=True)
updates = momentum(loss,
params,
momentum=0.9,
learning_rate=self.learning_rate)
self.set_training(input_var, target_var, loss, updates)
def get_output_for(self, inputs, mask=None, **kwargs):
"""
Compute this layer's output function given a symbolic input variable.
Parameters
----------
inputs : list of theano.TensorType
`inputs[0]` should always be the symbolic input variable. When
this layer has a mask input (i.e. was instantiated with
`mask_input != None`, indicating that the lengths of sequences in
each batch vary), `inputs` should have length 2, where `inputs[1]`
is the `mask`. The `mask` should be supplied as a Theano variable
denoting whether each time step in each sequence in the batch is
part of the sequence or not. `mask` should be a matrix of shape
``(n_batch, n_time_steps)`` where ``mask[i, j] = 1`` when ``j <=
(length of sequence i)`` and ``mask[i, j] = 0`` when ``j > (length
of sequence i)``. When the hidden state of this layer is to be
pre-filled (i.e. was set to a :class:`Layer` instance) `inputs`
should have length at least 2, and `inputs[-1]` is the hidden state
to prefill with.
Returns
-------
layer_output : theano.TensorType
Symbolic output variable.
"""
# Retrieve the layer input
input = inputs[0]
# Retrieve the mask when it is supplied
hid_init = None
if self.mask_incoming_index > 0:
mask = inputs[self.mask_incoming_index]
if self.hid_init_incoming_index > 0:
hid_init = inputs[self.hid_init_incoming_index]
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
if self.precompute_input:
# Because the input is given for all time steps, we can precompute
# the inputs to hidden before scanning. First we need to reshape
# from (seq_len, batch_size, trailing dimensions...) to
# (seq_len*batch_size, trailing dimensions...)
# This strange use of a generator in a tuple was because
# input.shape[2:] was raising a Theano error
trailing_dims = tuple(input.shape[n] for n in range(2, input.ndim))
input = T.reshape(input, (seq_len*num_batch,) + trailing_dims)
input = helper.get_output(
self.input_to_hidden, input, **kwargs)
# Reshape back to (seq_len, batch_size, trailing dimensions...)
trailing_dims = tuple(input.shape[n] for n in range(1, input.ndim))
input = T.reshape(input, (seq_len, num_batch) + trailing_dims)
# We will always pass the hidden-to-hidden layer params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
# When we are not precomputing the input, we also need to pass the
# input-to-hidden parameters to step
if not self.precompute_input:
non_seqs += helper.get_all_params(self.input_to_hidden)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_pre = helper.get_output(
self.hidden_to_hidden, hid_previous, **kwargs)
# If the dot product is precomputed then add it, otherwise
# calculate the input_to_hidden values and add them
if self.precompute_input:
hid_pre += input_n
else:
hid_pre += helper.get_output(
self.input_to_hidden, input_n, **kwargs)
# Clip gradients
if self.grad_clipping:
hid_pre = theano.gradient.grad_clip(
hid_pre, -self.grad_clipping, self.grad_clipping)
return self.nonlinearity(hid_pre)
def step_masked(input_n, mask_n, hid_previous, *args):
# Skip over any input with mask 0 by copying the previous
# hidden state; proceed normally for any input with mask 1.
hid = step(input_n, hid_previous, *args)
hid_out = T.switch(mask_n, hid, hid_previous)
return [hid_out]
if mask is not None:
mask = mask.dimshuffle(1, 0, 'x')
sequences = [input, mask]
step_fun = step_masked
else:
sequences = input
step_fun = step
if not isinstance(self.hid_init, Layer):
# The code below simply repeats self.hid_init num_batch times in
# its first dimension. Turns out using a dot product and a
# dimshuffle is faster than T.repeat.
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
if self.unroll_scan:
# Retrieve the dimensionality of the incoming layer
input_shape = self.input_shapes[0]
# Explicitly unroll the recurrence instead of using scan
hid_out = unroll_scan(
fn=step_fun,
sequences=sequences,
outputs_info=[hid_init],
go_backwards=self.backwards,
non_sequences=non_seqs,
n_steps=input_shape[1])[0]
else:
# Scan op iterates over first dimension of input and repeatedly
# applies the step function
hid_out = theano.scan(
fn=step_fun,
sequences=sequences,
go_backwards=self.backwards,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=self.gradient_steps,
strict=True)[0]
# When it is requested that we only return the final sequence step,
# we need to slice it out immediately after scan is applied
if self.only_return_final:
hid_out = hid_out[-1]
else:
# dimshuffle back to (n_batch, n_time_steps, n_features))
hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
# if scan is backward reverse the output
if self.backwards:
hid_out = hid_out[:, ::-1]
return hid_out
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(ConvTimeStep1DLayer, self).get_params(**tags)
# Combine with all parameters from the child layers
params += helper.get_all_params(self.conv1d, **tags)
return params
def get_output_for(self, inputs, **kwargs):
"""
Compute this layer's output function given a symbolic input variable.
Parameters
----------
inputs : list of theano.TensorType
`inputs[0]` should always be the symbolic input variable. When
this layer has a mask input (i.e. was instantiated with
`mask_input != None`, indicating that the lengths of sequences in
each batch vary), `inputs` should have length 2, where `inputs[1]`
is the `mask`. The `mask` should be supplied as a Theano variable
denoting whether each time step in each sequence in the batch is
part of the sequence or not. `mask` should be a matrix of shape
``(n_batch, n_time_steps)`` where ``mask[i, j] = 1`` when ``j <=
(length of sequence i)`` and ``mask[i, j] = 0`` when ``j > (length
of sequence i)``. When the hidden state of this layer is to be
pre-filled (i.e. was set to a :class:`Layer` instance) `inputs`
should have length at least 2, and `inputs[-1]` is the hidden state
to prefill with.
Returns
-------
layer_output : theano.TensorType
Symbolic output variable.
"""
# Retrieve the layer input
input = inputs[0]
# Retrieve the mask when it is supplied
mask = None
hid_init = None
if self.mask_incoming_index > 0:
mask = inputs[self.mask_incoming_index]
if self.hid_init_incoming_index > 0:
hid_init = inputs[self.hid_init_incoming_index]
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
if self.precompute_input:
# Because the input is given for all time steps, we can precompute
# the inputs to hidden before scanning. First we need to reshape
# from (seq_len, batch_size, trailing dimensions...) to
# (seq_len*batch_size, trailing dimensions...)
# This strange use of a generator in a tuple was because
# input.shape[2:] was raising a Theano error
trailing_dims = tuple(input.shape[n] for n in range(2, input.ndim))
input = T.reshape(input, (seq_len * num_batch, ) + trailing_dims)
input = helper.get_output(self.input_to_hidden, input, **kwargs)
# Reshape back to (seq_len, batch_size, trailing dimensions...)
trailing_dims = tuple(input.shape[n] for n in range(1, input.ndim))
input = T.reshape(input, (seq_len, num_batch) + trailing_dims)
# We will always pass the hidden-to-hidden layer params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
non_seqs += self._get_mi_params()
# When we are not precomputing the input, we also need to pass the
# input-to-hidden parameters to step
if not self.precompute_input:
non_seqs += helper.get_all_params(self.input_to_hidden)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_to_hid = helper.get_output(self.hidden_to_hidden, hid_previous,
**kwargs)
# Compute the input-to-hidden activation
if self.precompute_input:
# if the input is precomputed
in_to_hid = input_n
else:
# compute the input
in_to_hid = helper.get_output(self.input_to_hidden, input_n,
**kwargs)
# Compute the second order term
if self.a_g is not None:
second_order_term = (self.a_g * in_to_hid * hid_to_hid)
# second_order_term = in_to_hid * hid_to_hid
else:
second_order_term = 0
# Compute the first order hidden-to-hidden term
if self.b_g_hid_to_hid is not None:
f_o_hid_to_hid = self.b_g_hid_to_hid * hid_to_hid
else:
f_o_hid_to_hid = 0
# Compute first order input to hidden term
if self.b_g_in_to_hid is not None:
f_o_in_to_hid = self.b_g_in_to_hid * in_to_hid
else:
# if all else is None, it will output zeros of the right size
f_o_in_to_hid = T.zeros_like(in_to_hid)
hid_pre = second_order_term + f_o_in_to_hid + f_o_hid_to_hid
if self.b is not None:
hid_pre = hid_pre + self.b
return self.nonlinearity(hid_pre)
def step_masked(input_n, mask_n, hid_previous, *args):
# Skip over any input with mask 0 by copying the previous
# hidden state; proceed normally for any input with mask 1.
hid = step(input_n, hid_previous, *args)
hid_out = T.switch(mask_n, hid, hid_previous)
return [hid_out]
if mask is not None:
mask = mask.dimshuffle(1, 0, 'x')
sequences = [input, mask]
step_fun = step_masked
else:
sequences = input
step_fun = step
if not isinstance(self.hid_init, Layer):
# The code below simply repeats self.hid_init num_batch times in
# its first dimension. Turns out using a dot product and a
# dimshuffle is faster than T.repeat.
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
if self.unroll_scan:
# Retrieve the dimensionality of the incoming layer
input_shape = self.input_shapes[0]
# Explicitly unroll the recurrence instead of using scan
hid_out = unroll_scan(fn=step_fun,
sequences=sequences,
outputs_info=[hid_init],
go_backwards=self.backwards,
non_sequences=non_seqs,
n_steps=input_shape[1])[0]
else:
# Scan op iterates over first dimension of input and repeatedly
# applies the step function
hid_out = theano.scan(fn=step_fun,
sequences=sequences,
go_backwards=self.backwards,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=self.gradient_steps,
strict=True)[0]
# When it is requested that we only return the final sequence step,
# we need to slice it out immediately after scan is applied
if self.only_return_final:
hid_out = hid_out[-1]
else:
# dimshuffle back to (n_batch, n_time_steps, n_features))
hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
# if scan is backward reverse the output
if self.backwards:
hid_out = hid_out[:, ::-1]
return hid_out
y = data['target']
P = compute_joint_probabilities(X,
batch_size=batch_size,
d=2,
perplexity=30,
tol=1e-5,
verbose=0)
x = Input((None, X.shape[1]))
z = Dense(x, num_units=256, nonlinearity=rectify)
z = Dense(z, num_units=2, nonlinearity=linear)
z_pred = get_output(z)
P_real = T.matrix()
loss = tsne_loss(P_real, z_pred)
params = get_all_params(z, trainable=True)
lr = theano.shared(np.array(0.01, dtype=floatX))
updates = updates.adam(loss, params, learning_rate=lr)
train_fn = theano.function([x.input_var, P_real], loss, updates=updates)
encode = theano.function([x.input_var], z_pred)
X_train = X
Y_train = P
for epoch in range(1000):
total_loss = 0
nb = 0
for xt in iterate_minibatches(X_train,
batch_size=batch_size,
shuffle=False):
yt = Y_train[nb]
total_loss += train_fn(xt, yt)
def get_output_for(self, inputs, **kwargs):
# Retrieve the layer input
input = inputs[0]
# Retrieve the mask when it is supplied
mask = None
hid_init = None
if self.mask_incoming_index > 0:
mask = inputs[self.mask_incoming_index]
if self.hid_init_incoming_index > 0:
hid_init = inputs[self.hid_init_incoming_index]
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
#input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
# We will always pass the hidden-to-hidden layer params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_pre = helper.get_output(
self.hidden_to_hidden, hid_previous, **kwargs)
hid_pre += input_n
# Clip gradients
if self.grad_clipping:
hid_pre = theano.gradient.grad_clip(
hid_pre, -self.grad_clipping, self.grad_clipping)
return self.nonlinearity(hid_pre)
def step_masked(input_n, mask_n, hid_previous, *args):
# Skip over any input with mask 0 by copying the previous
# hidden state; proceed normally for any input with mask 1.
hid = step(input_n, hid_previous, *args)
hid_out = T.switch(mask_n, hid, hid_previous)
return [hid_out]
if mask is not None:
mask = mask.dimshuffle(1, 0, 'x')
sequences = [input, mask]
step_fun = step_masked
else:
sequences = input
step_fun = step
if not isinstance(self.hid_init, Layer):
# The code below simply repeats self.hid_init num_batch times in
# its first dimension. Turns out using a dot product and a
# dimshuffle is faster than T.repeat.
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
if self.unroll_scan:
# Retrieve the dimensionality of the incoming layer
input_shape = self.input_shapes[0]
# Explicitly unroll the recurrence instead of using scan
hid_out = unroll_scan(
fn=step_fun,
sequences=sequences,
outputs_info=[hid_init],
go_backwards=self.backwards,
non_sequences=non_seqs,
n_steps=input_shape[1])[0]
else:
# Scan op iterates over first dimension of input and repeatedly
# applies the step function
hid_out = theano.scan(
fn=step_fun,
sequences=sequences,
go_backwards=self.backwards,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=self.gradient_steps,
strict=True)[0]
# When it is requested that we only return the final sequence step,
# we need to slice it out immediately after scan is applied
if self.only_return_final:
hid_out = hid_out[-1]
else:
# dimshuffle back to (n_batch, n_time_steps, n_features))
#hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
# if scan is backward reverse the output
if self.backwards:
hid_out = hid_out[::-1,:]
return hid_out
def num_trainable_parameters(self):
return sum(
[p.get_value().size for p in get_all_params(self.layers[-1])])
def get_params(self, **tags): # Get all parameters from this layer, the master layer params = super(PermutationalLayer, self).get_params(**tags) # Combine with all parameters from the child layers params += helper.get_all_params(self.subnet, **tags) return params
def main(num_epochs=10, layers=1, load_file=None, batch_size=128, seq_len=96, suffix='', test=False, model_name='model'):
print "Building network ..."
print theano.config.floatX
BATCH_SIZE = batch_size
SEQ_LENGTH = seq_len
# Recurrent layers expect input of shape (batch size, SEQ_LENGTH, num_features)
x = T.imatrix('x')
mask = T.matrix('mask')
target_values = T.ivector('target_output')
# We now build a layer for the embeddings.
U = np.random.randn(vocab_size, char_dims).astype(theano.config.floatX)
embeddings = theano.shared(U, name='embeddings', borrow=True)
x_embedded = embeddings[x]
l_in = lasagne.layers.InputLayer(shape=(BATCH_SIZE, SEQ_LENGTH, char_dims), input_var=x_embedded)
l_mask = lasagne.layers.InputLayer(shape=(BATCH_SIZE, SEQ_LENGTH), input_var=mask)
recurrent_type = lasagne.layers.LSTMLayer
l_forward_1 = recurrent_type(l_in, N_HIDDEN,
grad_clipping=GRAD_CLIP,
nonlinearity=lasagne.nonlinearities.tanh,
mask_input=l_mask)
l_backward_1 = recurrent_type(l_in, N_HIDDEN,
grad_clipping=GRAD_CLIP,
nonlinearity=lasagne.nonlinearities.tanh,
backwards=True,
mask_input=l_mask)
if layers == 2:
l_forward_2 = recurrent_type(l_forward_1, N_HIDDEN,
grad_clipping=GRAD_CLIP,
nonlinearity=lasagne.nonlinearities.tanh,
mask_input=l_mask)
l_backward_2 = recurrent_type(l_backward_1, N_HIDDEN,
grad_clipping=GRAD_CLIP,
nonlinearity=lasagne.nonlinearities.tanh,
backwards=True,
mask_input=l_mask)
l_forward_slice = lasagne.layers.get_output(l_forward_2)[:,-1,:]
l_backward_slice = lasagne.layers.get_output(l_backward_2)[:,-1,:]
else:
l_forward_slice = lasagne.layers.get_output(l_forward_1)[:,-1,:]
l_backward_slice = lasagne.layers.get_output(l_backward_1)[:,-1,:]
# Now combine the LSTM layers.
_Wf, _Wb = np.random.randn(N_HIDDEN, dim_out).astype(theano.config.floatX), np.random.randn(N_HIDDEN, dim_out).astype(theano.config.floatX)
_bias = np.random.randn(dim_out).astype(theano.config.floatX)
wf = theano.shared(_Wf, name='join forward weights', borrow=True)
wb = theano.shared(_Wb, name='join backward weights', borrow=True)
bias = theano.shared(_bias, name='join bias', borrow=True)
joined = T.dot(l_forward_slice, wf) + T.dot(l_backward_slice, wb) + bias
tmp = lasagne.layers.InputLayer(shape=(BATCH_SIZE, dim_out))
l_out = lasagne.layers.DenseLayer(tmp, num_units=NUM_TAGS, W = lasagne.init.Normal(), nonlinearity=lasagne.nonlinearities.softmax)
# lasagne.layers.get_output produces a variable for the output of the net
network_output = l_out.get_output_for(joined)
# The loss function is calculated as the mean of the (categorical) cross-entropy between the prediction and target.
cost = T.nnet.categorical_crossentropy(network_output,target_values).mean()
# Retrieve all parameters from the network
if layers == 1:
all_params = helper.get_all_params(l_forward_1) + helper.get_all_params(l_backward_1)
else:
all_params = helper.get_all_params(l_forward_2) + helper.get_all_params(l_backward_2)
all_params += helper.get_all_params(l_out) + [wf, wb, bias, embeddings]
print len(all_params)
grads = T.grad(cost, all_params)
get_grads = theano.function([x, mask, target_values], grads)
# Compute AdaGrad updates for training
print("Computing updates ...")
updates = lasagne.updates.adam(cost, all_params)
# Theano functions for training and computing cost
print("Compiling functions ...")
train = theano.function([x, mask, target_values], cost, updates=updates, allow_input_downcast=True)
compute_cost = theano.function([x, mask, target_values], cost, allow_input_downcast=True)
pred = T.argmax(network_output, axis=1)
get_preds = theano.function([x, mask], pred, allow_input_downcast=True)
errors = T.sum(T.neq(pred, target_values))
count_errors = theano.function([x, mask, target_values], errors, allow_input_downcast=True)
def get_data(fname):
import cPickle
with open(fname, 'rb') as handle:
data = cPickle.load(handle)
xs = [d.astype('int32') for d in data[0]]
return xs, data[1]
print 'Loading train'
train_xs, train_ys = get_data('train%s' % suffix)
print 'Loading dev'
dev_xs, dev_ys = get_data('dev%s' % suffix)
print 'Loading test'
test_xs, test_ys = get_data('test%s' % suffix)
print 'Sizes:\tTrain: %d\tDev: %d\tTest: %d\n' % (len(train_xs) * BATCH_SIZE, len(dev_xs) * BATCH_SIZE, len(test_xs) * BATCH_SIZE)
def get_accuracy(pXs, pYs):
total = sum([len(batch) for batch in pXs])
errors = sum([count_errors(tx, get_mask(tx), ty) for tx, ty in zip(pXs, pYs)])
return float(total-errors)/total
def save_preds(pXs, pYs):
preds = [get_preds(tx, get_mask(tx)) for tx, _ in zip(pXs, pYs)]
with open('pred.pkl', 'wb') as handle:
handle.dump(preds, handle)
if not load_file is None:
print 'Loading params...'
with open(load_file, 'rb') as handle:
params = cPickle.load(handle)
print len(params)
for ix, _ in enumerate(zip(params, all_params)):
all_params[ix].set_value(params[ix].astype('float32'))
print("Training ...")
try:
if test:
dev_acc = get_accuracy(dev_xs, dev_ys)
save_preds(dev_xs, dev_ys)
print dev_acc
return
best_acc = 0.0
for it in xrange(num_epochs):
data = zip(train_xs, train_ys)
random.shuffle(data)
train_xs, train_ys = zip(*data)
avg_cost = 0;
total = 0.
for x, y in zip(train_xs, train_ys):
avg_cost += train(x, get_mask(x), y)
total += 1.
train_acc = 0.
#train_acc = get_accuracy(train_xs, train_ys)
dev_acc = get_accuracy(dev_xs, dev_ys)
test_acc = get_accuracy(test_xs, test_ys)
if dev_acc > best_acc:
params = [np.asarray(p.eval()) for p in all_params]
with open('%s_%f.pkl' % (model_name, dev_acc), 'wb') as handle:
cPickle.dump(params, handle)
best_acc = dev_acc
print("Epoch {} average loss = {}".format(it, avg_cost / total))
print "Accuracies:\t train: %f\tdev: %f\ttest: %f\n" % (train_acc, dev_acc, test_acc)
print
except KeyboardInterrupt:
pass
def get_output_for(self, inputs, **kwargs):
"""
Compute this layer's output function given a symbolic input variable.
Parameters
----------
inputs : list of theano.TensorType
`inputs[0]` should always be the symbolic input variable. When
this layer has a mask input (i.e. was instantiated with
`mask_input != None`, indicating that the lengths of sequences in
each batch vary), `inputs` should have length 2, where `inputs[1]`
is the `mask`. The `mask` should be supplied as a Theano variable
denoting whether each time step in each sequence in the batch is
part of the sequence or not. `mask` should be a matrix of shape
``(n_batch, n_time_steps)`` where ``mask[i, j] = 1`` when ``j <=
(length of sequence i)`` and ``mask[i, j] = 0`` when ``j > (length
of sequence i)``.
Returns
-------
layer_output : theano.TensorType
Symbolic output variable.
"""
# Retrieve the layer input
input = inputs[0]
# Retrieve the mask when it is supplied
mask = inputs[1] if len(inputs) > 1 else None
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
if self.precompute_input:
# Because the input is given for all time steps, we can precompute
# the inputs to hidden before scanning. First we need to reshape
# from (seq_len, batch_size, trailing dimensions...) to
# (seq_len*batch_size, trailing dimensions...)
# This strange use of a generator in a tuple was because
# input.shape[2:] was raising a Theano error
trailing_dims = tuple(input.shape[n] for n in range(2, input.ndim))
input = T.reshape(input, (seq_len * num_batch, ) + trailing_dims)
input = helper.get_output(self.input_to_hidden, input, **kwargs)
# Reshape back to (seq_len, batch_size, trailing dimensions...)
trailing_dims = tuple(input.shape[n] for n in range(1, input.ndim))
input = T.reshape(input, (seq_len, num_batch) + trailing_dims)
# We will always pass the hidden-to-hidden layer params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
non_seqs += helper.get_all_params(self.output_to_hidden)
# When we are not precomputing the input, we also need to pass the
# input-to-hidden parameters to step
if not self.precompute_input:
non_seqs += helper.get_all_params(self.input_to_hidden)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_pre = helper.get_output(self.hidden_to_hidden, hid_previous,
**kwargs)
# out_layers = helper.get_all_layers(self.output_to_hidden)
# out_layers[1].incoming_layer = self.hidden_to_hidden
hid_pre += helper.get_output(self.output_to_hidden, hid_previous,
**kwargs)
# If the dot product is precomputed then add it, otherwise
# calculate the input_to_hidden values and add them
if self.precompute_input:
hid_pre += input_n
else:
hid_pre += helper.get_output(self.input_to_hidden, input_n,
**kwargs)
# Clip gradients
if self.grad_clipping:
hid_pre = theano.gradient.grad_clip(hid_pre,
-self.grad_clipping,
self.grad_clipping)
return self.nonlinearity(hid_pre)
def step_masked(input_n, mask_n, hid_previous, *args):
# Skip over any input with mask 0 by copying the previous
# hidden state; proceed normally for any input with mask 1.
hid = step(input_n, hid_previous, *args)
hid_out = hid * mask_n + hid_previous * (1 - mask_n)
return [hid_out]
if mask is not None:
mask = mask.dimshuffle(1, 0, 'x')
sequences = [input, mask]
step_fun = step_masked
else:
sequences = input
step_fun = step
# When hid_init is provided as a TensorVariable, use it as-is
if isinstance(self.hid_init, T.TensorVariable):
hid_init = self.hid_init
else:
# The code below simply repeats self.hid_init num_batch times in
# its first dimension. Turns out using a dot product and a
# dimshuffle is faster than T.repeat.
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
if self.unroll_scan:
# Retrieve the dimensionality of the incoming layer
input_shape = self.input_shapes[0]
# Explicitly unroll the recurrence instead of using scan
hid_out = unroll_scan(fn=step_fun,
sequences=sequences,
outputs_info=[hid_init],
go_backwards=self.backwards,
non_sequences=non_seqs,
n_steps=input_shape[1])[0]
else:
# Scan op iterates over first dimension of input and repeatedly
# applies the step function
hid_out = theano.scan(fn=step_fun,
sequences=sequences,
go_backwards=self.backwards,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=self.gradient_steps,
strict=True)[0]
# dimshuffle back to (n_batch, n_time_steps, n_features))
hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
# if scan is backward reverse the output
if self.backwards:
hid_out = hid_out[:, ::-1]
return hid_out
def get_params(self, **tags):
# Get all parameters from this layer, the master layer
params = super(ConvTimeStep1DLayer, self).get_params(**tags)
# Combine with all parameters from the child layers
params += helper.get_all_params(self.conv1d, **tags)
return params
def num_trainable_parameters(self):
return sum(
[p.get_value().size for p in get_all_params(self.layers[-1])])
def get_output_for(self, inputs, **kwargs):
"""
Compute this layer's output function given a symbolic input variable
Parameters
----------
inputs : list of theano.TensorType
`inputs[0]` should always be the symbolic input variable. When
this layer has a mask input (i.e. was instantiated with
`mask_input != None`, indicating that the lengths of sequences in
each batch vary), `inputs` should have length 2, where `inputs[1]`
is the `mask`. The `mask` should be supplied as a Theano variable
denoting whether each time step in each sequence in the batch is
part of the sequence or not. `mask` should be a matrix of shape
``(n_batch, n_time_steps)`` where ``mask[i, j] = 1`` when ``j <=
(length of sequence i)`` and ``mask[i, j] = 0`` when ``j > (length
of sequence i)``. When the hidden state of this layer is to be
pre-filled (i.e. was set to a :class:`Layer` instance) `inputs`
should have length at least 2, and `inputs[-1]` is the hidden state
to prefill with.
Returns
-------
layer_output : theano.TensorType
Symbolic output variable.
"""
# Retrieve the layer input
input_p = inputs[0]
input_q = inputs[1]
z_init = inputs[2]
mu_p_init = inputs[3]
# Retrieve the mask when it is supplied
mask = None
if self.mask_incoming_index > 0:
mask = inputs[self.mask_incoming_index]
# Because scan iterates over the first dimension we dimshuffle to
# (n_time_steps, n_batch, n_features)
input_p = input_p.dimshuffle(1, 0, 2)
input_q = input_q.dimshuffle(1, 0, 2)
seq_len, num_batch, _ = input_p.shape
# Create single recurrent computation step function
# input__n is the n'th vector of the input
def log_sum_exp(a, b):
return T.log(T.exp(a) + T.exp(b))
def step(noise_n, input_p_n, input_q_n, z_previous, mu_p_previous,
logvar_p_previous, mu_q_previous, logvar_q_previous, *args):
input_p = T.concatenate([input_p_n, z_previous], axis=1)
mu_p = get_output(self.mu_p_mlp, input_p)
logvar_p = get_output(self.logvar_p_mlp, input_p)
logvar_p = T.log(T.exp(logvar_p) + self.cons)
q_input_n = T.concatenate([input_q_n, z_previous], axis=1)
mu_q = get_output(self.q_mu_mlp, q_input_n)
if self.use_mu_residual_q:
print "Using residuals for mean_q"
mu_q += mu_p
logvar_q = get_output(self.q_logvar_mlp, q_input_n)
# Numerical stability
logvar_q = T.log(T.exp(logvar_q) + self.cons)
z_n = mu_q + T.exp(0.5 * logvar_q) * noise_n
return z_n, mu_p, logvar_p, mu_q, logvar_q
def step_masked(noise_n, input_p_n, input_q_n, mask_n, z_previous,
mu_p_previous, logvar_p_previous, mu_q_previous,
logvar_q_previous, *args):
# Skip over any input with mask 0 by copying the previous
# hidden state; proceed normally for any input with mask 1.
z_n, mu_p, logvar_p, mu_q, logvar_q = step(
noise_n, input_p_n, input_q_n, z_previous, mu_p_previous,
logvar_p_previous, mu_q_previous, logvar_q_previous, *args)
z_n = T.switch(mask_n, z_n, z_previous)
mu_p = T.switch(mask_n, mu_p, mu_p_previous)
logvar_p = T.switch(mask_n, logvar_p, logvar_p_previous)
mu_q = T.switch(mask_n, mu_q, mu_q_previous)
logvar_q = T.switch(mask_n, logvar_q, logvar_q_previous)
return z_n, mu_p, logvar_p, mu_q, logvar_q
eps = self._srng.normal(size=(seq_len, num_batch, self.num_units),
avg=0.0,
std=1.0)
logvar_init = T.zeros((num_batch, self.num_units))
if mask is not None:
# mask is given as (batch_size, seq_len). Because scan iterates
# over first dimension, we dimshuffle to (seq_len, batch_size) and
# add a broadcastable dimension
mask = mask.dimshuffle(1, 0, 'x')
sequences = [eps, input_p, input_q, mask]
step_fun = step_masked
else:
sequences = [eps, input_p, input_q]
step_fun = step
# The hidden-to-hidden weight matrix is always used in step
non_seqs = helper.get_all_params(self.logvar_p_mlp)
non_seqs += helper.get_all_params(self.mu_p_mlp)
non_seqs += helper.get_all_params(self.q_mu_mlp)
non_seqs += helper.get_all_params(self.q_logvar_mlp)
if self.unroll_scan:
# Retrieve the dimensionality of the incoming layer
input_shape = self.input_shapes[0]
# Explicitly unroll the recurrence instead of using scan
scan_out = unroll_scan(fn=step_fun,
sequences=sequences,
outputs_info=[
z_init, mu_p_init, logvar_init,
mu_p_init, logvar_init
],
go_backwards=self.backwards,
non_sequences=non_seqs,
n_steps=input_shape[1])
else:
# Scan op iterates over first dimension of input and repeatedly
# applies the step function
scan_out = theano.scan(fn=step_fun,
sequences=sequences,
go_backwards=self.backwards,
outputs_info=[
z_init, mu_p_init, logvar_init,
mu_p_init, logvar_init
],
non_sequences=non_seqs,
truncate_gradient=self.gradient_steps,
strict=True)[0]
z, mu_p, logvar_p, mu_q, logvar_q = scan_out
# When it is requested that we only return the final sequence step,
# we need to slice it out immediately after scan is applied
if self.only_return_final:
assert False
else:
# dimshuffle back to (n_batch, n_time_steps, n_features))
z = z.dimshuffle(1, 0, 2)
mu_p = mu_p.dimshuffle(1, 0, 2)
logvar_p = logvar_p.dimshuffle(1, 0, 2)
mu_q = mu_q.dimshuffle(1, 0, 2)
logvar_q = logvar_q.dimshuffle(1, 0, 2)
# if scan is backward reverse the output
if self.backwards:
z = z[:, ::-1]
mu_p = mu_p[:, ::-1]
logvar_p = logvar_p[:, ::-1]
mu_q = mu_q[:, ::-1]
logvar_q = logvar_q[:, ::-1]
return z, mu_p, logvar_p, mu_q, logvar_q
def get_output_for(self, inputs, **kwargs):
input = inputs[0]
hid_init = None
if self.hid_init_incoming_index > 0:
hid_init = inputs[self.hid_init_incoming_index]
# Input should be provided as (n_batch, n_time_steps, n_features)
# but scan requires the iterable dimension to be first
# So, we need to dimshuffle to (n_time_steps, n_batch, n_features)
input = input.dimshuffle(1, 0, *range(2, input.ndim))
seq_len, num_batch = input.shape[0], input.shape[1]
# precompute inputs before scanning
trailing_dims = tuple(input.shape[n] for n in range(2, input.ndim))
input = T.reshape(input, (seq_len*num_batch,) + trailing_dims)
input = helper.get_output(
self.input_to_hidden, input, **kwargs)
# Reshape back to (seq_len, batch_size, trailing dimensions...)
trailing_dims = tuple(input.shape[n] for n in range(1, input.ndim))
input = T.reshape(input, (seq_len, num_batch) + trailing_dims)
# pass params to step
non_seqs = helper.get_all_params(self.hidden_to_hidden)
non_seqs += helper.get_all_params(self.post_concat)
# Create single recurrent computation step function
def step(input_n, hid_previous, *args):
# Compute the hidden-to-hidden activation
hid_pre = helper.get_output(
self.hidden_to_hidden, hid_previous, **kwargs)
hid_pre = T.concatenate([hid_pre, input_n], axis=1)
hid_pre = helper.get_output(self.post_concat, hid_pre, **kwargs)
if self.grad_clipping:
hid_pre = theano.gradient.grad_clip(
hid_pre, -self.grad_clipping, self.grad_clipping)
return hid_pre
sequences = input
step_fun = step
if not isinstance(self.hid_init, Layer):
# repeats self.hid_init num_batch times in first dimension
dot_dims = (list(range(1, self.hid_init.ndim - 1)) +
[0, self.hid_init.ndim - 1])
hid_init = T.dot(T.ones((num_batch, 1)),
self.hid_init.dimshuffle(dot_dims))
hid_out = theano.scan(
fn=step_fun,
sequences=sequences,
go_backwards=False,
outputs_info=[hid_init],
non_sequences=non_seqs,
truncate_gradient=-1,
strict=True)[0]
# dimshuffle back to (n_batch, n_time_steps, n_features))
hid_out = hid_out.dimshuffle(1, 0, *range(2, hid_out.ndim))
return hid_out