def test_broadcast(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
ds = DimshuffleLayer(input_layer, [0, 1, 2, 3, 4, 'x'])
assert ds.output_shape == (2, 3, 1, 5, 7, 1)
assert ds.get_output_for(input_var).eval({
input_var: input_data
}).shape == (2, 3, 1, 5, 7, 1)
def test_rearrange(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
ds = DimshuffleLayer(input_layer, [4, 3, 2, 1, 0])
assert ds.output_shape == (7, 5, 1, 3, 2)
assert ds.get_output_for(input_var).eval({
input_var: input_data
}).shape == (7, 5, 1, 3, 2)
def test_collapse_None(self, input_data, input_var, input_layer_with_None):
from lasagne.layers.shape import DimshuffleLayer
ds_ok = DimshuffleLayer(input_layer_with_None, [0, 1, 3, 4])
assert ds_ok.output_shape == (2, 3, 5, 7)
assert ds_ok.get_output_for(input_var).eval(
{input_var: input_data}).shape == (2, 3, 5, 7)
with pytest.raises(ValueError):
DimshuffleLayer(input_layer_with_None, [0, 1, 2, 4])
def test_collapse_None(self, input_data, input_var, input_layer_with_None):
from lasagne.layers.shape import DimshuffleLayer
ds_ok = DimshuffleLayer(input_layer_with_None, [0, 1, 3, 4])
assert ds_ok.output_shape == (2, 3, 5, 7)
assert ds_ok.get_output_for(input_var).eval(
{input_var: input_data}).shape == (2, 3, 5, 7)
with pytest.raises(ValueError):
DimshuffleLayer(input_layer_with_None, [0, 1, 2, 4])
def test_invalid_pattern(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
with pytest.raises(ValueError):
DimshuffleLayer(input_layer, ['q'])
with pytest.raises(ValueError):
DimshuffleLayer(input_layer, [0, 0, 1, 3, 4])
with pytest.raises(ValueError):
# There is no dimension 42
DimshuffleLayer(input_layer, [0, 1, 2, 4, 42])
def test_invalid_pattern(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
with pytest.raises(ValueError):
DimshuffleLayer(input_layer, ['q'])
with pytest.raises(ValueError):
DimshuffleLayer(input_layer, [0, 0, 1, 3, 4])
# There is no dimension 42
ds_bad = DimshuffleLayer(input_layer, [0, 1, 2, 4, 42])
with pytest.raises(ValueError):
ds_bad.get_output_shape()
def get_layers(self):
l = InputLayer([None, self.in_chans, self.input_time_length, 1])
if self.split_first_layer:
l = DimshuffleLayer(l, pattern=[0, 3, 2, 1])
l = Conv2DLayer(l,
num_filters=self.n_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
l = Conv2DAllColsLayer(l,
num_filters=self.n_filters_spat,
filter_size=[1, -1],
nonlinearity=identity,
name='spat_conv')
else: #keep channel dim in first dim, so it will also be convolved over
l = Conv2DLayer(l,
num_filters=self.num_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
if self.batch_norm:
l = BatchNormLayer(l,
epsilon=1e-4,
alpha=self.batch_norm_alpha,
nonlinearity=self.conv_nonlin)
else:
l = NonlinearityLayer(l, nonlinearity=self.conv_nonlin)
l = Pool2DLayer(l,
pool_size=[self.pool_time_length, 1],
stride=[1, 1],
mode=self.pool_mode)
l = NonlinearityLayer(l, self.pool_nonlin)
l = StrideReshapeLayer(l, n_stride=self.pool_time_stride)
l = DropoutLayer(l, p=self.drop_prob)
l = Conv2DLayer(l,
num_filters=self.n_classes,
filter_size=[self.final_dense_length, 1],
nonlinearity=identity,
name='final_dense')
l = FinalReshapeLayer(l)
l = NonlinearityLayer(l, softmax)
return lasagne.layers.get_all_layers(l)
def get_layers(self):
in_l = InputLayer((self.n_examples, self.n_time_steps, self.n_chans))
in_bandpass = InputLayer(
(self.n_examples, self.n_time_steps, self.n_chans, self.n_filters))
l_bandpass = BandpassLayer([in_l, in_bandpass],
n_filt_order=self.n_filt_order,
truncate_gradient=self.truncate_gradient)
# out comes examples x timesteps x chans x filters
l_spat_filt = TensorDotLayer(l_bandpass,
n_filters=self.n_spat_filters,
axis=2)
# still examples x timesteps x chans x filters
l_square = NonlinearityLayer(l_spat_filt, T.sqr)
# now adding empty chan dim so we can make pooling per output chan
l_shape_pad = DimshuffleLayer(l_square, (0, 'x', 1, 2, 3))
# examples x convchans x timesteps x chans x filters
l_pooled = Pool3DDNNLayer(l_shape_pad,
pool_size=(self.n_pool_len, 1, 1),
stride=1,
mode='average_exc_pad')
l_log = NonlinearityLayer(l_pooled, safe_log)
# removing empty convchan dim again
l_sliced = SliceLayer(l_log, indices=0, axis=1)
# now examples x timesteps x chans x filters
l_flat = FlattenLayer(l_sliced, outdim=3)
# now examples x timesteps x features (chans * filters)
l_dense = TensorDotLayer(l_flat, n_filters=1, axis=2)
# now examples x timesteps x 1
l_nonlin = NonlinearityLayer(l_dense, sigmoid)
return lasagne.layers.get_all_layers(l_nonlin)
def test_broadcast(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
ds = DimshuffleLayer(input_layer, [0, 1, 2, 3, 4, 'x'])
assert ds.output_shape == (2, 3, 1, 5, 7, 1)
assert ds.get_output_for(input_var).eval(
{input_var: input_data}).shape == (2, 3, 1, 5, 7, 1)
def test_rearrange(self, input_data, input_var, input_layer):
from lasagne.layers.shape import DimshuffleLayer
ds = DimshuffleLayer(input_layer, [4, 3, 2, 1, 0])
assert ds.output_shape == (7, 5, 1, 3, 2)
assert ds.get_output_for(input_var).eval(
{input_var: input_data}).shape == (7, 5, 1, 3, 2)
def get_layers(self):
l = InputLayer([None, self.in_chans, self.input_time_length, 1])
if self.split_first_layer:
l = DimshuffleLayer(l, pattern=[0, 3, 2, 1])
l = DropoutLayer(l, p=self.drop_in_prob)
l = Conv2DLayer(l,
num_filters=self.num_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
if self.double_time_convs:
l = Conv2DLayer(l,
num_filters=self.num_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
l = Conv2DAllColsLayer(l,
num_filters=self.num_filters_spat,
filter_size=[1, -1],
nonlinearity=identity,
name='spat_conv')
else: #keep channel dim in first dim, so it will also be convolved over
l = DropoutLayer(l, p=self.drop_in_prob)
l = Conv2DLayer(l,
num_filters=self.num_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
if self.double_time_convs:
l = Conv2DLayer(l,
num_filters=self.num_filters_time,
filter_size=[self.filter_time_length, 1],
nonlinearity=identity,
name='time_conv')
if self.batch_norm:
l = BatchNormLayer(l,
epsilon=1e-4,
alpha=self.batch_norm_alpha,
nonlinearity=self.first_nonlin)
else:
l = NonlinearityLayer(l, nonlinearity=self.first_nonlin)
l = Pool2DLayer(l,
pool_size=[self.pool_time_length, 1],
stride=[1, 1],
mode=self.first_pool_mode)
l = StrideReshapeLayer(l, n_stride=self.pool_time_stride)
l = NonlinearityLayer(l, self.first_pool_nonlin)
def conv_pool_block(l, num_filters, filter_length, i_block):
l = DropoutLayer(l, p=self.drop_prob)
l = Conv2DLayer(l,
num_filters=num_filters,
filter_size=[filter_length, 1],
nonlinearity=identity,
name='combined_conv_{:d}'.format(i_block))
if self.double_time_convs:
l = Conv2DLayer(l,
num_filters=num_filters,
filter_size=[filter_length, 1],
nonlinearity=identity,
name='combined_conv_{:d}'.format(i_block))
if self.batch_norm:
l = BatchNormLayer(l,
epsilon=1e-4,
alpha=self.batch_norm_alpha,
nonlinearity=self.later_nonlin)
else:
l = NonlinearityLayer(l, nonlinearity=self.later_nonlin)
l = Pool2DLayer(l,
pool_size=[self.pool_time_length, 1],
stride=[1, 1],
mode=self.later_pool_mode)
l = StrideReshapeLayer(l, n_stride=self.pool_time_stride)
l = NonlinearityLayer(l, self.later_pool_nonlin)
return l
l = conv_pool_block(l, self.num_filters_2, self.filter_length_2, 2)
l = conv_pool_block(l, self.num_filters_3, self.filter_length_3, 3)
l = conv_pool_block(l, self.num_filters_4, self.filter_length_4, 4)
# Final part, transformed dense layer
l = DropoutLayer(l, p=self.drop_prob)
l = Conv2DLayer(l,
num_filters=self.n_classes,
filter_size=[self.final_dense_length, 1],
nonlinearity=identity,
name='final_dense')
l = FinalReshapeLayer(l)
l = NonlinearityLayer(l, self.final_nonlin)
return lasagne.layers.get_all_layers(l)
def get_layers(self):
def resnet_residual_block(model,
increase_units_factor=None,
half_time=False):
"""Calling residual_block function with correct attributes
from this object.
Parameters
----------
model :
increase_units_factor :
(Default value = None)
half_time :
(Default value = False)
Returns
-------
Final layer of created residual block.
"""
return residual_block(model,
batch_norm_epsilon=self.batch_norm_epsilon,
batch_norm_alpha=self.batch_norm_alpha,
increase_units_factor=increase_units_factor,
half_time=half_time,
nonlinearity=self.nonlinearity,
projection=self.projection,
survival_prob=self.survival_prob,
add_after_nonlin=self.add_after_nonlin,
reduction_method=self.reduction_method,
reduction_pool_mode=self.reduction_pool_mode)
model = InputLayer([None, self.in_chans, self.input_time_length, 1])
if self.split_first_layer:
# shift channel dim out
model = DimshuffleLayer(model, (0, 3, 2, 1))
# first timeconv
model = Conv2DLayer(model,
num_filters=self.n_first_filters,
filter_size=(self.first_filter_length, 1),
stride=(1, 1),
nonlinearity=identity,
pad='same',
W=lasagne.init.HeNormal(gain='relu'))
# now spatconv
model = batch_norm(Conv2DLayer(
model,
num_filters=self.n_first_filters,
filter_size=(1, self.in_chans),
stride=(1, 1),
nonlinearity=self.nonlinearity,
pad=0,
W=lasagne.init.HeNormal(gain='relu')),
epsilon=self.batch_norm_epsilon,
alpha=self.batch_norm_alpha)
else:
model = batch_norm(Conv2DLayer(
model,
num_filters=self.n_first_filters,
filter_size=(self.first_filter_length, 1),
stride=(1, 1),
nonlinearity=self.nonlinearity,
pad='same',
W=lasagne.init.HeNormal(gain='relu')),
epsilon=self.batch_norm_epsilon,
alpha=self.batch_norm_alpha)
for _ in range(self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model,
increase_units_factor=2,
half_time=True)
for _ in range(1, self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model,
increase_units_factor=1.5,
half_time=True)
for _ in range(1, self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model, half_time=True)
for _ in range(1, self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model, half_time=True)
for _ in range(1, self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model, half_time=True)
for _ in range(1, self.n_layers_per_block):
model = resnet_residual_block(model)
model = resnet_residual_block(model, half_time=True)
if self.drop_before_pool:
model = DropoutLayer(model, p=0.5)
# Replacement for global mean pooling
if self.final_aggregator == 'pool':
model = Pool2DLayer(model,
pool_size=(self.final_pool_length, 1),
stride=(1, 1),
mode='average_exc_pad')
model = Conv2DLayer(model,
filter_size=(1, 1),
num_filters=4,
W=lasagne.init.HeNormal(),
nonlinearity=identity)
elif self.final_aggregator == 'conv':
model = Conv2DLayer(model,
filter_size=(self.final_pool_length, 1),
num_filters=4,
W=lasagne.init.HeNormal(),
nonlinearity=identity)
else:
raise ValueError("Unknown final aggregator {:s}".format(
self.final_aggregator))
model = FinalReshapeLayer(model)
model = NonlinearityLayer(model, nonlinearity=self.final_nonlin)
model = set_survival_probs_to_linear_decay(model, self.survival_prob)
return lasagne.layers.get_all_layers(model)
def build_nmt_encoder_decoder(dim_word=1,
n_embd=100,
n_units=500,
n_proj=200,
state=None,
rev_state=None,
context_type=None,
attention=False,
drop_p=None):
enc = OrderedDict()
enc['input'] = InputLayer((None, None), name='input')
enc_mask = enc['mask'] = InputLayer((None, None), name='mask')
enc_rev_mask = enc['rev_mask'] = InputLayer((None, None), name='rev_mask')
enc['input_emb'] = EmbeddingLayer(enc.values()[-1],
input_size=dim_word,
output_size=n_embd,
name='input_emb')
### ENCODER PART ###
# rnn encoder unit
hid_init = Constant(0.)
hid_init_rev = Constant(0.)
encoder_unit = get_rnn_unit(enc.values()[-1],
enc_mask,
enc_rev_mask,
hid_init,
hid_init_rev,
n_units,
prefix='encoder_')
enc.update(encoder_unit)
# context layer = decoder's initial state of shape (batch_size, num_units)
context = enc.values()[-1] # net['context']
if context_type == 'last':
enc['context2init'] = SliceLayer(context,
indices=-1,
axis=1,
name='last_encoder_context')
elif context_type == 'mean':
enc['context2init'] = ExpressionLayer(context,
mean_over_1_axis,
output_shape='auto',
name='mean_encoder_context')
### DECODER PART ###
W_init2proj, b_init2proj = GlorotUniform(), Constant(0.)
enc['init_state'] = DenseLayer(enc['context2init'],
num_units=n_units,
W=W_init2proj,
b=b_init2proj,
nonlinearity=tanh,
name='decoder_init_state')
if state is None:
init_state = enc['init_state']
init_state_rev = None #if rev_state is None else init_state
if not attention:
# if simple attetion the context is 2D, else 3D
context = enc['context2init']
else:
init_state = state
init_state_rev = rev_state
context = enc['context_input'] = \
InputLayer((None, n_units), name='ctx_input')
# (batch_size, nfeats)
# (batch_size, valid ntsteps)
enc['target'] = InputLayer((None, None), name='target')
dec_mask = enc['target_mask'] = InputLayer((None, None),
name='target_mask')
enc['target_emb'] = EmbeddingLayer(enc.values()[-1],
input_size=dim_word,
output_size=n_embd,
name='target_emb')
prevdim = n_embd
prev2rnn = enc.values()[-1] # it's either emb or prev2rnn/noise
decoder_unit = get_rnn_unit(prev2rnn,
dec_mask,
None,
init_state,
None,
n_units,
prefix='decoder_',
context=context,
attention=attention)
enc.update(decoder_unit)
if attention:
ctxs = enc.values()[-1]
ctxs_shape = ctxs.output_shape
def get_ctx(x):
return ctxs.ctx
context = enc['context'] = ExpressionLayer(ctxs,
function=get_ctx,
output_shape=ctxs_shape,
name='context')
# return all values'
# reshape for feed-forward layer
# 2D shapes of (batch_size * num_steps, num_units/num_feats)
enc['rnn2proj'] = rnn2proj = ReshapeLayer(enc.values()[-1], (-1, n_units),
name='flatten_rnn2proj')
enc['prev2proj'] = prev2proj = ReshapeLayer(prev2rnn, (-1, prevdim),
name='flatten_prev')
if isinstance(context, ExpressionLayer):
ctx2proj = enc['ctx2proj'] = ReshapeLayer(context,
(-1, ctxs_shape[-1]),
name='flatten_ctxs')
else:
ctx2proj = context
# load shared parameters
W_rnn2proj, b_rnn2proj = GlorotUniform(), Constant(0.)
W_prev2proj, b_prev2proj = GlorotUniform(), Constant(0.)
W_ctx2proj, b_ctx2proj = GlorotUniform(), Constant(0.)
# perturb rnn-to-projection by noise
if drop_p is not None:
rnn2proj = enc['noise_rnn2proj'] = DropoutLayer(rnn2proj,
sigma=drop_p,
name='noise_rnn2proj')
prev2proj = enc['drop_prev2proj'] = DropoutLayer(prev2proj,
sigma=drop_p,
name='drop_prev2proj')
ctx2proj = enc['noise_ctx2proj'] = DropoutLayer(ctx2proj,
sigma=drop_p,
name='noise_ctx2proj')
# project rnn
enc['rnn_proj'] = DenseLayer(rnn2proj,
num_units=n_proj,
nonlinearity=linear,
W=W_rnn2proj,
b=b_rnn2proj,
name='rnn_proj')
# project raw targets
enc['prev_proj'] = DenseLayer(prev2proj,
num_units=n_proj,
nonlinearity=linear,
W=W_prev2proj,
b=b_prev2proj,
name='prev_proj')
# project context
enc['ctx_proj'] = DenseLayer(ctx2proj,
num_units=n_proj,
nonlinearity=linear,
W=W_ctx2proj,
b=b_ctx2proj,
name='ctx_proj')
# reshape back for merging
n_batch = enc['input'].input_var.shape[0]
rnn2merge = enc['rnn2merge'] = ReshapeLayer(enc['rnn_proj'],
(n_batch, -1, n_proj),
name='reshaped_rnn2proj')
prev2merge = enc['prev2merge'] = ReshapeLayer(enc['prev_proj'],
(n_batch, -1, n_proj),
name='reshaped_prev')
if isinstance(context, ExpressionLayer):
ctx2merge = ReshapeLayer(enc['ctx_proj'], (n_batch, -1, n_proj),
name='reshaped_prev')
else:
ctx2merge = enc['ctx2merge'] = DimshuffleLayer(enc['ctx_proj'],
pattern=(0, 'x', 1),
name='reshaped_context')
# combine projections into shape (batch_size, n_steps, n_proj)
enc['proj_merge'] = ElemwiseMergeLayer([rnn2merge, prev2merge, ctx2merge],
merge_function=tanh_add,
name='proj_merge')
# reshape for output regression projection
enc['merge2proj'] = ReshapeLayer(enc.values()[-1], (-1, n_proj),
name='flatten_proj_merge')
# perturb concatenated regressors by noise
if drop_p is not None:
# if noise_type == 'binary':
enc['noise_output'] = DropoutLayer(enc.values()[-1],
p=drop_p,
name='noise_output')
# regress on combined (perturbed) projections
out = get_output_unit(enc['target'], enc.values()[-1], dim_word)
enc.update(out) # update graph
return enc