def apply(self, input_lb, input_un, target):
batch_size = input_lb.shape[0]
get_labeled = lambda x: x[:batch_size] if x is not None else x
input = T.concatenate([input_lb, input_un], axis=0)
self.layer_dims = {0: self.input_dim}
self.lr = self.shared(self.default_lr, 'learning_rate', role=None)
top = len(self.layers) - 1
clean = self.encoder(input, noise_std=[0])
corr = self.encoder(input, noise_std=self.noise_std)
ests, costs = self.decoder(clean, corr, batch_size)
# Costs
y = target.flatten()
costs.class_clean = CategoricalCrossEntropy().apply(
y, get_labeled(clean.h[top]))
costs.class_clean.name = 'CE_clean'
costs.class_corr = CategoricalCrossEntropy().apply(
y, get_labeled(corr.h[top]))
costs.class_corr.name = 'CE_corr'
costs.total = costs.class_corr * 1.0
for i in range(len(self.layers)):
costs.total += costs.denois[i] * self.denoising_cost_x[i]
costs.total.name = 'Total_cost'
self.costs = costs
# Classification error
mr = MisclassificationRate()
self.error = mr.apply(y, get_labeled(clean.h[top])) * np.float32(100.)
self.error.name = 'Error_rate'
def main(save_to, num_epochs):
mlp = MLP([Tanh(), Softmax()], [784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
probs = mlp.apply(tensor.flatten(x, outdim=2))
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost])
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * (W1**2).sum() + .00005 * (W2**2).sum()
cost.name = 'final_cost'
mnist_train = MNIST(("train", ))
mnist_test = MNIST(("test", ))
algorithm = GradientDescent(cost=cost,
parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [
Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate],
Flatten(DataStream.default_stream(
mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
which_sources=('features', )),
prefix="test"),
TrainingDataMonitoring([
cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)
],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()
]
if BLOCKS_EXTRAS_AVAILABLE:
extensions.append(
Plot('MNIST example',
channels=[[
'test_final_cost',
'test_misclassificationrate_apply_error_rate'
], ['train_total_gradient_norm']]))
main_loop = MainLoop(algorithm,
Flatten(DataStream.default_stream(
mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 50)),
which_sources=('features', )),
model=Model(cost),
extensions=extensions)
main_loop.run()
def setup_model(configs):
tensor5 = theano.tensor.TensorType(config.floatX, (False,) * 5)
# shape: T x B x C x X x Y
input_ = tensor5("features")
tensor3 = theano.tensor.TensorType(config.floatX, (False,) * 3)
locs = tensor3("locs")
# shape: B x Classes
target = T.ivector("targets")
model = LSTMAttention(configs, weights_init=Glorot(), biases_init=Constant(0))
model.initialize()
(h, c, location, scale, alpha, patch, downn_sampled_input, conved_part_1, conved_part_2, pre_lstm) = model.apply(
input_, locs
)
model.location = location
model.scale = scale
model.alpha = location
model.patch = patch
classifier = MLP(
[Rectifier(), Softmax()], configs["classifier_dims"], weights_init=Glorot(), biases_init=Constant(0)
)
classifier.initialize()
probabilities = classifier.apply(h[-1])
cost = CategoricalCrossEntropy().apply(target, probabilities)
cost.name = "CE"
error_rate = MisclassificationRate().apply(target, probabilities)
error_rate.name = "ER"
model.cost = cost
model.error_rate = error_rate
model.probabilities = probabilities
if configs["load_pretrained"]:
blocks_model = Model(model.cost)
all_params = blocks_model.parameters
with open("VGG_CNN_params.npz") as f:
loaded = np.load(f)
all_conv_params = loaded.keys()
for param in all_params:
if param.name in loaded.keys():
assert param.get_value().shape == loaded[param.name].shape
param.set_value(loaded[param.name])
all_conv_params.pop(all_conv_params.index(param.name))
print "the following parameters did not match: " + str(all_conv_params)
if configs["test_model"]:
print "TESTING THE MODEL: CHECK THE INPUT SIZE!"
cg = ComputationGraph(model.cost)
f = theano.function(cg.inputs, [model.cost], on_unused_input="ignore", allow_input_downcast=True)
data = configs["get_streams"](configs["batch_size"])[0].get_epoch_iterator().next()
f(data[1], data[0], data[2])
print "Test passed! ;)"
model.monitorings = [cost, error_rate]
return model
def main(save_to, num_epochs, bokeh=False):
mlp = MLP([Tanh(), Softmax()], [784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
probs = mlp.apply(x)
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost])
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * (W1 ** 2).sum() + .00005 * (W2 ** 2).sum()
cost.name = 'final_cost'
mnist_train = MNIST("train")
mnist_test = MNIST("test")
algorithm = GradientDescent(
cost=cost, params=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(
[cost, error_rate],
DataStream(mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
prefix="test"),
TrainingDataMonitoring(
[cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()]
if bokeh:
extensions.append(Plot(
'MNIST example',
channels=[
['test_final_cost',
'test_misclassificationrate_apply_error_rate'],
['train_total_gradient_norm']]))
main_loop = MainLoop(
algorithm,
DataStream(mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 50)),
model=Model(cost),
extensions=extensions)
main_loop.run()
def apply(self, input_, target):
mlp = MLP(self.non_lins, self.dims,
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0),
name=self.name)
mlp.initialize()
probs = mlp.apply(T.flatten(input_, outdim=2))
probs.name = 'probs'
cost = CategoricalCrossEntropy().apply(target.flatten(), probs)
cost.name = "CE"
self.outputs = {}
self.outputs['probs'] = probs
self.outputs['cost'] = cost
def apply(self, input_, target):
mlp = MLP(self.non_lins,
self.dims,
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0),
name=self.name)
mlp.initialize()
probs = mlp.apply(T.flatten(input_, outdim=2))
probs.name = 'probs'
cost = CategoricalCrossEntropy().apply(target.flatten(), probs)
cost.name = "CE"
self.outputs = {}
self.outputs['probs'] = probs
self.outputs['cost'] = cost
def main(save_to, num_epochs):
mlp = MLP([Tanh(), Softmax()], [784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
probs = mlp.apply(x)
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost])
W1, W2 = VariableFilter(roles=[WEIGHTS])(cg.variables)
cost = cost + .00005 * (W1**2).sum() + .00005 * (W2**2).sum()
cost.name = 'final_cost'
mnist_train = MNIST("train")
mnist_test = MNIST("test")
algorithm = GradientDescent(cost=cost,
step_rule=SteepestDescent(learning_rate=0.1))
main_loop = MainLoop(
mlp,
DataStream(mnist_train,
iteration_scheme=SequentialScheme(mnist_train.num_examples,
50)),
algorithm,
extensions=[
Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate],
DataStream(mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
prefix="test"),
TrainingDataMonitoring([
cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)
],
prefix="train",
after_every_epoch=True),
SerializeMainLoop(save_to),
Plot('MNIST example',
channels=[[
'test_final_cost',
'test_misclassificationrate_apply_error_rate'
], ['train_total_gradient_norm']]),
Printing()
])
main_loop.run()
def main(save_to, num_epochs, batch_size):
mlp = MLP([Tanh(), Tanh(), Tanh(), Softmax()], [3072, 4096, 1024, 512, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tt.tensor4('features', dtype='float32')
y = tt.vector('label', dtype='int32')
probs = mlp.apply(x.reshape((-1, 3072)))
cost = CategoricalCrossEntropy().apply(y, probs)
error_rate = MisclassificationRate().apply(y, probs)
cg = ComputationGraph([cost])
ws = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * sum(([(w**2).sum() for w in ws]))
cost.name = 'final_cost'
train_dataset = Cifar10Dataset(data_dir='/home/belohlavek/data/cifar10',
is_train=True)
valid_dataset = Cifar10Dataset(data_dir='/home/belohlavek/data/cifar10',
is_train=False)
train_stream = train_dataset.get_stream(batch_size)
valid_stream = valid_dataset.get_stream(batch_size)
algorithm = GradientDescent(cost=cost,
parameters=cg.parameters,
step_rule=Adam(learning_rate=0.001))
extensions = [
Timing(),
LogExtension('/home/belohlavek/ALI/mlp.log'),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate], valid_stream, prefix="test"),
TrainingDataMonitoring([
cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)
],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()
]
main_loop = MainLoop(algorithm,
train_stream,
model=Model(cost),
extensions=extensions)
main_loop.run()
def build_model(images, labels):
# Construct a bottom convolutional sequence
bottom_conv_sequence = convolutional_sequence((3,3), 16, (160, 160))
bottom_conv_sequence._push_allocation_config()
# Flatten layer
flattener = Flattener()
# Construct a top MLP
conv_out_dim = numpy.prod(bottom_conv_sequence.get_dim('output'))
#top_mlp = MLP([Rectifier(name='non_linear_9'), Softmax(name='non_linear_11')], [conv_out_dim, 1024, 10], weights_init=IsotropicGaussian(), biases_init=Constant(0))
top_mlp = BatchNormalizedMLP([Rectifier(name='non_linear_9'), Softmax(name='non_linear_11')], [conv_out_dim, 1024, 10], weights_init=IsotropicGaussian(), biases_init=Constant(0))
# Construct feedforward sequence
ss_seq = FeedforwardSequence([bottom_conv_sequence.apply, flattener.apply, top_mlp.apply])
ss_seq.push_initialization_config()
ss_seq.initialize()
prediction = ss_seq.apply(images)
cost_noreg = CategoricalCrossEntropy().apply(labels.flatten(), prediction)
# add regularization
selector = Selector([top_mlp])
Ws = selector.get_parameters('W')
mlp_brick_name = 'batchnormalizedmlp'
W0 = Ws['/%s/linear_0.W' % mlp_brick_name]
W1 = Ws['/%s/linear_1.W' % mlp_brick_name]
cost = cost_noreg + .01 * (W0 ** 2).mean() + .01 * (W1 ** 2).mean()
return cost
def __init__(self, config):
self.X = T.tensor4("features")
c = config
seq = BrickSequence(
input_dim=(3, 32, 32),
bricks=[
conv3(c['n_l1']),
conv3(c['n_l2']),
max_pool(),
conv3(c['n_l3']),
conv3(c['n_l4']),
max_pool(),
#conv3(10),
#conv3(10),
Flattener(),
linear(c['n_l5']),
Softmax()
])
seq.initialize()
self.pred = seq.apply(self.X)
self.Y = T.imatrix("targets")
self.cost = CategoricalCrossEntropy().apply(self.Y.flatten(),
self.pred)
self.cost.name = "cost"
self.accur = 1.0 - MisclassificationRate().apply(
self.Y.flatten(), self.pred)
self.accur.name = "accur"
def build_model(images, labels):
# Construct a bottom convolutional sequence
bottom_conv_sequence = convolutional_sequence((3, 3), 64, (150, 150))
bottom_conv_sequence._push_allocation_config()
# Flatten layer
flattener = Flattener()
# Construct a top MLP
conv_out_dim = numpy.prod(bottom_conv_sequence.get_dim('output'))
top_mlp = MLP([
LeakyRectifier(name='non_linear_9'),
LeakyRectifier(name='non_linear_10'),
Softmax(name='non_linear_11')
], [conv_out_dim, 2048, 612, 10],
weights_init=IsotropicGaussian(),
biases_init=Constant(1))
# Construct feedforward sequence
ss_seq = FeedforwardSequence(
[bottom_conv_sequence.apply, flattener.apply, top_mlp.apply])
ss_seq.push_initialization_config()
ss_seq.initialize()
prediction = ss_seq.apply(images)
cost = CategoricalCrossEntropy().apply(labels.flatten(), prediction)
return cost
def setup_model():
# shape: T x B x F
input_ = T.tensor3('features')
# shape: B
target = T.lvector('targets')
model = LSTMAttention(input_dim=10000,
dim=500,
mlp_hidden_dims=[2000, 500, 4],
batch_size=100,
image_shape=(100, 100),
patch_shape=(28, 28),
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
model.initialize()
h, c = model.apply(input_)
classifier = MLP([Rectifier(), Softmax()], [500, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
classifier.initialize()
probabilities = classifier.apply(h[-1])
cost = CategoricalCrossEntropy().apply(target, probabilities)
error_rate = MisclassificationRate().apply(target, probabilities)
return cost, error_rate
def __init__(self, split_idx, domain_classifier, **kwargs):
super(DomainUnsupervisedCost, self).__init__(**kwargs)
batchwise_split = BatchwiseSplit(split_idx)
gradient_reversal = GradientReversal()
cost = CategoricalCrossEntropy()
self.children = [
gradient_reversal, domain_classifier, batchwise_split, cost
]
def main(save_to, num_epochs, batch_size):
mlp = MLP([Tanh(), Tanh(), Tanh(), Softmax()], [3072, 4096, 1024, 512, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tt.tensor4('features', dtype='float32')
y = tt.vector('label', dtype='int32')
probs = mlp.apply(x.reshape((-1,3072)))
cost = CategoricalCrossEntropy().apply(y, probs)
error_rate = MisclassificationRate().apply(y, probs)
cg = ComputationGraph([cost])
ws = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * sum(([(w**2).sum() for w in ws]))
cost.name = 'final_cost'
train_dataset = Cifar10Dataset(data_dir='/home/belohlavek/data/cifar10', is_train=True)
valid_dataset = Cifar10Dataset(data_dir='/home/belohlavek/data/cifar10', is_train=False)
train_stream = train_dataset.get_stream(batch_size)
valid_stream = valid_dataset.get_stream(batch_size)
algorithm = GradientDescent(
cost=cost, parameters=cg.parameters,
step_rule=Adam(learning_rate=0.001))
extensions = [Timing(),
LogExtension('/home/belohlavek/ALI/mlp.log'),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate], valid_stream, prefix="test"),
TrainingDataMonitoring(
[cost, error_rate, aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()]
main_loop = MainLoop(algorithm,
train_stream,
model=Model(cost),
extensions=extensions)
main_loop.run()
def setup_model():
# shape: T x B x F
input_ = T.tensor3('features')
# shape: B
target = T.lvector('targets')
model = LSTMAttention(dim=256,
mlp_hidden_dims=[256, 4],
batch_size=100,
image_shape=(64, 64),
patch_shape=(16, 16),
weights_init=Glorot(),
biases_init=Constant(0))
model.initialize()
h, c, location, scale = model.apply(input_)
classifier = MLP([Rectifier(), Softmax()], [256 * 2, 200, 10],
weights_init=Glorot(),
biases_init=Constant(0))
model.h = h
model.c = c
model.location = location
model.scale = scale
classifier.initialize()
probabilities = classifier.apply(T.concatenate([h[-1], c[-1]], axis=1))
cost = CategoricalCrossEntropy().apply(target, probabilities)
error_rate = MisclassificationRate().apply(target, probabilities)
model.cost = cost
location_x_0_avg = T.mean(location[0, :, 0])
location_x_0_avg.name = 'location_x_0_avg'
location_x_10_avg = T.mean(location[10, :, 0])
location_x_10_avg.name = 'location_x_10_avg'
location_x_20_avg = T.mean(location[-1, :, 0])
location_x_20_avg.name = 'location_x_20_avg'
scale_x_0_avg = T.mean(scale[0, :, 0])
scale_x_0_avg.name = 'scale_x_0_avg'
scale_x_10_avg = T.mean(scale[10, :, 0])
scale_x_10_avg.name = 'scale_x_10_avg'
scale_x_20_avg = T.mean(scale[-1, :, 0])
scale_x_20_avg.name = 'scale_x_20_avg'
monitorings = [
error_rate, location_x_0_avg, location_x_10_avg, location_x_20_avg,
scale_x_0_avg, scale_x_10_avg, scale_x_20_avg
]
model.monitorings = monitorings
return model
def test_dataset_evaluators():
X = theano.tensor.vector('X')
Y = theano.tensor.vector('Y')
data = [
numpy.arange(1, 7, dtype=theano.config.floatX).reshape(3, 2),
numpy.arange(11, 17, dtype=theano.config.floatX).reshape(3, 2)
]
data_stream = IterableDataset(dict(X=data[0],
Y=data[1])).get_example_stream()
validator = DatasetEvaluator([
CrossEntropy(requires=[X, Y], name="monitored_cross_entropy0"),
# to test two same quantities and make sure that state will be reset
CrossEntropy(requires=[X, Y], name="monitored_cross_entropy1"),
CategoricalCrossEntropy().apply(X, Y),
])
values = validator.evaluate(data_stream)
numpy.testing.assert_allclose(values['monitored_cross_entropy1'],
values['categoricalcrossentropy_apply_cost'])
def test_softmax_vector():
x = tensor.matrix('x')
y = tensor.lvector('y')
softmax_out = Softmax().apply(x)
cost = CategoricalCrossEntropy().apply(y, softmax_out)
cost_stable = Softmax().categorical_cross_entropy(y, x)
softmax_cost_func = function([x, y], cost)
softmax_cost_stable_func = function([x, y], cost_stable)
batch_size = 100
x_size = 10
rng = numpy.random.RandomState(1)
x_val = rng.randn(batch_size, x_size).astype(theano.config.floatX)
y_val = rng.randint(low=0, high=x_size, size=(batch_size))
softmax_cost = softmax_cost_func(x_val, y_val)
softmax_cost_stable = softmax_cost_stable_func(x_val, y_val)
assert_allclose(softmax_cost, softmax_cost_stable)
def test_softmax_matrix():
x = tensor.matrix('x')
y = tensor.matrix('y')
softmax_out = Softmax().apply(x)
cost = CategoricalCrossEntropy().apply(y, softmax_out)
cost_stable = Softmax().categorical_cross_entropy(y, x)
softmax_cost_func = function([x, y], cost)
softmax_cost_stable_func = function([x, y], cost_stable)
batch_size = 2
x_size = 2
rng = numpy.random.RandomState(1)
x_val = rng.randn(batch_size, x_size).astype(theano.config.floatX)
y_val_us = rng.uniform(size=(batch_size,
x_size)).astype(theano.config.floatX)
y_val = y_val_us / numpy.expand_dims(y_val_us.sum(axis=1), axis=1)
softmax_cost = softmax_cost_func(x_val, y_val)
softmax_cost_stable = softmax_cost_stable_func(x_val, y_val)
assert_allclose(softmax_cost, softmax_cost_stable, rtol=1e-5)
def create_model(self, symbols_num = 500):
# Hyperparameters
# The dimension of the hidden state of the GRUs in each direction.
hidden_states = self.args.encoder_hidden_dims
# Dimension of the word-embedding space
embedding_dims = self.args.source_embeddings_dim
###################
# Declaration of the Theano variables that come from the data stream
###################
# The context document.
context_bt = tt.lmatrix('context')
# Context document mask used to distinguish real symbols from the sequence and padding symbols that are at the end
context_mask_bt = tt.matrix('context_mask')
# The question
question_bt = tt.lmatrix('question')
question_mask_bt = tt.matrix('question_mask')
# The correct answer
y = tt.lmatrix('answer')
y = y[:,0] # originally answers are in a 2d matrix, here we convert it to a vector
# The candidates among which the answer is selected
candidates_bi = tt.lmatrix("candidates")
candidates_bi_mask = tt.matrix("candidates_mask")
###################
# Network's components
###################
# Lookup table with randomly initialized word embeddings
lookup = LookupTable(symbols_num, embedding_dims, weights_init=Uniform(width=0.2))
# bidirectional encoder that translates context
context_encoder = self.create_bidi_encoder("context_encoder", embedding_dims, hidden_states)
# bidirectional encoder for question
question_encoder = self.create_bidi_encoder("question_encoder", embedding_dims, hidden_states)
# Initialize the components (where not done upon creation)
lookup.initialize()
###################
# Wiring the components together
#
# Where present, the 3 letters at the end of the variable name identify its dimensions:
# b ... position of the example within the batch
# t ... position of the word within the document/question
# f ... features of the embedding vector
###################
### Read the context document
# Map token indices to word embeddings
context_embedding_tbf = lookup.apply(context_bt.T)
# Read the embedded context document using the bidirectional GRU and produce the contextual embedding of each word
memory_encoded_btf = context_encoder.apply(context_embedding_tbf, context_mask_bt.T).dimshuffle(1,0,2)
memory_encoded_btf.name = "memory_encoded_btf"
### Correspondingly, read the query
x_embedded_tbf = lookup.apply(question_bt.T)
x_encoded_btf = question_encoder.apply(x_embedded_tbf, question_mask_bt.T).dimshuffle(1,0,2)
# The query encoding is a concatenation of the final states of the forward and backward GRU encoder
x_forward_encoded_bf = x_encoded_btf[:,-1,0:hidden_states]
x_backward_encoded_bf = x_encoded_btf[:,0,hidden_states:hidden_states*2]
query_representation_bf = tt.concatenate([x_forward_encoded_bf,x_backward_encoded_bf],axis=1)
# Compute the attention on each word in the context as a dot product of its contextual embedding and the query
mem_attention_presoft_bt = tt.batched_dot(query_representation_bf, memory_encoded_btf.dimshuffle(0,2,1))
# TODO is this pre-masking necessary?
mem_attention_presoft_masked_bt = tt.mul(mem_attention_presoft_bt,context_mask_bt)
# Normalize the attention using softmax
mem_attention_bt = SoftmaxWithMask(name="memory_query_softmax").apply(mem_attention_presoft_masked_bt,context_mask_bt)
if self.args.weighted_att:
# compute weighted attention over original word vectors
att_weighted_responses_bf = theano.tensor.batched_dot(mem_attention_bt, context_embedding_tbf.dimshuffle(1,0,2))
# compare desired response to all candidate responses
# select relevant candidate answer words
candidates_embeddings_bfi = lookup.apply(candidates_bi).dimshuffle(0,2,1)
# convert it to output symbol probabilities
y_hat_presoft = tt.batched_dot(att_weighted_responses_bf, candidates_embeddings_bfi)
y_hat = SoftmaxWithMask(name="output_softmax").apply(y_hat_presoft,candidates_bi_mask)
else:
# Sum the attention of each candidate word across the whole context document,
# this is the key innovation of the model
# TODO: Get rid of sentence-by-sentence processing?
# TODO: Rewrite into matrix notation instead of scans?
def sum_prob_of_word(word_ix, sentence_ixs, sentence_attention_probs):
word_ixs_in_sentence = tt.eq(sentence_ixs,word_ix).nonzero()[0]
return sentence_attention_probs[word_ixs_in_sentence].sum()
def sum_probs_single_sentence(candidate_indices_i, sentence_ixs_t, sentence_attention_probs_t):
result, updates = theano.scan(
fn=sum_prob_of_word,
sequences=[candidate_indices_i],
non_sequences=[sentence_ixs_t, sentence_attention_probs_t])
return result
def sum_probs_batch(candidate_indices_bt,sentence_ixs_bt, sentence_attention_probs_bt):
result, updates = theano.scan(
fn=sum_probs_single_sentence,
sequences=[candidate_indices_bt, sentence_ixs_bt, sentence_attention_probs_bt],
non_sequences=None)
return result
# Sum the attention of each candidate word across the whole context document
y_hat = sum_probs_batch(candidates_bi, context_bt, mem_attention_bt)
y_hat.name = "y_hat"
# We use the convention that ground truth is always at index 0, so the following are the target answers
y = y.zeros_like()
# We use Cross Entropy as the training objective
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
cost.name = "cost"
predicted_response_index = tt.argmax(y_hat,axis=1)
accuracy = tt.eq(y,predicted_response_index).mean()
accuracy.name = "accuracy"
return cost, accuracy, mem_attention_bt, y_hat, context_bt, candidates_bi, candidates_bi_mask, y, context_mask_bt, question_bt, question_mask_bt
sampler = q_sampler,
classifier=classifier_mlp)
draw.initialize()
#------------------------------------------------------------------------
x = tensor.matrix(u'features')
y = tensor.lmatrix(u'targets')
#y = theano.tensor.extra_ops.to_one_hot(tensor.lmatrix(u'targets'),2)
#probs, h_enc, c_enc, i_dec, h_dec, c_dec, center_y, center_x, delta = draw.reconstruct(x)
probs, h_enc, c_enc, center_y, center_x, delta = draw.reconstruct(x)
trim_probs = probs[-1,:,:] #Only take information from the last iteration
labels = y.flatten()
#cost = BinaryCrossEntropy().apply(labels, trim_probs)
cost = CategoricalCrossEntropy().apply(y, trim_probs)
error_rate = MisclassificationRate().apply(labels, trim_probs)
cost.name = "CCE"
#------------------------------------------------------------
cg = ComputationGraph([cost])
params = VariableFilter(roles=[PARAMETER])(cg.variables)
algorithm = GradientDescent(
cost=cost,
parameters=params,
step_rule=CompositeRule([
StepClipping(10.),
Adam(learning_rate),
]),
on_unused_sources='ignore',
def main(save_to, num_epochs):
mlp = MLP([Tanh(), Softmax()], [784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
probs = mlp.apply(tensor.flatten(x, outdim=2))
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost])
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * (W1 ** 2).sum() + .00005 * (W2 ** 2).sum()
cost.name = 'final_cost'
mnist_train = MNIST(("train",))
mnist_test = MNIST(("test",))
algorithm = GradientDescent(
cost=cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(
[cost, error_rate],
Flatten(
DataStream.default_stream(
mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
which_sources=('features',)),
prefix="test"),
TrainingDataMonitoring(
[cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to, save_separately=['log'], after_batch=True),
Printing()]
if BLOCKS_EXTRAS_AVAILABLE:
extensions.append(Plot(
'MNIST example',
channels=[
['test_final_cost',
'test_misclassificationrate_apply_error_rate'],
['train_total_gradient_norm']]))
main_loop = MainLoop(
algorithm,
Flatten(
DataStream.default_stream(
mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 50)),
which_sources=('features',)),
model=Model(cost),
extensions=extensions)
main_loop.run()
import cPickle
import pandas
with open('mnist_log.pkl') as f:
log = cPickle.load(f)
data_frame = pandas.DataFrame.from_dict(log, orient='index')
weights_init=IsotropicGaussian(),
biases_init=IsotropicGaussian(),
prototype=input_mlp,
)
parallel_nets.initialize()
l_h, r_h = parallel_nets.apply(l_x=l_x, r_x=r_x)
# Concatenate the inputs from the two hidden subnets into a single variable
# for input into the next layer.
merge = tensor.concatenate([l_h, r_h], axis=1)
y_hat = output_mlp.apply(merge)
# Define a cost function to optimize, and a classification error rate:
# Also apply the outputs from the net, and corresponding targets:
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
error = MisclassificationRate().apply(y.flatten(), y_hat)
error.name = 'error'
# Need to define the computation graph:
graph = ComputationGraph(cost)
# This returns a list of weight vectors for each layer
W = VariableFilter(roles=[WEIGHT])(graph.variables)
# Add some regularization to this model:
lam = 0.001
cost += lam * l2_norm(W)
cost.name = 'entropy'
# This is the model without dropout, but with l2 reg.
# In[5]:
from blocks.bricks import Linear, Logistic, Softmax
# In[10]:
hidden_layer_size = 100
input_to_hidden = Linear(name='input_to_hidden', input_dim=117, output_dim=hidden_layer_size)
h = Logistic().apply(input_to_hidden.apply(x))
hidden_to_output = Linear(name='hidden_to_output', input_dim=hidden_layer_size, output_dim=2)
y_hat = Softmax().apply(hidden_to_output.apply(h))
y = tensor.lmatrix('targets')
from blocks.bricks.cost import CategoricalCrossEntropy, MisclassificationRate
cost = CategoricalCrossEntropy().apply(y, y_hat)
error_rate = MisclassificationRate().apply(y.argmax(axis=1), y_hat)
error_rate.name = "error_rate"
# >>> from blocks.roles import WEIGHT
from blocks.graph import ComputationGraph
# >>> from blocks.filter import VariableFilter
cg = ComputationGraph(cost)
# >>> W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
# >>> cost = cost + 0.005 * (W1 ** 2).sum() + 0.005 * (W2 ** 2).sum()
# >>> cost.name = 'cost_with_regularization'
cost.name = 'cost_simple_xentropy'
from blocks.initialization import IsotropicGaussian, Constant
input_to_hidden.weights_init = hidden_to_output.weights_init = IsotropicGaussian(0.01)
input_to_hidden.biases_init = hidden_to_output.biases_init = Constant(0)
def main(num_epochs=100):
x = tensor.matrix('features')
m = tensor.matrix('features_mask')
x_int = x.astype(dtype='int32').T
train_dataset = TextFile('inspirational.txt')
train_dataset.indexables[0] = numpy.array(sorted(
train_dataset.indexables[0], key=len
))
n_voc = len(train_dataset.dict.keys())
init_probs = numpy.array(
[sum(filter(lambda idx:idx == w,
[s[0] for s in train_dataset.indexables[
train_dataset.sources.index('features')]]
)) for w in xrange(n_voc)],
dtype=theano.config.floatX
)
init_probs = init_probs / init_probs.sum()
n_h = 100
linear_embedding = LookupTable(
length=n_voc,
dim=n_h,
weights_init=Uniform(std=0.01),
biases_init=Constant(0.)
)
linear_embedding.initialize()
lstm_biases = numpy.zeros(4 * n_h).astype(dtype=theano.config.floatX)
lstm_biases[n_h:(2 * n_h)] = 4.
rnn = SimpleRecurrent(
dim=n_h,
activation=Tanh(),
weights_init=Uniform(std=0.01),
biases_init=Constant(0.)
)
rnn.initialize()
score_layer = Linear(
input_dim=n_h,
output_dim=n_voc,
weights_init=Uniform(std=0.01),
biases_init=Constant(0.)
)
score_layer.initialize()
embedding = (linear_embedding.apply(x_int[:-1])
* tensor.shape_padright(m.T[1:]))
rnn_out = rnn.apply(inputs=embedding, mask=m.T[1:])
probs = softmax(
sequence_map(score_layer.apply, rnn_out, mask=m.T[1:])[0]
)
idx_mask = m.T[1:].nonzero()
cost = CategoricalCrossEntropy().apply(
x_int[1:][idx_mask[0], idx_mask[1]],
probs[idx_mask[0], idx_mask[1]]
)
cost.name = 'cost'
misclassification = MisclassificationRate().apply(
x_int[1:][idx_mask[0], idx_mask[1]],
probs[idx_mask[0], idx_mask[1]]
)
misclassification.name = 'misclassification'
cg = ComputationGraph([cost])
params = cg.parameters
algorithm = GradientDescent(
cost=cost,
params=params,
step_rule=Adam()
)
train_data_stream = Padding(
data_stream=DataStream(
dataset=train_dataset,
iteration_scheme=BatchwiseShuffledScheme(
examples=train_dataset.num_examples,
batch_size=10,
)
),
mask_sources=('features',)
)
model = Model(cost)
extensions = []
extensions.append(Timing())
extensions.append(FinishAfter(after_n_epochs=num_epochs))
extensions.append(TrainingDataMonitoring(
[cost, misclassification],
prefix='train',
after_epoch=True))
batch_size = 10
length = 30
trng = MRG_RandomStreams(18032015)
u = trng.uniform(size=(length, batch_size, n_voc))
gumbel_noise = -tensor.log(-tensor.log(u))
init_samples = (tensor.log(init_probs).dimshuffle(('x', 0))
+ gumbel_noise[0]).argmax(axis=-1)
init_states = rnn.initial_state('states', batch_size)
def sampling_step(g_noise, states, samples_step):
embedding_step = linear_embedding.apply(samples_step)
next_states = rnn.apply(inputs=embedding_step,
states=states,
iterate=False)
probs_step = softmax(score_layer.apply(next_states))
next_samples = (tensor.log(probs_step)
+ g_noise).argmax(axis=-1)
return next_states, next_samples
[_, samples], _ = theano.scan(
fn=sampling_step,
sequences=[gumbel_noise[1:]],
outputs_info=[init_states, init_samples]
)
sampling = theano.function([], samples.owner.inputs[0].T)
plotters = []
plotters.append(Plotter(
channels=[['train_cost', 'train_misclassification']],
titles=['Costs']))
extensions.append(PlotManager('Language modelling example',
plotters=plotters,
after_epoch=True,
after_training=True))
extensions.append(Printing())
extensions.append(PrintSamples(sampler=sampling,
voc=train_dataset.inv_dict))
main_loop = MainLoop(model=model,
data_stream=train_data_stream,
algorithm=algorithm,
extensions=extensions)
main_loop.run()
def run(epochs=1, corpus="data/", HIDDEN_DIMS=100, path="./"):
brown = BrownDataset(corpus)
INPUT_DIMS = brown.get_vocabulary_size()
OUTPUT_DIMS = brown.get_vocabulary_size()
# These are theano variables
x = tensor.lmatrix('context')
y = tensor.ivector('output')
# Construct the graph
input_to_hidden = LookupTable(name='input_to_hidden', length=INPUT_DIMS,
dim=HIDDEN_DIMS)
# Compute the weight matrix for every word in the context and then compute
# the average.
h = tensor.mean(input_to_hidden.apply(x), axis=1)
hidden_to_output = Linear(name='hidden_to_output', input_dim=HIDDEN_DIMS,
output_dim=OUTPUT_DIMS)
y_hat = Softmax().apply(hidden_to_output.apply(h))
# And initialize with random varibales and set the bias vector to 0
weights = IsotropicGaussian(0.01)
input_to_hidden.weights_init = hidden_to_output.weights_init = weights
input_to_hidden.biases_init = hidden_to_output.biases_init = Constant(0)
input_to_hidden.initialize()
hidden_to_output.initialize()
# And now the cost function
cost = CategoricalCrossEntropy().apply(y, y_hat)
cg = ComputationGraph(cost)
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + 0.01 * (W1 ** 2).sum() + 0.01 * (W2 ** 2).sum()
cost.name = 'cost_with_regularization'
mini_batch = SequentialScheme(brown.num_instances(), 512)
data_stream = DataStream.default_stream(brown, iteration_scheme=mini_batch)
# Now we tie up lose ends and construct the algorithm for the training
# and define what happens in the main loop.
algorithm = GradientDescent(cost=cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [
ProgressBar(),
FinishAfter(after_n_epochs=epochs),
Printing(),
# TrainingDataMonitoring(variables=[cost]),
SaveWeights(layers=[input_to_hidden, hidden_to_output],
prefixes=['%sfirst' % path, '%ssecond' % path]),
# Plot(
# 'Word Embeddings',
# channels=[
# [
# 'cost_with_regularization'
# ]
# ])
]
logger.info("Starting main loop...")
main = MainLoop(data_stream=data_stream,
algorithm=algorithm,
extensions=extensions)
main.run()
pickle.dump(cg, open('%scg.pickle' % path, 'wb'))
def _create_main_loop(self):
# hyper parameters
hp = self.params
batch_size = hp['batch_size']
biases_init = Constant(0)
batch_normalize = hp['batch_normalize']
### Build fprop
tensor5 = T.TensorType(config.floatX, (False,)*5)
X = tensor5("images")
#X = T.tensor4("images")
y = T.lvector('targets')
gnet_params = OrderedDict()
#X_shuffled = X[:, :, :, :, [2, 1, 0]]
#X_shuffled = gpu_contiguous(X.dimshuffle(0, 1, 4, 2, 3)) * 255
X = X[:, :, :, :, [2, 1, 0]]
X_shuffled = X.dimshuffle((0, 1, 4, 2, 3)) * 255
X_r = X_shuffled.reshape((X_shuffled.shape[0],
X_shuffled.shape[1]*X_shuffled.shape[2],
X_shuffled.shape[3], X_shuffled.shape[4]))
X_r = X_r - (np.array([104, 117, 123])[None, :, None, None]).astype('float32')
expressions, input_data, param = stream_layer_exp(inputs = ('data', X_r),
mode='rgb')
res = expressions['outloss']
y_hat = res.flatten(ndim=2)
import pdb; pdb.set_trace()
### Build Cost
cost = CategoricalCrossEntropy().apply(y, y_hat)
cost = T.cast(cost, theano.config.floatX)
cost.name = 'cross_entropy'
y_pred = T.argmax(y_hat, axis=1)
misclass = T.cast(T.mean(T.neq(y_pred, y)), theano.config.floatX)
misclass.name = 'misclass'
monitored_channels = []
monitored_quantities = [cost, misclass, y_hat, y_pred]
model = Model(cost)
training_cg = ComputationGraph(monitored_quantities)
inference_cg = ComputationGraph(monitored_quantities)
### Get evaluation function
#training_eval = training_cg.get_theano_function(additional_updates=bn_updates)
training_eval = training_cg.get_theano_function()
#inference_eval = inference_cg.get_theano_function()
# Dataset
test = JpegHDF5Dataset('test',
#name='jpeg_data_flows.hdf5',
load_in_memory=True)
#mean = np.load(os.path.join(os.environ['UCF101'], 'mean.npy'))
import pdb; pdb.set_trace()
### Eval
labels = np.zeros(test.num_video_examples)
y_hat = np.zeros((test.num_video_examples, 101))
labels_flip = np.zeros(test.num_video_examples)
y_hat_flip = np.zeros((test.num_video_examples, 101))
### Important to shuffle list for batch normalization statistic
#rng = np.random.RandomState()
#examples_list = range(test.num_video_examples)
#import pdb; pdb.set_trace()
#rng.shuffle(examples_list)
nb_frames=1
for i in xrange(24):
scheme = HDF5SeqScheme(test.video_indexes,
examples=test.num_video_examples,
batch_size=batch_size,
f_subsample=i,
nb_subsample=25,
frames_per_video=nb_frames)
#for crop in ['upleft', 'upright', 'downleft', 'downright', 'center']:
for crop in ['center']:
stream = JpegHDF5Transformer(
input_size=(240, 320), crop_size=(224, 224),
#input_size=(256, 342), crop_size=(224, 224),
crop_type=crop,
translate_labels = True,
flip='noflip', nb_frames = nb_frames,
data_stream=ForceFloatX(DataStream(
dataset=test, iteration_scheme=scheme)))
stream_flip = JpegHDF5Transformer(
input_size=(240, 320), crop_size=(224, 224),
#input_size=(256, 342), crop_size=(224, 224),
crop_type=crop,
translate_labels = True,
flip='flip', nb_frames = nb_frames,
data_stream=ForceFloatX(DataStream(
dataset=test, iteration_scheme=scheme)))
## Do the evaluation
epoch = stream.get_epoch_iterator()
for j, batch in enumerate(epoch):
output = training_eval(batch[0], batch[1])
# import cv2
# cv2.imshow('img', batch[0][0, 0, :, :, :])
# cv2.waitKey(160)
# cv2.destroyAllWindows()
#import pdb; pdb.set_trace()
labels_flip[batch_size*j:batch_size*(j+1)] = batch[1]
y_hat_flip[batch_size*j:batch_size*(j+1), :] += output[2]
preds = y_hat_flip.argmax(axis=1)
misclass = np.sum(labels_flip != preds) / float(len(preds))
print i, crop, "flip Misclass:", misclass
epoch = stream_flip.get_epoch_iterator()
for j, batch in enumerate(epoch):
output = training_eval(batch[0], batch[1])
labels[batch_size*j:batch_size*(j+1)] = batch[1]
y_hat[batch_size*j:batch_size*(j+1), :] += output[2]
preds = y_hat.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print i, crop, "noflip Misclass:", misclass
y_merge = y_hat + y_hat_flip
preds = y_merge.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print i, crop, "avg Misclass:", misclass
### Compute misclass
y_hat += y_hat_flip
preds = y_hat.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print "Misclass:", misclass
def shroom_mlp(shrooms_train, shrooms_test, num_epochs, hidden_dims,
activation_function):
# These are theano variables
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
# Construct the graph
input_to_hidden = Linear(name='input_to_hidden', input_dim=117,
output_dim=hidden_dims)
h = activation_function.apply(input_to_hidden.apply(x))
hidden_to_output = Linear(name='hidden_to_output', input_dim=hidden_dims,
output_dim=2)
y_hat = Softmax().apply(hidden_to_output.apply(h))
# And initialize with random varibales and set the bias vector to 0
weights = IsotropicGaussian(0.01)
input_to_hidden.weights_init = hidden_to_output.weights_init = weights
input_to_hidden.biases_init = hidden_to_output.biases_init = Constant(0)
input_to_hidden.initialize()
hidden_to_output.initialize()
# And now the cost function
cost = CategoricalCrossEntropy().apply(y, y_hat)
cg = ComputationGraph(cost)
# Not needed for now:
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + 0.01 * (W1 ** 2).sum() + 0.01 * (W2 ** 2).sum()
cost.name = 'cost_with_regularization'
error_rate = MisclassificationRate().apply(y.argmax(axis=1), y_hat)
# The data streams give us access to our corpus and allow us to perform a
# mini-batch training.
data_stream = Flatten(DataStream.default_stream(
shrooms_train,
iteration_scheme=SequentialScheme(shrooms_train.num_examples,
batch_size=128)))
test_data_stream = Flatten(DataStream.default_stream(
shrooms_test,
iteration_scheme=SequentialScheme(shrooms_test.num_examples,
batch_size=1000)))
extensions = [
ProgressBar(),
PlotWeights(after_epoch=True,
folder="results_logistic_40_interpolation",
computation_graph=cg,
folder_per_layer=True,
dpi=150),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(variables=[cost, error_rate],
data_stream=test_data_stream, prefix="test"),
Printing()
]
# Now we tie up lose ends and construct the algorithm for the training
# and define what happens in the main loop.
algorithm = GradientDescent(cost=cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
main = MainLoop(data_stream=data_stream,
algorithm=algorithm,
extensions=extensions)
main.run()
return 0
def train(algorithm, learning_rate, clipping, momentum,
layer_size, epochs, test_cost, experiment_path,
initialization, init_width, weight_noise, z_prob,
z_prob_states, z_prob_cells, drop_prob_igates, ogates_zoneout,
batch_size, stoch_depth, share_mask, gaussian_drop, rnn_type,
num_layers, norm_cost_coeff, penalty, testing, seq_len,
decrease_lr_after_epoch, lr_decay,
**kwargs):
print '.. PTB experiment'
print '.. arguments:', ' '.join(sys.argv)
t0 = time.time()
###########################################
#
# LOAD DATA
#
###########################################
def onehot(x, numclasses=None):
""" Convert integer encoding for class-labels (starting with 0 !)
to one-hot encoding.
The output is an array whose shape is the shape of the input array
plus an extra dimension, containing the 'one-hot'-encoded labels.
"""
if x.shape == ():
x = x[None]
if numclasses is None:
numclasses = x.max() + 1
result = numpy.zeros(list(x.shape) + [numclasses], dtype="int")
z = numpy.zeros(x.shape, dtype="int")
for c in range(numclasses):
z *= 0
z[numpy.where(x == c)] = 1
result[..., c] += z
return result.astype(theano.config.floatX)
alphabetsize = 10000
data = np.load('penntree_char_and_word.npz')
trainset = data['train_words']
validset = data['valid_words']
testset = data['test_words']
if testing:
trainset = trainset[:3000]
validset = validset[:3000]
if share_mask:
if not z_prob:
raise ValueError('z_prob must be provided when using share_mask')
if z_prob_cells or z_prob_states:
raise ValueError('z_prob_states and z_prob_cells must not be provided when using share_mask (use z_prob instead)')
z_prob_cells = z_prob
# we don't want to actually use these masks, so this is to debug
z_prob_states = None
else:
if z_prob:
raise ValueError('z_prob is only used with share_mask')
z_prob_cells = z_prob_cells or '1'
z_prob_states = z_prob_states or '1'
# rng = np.random.RandomState(seed)
###########################################
#
# MAKE STREAMS
#
###########################################
def prep_dataset(dataset):
dataset = dataset[:(len(dataset) - (len(dataset) % (seq_len * batch_size)))]
dataset = dataset.reshape(batch_size, -1, seq_len).transpose((1, 0, 2))
stream = DataStream(IndexableDataset(indexables=OrderedDict([
('data', dataset)])),
iteration_scheme=SequentialExampleScheme(dataset.shape[0]))
stream = Transpose(stream, [(1, 0)])
stream = SampleDropsNPWord(
stream, z_prob_states, z_prob_cells, drop_prob_igates,
layer_size, num_layers, False, stoch_depth, share_mask,
gaussian_drop, alphabetsize)
stream.sources = ('data',) * 3 + stream.sources + ('zoneouts_states', 'zoneouts_cells', 'zoneouts_igates')
return (stream,)
train_stream, = prep_dataset(trainset)
valid_stream, = prep_dataset(validset)
test_stream, = prep_dataset(testset)
####################
data = train_stream.get_epoch_iterator(as_dict=True).next()
####################
###########################################
#
# BUILD MODEL
#
###########################################
print '.. building model'
x = T.tensor3('data')
y = x
zoneouts_states = T.tensor3('zoneouts_states')
zoneouts_cells = T.tensor3('zoneouts_cells')
zoneouts_igates = T.tensor3('zoneouts_igates')
x.tag.test_value = data['data']
zoneouts_states.tag.test_value = data['zoneouts_states']
zoneouts_cells.tag.test_value = data['zoneouts_cells']
zoneouts_igates.tag.test_value = data['zoneouts_igates']
if init_width and not initialization == 'uniform':
raise ValueError('Width is only for uniform init, whassup?')
if initialization == 'glorot':
weights_init = NormalizedInitialization()
elif initialization == 'uniform':
weights_init = Uniform(width=init_width)
elif initialization == 'ortho':
weights_init = OrthogonalInitialization()
else:
raise ValueError('No such initialization')
if rnn_type.lower() == 'lstm':
in_to_hids = [Linear(layer_size if l > 0 else alphabetsize, layer_size*4, name='in_to_hid%d'%l,
weights_init=weights_init, biases_init=Constant(0.0)) for l in range(num_layers)]
recurrent_layers = [DropLSTM(dim=layer_size, weights_init=weights_init, activation=Tanh(), model_type=6, name='rnn%d'%l, ogates_zoneout=ogates_zoneout) for l in range(num_layers)]
elif rnn_type.lower() == 'gru':
in_to_hids = [Linear(layer_size if l > 0 else alphabetsize, layer_size*3, name='in_to_hid%d'%l,
weights_init=weights_init, biases_init=Constant(0.0)) for l in range(num_layers)]
recurrent_layers = [DropGRU(dim=layer_size, weights_init=weights_init, activation=Tanh(), name='rnn%d'%l) for l in range(num_layers)]
elif rnn_type.lower() == 'srnn': # FIXME!!! make ReLU
in_to_hids = [Linear(layer_size if l > 0 else alphabetsize, layer_size, name='in_to_hid%d'%l,
weights_init=weights_init, biases_init=Constant(0.0)) for l in range(num_layers)]
recurrent_layers = [DropSimpleRecurrent(dim=layer_size, weights_init=weights_init, activation=Rectifier(), name='rnn%d'%l) for l in range(num_layers)]
else:
raise NotImplementedError
hid_to_out = Linear(layer_size, alphabetsize, name='hid_to_out',
weights_init=weights_init, biases_init=Constant(0.0))
for layer in in_to_hids:
layer.initialize()
for layer in recurrent_layers:
layer.initialize()
hid_to_out.initialize()
layer_input = x #in_to_hid.apply(x)
init_updates = OrderedDict()
for l, (in_to_hid, layer) in enumerate(zip(in_to_hids, recurrent_layers)):
rnn_embedding = in_to_hid.apply(layer_input)
if rnn_type.lower() == 'lstm':
states_init = theano.shared(np.zeros((batch_size, layer_size), dtype=floatX))
cells_init = theano.shared(np.zeros((batch_size, layer_size), dtype=floatX))
states_init.name, cells_init.name = "states_init", "cells_init"
states, cells = layer.apply(rnn_embedding,
zoneouts_states[:, :, l * layer_size : (l + 1) * layer_size],
zoneouts_cells[:, :, l * layer_size : (l + 1) * layer_size],
zoneouts_igates[:, :, l * layer_size : (l + 1) * layer_size],
states_init,
cells_init)
init_updates.update([(states_init, states[-1]), (cells_init, cells[-1])])
elif rnn_type.lower() in ['gru', 'srnn']:
# untested!
states_init = theano.shared(np.zeros((batch_size, layer_size), dtype=floatX))
states_init.name = "states_init"
states = layer.apply(rnn_embedding, zoneouts_states, zoneouts_igates, states_init)
init_updates.update([(states_init, states[-1])])
else:
raise NotImplementedError
layer_input = states
y_hat_pre_softmax = hid_to_out.apply(T.join(0, [states_init], states[:-1]))
shape_ = y_hat_pre_softmax.shape
y_hat = Softmax().apply(
y_hat_pre_softmax.reshape((-1, alphabetsize)))
####################
###########################################
#
# SET UP COSTS AND MONITORS
#
###########################################
cost = CategoricalCrossEntropy().apply(y.reshape((-1, alphabetsize)), y_hat).copy('cost')
bpc = (cost/np.log(2.0)).copy(name='bpr')
perp = T.exp(cost).copy(name='perp')
cost_train = cost.copy(name='train_cost')
cg_train = ComputationGraph([cost_train])
###########################################
#
# NORM STABILIZER
#
###########################################
norm_cost = 0.
def _magnitude(x, axis=-1):
return T.sqrt(T.maximum(T.sqr(x).sum(axis=axis), numpy.finfo(x.dtype).tiny))
if penalty == 'cells':
assert VariableFilter(roles=[MEMORY_CELL])(cg_train.variables)
for cell in VariableFilter(roles=[MEMORY_CELL])(cg_train.variables):
norms = _magnitude(cell)
norm_cost += T.mean(T.sum((norms[1:] - norms[:-1])**2, axis=0) / (seq_len - 1))
elif penalty == 'hids':
for l in range(num_layers):
assert 'rnn%d_apply_states'%l in [o.name for o in VariableFilter(roles=[OUTPUT])(cg_train.variables)]
for output in VariableFilter(roles=[OUTPUT])(cg_train.variables):
for l in range(num_layers):
if output.name == 'rnn%d_apply_states'%l:
norms = _magnitude(output)
norm_cost += T.mean(T.sum((norms[1:] - norms[:-1])**2, axis=0) / (seq_len - 1))
norm_cost.name = 'norm_cost'
#cost_valid = cost_train
cost_train += norm_cost_coeff * norm_cost
cost_train = cost_train.copy('cost_train') #should this be cost_train.outputs[0]? no.
cg_train = ComputationGraph([cost_train])
###########################################
#
# WEIGHT NOISE
#
###########################################
if weight_noise > 0:
weights = VariableFilter(roles=[WEIGHT])(cg_train.variables)
cg_train = apply_noise(cg_train, weights, weight_noise)
cost_train = cg_train.outputs[0].copy(name='cost_train')
model = Model(cost_train)
learning_rate = float(learning_rate)
clipping = StepClipping(threshold=np.cast[floatX](clipping))
if algorithm == 'adam':
adam = Adam(learning_rate=learning_rate)
learning_rate = adam.learning_rate
step_rule = CompositeRule([adam, clipping])
elif algorithm == 'rms_prop':
rms_prop = RMSProp(learning_rate=learning_rate)
learning_rate = rms_prop.learning_rate
step_rule = CompositeRule([clipping, rms_prop])
elif algorithm == 'momentum':
sgd_momentum = Momentum(learning_rate=learning_rate, momentum=momentum)
learning_rate = sgd_momentum.learning_rate
step_rule = CompositeRule([clipping, sgd_momentum])
elif algorithm == 'sgd':
sgd = Scale(learning_rate=learning_rate)
learning_rate = sgd.learning_rate
step_rule = CompositeRule([clipping, sgd])
else:
raise NotImplementedError
algorithm = GradientDescent(step_rule=step_rule,
cost=cost_train,
parameters=cg_train.parameters)
# theano_func_kwargs={"mode": theano.compile.MonitorMode(post_func=detect_nan)})
algorithm.add_updates(init_updates)
def cond_number(x):
_, _, sing_vals = T.nlinalg.svd(x, True, True)
sing_mags = abs(sing_vals)
return T.max(sing_mags) / T.min(sing_mags)
def rms(x):
return (x*x).mean().sqrt()
whysplode_cond = []
whysplode_rms = []
for i, p in enumerate(init_updates):
v = p.get_value()
if p.get_value().shape == 2:
whysplode_cond.append(cond_number(p).copy('ini%d:%s_cond(%s)'%(i, p.name, "x".join(map(str, p.get_value().shape)))))
whysplode_rms.append(rms(p).copy('ini%d:%s_rms(%s)'%(i, p.name, "x".join(map(str, p.get_value().shape)))))
for i, p in enumerate(cg_train.parameters):
v = p.get_value()
if p.get_value().shape == 2:
whysplode_cond.append(cond_number(p).copy('ini%d:%s_cond(%s)'%(i, p.name, "x".join(map(str, p.get_value().shape)))))
whysplode_rms.append(rms(p).copy('ini%d:%s_rms(%s)'%(i, p.name, "x".join(map(str, p.get_value().shape)))))
observed_vars = [cost_train, cost, bpc, perp, learning_rate,
aggregation.mean(algorithm.total_gradient_norm).copy("gradient_norm_mean")] # + whysplode_rms
parameters = model.get_parameter_dict()
for name, param in parameters.iteritems():
observed_vars.append(param.norm(2).copy(name=name + "_norm"))
observed_vars.append(
algorithm.gradients[param].norm(2).copy(name=name + "_grad_norm"))
train_monitor = TrainingDataMonitoring(
variables=observed_vars,
prefix="train", after_epoch=True
)
dev_inits = [p.clone() for p in init_updates]
cg_dev = ComputationGraph([cost, bpc, perp] + init_updates.values()).replace(zip(init_updates.keys(), dev_inits))
dev_cost, dev_bpc, dev_perp = cg_dev.outputs[:3]
dev_init_updates = OrderedDict(zip(dev_inits, cg_dev.outputs[3:]))
dev_monitor = DataStreamMonitoring(
variables=[dev_cost, dev_bpc, dev_perp],
data_stream=valid_stream, prefix="dev",
updates=dev_init_updates
)
# noone does this
if 'load_path' in kwargs:
with open(kwargs['load_path']) as f:
loaded = np.load(f)
model = Model(cost_train)
params_dicts = model.get_parameter_dict()
params_names = params_dicts.keys()
for param_name in params_names:
param = params_dicts[param_name]
# '/f_6_.W' --> 'f_6_.W'
slash_index = param_name.find('/')
param_name = param_name[slash_index + 1:]
if param.get_value().shape == loaded[param_name].shape:
print 'Found: ' + param_name
param.set_value(loaded[param_name])
else:
print 'Not found: ' + param_name
extensions = []
extensions.extend([FinishAfter(after_n_epochs=epochs),
train_monitor, dev_monitor])
if test_cost:
test_inits = [p.clone() for p in init_updates]
cg_test = ComputationGraph([cost, bpc, perp] + init_updates.values()).replace(zip(init_updates.keys(), test_inits))
test_cost, test_bpc, test_perp = cg_test.outputs[:3]
test_init_updates = OrderedDict(zip(test_inits, cg_test.outputs[3:]))
test_monitor = DataStreamMonitoring(
variables=[test_cost, test_bpc, test_perp],
data_stream=test_stream,
prefix="test",
updates=test_init_updates
)
extensions.extend([test_monitor])
if not os.path.exists(experiment_path):
os.makedirs(experiment_path)
log_path = os.path.join(experiment_path, 'log.txt')
fh = logging.FileHandler(filename=log_path)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
extensions.append(SaveParams('dev_cost', model, experiment_path,
every_n_epochs=1))
extensions.append(SaveLog(every_n_epochs=1))
extensions.append(ProgressBar())
extensions.append(Printing())
class RollsExtension(TrainingExtension):
""" rolls the cell and state activations between epochs so that first batch gets correct initial activations """
def __init__(self, shvars):
self.shvars = shvars
def before_epoch(self):
for v in self.shvars:
v.set_value(np.roll(v.get_value(), 1, 0))
extensions.append(RollsExtension(init_updates.keys() + dev_init_updates.keys() + (test_init_updates.keys() if test_cost else [])))
class LearningRateSchedule(TrainingExtension):
""" Lets you set a number to divide learning rate by each epoch + when to start doing that """
def __init__(self):
self.epoch_number = 0
def after_epoch(self):
self.epoch_number += 1
if self.epoch_number > decrease_lr_after_epoch:
learning_rate.set_value(learning_rate.get_value()/lr_decay)
if bool(lr_decay) != bool(decrease_lr_after_epoch):
raise ValueError('Need to define both lr_decay and decrease_lr_after_epoch')
if lr_decay and decrease_lr_after_epoch:
extensions.append(LearningRateSchedule())
main_loop = MainLoop(model=model, data_stream=train_stream,
algorithm=algorithm, extensions=extensions)
t1 = time.time()
print "Building time: %f" % (t1 - t0)
main_loop.run()
print "Execution time: %f" % (time.time() - t1)
def main(job_id, params):
config = ConfigParser.ConfigParser()
config.readfp(open('./params'))
max_epoch = int(config.get('hyperparams', 'max_iter', 100))
base_lr = float(config.get('hyperparams', 'base_lr', 0.01))
train_batch = int(config.get('hyperparams', 'train_batch', 256))
valid_batch = int(config.get('hyperparams', 'valid_batch', 512))
test_batch = int(config.get('hyperparams', 'valid_batch', 512))
hidden_units = int(config.get('hyperparams', 'hidden_units', 16))
W_sd = float(config.get('hyperparams', 'W_sd', 0.01))
W_mu = float(config.get('hyperparams', 'W_mu', 0.0))
b_sd = float(config.get('hyperparams', 'b_sd', 0.01))
b_mu = float(config.get('hyperparams', 'b_mu', 0.0))
dropout_ratio = float(config.get('hyperparams', 'dropout_ratio', 0.2))
weight_decay = float(config.get('hyperparams', 'weight_decay', 0.001))
max_norm = float(config.get('hyperparams', 'max_norm', 100.0))
solver = config.get('hyperparams', 'solver_type', 'rmsprop')
data_file = config.get('hyperparams', 'data_file')
fine_tune = config.getboolean('hyperparams', 'fine_tune')
# Spearmint optimization parameters:
if params:
base_lr = float(params['base_lr'][0])
dropout_ratio = float(params['dropout_ratio'][0])
hidden_units = params['hidden_units'][0]
weight_decay = params['weight_decay'][0]
if 'adagrad' in solver:
solver_type = CompositeRule([AdaGrad(learning_rate=base_lr), VariableClipping(threshold=max_norm)])
else:
solver_type = CompositeRule([RMSProp(learning_rate=base_lr), VariableClipping(threshold=max_norm)])
rn_file = '/projects/francisco/repositories/NI-ML/models/deepnets/blocks/ff/models/rnet/2015-06-25-18:13'
ln_file = '/projects/francisco/repositories/NI-ML/models/deepnets/blocks/ff/models/lnet/2015-06-29-11:45'
right_dim = 10519
left_dim = 11427
train = H5PYDataset(data_file, which_set='train')
valid = H5PYDataset(data_file, which_set='valid')
test = H5PYDataset(data_file, which_set='test')
l_x = tensor.matrix('l_features')
r_x = tensor.matrix('r_features')
y = tensor.lmatrix('targets')
lnet = load(ln_file).model.get_top_bricks()[0]
rnet = load(rn_file).model.get_top_bricks()[0]
# Pre-trained layers:
# Inputs -> hidden_1 -> hidden 2
for side, net in zip(['l', 'r'], [lnet, rnet]):
for child in net.children:
child.name = side + '_' + child.name
ll1 = lnet.children[0]
lr1 = lnet.children[1]
ll2 = lnet.children[2]
lr2 = lnet.children[3]
rl1 = rnet.children[0]
rr1 = rnet.children[1]
rl2 = rnet.children[2]
rr2 = rnet.children[3]
l_h = lr2.apply(ll2.apply(lr1.apply(ll1.apply(l_x))))
r_h = rr2.apply(rl2.apply(rr1.apply(rl1.apply(r_x))))
input_dim = ll2.output_dim + rl2.output_dim
# hidden_2 -> hidden_3 -> hidden_4 -> Logistic output
output_mlp = MLP(activations=[
Rectifier(name='h3'),
Rectifier(name='h4'),
Softmax(name='output'),
],
dims=[
input_dim,
hidden_units,
hidden_units,
2,
],
weights_init=IsotropicGaussian(std=W_sd, mean=W_mu),
biases_init=IsotropicGaussian(std=W_sd, mean=W_mu))
output_mlp.initialize()
# # Concatenate the inputs from the two hidden subnets into a single variable
# # for input into the next layer.
merge = tensor.concatenate([l_h, r_h], axis=1)
#
y_hat = output_mlp.apply(merge)
# Define a cost function to optimize, and a classification error rate.
# Also apply the outputs from the net and corresponding targets:
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
error = MisclassificationRate().apply(y.flatten(), y_hat)
error.name = 'error'
# This is the model: before applying dropout
model = Model(cost)
# Need to define the computation graph for the cost func:
cost_graph = ComputationGraph([cost])
# This returns a list of weight vectors for each layer
W = VariableFilter(roles=[WEIGHT])(cost_graph.variables)
# Add some regularization to this model:
cost += weight_decay * l2_norm(W)
cost.name = 'entropy'
# computational graph with l2 reg
cost_graph = ComputationGraph([cost])
# Apply dropout to inputs:
inputs = VariableFilter([INPUT])(cost_graph.variables)
dropout_inputs = [input for input in inputs if input.name.startswith('linear_')]
dropout_graph = apply_dropout(cost_graph, [dropout_inputs[0]], 0.2)
dropout_graph = apply_dropout(dropout_graph, dropout_inputs[1:], dropout_ratio)
dropout_cost = dropout_graph.outputs[0]
dropout_cost.name = 'dropout_entropy'
# If no fine-tuning of l-r models is wanted, find the params for only
# the joint layers:
if fine_tune:
params_to_update = dropout_graph.parameters
else:
params_to_update = VariableFilter([PARAMETER], bricks=output_mlp.children)(cost_graph)
# Learning Algorithm:
algo = GradientDescent(
step_rule=solver_type,
params=params_to_update,
cost=dropout_cost)
# algo.step_rule.learning_rate.name = 'learning_rate'
# Data stream used for training model:
training_stream = Flatten(
DataStream.default_stream(
dataset=train,
iteration_scheme=ShuffledScheme(
train.num_examples,
batch_size=train_batch)))
training_monitor = TrainingDataMonitoring([dropout_cost,
aggregation.mean(error),
aggregation.mean(algo.total_gradient_norm)],
after_batch=True)
# Use the 'valid' set for validation during training:
validation_stream = Flatten(
DataStream.default_stream(
dataset=valid,
iteration_scheme=ShuffledScheme(
valid.num_examples,
batch_size=valid_batch)))
validation_monitor = DataStreamMonitoring(
variables=[cost, error],
data_stream=validation_stream,
prefix='validation',
after_epoch=True)
test_stream = Flatten(
DataStream.default_stream(
dataset=test,
iteration_scheme=ShuffledScheme(
test.num_examples,
batch_size=test_batch)))
test_monitor = DataStreamMonitoring(
variables=[error],
data_stream=test_stream,
prefix='test',
after_training=True)
plotting = Plot('AdniNet_LeftRight',
channels=[
['dropout_entropy'],
['error', 'validation_error'],
],
)
# Checkpoint class used to save model and log:
stamp = datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d-%H:%M')
checkpoint = Checkpoint('./models/{}'.format(stamp),
save_separately=['model', 'log'],
every_n_epochs=1)
# The main loop will train the network and output reports, etc
main_loop = MainLoop(
data_stream=training_stream,
model=model,
algorithm=algo,
extensions=[
validation_monitor,
training_monitor,
plotting,
FinishAfter(after_n_epochs=max_epoch),
FinishIfNoImprovementAfter(notification_name='validation_error', epochs=1),
Printing(),
ProgressBar(),
checkpoint,
test_monitor,
])
main_loop.run()
ve = float(main_loop.log.last_epoch_row['validation_error'])
te = float(main_loop.log.last_epoch_row['error'])
spearmint_loss = ve + abs(te - ve)
print 'Spearmint Loss: {}'.format(spearmint_loss)
return spearmint_loss
def main():
parser = argparse.ArgumentParser()
parser.add_argument("every_n_batches", type=int, default=[1], nargs=1)
args = parser.parse_args()
print("We were asked to sync with legion at every_n_batches = %s" % str(args.every_n_batches[0]))
# The rest is a copy paste from the blocks tutorial, except for the inclusion of the sync extension
# at the creation of the MainLoop blocks object.
x = tensor.matrix('features')
input_to_hidden = Linear(name='input_to_hidden', input_dim=784, output_dim=100)
h = Rectifier().apply(input_to_hidden.apply(x))
hidden_to_output = Linear(name='hidden_to_output', input_dim=100, output_dim=10)
y_hat = Softmax().apply(hidden_to_output.apply(h))
y = tensor.lmatrix('targets')
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
cg = ComputationGraph(cost)
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + 0.005 * (W1 ** 2).sum() + 0.005 * (W2 ** 2).sum()
cost.name = 'cost_with_regularization'
input_to_hidden.weights_init = hidden_to_output.weights_init = IsotropicGaussian(0.01)
input_to_hidden.biases_init = hidden_to_output.biases_init = Constant(0)
input_to_hidden.initialize()
hidden_to_output.initialize()
mnist = MNIST(("train",))
data_stream = Flatten(
DataStream.default_stream(
mnist,
iteration_scheme=SequentialScheme(mnist.num_examples, batch_size=256)))
algorithm = GradientDescent(
cost=cost,
params=cg.parameters,
step_rule=Scale(learning_rate=0.1)
)
mnist_test = MNIST(("test",))
data_stream_test = Flatten(DataStream.default_stream(
mnist_test,
iteration_scheme=SequentialScheme(mnist_test.num_examples,
batch_size=1024)))
monitor = DataStreamMonitoring(variables=[cost],
data_stream=data_stream_test,
prefix="test")
# Except for this line
b1, b2 = VariableFilter(roles=[BIAS])(cg.variables)
main_loop = MainLoop(data_stream=data_stream,
algorithm=algorithm,
extensions=[monitor,
FinishAfter(after_n_epochs=500),
Printing(),
# And the inclusion of the legion sync module, SharedParamsRateLimited:
SharedParamsRateLimited(
params={"W1": W1,
"W2": W2,
"b1": b1,
"b2": b2
},
alpha=.5,
beta=.5,
every_n_batches=args.every_n_batches[0],
maximum_rate=0.1)])
main_loop.run()
def build_submodel(input_shape,
output_dim,
L_dim_conv_layers,
L_filter_size,
L_pool_size,
L_activation_conv,
L_dim_full_layers,
L_activation_full,
L_exo_dropout_conv_layers,
L_exo_dropout_full_layers,
L_endo_dropout_conv_layers,
L_endo_dropout_full_layers,
L_border_mode=None,
L_filter_step=None,
L_pool_step=None):
# TO DO : target size and name of the features
x = T.tensor4('features')
y = T.imatrix('targets')
assert len(input_shape) == 3, "input_shape must be a 3d tensor"
num_channels = input_shape[0]
image_size = tuple(input_shape[1:])
print image_size
print num_channels
prediction = output_dim
# CONVOLUTION
output_conv = x
output_dim = num_channels*np.prod(image_size)
conv_layers = []
assert len(L_dim_conv_layers) == len(L_filter_size)
if L_filter_step is None:
L_filter_step = [None] * len(L_dim_conv_layers)
assert len(L_dim_conv_layers) == len(L_pool_size)
if L_pool_step is None:
L_pool_step = [None] * len(L_dim_conv_layers)
assert len(L_dim_conv_layers) == len(L_pool_step)
assert len(L_dim_conv_layers) == len(L_activation_conv)
if L_border_mode is None:
L_border_mode = ["valid"] * len(L_dim_conv_layers)
assert len(L_dim_conv_layers) == len(L_border_mode)
assert len(L_dim_conv_layers) == len(L_endo_dropout_conv_layers)
assert len(L_dim_conv_layers) == len(L_exo_dropout_conv_layers)
# regarding the batch dropout : the dropout is applied on the filter
# which is equivalent to the output dimension
# you have to look at the dropout_rate of the next layer
# that is why we need to have the first dropout value of L_exo_dropout_full_layers
# the first value has to be 0.0 in this context, and we'll
# assume that it is, but let's have an assert
assert L_exo_dropout_conv_layers[0] == 0.0, "L_exo_dropout_conv_layers[0] has to be 0.0 in this context. There are ways to make it work, of course, but we don't support this with this scripts."
# here modifitication of L_exo_dropout_conv_layers
L_exo_dropout_conv_layers = L_exo_dropout_conv_layers[1:] + [L_exo_dropout_full_layers[0]]
if len(L_dim_conv_layers):
for (num_filters, filter_size, filter_step,
pool_size, pool_step, activation_str, border_mode,
dropout, index) in zip(L_dim_conv_layers,
L_filter_size,
L_filter_step,
L_pool_size,
L_pool_step,
L_activation_conv,
L_border_mode,
L_exo_dropout_conv_layers,
xrange(len(L_dim_conv_layers))
):
# convert filter_size and pool_size in tuple
filter_size = tuple(filter_size)
if filter_step is None:
filter_step = (1, 1)
else:
filter_step = tuple(filter_step)
if pool_size is None:
pool_size = (0,0)
else:
pool_size = tuple(pool_size)
# TO DO : leaky relu
if activation_str.lower() == 'rectifier':
activation = Rectifier().apply
elif activation_str.lower() == 'tanh':
activation = Tanh().apply
elif activation_str.lower() in ['sigmoid', 'logistic']:
activation = Logistic().apply
elif activation_str.lower() in ['id', 'identity']:
activation = Identity().apply
else:
raise Exception("unknown activation function : %s", activation_str)
assert 0.0 <= dropout and dropout < 1.0
num_filters = num_filters - int(num_filters*dropout)
print "border_mode : %s" % border_mode
# filter_step
# http://blocks.readthedocs.org/en/latest/api/bricks.html#module-blocks.bricks.conv
kwargs = {}
if filter_step is None or filter_step == (1,1):
pass
else:
# there's a bit of a mix of names because `Convolutional` takes
# a "step" argument, but `ConvolutionActivation` takes "conv_step" argument
kwargs['conv_step'] = filter_step
if (pool_size[0] == 0 and pool_size[1] == 0):
layer_conv = ConvolutionalActivation(activation=activation,
filter_size=filter_size,
num_filters=num_filters,
border_mode=border_mode,
name="layer_%d" % index,
**kwargs)
else:
if pool_step is None:
pass
else:
kwargs['pooling_step'] = tuple(pool_step)
layer_conv = ConvolutionalLayer(activation=activation,
filter_size=filter_size,
num_filters=num_filters,
border_mode=border_mode,
pooling_size=pool_size,
name="layer_%d" % index,
**kwargs)
conv_layers.append(layer_conv)
convnet = ConvolutionalSequence(conv_layers, num_channels=num_channels,
image_size=image_size,
weights_init=Uniform(width=0.1),
biases_init=Constant(0.0),
name="conv_section")
convnet.push_allocation_config()
convnet.initialize()
output_dim = np.prod(convnet.get_dim('output'))
output_conv = convnet.apply(output_conv)
output_conv = Flattener().apply(output_conv)
# FULLY CONNECTED
output_mlp = output_conv
full_layers = []
assert len(L_dim_full_layers) == len(L_activation_full)
assert len(L_dim_full_layers) + 1 == len(L_endo_dropout_full_layers)
assert len(L_dim_full_layers) + 1 == len(L_exo_dropout_full_layers)
# reguarding the batch dropout : the dropout is applied on the filter
# which is equivalent to the output dimension
# you have to look at the dropout_rate of the next layer
# that is why we throw away the first value of L_exo_dropout_full_layers
L_exo_dropout_full_layers = L_exo_dropout_full_layers[1:]
pre_dim = output_dim
print "When constructing the model, the output_dim of the conv section is %d." % output_dim
if len(L_dim_full_layers):
for (dim, activation_str,
dropout, index) in zip(L_dim_full_layers,
L_activation_full,
L_exo_dropout_full_layers,
range(len(L_dim_conv_layers),
len(L_dim_conv_layers)+
len(L_dim_full_layers))
):
# TO DO : leaky relu
if activation_str.lower() == 'rectifier':
activation = Rectifier().apply
elif activation_str.lower() == 'tanh':
activation = Tanh().apply
elif activation_str.lower() in ['sigmoid', 'logistic']:
activation = Logistic().apply
elif activation_str.lower() in ['id', 'identity']:
activation = Identity().apply
else:
raise Exception("unknown activation function : %s", activation_str)
assert 0.0 <= dropout and dropout < 1.0
dim = dim - int(dim*dropout)
print "When constructing the fully-connected section, we apply dropout %f to add an MLP going from pre_dim %d to dim %d." % (dropout, pre_dim, dim)
layer_full = MLP(activations=[activation], dims=[pre_dim, dim],
weights_init=Uniform(width=0.1),
biases_init=Constant(0.0),
name="layer_%d" % index)
layer_full.initialize()
full_layers.append(layer_full)
pre_dim = dim
for layer in full_layers:
output_mlp = layer.apply(output_mlp)
output_dim = L_dim_full_layers[-1] - int(L_dim_full_layers[-1]*L_exo_dropout_full_layers[-1])
# COST FUNCTION
output_layer = Linear(output_dim, prediction,
weights_init=Uniform(width=0.1),
biases_init=Constant(0.0),
name="layer_"+str(len(L_dim_conv_layers)+
len(L_dim_full_layers))
)
output_layer.initialize()
full_layers.append(output_layer)
y_pred = output_layer.apply(output_mlp)
y_hat = Softmax().apply(y_pred)
# SOFTMAX and log likelihood
y_pred = Softmax().apply(y_pred)
# be careful. one version expects the output of a softmax; the other expects just the
# output of the network
cost = CategoricalCrossEntropy().apply(y.flatten(), y_pred)
#cost = Softmax().categorical_cross_entropy(y.flatten(), y_pred)
cost.name = "cost"
# Misclassification
error_rate_brick = MisclassificationRate()
error_rate = error_rate_brick.apply(y.flatten(), y_hat)
error_rate.name = "error_rate"
# put names
D_params, D_kind = build_params(x, T.matrix(), conv_layers, full_layers)
# test computation graph
cg = ComputationGraph(cost)
# DROPOUT
L_endo_dropout = L_endo_dropout_conv_layers + L_endo_dropout_full_layers
cg_dropout = cg
inputs = VariableFilter(roles=[INPUT])(cg.variables)
for (index, drop_rate) in enumerate(L_endo_dropout):
for input_ in inputs:
m = re.match(r"layer_(\d+)_apply.*", input_.name)
if m and index == int(m.group(1)):
if drop_rate < 0.0001:
print "Skipped applying dropout on %s because the dropout rate was under 0.0001." % input_.name
break
else:
cg_dropout = apply_dropout(cg, [input_], drop_rate)
print "Applied dropout %f on %s." % (drop_rate, input_.name)
break
cg = cg_dropout
return (cg, error_rate, cost, D_params, D_kind)
from fuel.streams import DataStream
from fuel.schemes import SequentialScheme
from fuel.transformers import Flatten
# Construct the model
mlp = MLP(activations=[Tanh(), Softmax()],
dims=[784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
# Calculate the loss function
x = T.matrix('features')
y = T.lmatrix('targets')
y_hat = mlp.apply(x)
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
error_rate = MisclassificationRate().apply(y.flatten(), y_hat)
# load training data using Fuel
mnist_train = MNIST("train")
train_stream = Flatten(
DataStream.default_stream(dataset=mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 128)), )
# load testing data
mnist_test = MNIST("test")
test_stream = Flatten(
DataStream.default_stream(dataset=mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 1024)), )
update_prob=update_prob, name="rnn")
h1, sd = rnn.apply(pre_rnn[:, :, :h_dim],
pre_rnn[:, :, h_dim:],
drops, is_for_test)
h1_to_o = Linear(name='h1_to_o',
input_dim=h_dim,
output_dim=y_dim)
pre_softmax = h1_to_o.apply(h1)
softmax = Softmax()
shape = pre_softmax.shape
softmax_out = softmax.apply(pre_softmax.reshape((-1, y_dim)))
softmax_out = softmax_out.reshape(shape)
softmax_out.name = 'softmax_out'
# comparing only last time-step
cost = CategoricalCrossEntropy().apply(y, softmax_out[-1])
cost.name = 'CrossEntropy'
error_rate = MisclassificationRate().apply(y, softmax_out[-1])
error_rate.name = 'error_rate'
# Initialization
for brick in (x_to_h1, h1_to_o, rnn):
brick.weights_init = Glorot()
brick.biases_init = Constant(0)
brick.initialize()
train_stream = get_stream('train', batch_size, h_dim, False)
data = train_stream.get_epoch_iterator(as_dict=True).next()
cg = ComputationGraph(cost)
f = theano.function(cg.inputs, cost)
print f(data['y'], data['x'], data['is_for_test'], data['drops'])
def main(save_to, num_epochs):
mlp = MLP([Tanh(), Tanh(), Softmax()], [784, 100, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
probs = mlp.apply(tensor.flatten(x, outdim=2))
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost, error_rate])
cost.name = 'final_cost'
test_cost = cost
for_dropout = VariableFilter(roles=[INPUT],
bricks=mlp.linear_transformations[1:])(cg.variables)
dropout_graph = apply_dropout(cg, for_dropout, 0.5)
dropout_graph = apply_dropout(dropout_graph, [x], 0.1)
dropout_cost, dropout_error_rate = dropout_graph.outputs
mnist_train = MNIST(("train",))
mnist_test = MNIST(("test",))
algorithm = GradientDescent(
cost=dropout_cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(
[cost, error_rate],
Flatten(
DataStream.default_stream(
mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
which_sources=('features',)),
prefix="test"),
TrainingDataMonitoring(
[dropout_cost, dropout_error_rate,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()]
if BLOCKS_EXTRAS_AVAILABLE:
extensions.append(Plot(
'MNIST example',
channels=[
['test_final_cost',
'test_misclassificationrate_apply_error_rate'],
['train_total_gradient_norm']]))
main_loop = MainLoop(
algorithm,
Flatten(
DataStream.default_stream(
mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 50)),
which_sources=('features',)),
model=Model(dropout_cost),
extensions=extensions)
main_loop.run()
def main(job_id, params, config_file='params.ec'):
config = ConfigParser.ConfigParser()
config.readfp(open('./configs/{}'.format(config_file)))
pr = pprint.PrettyPrinter(indent=4)
pr.pprint(config)
net_name = config.get('hyperparams', 'net_name', 'adni')
struct_name = net_name.split('_')[0]
max_epoch = int(config.get('hyperparams', 'max_iter', 100))
base_lr = float(config.get('hyperparams', 'base_lr', 0.01))
train_batch = int(config.get('hyperparams', 'train_batch', 256))
valid_batch = int(config.get('hyperparams', 'valid_batch', 512))
test_batch = int(config.get('hyperparams', 'valid_batch', 512))
W_sd = float(config.get('hyperparams', 'W_sd', 0.01))
W_mu = float(config.get('hyperparams', 'W_mu', 0.0))
b_sd = float(config.get('hyperparams', 'b_sd', 0.01))
b_mu = float(config.get('hyperparams', 'b_mu', 0.0))
hidden_units = int(config.get('hyperparams', 'hidden_units', 32))
input_dropout_ratio = float(config.get('hyperparams', 'input_dropout_ratio', 0.2))
dropout_ratio = float(config.get('hyperparams', 'dropout_ratio', 0.2))
weight_decay = float(config.get('hyperparams', 'weight_decay', 0.001))
max_norm = float(config.get('hyperparams', 'max_norm', 100.0))
solver = config.get('hyperparams', 'solver_type', 'rmsprop')
data_file = config.get('hyperparams', 'data_file')
side = config.get('hyperparams', 'side', 'b')
input_dim = input_dims[struct_name]
# Spearmint optimization parameters:
if params:
base_lr = float(params['base_lr'][0])
dropout_ratio = float(params['dropout_ratio'][0])
hidden_units = params['hidden_units'][0]
weight_decay = params['weight_decay'][0]
if 'adagrad' in solver:
solver_type = CompositeRule([AdaGrad(learning_rate=base_lr), VariableClipping(threshold=max_norm)])
else:
solver_type = CompositeRule([RMSProp(learning_rate=base_lr), VariableClipping(threshold=max_norm)])
data_file = config.get('hyperparams', 'data_file')
if 'b' in side:
train = H5PYDataset(data_file, which_set='train')
valid = H5PYDataset(data_file, which_set='valid')
test = H5PYDataset(data_file, which_set='test')
x_l = tensor.matrix('l_features')
x_r = tensor.matrix('r_features')
x = tensor.concatenate([x_l, x_r], axis=1)
else:
train = H5PYDataset(data_file, which_set='train', sources=['{}_features'.format(side), 'targets'])
valid = H5PYDataset(data_file, which_set='valid', sources=['{}_features'.format(side), 'targets'])
test = H5PYDataset(data_file, which_set='test', sources=['{}_features'.format(side), 'targets'])
x = tensor.matrix('{}_features'.format(side))
y = tensor.lmatrix('targets')
# Define a feed-forward net with an input, two hidden layers, and a softmax output:
model = MLP(activations=[
Rectifier(name='h1'),
Rectifier(name='h2'),
Softmax(name='output'),
],
dims=[
input_dim[side],
hidden_units,
hidden_units,
2],
weights_init=IsotropicGaussian(std=W_sd, mean=W_mu),
biases_init=IsotropicGaussian(b_sd, b_mu))
# Don't forget to initialize params:
model.initialize()
# y_hat is the output of the neural net with x as its inputs
y_hat = model.apply(x)
# Define a cost function to optimize, and a classification error rate.
# Also apply the outputs from the net and corresponding targets:
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
error = MisclassificationRate().apply(y.flatten(), y_hat)
error.name = 'error'
# This is the model: before applying dropout
model = Model(cost)
# Need to define the computation graph for the cost func:
cost_graph = ComputationGraph([cost])
# This returns a list of weight vectors for each layer
W = VariableFilter(roles=[WEIGHT])(cost_graph.variables)
# Add some regularization to this model:
cost += weight_decay * l2_norm(W)
cost.name = 'entropy'
# computational graph with l2 reg
cost_graph = ComputationGraph([cost])
# Apply dropout to inputs:
inputs = VariableFilter([INPUT])(cost_graph.variables)
dropout_inputs = [input for input in inputs if input.name.startswith('linear_')]
dropout_graph = apply_dropout(cost_graph, [dropout_inputs[0]], input_dropout_ratio)
dropout_graph = apply_dropout(dropout_graph, dropout_inputs[1:], dropout_ratio)
dropout_cost = dropout_graph.outputs[0]
dropout_cost.name = 'dropout_entropy'
# Learning Algorithm (notice: we use the dropout cost for learning):
algo = GradientDescent(
step_rule=solver_type,
params=dropout_graph.parameters,
cost=dropout_cost)
# algo.step_rule.learning_rate.name = 'learning_rate'
# Data stream used for training model:
training_stream = Flatten(
DataStream.default_stream(
dataset=train,
iteration_scheme=ShuffledScheme(
train.num_examples,
batch_size=train_batch)))
training_monitor = TrainingDataMonitoring([dropout_cost,
aggregation.mean(error),
aggregation.mean(algo.total_gradient_norm)],
after_batch=True)
# Use the 'valid' set for validation during training:
validation_stream = Flatten(
DataStream.default_stream(
dataset=valid,
iteration_scheme=ShuffledScheme(
valid.num_examples,
batch_size=valid_batch)))
validation_monitor = DataStreamMonitoring(
variables=[cost, error],
data_stream=validation_stream,
prefix='validation',
after_epoch=True)
test_stream = Flatten(
DataStream.default_stream(
dataset=test,
iteration_scheme=ShuffledScheme(
test.num_examples,
batch_size=test_batch)))
test_monitor = DataStreamMonitoring(
variables=[error],
data_stream=test_stream,
prefix='test',
after_training=True)
plotting = Plot('{}_{}'.format(net_name, side),
channels=[
['dropout_entropy'],
['error', 'validation_error'],
],
after_batch=False)
# Checkpoint class used to save model and log:
stamp = datetime.datetime.fromtimestamp(time.time()).strftime('%Y-%m-%d-%H:%M')
checkpoint = Checkpoint('./models/{}/{}/{}'.format(struct_name, side, stamp),
save_separately=['model', 'log'],
every_n_epochs=1)
# Home-brewed class for early stopping when we detect we have started to overfit:
# And by that I mean if the means of the val error and training error over the
# previous 'epochs' is greater than the 'threshold', we are overfitting.
early_stopper = FinishIfOverfitting(error_name='error',
validation_name='validation_error',
threshold=0.05,
epochs=5,
burn_in=100)
# The main loop will train the network and output reports, etc
main_loop = MainLoop(
data_stream=training_stream,
model=model,
algorithm=algo,
extensions=[
validation_monitor,
training_monitor,
plotting,
FinishAfter(after_n_epochs=max_epoch),
early_stopper,
Printing(),
ProgressBar(),
checkpoint,
test_monitor,
])
main_loop.run()
ve = float(main_loop.log.last_epoch_row['validation_error'])
te = float(main_loop.log.last_epoch_row['error'])
spearmint_loss = ve + abs(te - ve)
print 'Spearmint Loss: {}'.format(spearmint_loss)
return spearmint_loss
def _create_main_loop(self):
# hyper parameters
hp = self.params
batch_size = hp['batch_size']
biases_init = Constant(0)
batch_normalize = hp['batch_normalize']
### Build fprop
tensor5 = T.TensorType(config.floatX, (False, ) * 5)
X = tensor5("images")
#X = T.tensor4("images")
y = T.lvector('targets')
gnet_params = OrderedDict()
#X_shuffled = X[:, :, :, :, [2, 1, 0]]
#X_shuffled = gpu_contiguous(X.dimshuffle(0, 1, 4, 2, 3)) * 255
X = X[:, :, :, :, [2, 1, 0]]
X_shuffled = X.dimshuffle((0, 1, 4, 2, 3)) * 255
X_r = X_shuffled.reshape(
(X_shuffled.shape[0], X_shuffled.shape[1] * X_shuffled.shape[2],
X_shuffled.shape[3], X_shuffled.shape[4]))
X_r = X_r - (np.array([104, 117, 123])[None, :, None,
None]).astype('float32')
expressions, input_data, param = stream_layer_exp(inputs=('data', X_r),
mode='rgb')
res = expressions['outloss']
y_hat = res.flatten(ndim=2)
import pdb
pdb.set_trace()
### Build Cost
cost = CategoricalCrossEntropy().apply(y, y_hat)
cost = T.cast(cost, theano.config.floatX)
cost.name = 'cross_entropy'
y_pred = T.argmax(y_hat, axis=1)
misclass = T.cast(T.mean(T.neq(y_pred, y)), theano.config.floatX)
misclass.name = 'misclass'
monitored_channels = []
monitored_quantities = [cost, misclass, y_hat, y_pred]
model = Model(cost)
training_cg = ComputationGraph(monitored_quantities)
inference_cg = ComputationGraph(monitored_quantities)
### Get evaluation function
#training_eval = training_cg.get_theano_function(additional_updates=bn_updates)
training_eval = training_cg.get_theano_function()
#inference_eval = inference_cg.get_theano_function()
# Dataset
test = JpegHDF5Dataset(
'test',
#name='jpeg_data_flows.hdf5',
load_in_memory=True)
#mean = np.load(os.path.join(os.environ['UCF101'], 'mean.npy'))
import pdb
pdb.set_trace()
### Eval
labels = np.zeros(test.num_video_examples)
y_hat = np.zeros((test.num_video_examples, 101))
labels_flip = np.zeros(test.num_video_examples)
y_hat_flip = np.zeros((test.num_video_examples, 101))
### Important to shuffle list for batch normalization statistic
#rng = np.random.RandomState()
#examples_list = range(test.num_video_examples)
#import pdb; pdb.set_trace()
#rng.shuffle(examples_list)
nb_frames = 1
for i in xrange(24):
scheme = HDF5SeqScheme(test.video_indexes,
examples=test.num_video_examples,
batch_size=batch_size,
f_subsample=i,
nb_subsample=25,
frames_per_video=nb_frames)
#for crop in ['upleft', 'upright', 'downleft', 'downright', 'center']:
for crop in ['center']:
stream = JpegHDF5Transformer(
input_size=(240, 320),
crop_size=(224, 224),
#input_size=(256, 342), crop_size=(224, 224),
crop_type=crop,
translate_labels=True,
flip='noflip',
nb_frames=nb_frames,
data_stream=ForceFloatX(
DataStream(dataset=test, iteration_scheme=scheme)))
stream_flip = JpegHDF5Transformer(
input_size=(240, 320),
crop_size=(224, 224),
#input_size=(256, 342), crop_size=(224, 224),
crop_type=crop,
translate_labels=True,
flip='flip',
nb_frames=nb_frames,
data_stream=ForceFloatX(
DataStream(dataset=test, iteration_scheme=scheme)))
## Do the evaluation
epoch = stream.get_epoch_iterator()
for j, batch in enumerate(epoch):
output = training_eval(batch[0], batch[1])
# import cv2
# cv2.imshow('img', batch[0][0, 0, :, :, :])
# cv2.waitKey(160)
# cv2.destroyAllWindows()
#import pdb; pdb.set_trace()
labels_flip[batch_size * j:batch_size * (j + 1)] = batch[1]
y_hat_flip[batch_size * j:batch_size *
(j + 1), :] += output[2]
preds = y_hat_flip.argmax(axis=1)
misclass = np.sum(labels_flip != preds) / float(len(preds))
print i, crop, "flip Misclass:", misclass
epoch = stream_flip.get_epoch_iterator()
for j, batch in enumerate(epoch):
output = training_eval(batch[0], batch[1])
labels[batch_size * j:batch_size * (j + 1)] = batch[1]
y_hat[batch_size * j:batch_size * (j + 1), :] += output[2]
preds = y_hat.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print i, crop, "noflip Misclass:", misclass
y_merge = y_hat + y_hat_flip
preds = y_merge.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print i, crop, "avg Misclass:", misclass
### Compute misclass
y_hat += y_hat_flip
preds = y_hat.argmax(axis=1)
misclass = np.sum(labels != preds) / float(len(preds))
print "Misclass:", misclass
# MLP
mlp = MLP(activations=[Logistic(name='sigmoid_0'),
Softmax(name='softmax_1')], dims=[ 256, 256, 256, 2],
weights_init=IsotropicGaussian(0.01), biases_init=Constant(0))
[child.name for child in mlp.children]
['linear_0', 'sigmoid_0', 'linear_1', 'softmax_1']
Y = mlp.apply(conv_features)
mlp.initialize()
# Setting up the cost function
from blocks.bricks.cost import CategoricalCrossEntropy
cost = CategoricalCrossEntropy().apply(T.flatten(), Y)
from blocks.roles import WEIGHT
from blocks.graph import ComputationGraph
from blocks.filter import VariableFilter
cg = ComputationGraph(cost)
print(VariableFilter(roles=[WEIGHT])(cg.variables))
W1, W2, W3 = VariableFilter(roles=[WEIGHT])(cg.variables)
# cost with L2 regularization
cost = cost + 0.005 * (W2 ** 2).sum() + 0.005 * (W3 ** 2).sum()
cost.name = 'cost_with_regularization'
#print(cg.variables)
#print(VariableFilter(roles=[WEIGHT])(cg.variables))
# Use Blocks to train this network
o = l.apply(o)
o = Rectifier().apply(o)
l = Linear(input_dim=l.get_dim("output"),
output_dim=10,
weights_init=IsotropicGaussian(std=0.01),
biases_init=IsotropicGaussian(std=0.01))
l.initialize()
o = l.apply(o)
o = Softmax().apply(o)
Y = T.imatrix(name="targets")
cost = CategoricalCrossEntropy().apply(Y.flatten(), o)
cost.name = "cost"
miss_class = 1.0 - MisclassificationRate().apply(Y.flatten(), o)
miss_class.name = "accuracy"
cg = ComputationGraph(cost)
print cg.shared_variables
bricks = [get_brick(var) for var in cg.variables if get_brick(var)]
for i, b in enumerate(bricks):
b.name += str(i)
step_rule = AdaM()
algorithm = GradientDescent(cost=cost, step_rule=step_rule)
def main(save_to, num_epochs,
weight_decay=0.0001, noise_pressure=0, subset=None, num_batches=None,
batch_size=None, histogram=None, resume=False):
output_size = 10
prior_noise_level = -10
noise_step_rule = Scale(1e-6)
noise_rate = theano.shared(numpy.asarray(1e-5, dtype=theano.config.floatX))
convnet = create_res_net(out_noise=True, tied_noise=True, tied_sigma=True,
noise_rate=noise_rate,
prior_noise_level=prior_noise_level)
x = tensor.tensor4('features')
y = tensor.lmatrix('targets')
# Normalize input and apply the convnet
test_probs = convnet.apply(x)
test_cost = (CategoricalCrossEntropy().apply(y.flatten(), test_probs)
.copy(name='cost'))
test_error_rate = (MisclassificationRate().apply(y.flatten(), test_probs)
.copy(name='error_rate'))
test_confusion = (ConfusionMatrix().apply(y.flatten(), test_probs)
.copy(name='confusion'))
test_confusion.tag.aggregation_scheme = Sum(test_confusion)
test_cg = ComputationGraph([test_cost, test_error_rate])
# Apply dropout to all layer outputs except final softmax
# dropout_vars = VariableFilter(
# roles=[OUTPUT], bricks=[Convolutional],
# theano_name_regex="^conv_[25]_apply_output$")(test_cg.variables)
# drop_cg = apply_dropout(test_cg, dropout_vars, 0.5)
# Apply 0.2 dropout to the pre-averaging layer
# dropout_vars_2 = VariableFilter(
# roles=[OUTPUT], bricks=[Convolutional],
# theano_name_regex="^conv_8_apply_output$")(test_cg.variables)
# train_cg = apply_dropout(test_cg, dropout_vars_2, 0.2)
# Apply 0.2 dropout to the input, as in the paper
# train_cg = apply_dropout(test_cg, [x], 0.2)
# train_cg = drop_cg
# train_cg = apply_batch_normalization(test_cg)
# train_cost, train_error_rate, train_components = train_cg.outputs
with batch_normalization(convnet):
with training_noise(convnet):
train_probs = convnet.apply(x)
train_cost = (CategoricalCrossEntropy().apply(y.flatten(), train_probs)
.copy(name='cost'))
train_components = (ComponentwiseCrossEntropy().apply(y.flatten(),
train_probs).copy(name='components'))
train_error_rate = (MisclassificationRate().apply(y.flatten(),
train_probs).copy(name='error_rate'))
train_cg = ComputationGraph([train_cost,
train_error_rate, train_components])
population_updates = get_batch_normalization_updates(train_cg)
bn_alpha = 0.9
extra_updates = [(p, p * bn_alpha + m * (1 - bn_alpha))
for p, m in population_updates]
# for annealing
nit_penalty = theano.shared(numpy.asarray(noise_pressure, dtype=theano.config.floatX))
nit_penalty.name = 'nit_penalty'
# Compute noise rates for training graph
train_logsigma = VariableFilter(roles=[LOG_SIGMA])(train_cg.variables)
train_mean_log_sigma = tensor.concatenate([n.flatten() for n in train_logsigma]).mean()
train_mean_log_sigma.name = 'mean_log_sigma'
train_nits = VariableFilter(roles=[NITS])(train_cg.auxiliary_variables)
train_nit_rate = tensor.concatenate([n.flatten() for n in train_nits]).mean()
train_nit_rate.name = 'nit_rate'
train_nit_regularization = nit_penalty * train_nit_rate
train_nit_regularization.name = 'nit_regularization'
# Apply regularization to the cost
trainable_parameters = VariableFilter(roles=[WEIGHT, BIAS])(
train_cg.parameters)
mask_parameters = [p for p in trainable_parameters
if get_brick(p).name == 'mask']
noise_parameters = VariableFilter(roles=[NOISE])(train_cg.parameters)
biases = VariableFilter(roles=[BIAS])(train_cg.parameters)
weights = VariableFilter(roles=[WEIGHT])(train_cg.variables)
nonmask_weights = [p for p in weights if get_brick(p).name != 'mask']
l2_norm = sum([(W ** 2).sum() for W in nonmask_weights])
l2_norm.name = 'l2_norm'
l2_regularization = weight_decay * l2_norm
l2_regularization.name = 'l2_regularization'
# testversion
test_cost = test_cost + l2_regularization
test_cost.name = 'cost_with_regularization'
# Training version of cost
train_cost_without_regularization = train_cost
train_cost_without_regularization.name = 'cost_without_regularization'
train_cost = train_cost + l2_regularization + train_nit_regularization
train_cost.name = 'cost_with_regularization'
cifar10_train = CIFAR10(("train",))
cifar10_train_stream = RandomPadCropFlip(
NormalizeBatchLevels(DataStream.default_stream(
cifar10_train, iteration_scheme=ShuffledScheme(
cifar10_train.num_examples, batch_size)),
which_sources=('features',)),
(32, 32), pad=4, which_sources=('features',))
test_batch_size = 128
cifar10_test = CIFAR10(("test",))
cifar10_test_stream = NormalizeBatchLevels(DataStream.default_stream(
cifar10_test,
iteration_scheme=ShuffledScheme(
cifar10_test.num_examples, test_batch_size)),
which_sources=('features',))
momentum = Momentum(0.01, 0.9)
# Create a step rule that doubles the learning rate of biases, like Caffe.
# scale_bias = Restrict(Scale(2), biases)
# step_rule = CompositeRule([scale_bias, momentum])
# Create a step rule that reduces the learning rate of noise
scale_mask = Restrict(noise_step_rule, mask_parameters)
step_rule = CompositeRule([scale_mask, momentum])
# from theano.compile.nanguardmode import NanGuardMode
# Train with simple SGD
algorithm = GradientDescent(
cost=train_cost, parameters=trainable_parameters,
step_rule=step_rule)
algorithm.add_updates(extra_updates)
#,
# theano_func_kwargs={
# 'mode': NanGuardMode(
# nan_is_error=True, inf_is_error=True, big_is_error=True)})
exp_name = save_to.replace('.%d', '')
# `Timing` extension reports time for reading data, aggregating a batch
# and monitoring;
# `ProgressBar` displays a nice progress bar during training.
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs,
after_n_batches=num_batches),
EpochSchedule(momentum.learning_rate, [
(0, 0.01), # Warm up with 0.01 learning rate
(50, 0.1), # Then go back to 0.1
(100, 0.01),
(150, 0.001)
# (83, 0.01), # Follow the schedule in the paper
# (125, 0.001)
]),
EpochSchedule(noise_step_rule.learning_rate, [
(0, 1e-2),
(2, 1e-1),
(4, 1)
# (0, 1e-6),
# (2, 1e-5),
# (4, 1e-4)
]),
EpochSchedule(noise_rate, [
(0, 1e-2),
(2, 1e-1),
(4, 1)
# (0, 1e-6),
# (2, 1e-5),
# (4, 1e-4),
# (6, 3e-4),
# (8, 1e-3), # Causes nit rate to jump
# (10, 3e-3),
# (12, 1e-2),
# (15, 3e-2),
# (19, 1e-1),
# (24, 3e-1),
# (30, 1)
]),
NoiseExtension(
noise_parameters=noise_parameters),
NoisyDataStreamMonitoring(
[test_cost, test_error_rate, test_confusion],
cifar10_test_stream,
noise_parameters=noise_parameters,
prefix="test"),
TrainingDataMonitoring(
[train_cost, train_error_rate, train_nit_rate,
train_cost_without_regularization,
l2_regularization,
train_nit_regularization,
momentum.learning_rate,
train_mean_log_sigma,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
every_n_batches=17),
# after_epoch=True),
Plot('Training performance for ' + exp_name,
channels=[
['train_cost_with_regularization',
'train_cost_without_regularization',
'train_nit_regularization',
'train_l2_regularization'],
['train_error_rate'],
['train_total_gradient_norm'],
['train_mean_log_sigma'],
],
every_n_batches=17),
Plot('Test performance for ' + exp_name,
channels=[[
'train_error_rate',
'test_error_rate',
]],
after_epoch=True),
EpochCheckpoint(save_to, use_cpickle=True, after_epoch=True),
ProgressBar(),
Printing()]
if histogram:
attribution = AttributionExtension(
components=train_components,
parameters=cg.parameters,
components_size=output_size,
after_batch=True)
extensions.insert(0, attribution)
if resume:
extensions.append(Load(exp_name, True, True))
model = Model(train_cost)
main_loop = MainLoop(
algorithm,
cifar10_train_stream,
model=model,
extensions=extensions)
main_loop.run()
if histogram:
save_attributions(attribution, filename=histogram)
with open('execution-log.json', 'w') as outfile:
json.dump(main_loop.log, outfile, cls=NumpyEncoder)
# In[40]:
x = tensor.matrix("features")
from blocks.bricks import Linear, Rectifier, Softmax
input_to_hidden = Linear(name="input_to_hidden", input_dim=784, output_dim=50)
h = Rectifier().apply(input_to_hidden.apply(x))
hidden_to_output = Linear(name="hidden_to_output", input_dim=50, output_dim=10)
y_hat = Softmax().apply(hidden_to_output.apply(h))
y = tensor.lmatrix("targets")
from blocks.bricks.cost import CategoricalCrossEntropy
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
from blocks.roles import WEIGHT
from blocks.graph import ComputationGraph
from blocks.filter import VariableFilter
cg = ComputationGraph(cost)
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + 0.005 * (W1 ** 2).sum() + 0.005 * (W2 ** 2).sum()
cost.name = "cost_with_regularization"
from blocks.initialization import IsotropicGaussian, Constant
input_to_hidden.weights_init = hidden_to_output.weights_init = IsotropicGaussian(0.01)
input_to_hidden.biases_init = hidden_to_output.biases_init = Constant(0)
input_to_hidden.initialize()
def main(save_to, model, train, test, num_epochs, input_size = (150,150), learning_rate=0.01,
batch_size=50, num_batches=None, flatten_stream=False):
"""
save_to : where to save trained model
model : model given in input must be already initialised (works with convnet and mlp)
input_size : the shape of the reshaped image in input (before flattening is applied if flatten_stream is True)
"""
if flatten_stream :
x = tensor.matrix('image_features')
else :
x = tensor.tensor4('image_features')
y = tensor.lmatrix('targets')
#Data augmentation
#insert data augmentation here
#Generating stream
train_stream = DataStream.default_stream(
train,
iteration_scheme=ShuffledScheme(train.num_examples, batch_size)
)
test_stream = DataStream.default_stream(
test,
iteration_scheme=ShuffledScheme(test.num_examples, batch_size)
)
#Reshaping procedure
#Add a crop option in scikitresize so that the image is not deformed
#Resize to desired square shape
train_stream = ScikitResize(train_stream, input_size, which_sources=('image_features',))
test_stream = ScikitResize(test_stream, input_size, which_sources=('image_features',))
#Flattening the stream
if flatten_stream is True:
train_stream = Flatten(train_stream, which_sources=('image_features',))
test_stream = Flatten(test_stream, which_sources=('image_features',))
# Apply input to model
probs = model.apply(x)
#Defining cost and various indices to watch
#print(probs)
#cost = SquaredError().apply(y.flatten(),probs)
cost = CategoricalCrossEntropy().apply(y.flatten(), probs).copy(name='cost')
error_rate = MisclassificationRate().apply(y.flatten(), probs).copy(
name='error_rate')
#Building Computation Graph
cg = ComputationGraph([cost, error_rate])
# Train with simple SGD
algorithm = GradientDescent(
cost=cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=learning_rate))
#Defining extensions
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs,
after_n_batches=num_batches),
TrainingDataMonitoring([cost, error_rate,aggregation.mean(algorithm.total_gradient_norm)], prefix="train", every_n_batches=5),
DataStreamMonitoring([cost, error_rate],test_stream,prefix="test", every_n_batches=25),
Checkpoint(save_to),
ProgressBar(),
Printing(every_n_batches=5)]
# `Timing` extension reports time for reading data, aggregating a batch
# and monitoring;
# `ProgressBar` displays a nice progress bar during training.
model = Model(cost)
main_loop = MainLoop(
algorithm,
train_stream,
model=model,
extensions=extensions)
main_loop.run()
def start(self):
xx = T.matrix('features', config.floatX)
yy = T.imatrix('targets')
zm = BNUM*(xx.shape[0]//BNUM)
x = xx[:zm].reshape((BNUM, zm//BNUM, xx.shape[1])).dimshuffle(1, 0, 2)
y = yy[:zm].reshape((BNUM, zm//BNUM)).dimshuffle(1, 0)
# x = xx[:zm].reshape((zm//16, 16, xx.shape[1]))
# y = yy[:zm].reshape((zm//16, 16))
DIMS = [108*5, 200, 200, 200, LABEL]
NUMS = [1, 1, 1, 1, 1]
# DIMS = [108*5, 48]
# NUMS = [1, 1]
FUNCS = [
Rectifier,
Rectifier,
Rectifier,
# Rectifier,
# Rectifier,
# Maxout(num_pieces=5),
# Maxout(num_pieces=5),
# Maxout(num_pieces=5),
# SimpleRecurrent,
# SimpleRecurrent,
# SimpleRecurrent,
# LSTM,
# LSTM,
# LSTM,
# SequenceGenerator,
# Softmax,
None,
]
def lllistool(i, inp, func):
if func == LSTM:
NUMS[i+1] *= 4
sdim = DIMS[i]
if func == SimpleRecurrent or func == LSTM:
sdim = DIMS[i] + DIMS[i+1]
l = Linear(input_dim=DIMS[i], output_dim=DIMS[i+1] * NUMS[i+1],
weights_init=IsotropicGaussian(std=sdim**(-0.5)),
biases_init=IsotropicGaussian(std=sdim**(-0.5)),
name='Lin{}'.format(i))
l.initialize()
if func == SimpleRecurrent:
gong = func(dim=DIMS[i+1], activation=Rectifier(), weights_init=IsotropicGaussian(std=sdim**(-0.5)))
gong.initialize()
ret = gong.apply(l.apply(inp))
elif func == LSTM:
gong = func(dim=DIMS[i+1], activation=Tanh(), weights_init=IsotropicGaussian(std=sdim**(-0.5)))
gong.initialize()
print(inp)
ret, _ = gong.apply(
l.apply(inp),
T.zeros((inp.shape[1], DIMS[i+1])),
T.zeros((inp.shape[1], DIMS[i+1])),
)
elif func == SequenceGenerator:
gong = func(
readout=None,
transition=SimpleRecurrent(dim=100, activation=Rectifier(), weights_init=IsotropicGaussian(std=0.1)))
ret = None
elif func == None:
ret = l.apply(inp)
else:
gong = func()
ret = gong.apply(l.apply(inp))
return ret
oup = x
for i in range(len(DIMS)-1):
oup = lllistool(i, oup, FUNCS[i])
y_hat = oup
y_rsp = y.reshape((y.shape[0]*y.shape[1],))
y_dsf_rsp = y.dimshuffle(1, 0).reshape((y.shape[0]*y.shape[1],))
yh_rsp = y_hat.reshape((y_hat.shape[0]*y_hat.shape[1], y_hat.shape[2]))
yh_dsf_rsp = y_hat.dimshuffle(1, 0, 2).reshape((y_hat.shape[0]*y_hat.shape[1], y_hat.shape[2]))
sfmx = Softmax().apply(yh_rsp)
# cost = CategoricalCrossEntropy().apply(y, y_hat).astype(config.floatX)
# j, wlh = Yimumu(y_hat, y)
# cost = CategoricalCrossEntropy().apply(y_rsp, sfmx) + j
cost = CategoricalCrossEntropy().apply(y_rsp, sfmx)
# cost_p = cost_p.astype(config.floatX)
# cost = CTC_cost(y, y_hat)
cost = cost.astype(config.floatX)
cg = ComputationGraph(cost)
# cg_p = ComputationGraph(cost_p)
orig_cg = cg
ips = VariableFilter(roles=[INPUT])(cg.variables)
ops = VariableFilter(roles=[OUTPUT])(cg.variables)
# print(ips, ops)
# cg = apply_dropout(cg, ips[0:2:1], 0.2)
# cg = apply_dropout(cg, ips[2:-2:1], 0.5)
# cost = cg.outputs[0].astype(config.floatX)
cost.name = 'cost'
mps = theano.shared(np.array([ph2id(ph48239(id2ph(t))) for t in range(48)]))
# yh_dsf_rsp = theano.printing.Print('YapYapYap')(yh_dsf_rsp)
# z_hat = T.argmax(yh_dsf_rsp[:,:-1], axis=1)
z_hat = T.argmax(yh_dsf_rsp, axis=1)
# z_hat = theano.printing.Print('Yap')(z_hat)
# z_hat = Yimumu_Decode()(y_hat, wlh)
z_hat_hat = CTC_Decode()(y_hat)
y39,_ = scan(fn=lambda t: mps[t], outputs_info=None, sequences=[y_dsf_rsp])
y_hat39,_ = scan(fn=lambda t: mps[t], outputs_info=None, sequences=[z_hat])
y_hat_hat39 = y_hat39
# y_hat_hat39,_ = scan(fn=lambda t: mps[t], outputs_info=None, sequences=[z_hat_hat])
# trm = TrimOp()(y_hat_hat39)
# trm = trm[1:1+trm[0]]
# trm = theano.printing.Print('Trm')(trm)
lost01 = (T.sum(T.neq(y_hat39, y39)) / y39.shape[0]).astype(config.floatX)
lost01.name = '0/1 loss'
lost23 = (T.sum(T.neq(y_hat39, y39)) / y39.shape[0]).astype(config.floatX)
lost23.name = '2/3 loss'
edit01 = EditDistance()(y39, y_hat_hat39).astype(config.floatX) #+ T.sum(trm) * 1E-10
# edit01 = edit01.astype(config.floatX)
edit01.name = '0/1 edit'
edit23 = EditDistance()(y39, y_hat_hat39).astype(config.floatX)
edit23.name = '2/3 edit'
Ws = cg.parameters
# Ws = Ws + [wlh]
print(list(Ws))
norms = sum(w.norm(2) for w in Ws)
norms = norms.astype(config.floatX)
norms.name = 'norms'
path = pjoin(PATH['fuel'], 'train_train.hdf5')
data = H5PYDataset(path, which_set='train', load_in_memory=True, subset=slice(0, 100000))
# data = H5PYDataset(path, which_set='train', load_in_memory=True)
data_v = H5PYDataset(pjoin(PATH['fuel'], 'train_validate.hdf5'), which_set='validate', load_in_memory=True)
num = data.num_examples
data_stream = DataStream(data, iteration_scheme=ShuffledScheme(
num, batch_size=SLEN*BNUM))
data_stream_v = DataStream(data_v, iteration_scheme=SequentialScheme(
data_v.num_examples, batch_size=SLEN*BNUM))
algo = GradientDescent(cost=cost, params=Ws, step_rule=CompositeRule([
Momentum(0.005, 0.9)
# AdaDelta()
]))
# algo_p = GradientDescent(cost=cost_p, params=cg_p.parameters, step_rule=CompositeRule([
# Momentum(0.01, 0.9)
# # AdaDelta()
# ]))
monitor = DataStreamMonitoring( variables=[cost, lost01, edit01, norms],
data_stream=data_stream)
monitor_v = DataStreamMonitoring( variables=[lost23, edit23],
data_stream=data_stream_v)
plt = Plot('AlpYap', channels=[['0/1 loss', '2/3 loss'], ['0/1 edit', '2/3 edit']], after_epoch=True)
# main_loop_p = MainLoop(data_stream = data_stream,
# algorithm=algo_p,
# extensions=[monitor, monitor_v, FinishAfter(after_n_epochs=10), Printing(), plt])
# main_loop_p.run()
main_loop = MainLoop(data_stream = data_stream,
algorithm=algo,
extensions=[monitor, monitor_v, FinishAfter(after_n_epochs=2000), Printing(), plt])
main_loop.run()
pfile = open('zzz.pkl', 'wb')
pickle.dump(orig_cg, pfile)
# pickle.dump(wlh, pfile)
pfile.close()
################
test_feat = np.load(pjoin(PATH['numpy'], 'train_test_features.npy')).astype(config.floatX)
func = theano.function([xx], y_hat.astype(config.floatX))
test_hat = []
for i in range(19):
tmp = func(test_feat[i*10000:(i+1)*10000])
tmp = tmp.transpose((1, 0, 2)).reshape((tmp.shape[0]*tmp.shape[1], tmp.shape[2]))
test_hat.append(tmp)
test_hat = np.concatenate(test_hat, axis=0)
test_hat = np.concatenate((test_hat, np.zeros((2, LABEL))), axis=0)
alpha = T.tensor3(config.floatX)
beta = alpha.argmax(axis=2)
# beta = alpha[:,:,:-1].argmax(axis=2)
# beta = Yimumu_Decode()(alpha, wlh)
# beta = CTC_Decode()(alpha)
func2 = theano.function([alpha], beta)
lens = []
tags = []
with shelve.open(SHELVE['test']) as f:
names = f['names']
for n in names:
lens.append(len(f[n]))
for i in range(lens[-1]):
tags.append(n+'_'+str(i+1))
seq = []
seq2 = []
nowcnt = 0
for i in lens:
nxt = nowcnt + i
cur_hat = test_hat[nowcnt:nxt].reshape((i, 1, LABEL)).astype(config.floatX)
nowcnt = nxt
fc2 = func2(cur_hat).flatten()
fc3 = []
fc4 = []
for j in fc2:
fc3.append(ph48239(id2ph(j)))
fc4.append(ph2c(ph48239(id2ph(j))))
seq.append(fc3)
seq2.append(''.join(trim(fc4)))
seq_flat = np.concatenate(seq)
with open('hw1_outz.txt', 'w') as f:
f.write('id,prediction\n')
for t, i in zip(tags, seq_flat):
f.write(t+','+i+'\n')
with open('hw2_outz.txt', 'w') as f:
f.write('id,phone_sequence\n')
for n, i in zip(names, seq2):
f.write(n+','+i+'\n')
def train_net(net, train_stream, test_stream, L1 = None, L2=None, early_stopping=False,
finish=None, dropout=False, jobid=None, update=None,
duration= None,
**ignored):
x = tensor.tensor4('image_features')
y = tensor.lmatrix('targets')
y_hat = net.apply(x)
#Cost
cost_before = CategoricalCrossEntropy().apply(y.flatten(), y_hat)
cost_before.name = "cost_without_regularization"
#Error
#Taken from brodesf
error = MisclassificationRate().apply(y.flatten(), y_hat)
error.name = "Misclassification rate"
#Regularization
cg = ComputationGraph(cost_before)
WS = VariableFilter(roles=[WEIGHT])(cg.variables)
if dropout:
print("Dropout")
cg = apply_dropout(cg, WS, 0.5)
if L1:
print("L1 with lambda ",L1)
L1_reg = L1 * sum([abs(W).sum() for W in WS])
L1_reg.name = "L1 regularization"
cost_before += L1_reg
if L2:
print("L2 with lambda ",L2)
L2_reg = L2 * sum([(W ** 2).sum() for W in WS])
L2_reg.name = "L2 regularization"
cost_before += L2_reg
cost = cost_before
cost.name = 'cost_with_regularization'
#Initialization
print("Initilization")
net.initialize()
#Algorithm
step_rule = Scale(learning_rate=0.1)
if update is not None:
if update == "rmsprop":
print("Using RMSProp")
step_rule = RMSProp()
remove_not_finite = RemoveNotFinite(0.9)
step_rule = CompositeRule([step_rule, remove_not_finite])
algorithm = GradientDescent(cost=cost, parameters=cg.parameters, step_rule=step_rule)
print("Extensions")
extensions = []
#Monitoring
monitor = DataStreamMonitoring(variables=[cost, error], data_stream=test_stream, prefix="test")
extensions.append(monitor)
def filename(suffix=""):
prefix = jobid if jobid else str(os.getpid())
ctime = str(time.time())
return "checkpoints/" + prefix + "_" + ctime + "_" + suffix + ".zip"
#Serialization
#serialization = Checkpoint(filename())
#extensions.append(serialization)
notification = "test_"+error.name
track = TrackTheBest(notification)
best_notification = track.notification_name
checkpointbest = SaveBest(best_notification, filename("best"))
extensions.extend([track, checkpointbest])
if early_stopping:
print("Early stopping")
stopper = FinishIfNoImprovementAfterPlus(best_notification)
extensions.append(stopper)
#Other extensions
if finish != None:
print("Force finish ", finish)
extensions.append(FinishAfter(after_n_epochs=finish))
if duration != None:
print("Stop after " , duration, " seconds")
extensions.append(FinishAfterTime(duration))
extensions.extend([
Timing(),
Printing()
])
#Main loop
main_loop = MainLoop(data_stream=train_stream, algorithm=algorithm, extensions=extensions)
print("Main loop start")
main_loop.run()
Convolutional(filter_size=(1, 1), num_filters=1024, name='Convx3'),
Rectifier(),
MaxPooling((2, 2), name='MaxPol2'),
Convolutional(filter_size=(1, 1), num_filters=2, name='Convx4'),
Rectifier(),
])
conv_sequence1 = ConvolutionalSequence(conv_layers1,
num_channels=512,
image_size=(10, 10),
weights_init=Orthogonal(),
use_bias=False,
name='ConvSeq3')
conv_sequence1.initialize()
out_soft1 = Flattener(name='Flatt1').apply(conv_sequence1.apply(out5))
predict1 = NDimensionalSoftmax(name='Soft1').apply(out_soft1)
cost1 = CategoricalCrossEntropy(name='Cross1').apply(
y.flatten(), predict1).copy(name='cost1')
#SECOND SOFTMAX
conv_layers2 = list([
MaxPooling((2, 2), name='MaxPol2'),
Convolutional(filter_size=(1, 1), num_filters=128, name='Convx21'),
Rectifier(),
MaxPooling((2, 2), name='MaxPol11'),
Convolutional(filter_size=(1, 1), num_filters=1024, name='Convx31'),
Rectifier(),
MaxPooling((2, 2), name='MaxPol21'),
Convolutional(filter_size=(1, 1), num_filters=2, name='Convx41'),
Rectifier(),
])
conv_sequence2 = ConvolutionalSequence(conv_layers2,
num_channels=832,
def main():
feature_maps = [20, 50]
mlp_hiddens = [50]
conv_sizes = [5, 5]
pool_sizes = [3, 3]
save_to = "DvC.pkl"
batch_size = 500
image_size = (32, 32)
output_size = 2
learningRate = 0.1
num_epochs = 10
num_batches = None
host_plot = 'http://*****:*****@ %s' %
('CNN ', datetime.datetime.now(), socket.gethostname()),
channels=[['valid_cost', 'valid_error_rate'],
['train_total_gradient_norm']],
after_epoch=True,
server_url=host_plot))
model = Model(cost)
main_loop = MainLoop(algorithm,
stream_data_train,
model=model,
extensions=extensions)
main_loop.run()
Xs = tensor.imatrix("context")
y = tensor.ivector('center')
w1 = LookupTable(name="w1", length=VOCAB_DIM, dim=EMBEDDING_DIM)
w2 = Linear(name='w2', input_dim=EMBEDDING_DIM, output_dim=VOCAB_DIM)
hidden = tensor.mean(w1.apply(Xs), axis=1)
y_hat = Softmax().apply(w2.apply(hidden))
w1.weights_init = w2.weights_init = IsotropicGaussian(0.01)
w1.biases_init = w2.biases_init = Constant(0)
w1.initialize()
w2.initialize()
cost = CategoricalCrossEntropy().apply(y, y_hat)
cg = ComputationGraph(cost)
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + 0.005 * (W1 ** 2).sum() + 0.005 * (W2 ** 2).sum()
cost.name = "loss"
#
# the actual training of the model
#
main = MainLoop(data_stream = DataStream.default_stream(
dataset,
iteration_scheme=SequentialScheme(dataset.num_instances, batch_size=512)),
algorithm = GradientDescent(
def main(save_to,
num_epochs,
feature_maps=None,
mlp_hiddens=None,
conv_sizes=None,
pool_sizes=None,
batch_size=500):
if feature_maps is None:
feature_maps = [20, 50]
if mlp_hiddens is None:
mlp_hiddens = [500]
if conv_sizes is None:
conv_sizes = [5, 5]
if pool_sizes is None:
pool_sizes = [2, 2]
image_size = (28, 28)
output_size = 10
# Use ReLUs everywhere and softmax for the final prediction
conv_activations = [Rectifier() for _ in feature_maps]
mlp_activations = [Rectifier() for _ in mlp_hiddens] + [Softmax()]
convnet = LeNet(conv_activations,
1,
image_size,
filter_sizes=zip(conv_sizes, conv_sizes),
feature_maps=feature_maps,
pooling_sizes=zip(pool_sizes, pool_sizes),
top_mlp_activations=mlp_activations,
top_mlp_dims=mlp_hiddens + [output_size],
border_mode='full',
weights_init=Uniform(width=.2),
biases_init=Constant(0))
# We push initialization config to set different initialization schemes
# for convolutional layers.
convnet.push_initialization_config()
convnet.layers[0].weights_init = Uniform(width=.2)
convnet.layers[1].weights_init = Uniform(width=.09)
convnet.top_mlp.linear_transformations[0].weights_init = Uniform(width=.08)
convnet.top_mlp.linear_transformations[1].weights_init = Uniform(width=.11)
convnet.initialize()
logging.info(
"Input dim: {} {} {}".format(*convnet.children[0].get_dim('input_')))
for i, layer in enumerate(convnet.layers):
logging.info("Layer {} dim: {} {} {}".format(i,
*layer.get_dim('output')))
x = tensor.tensor4('features')
y = tensor.lmatrix('targets')
# Normalize input and apply the convnet
probs = convnet.apply(x)
cost = named_copy(CategoricalCrossEntropy().apply(y.flatten(), probs),
'cost')
error_rate = named_copy(MisclassificationRate().apply(y.flatten(), probs),
'error_rate')
cg = ComputationGraph([cost, error_rate])
mnist_train = MNIST(("train", ))
mnist_train_stream = DataStream.default_stream(
mnist_train,
iteration_scheme=ShuffledScheme(mnist_train.num_examples, batch_size))
mnist_test = MNIST(("test", ))
mnist_test_stream = DataStream.default_stream(
mnist_test,
iteration_scheme=ShuffledScheme(mnist_test.num_examples, batch_size))
# Train with simple SGD
algorithm = GradientDescent(cost=cost,
parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
# `Timing` extension reports time for reading data, aggregating a batch
# and monitoring;
# `ProgressBar` displays a nice progress bar during training.
extensions = [
Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate],
mnist_test_stream,
prefix="test"),
TrainingDataMonitoring([
cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)
],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
ProgressBar(),
Printing()
]
model = Model(cost)
main_loop = MainLoop(algorithm,
mnist_train_stream,
model=model,
extensions=extensions)
main_loop.run()
def start(self):
x = T.matrix('features', config.floatX)
y = T.imatrix('targets')
self.x = x
DIMS = [108*5, 1000, 1000, 1000, 1000, 1943]
NUMS = [1, 1, 1, 1, 1, 1]
FUNCS = [
Rectifier,
Rectifier,
Rectifier,
Rectifier,
# Rectifier,
# Maxout(num_pieces=5),
# Maxout(num_pieces=5),
# Maxout(num_pieces=5),
# SimpleRecurrent,
# SimpleRecurrent,
# SimpleRecurrent,
Softmax,
]
def lllistool(i, inp, func):
l = Linear(input_dim=DIMS[i], output_dim=DIMS[i+1] * NUMS[i+1],
weights_init=IsotropicGaussian(std=DIMS[i]**(-0.5)),
biases_init=IsotropicGaussian(std=DIMS[i]**(-0.5)),
name='Lin{}'.format(i))
l.initialize()
func.name='Fun{}'.format(i)
if func == SimpleRecurrent:
gong = func(dim=DIMS[i+1], activation=Rectifier(), weights_init=IsotropicGaussian(std=(DIMS[i]+DIMS[i+1])**(-0.5)))
else:
gong = func()
ret = gong.apply(l.apply(inp))
return ret
oup = x
for i in range(len(DIMS)-1):
oup = lllistool(i, oup, FUNCS[i])
y_hat = oup
self.y_hat_prob = y_hat
cost = CategoricalCrossEntropy().apply(y.flatten(), y_hat).astype(config.floatX)
cg = ComputationGraph(cost)
orig_cg = cg
ips = VariableFilter(roles=[INPUT])(cg.variables)
ops = VariableFilter(roles=[OUTPUT])(cg.variables)
cg = apply_dropout(cg, ips[0:2:1], 0.2)
cg = apply_dropout(cg, ips[2:-2:1], 0.5)
cost = cg.outputs[0]
cost.name = 'cost'
# mps = theano.shared(np.array([ph2id(ph48239(id2ph(t))) for t in range(48)]))
mps = theano.shared(np.array([ph2id(state239(t)) for t in range(1943)]))
z_hat = T.argmax(y_hat, axis=1)
y39,_ = scan(fn=lambda t: mps[t], outputs_info=None, sequences=[y.flatten()])
y_hat39,_ = scan(fn=lambda t: mps[t], outputs_info=None, sequences=[z_hat])
self.y_hat39 = y_hat39
lost01 = (T.sum(T.neq(y_hat39, y39)) / y39.shape[0]).astype(config.floatX)
lost01.name = '0/1 loss'
lost23 = (T.sum(T.neq(y_hat39, y39)) / y39.shape[0]).astype(config.floatX)
#lost23 = MisclassificationRate().apply(y39, y_hat39).astype(config.floatX)
lost23.name = '2/3 loss'
Ws = VariableFilter(roles=[WEIGHT])(cg.variables)
norms = sum(w.norm(2) for w in Ws)
norms.name = 'norms'
path = pjoin(PATH['fuel'], pfx+'_train.hdf5')
data = H5PYDataset(path, which_set='train', load_in_memory=True, subset=slice(0, 100000))
# data = H5PYDataset(path, which_set='train', load_in_memory=True)
data_v = H5PYDataset(pjoin(PATH['fuel'], pfx+'_validate.hdf5'), which_set='validate', load_in_memory=True)
num = data.num_examples
data_stream = DataStream(data, iteration_scheme=ShuffledScheme(
num, batch_size=128))
data_stream_v = DataStream(data_v, iteration_scheme=SequentialScheme(
data_v.num_examples, batch_size=128))
algo = GradientDescent(cost=cost, params=cg.parameters, step_rule=CompositeRule([Momentum(0.002, 0.9)]))
monitor = DataStreamMonitoring( variables=[cost, lost01, norms],
data_stream=data_stream)
monitor_v = DataStreamMonitoring( variables=[lost23],
data_stream=data_stream_v)
plt = Plot('AlpAlpAlp', channels=[['0/1 loss', '2/3 loss']], after_epoch=True)
main_loop = MainLoop(data_stream = data_stream,
algorithm=algo,
extensions=[monitor, monitor_v, FinishAfter(after_n_epochs=2000), Printing(), plt])
main_loop.run()
def train(algorithm, learning_rate, clipping, momentum, layer_size, epochs,
test_cost, experiment_path, initialization, init_width, weight_noise,
z_prob, z_prob_states, z_prob_cells, drop_prob_igates,
ogates_zoneout, batch_size, stoch_depth, share_mask, gaussian_drop,
rnn_type, num_layers, norm_cost_coeff, penalty, testing, seq_len,
decrease_lr_after_epoch, lr_decay, **kwargs):
print '.. PTB experiment'
print '.. arguments:', ' '.join(sys.argv)
t0 = time.time()
###########################################
#
# LOAD DATA
#
###########################################
def onehot(x, numclasses=None):
""" Convert integer encoding for class-labels (starting with 0 !)
to one-hot encoding.
The output is an array whose shape is the shape of the input array
plus an extra dimension, containing the 'one-hot'-encoded labels.
"""
if x.shape == ():
x = x[None]
if numclasses is None:
numclasses = x.max() + 1
result = numpy.zeros(list(x.shape) + [numclasses], dtype="int")
z = numpy.zeros(x.shape, dtype="int")
for c in range(numclasses):
z *= 0
z[numpy.where(x == c)] = 1
result[..., c] += z
return result.astype(theano.config.floatX)
alphabetsize = 10000
data = np.load('penntree_char_and_word.npz')
trainset = data['train_words']
validset = data['valid_words']
testset = data['test_words']
if testing:
trainset = trainset[:3000]
validset = validset[:3000]
if share_mask:
if not z_prob:
raise ValueError('z_prob must be provided when using share_mask')
if z_prob_cells or z_prob_states:
raise ValueError(
'z_prob_states and z_prob_cells must not be provided when using share_mask (use z_prob instead)'
)
z_prob_cells = z_prob
# we don't want to actually use these masks, so this is to debug
z_prob_states = None
else:
if z_prob:
raise ValueError('z_prob is only used with share_mask')
z_prob_cells = z_prob_cells or '1'
z_prob_states = z_prob_states or '1'
# rng = np.random.RandomState(seed)
###########################################
#
# MAKE STREAMS
#
###########################################
def prep_dataset(dataset):
dataset = dataset[:(len(dataset) - (len(dataset) %
(seq_len * batch_size)))]
dataset = dataset.reshape(batch_size, -1, seq_len).transpose((1, 0, 2))
stream = DataStream(
IndexableDataset(indexables=OrderedDict([('data', dataset)])),
iteration_scheme=SequentialExampleScheme(dataset.shape[0]))
stream = Transpose(stream, [(1, 0)])
stream = SampleDropsNPWord(stream, z_prob_states, z_prob_cells,
drop_prob_igates, layer_size, num_layers,
False, stoch_depth, share_mask,
gaussian_drop, alphabetsize)
stream.sources = ('data', ) * 3 + stream.sources + (
'zoneouts_states', 'zoneouts_cells', 'zoneouts_igates')
return (stream, )
train_stream, = prep_dataset(trainset)
valid_stream, = prep_dataset(validset)
test_stream, = prep_dataset(testset)
####################
data = train_stream.get_epoch_iterator(as_dict=True).next()
####################
###########################################
#
# BUILD MODEL
#
###########################################
print '.. building model'
x = T.tensor3('data')
y = x
zoneouts_states = T.tensor3('zoneouts_states')
zoneouts_cells = T.tensor3('zoneouts_cells')
zoneouts_igates = T.tensor3('zoneouts_igates')
x.tag.test_value = data['data']
zoneouts_states.tag.test_value = data['zoneouts_states']
zoneouts_cells.tag.test_value = data['zoneouts_cells']
zoneouts_igates.tag.test_value = data['zoneouts_igates']
if init_width and not initialization == 'uniform':
raise ValueError('Width is only for uniform init, whassup?')
if initialization == 'glorot':
weights_init = NormalizedInitialization()
elif initialization == 'uniform':
weights_init = Uniform(width=init_width)
elif initialization == 'ortho':
weights_init = OrthogonalInitialization()
else:
raise ValueError('No such initialization')
if rnn_type.lower() == 'lstm':
in_to_hids = [
Linear(layer_size if l > 0 else alphabetsize,
layer_size * 4,
name='in_to_hid%d' % l,
weights_init=weights_init,
biases_init=Constant(0.0)) for l in range(num_layers)
]
recurrent_layers = [
DropLSTM(dim=layer_size,
weights_init=weights_init,
activation=Tanh(),
model_type=6,
name='rnn%d' % l,
ogates_zoneout=ogates_zoneout) for l in range(num_layers)
]
elif rnn_type.lower() == 'gru':
in_to_hids = [
Linear(layer_size if l > 0 else alphabetsize,
layer_size * 3,
name='in_to_hid%d' % l,
weights_init=weights_init,
biases_init=Constant(0.0)) for l in range(num_layers)
]
recurrent_layers = [
DropGRU(dim=layer_size,
weights_init=weights_init,
activation=Tanh(),
name='rnn%d' % l) for l in range(num_layers)
]
elif rnn_type.lower() == 'srnn': # FIXME!!! make ReLU
in_to_hids = [
Linear(layer_size if l > 0 else alphabetsize,
layer_size,
name='in_to_hid%d' % l,
weights_init=weights_init,
biases_init=Constant(0.0)) for l in range(num_layers)
]
recurrent_layers = [
DropSimpleRecurrent(dim=layer_size,
weights_init=weights_init,
activation=Rectifier(),
name='rnn%d' % l) for l in range(num_layers)
]
else:
raise NotImplementedError
hid_to_out = Linear(layer_size,
alphabetsize,
name='hid_to_out',
weights_init=weights_init,
biases_init=Constant(0.0))
for layer in in_to_hids:
layer.initialize()
for layer in recurrent_layers:
layer.initialize()
hid_to_out.initialize()
layer_input = x #in_to_hid.apply(x)
init_updates = OrderedDict()
for l, (in_to_hid, layer) in enumerate(zip(in_to_hids, recurrent_layers)):
rnn_embedding = in_to_hid.apply(layer_input)
if rnn_type.lower() == 'lstm':
states_init = theano.shared(
np.zeros((batch_size, layer_size), dtype=floatX))
cells_init = theano.shared(
np.zeros((batch_size, layer_size), dtype=floatX))
states_init.name, cells_init.name = "states_init", "cells_init"
states, cells = layer.apply(
rnn_embedding,
zoneouts_states[:, :, l * layer_size:(l + 1) * layer_size],
zoneouts_cells[:, :, l * layer_size:(l + 1) * layer_size],
zoneouts_igates[:, :, l * layer_size:(l + 1) * layer_size],
states_init, cells_init)
init_updates.update([(states_init, states[-1]),
(cells_init, cells[-1])])
elif rnn_type.lower() in ['gru', 'srnn']:
# untested!
states_init = theano.shared(
np.zeros((batch_size, layer_size), dtype=floatX))
states_init.name = "states_init"
states = layer.apply(rnn_embedding, zoneouts_states,
zoneouts_igates, states_init)
init_updates.update([(states_init, states[-1])])
else:
raise NotImplementedError
layer_input = states
y_hat_pre_softmax = hid_to_out.apply(T.join(0, [states_init], states[:-1]))
shape_ = y_hat_pre_softmax.shape
y_hat = Softmax().apply(y_hat_pre_softmax.reshape((-1, alphabetsize)))
####################
###########################################
#
# SET UP COSTS AND MONITORS
#
###########################################
cost = CategoricalCrossEntropy().apply(y.reshape((-1, alphabetsize)),
y_hat).copy('cost')
bpc = (cost / np.log(2.0)).copy(name='bpr')
perp = T.exp(cost).copy(name='perp')
cost_train = cost.copy(name='train_cost')
cg_train = ComputationGraph([cost_train])
###########################################
#
# NORM STABILIZER
#
###########################################
norm_cost = 0.
def _magnitude(x, axis=-1):
return T.sqrt(
T.maximum(T.sqr(x).sum(axis=axis),
numpy.finfo(x.dtype).tiny))
if penalty == 'cells':
assert VariableFilter(roles=[MEMORY_CELL])(cg_train.variables)
for cell in VariableFilter(roles=[MEMORY_CELL])(cg_train.variables):
norms = _magnitude(cell)
norm_cost += T.mean(
T.sum((norms[1:] - norms[:-1])**2, axis=0) / (seq_len - 1))
elif penalty == 'hids':
for l in range(num_layers):
assert 'rnn%d_apply_states' % l in [
o.name
for o in VariableFilter(roles=[OUTPUT])(cg_train.variables)
]
for output in VariableFilter(roles=[OUTPUT])(cg_train.variables):
for l in range(num_layers):
if output.name == 'rnn%d_apply_states' % l:
norms = _magnitude(output)
norm_cost += T.mean(
T.sum((norms[1:] - norms[:-1])**2, axis=0) /
(seq_len - 1))
norm_cost.name = 'norm_cost'
#cost_valid = cost_train
cost_train += norm_cost_coeff * norm_cost
cost_train = cost_train.copy(
'cost_train') #should this be cost_train.outputs[0]? no.
cg_train = ComputationGraph([cost_train])
###########################################
#
# WEIGHT NOISE
#
###########################################
if weight_noise > 0:
weights = VariableFilter(roles=[WEIGHT])(cg_train.variables)
cg_train = apply_noise(cg_train, weights, weight_noise)
cost_train = cg_train.outputs[0].copy(name='cost_train')
model = Model(cost_train)
learning_rate = float(learning_rate)
clipping = StepClipping(threshold=np.cast[floatX](clipping))
if algorithm == 'adam':
adam = Adam(learning_rate=learning_rate)
learning_rate = adam.learning_rate
step_rule = CompositeRule([adam, clipping])
elif algorithm == 'rms_prop':
rms_prop = RMSProp(learning_rate=learning_rate)
learning_rate = rms_prop.learning_rate
step_rule = CompositeRule([clipping, rms_prop])
elif algorithm == 'momentum':
sgd_momentum = Momentum(learning_rate=learning_rate, momentum=momentum)
learning_rate = sgd_momentum.learning_rate
step_rule = CompositeRule([clipping, sgd_momentum])
elif algorithm == 'sgd':
sgd = Scale(learning_rate=learning_rate)
learning_rate = sgd.learning_rate
step_rule = CompositeRule([clipping, sgd])
else:
raise NotImplementedError
algorithm = GradientDescent(step_rule=step_rule,
cost=cost_train,
parameters=cg_train.parameters)
# theano_func_kwargs={"mode": theano.compile.MonitorMode(post_func=detect_nan)})
algorithm.add_updates(init_updates)
def cond_number(x):
_, _, sing_vals = T.nlinalg.svd(x, True, True)
sing_mags = abs(sing_vals)
return T.max(sing_mags) / T.min(sing_mags)
def rms(x):
return (x * x).mean().sqrt()
whysplode_cond = []
whysplode_rms = []
for i, p in enumerate(init_updates):
v = p.get_value()
if p.get_value().shape == 2:
whysplode_cond.append(
cond_number(p).copy(
'ini%d:%s_cond(%s)' %
(i, p.name, "x".join(map(str,
p.get_value().shape)))))
whysplode_rms.append(
rms(p).copy('ini%d:%s_rms(%s)' %
(i, p.name, "x".join(map(str,
p.get_value().shape)))))
for i, p in enumerate(cg_train.parameters):
v = p.get_value()
if p.get_value().shape == 2:
whysplode_cond.append(
cond_number(p).copy(
'ini%d:%s_cond(%s)' %
(i, p.name, "x".join(map(str,
p.get_value().shape)))))
whysplode_rms.append(
rms(p).copy('ini%d:%s_rms(%s)' %
(i, p.name, "x".join(map(str,
p.get_value().shape)))))
observed_vars = [
cost_train, cost, bpc, perp, learning_rate,
aggregation.mean(
algorithm.total_gradient_norm).copy("gradient_norm_mean")
] # + whysplode_rms
parameters = model.get_parameter_dict()
for name, param in parameters.iteritems():
observed_vars.append(param.norm(2).copy(name=name + "_norm"))
observed_vars.append(
algorithm.gradients[param].norm(2).copy(name=name + "_grad_norm"))
train_monitor = TrainingDataMonitoring(variables=observed_vars,
prefix="train",
after_epoch=True)
dev_inits = [p.clone() for p in init_updates]
cg_dev = ComputationGraph([cost, bpc, perp] +
init_updates.values()).replace(
zip(init_updates.keys(), dev_inits))
dev_cost, dev_bpc, dev_perp = cg_dev.outputs[:3]
dev_init_updates = OrderedDict(zip(dev_inits, cg_dev.outputs[3:]))
dev_monitor = DataStreamMonitoring(variables=[dev_cost, dev_bpc, dev_perp],
data_stream=valid_stream,
prefix="dev",
updates=dev_init_updates)
# noone does this
if 'load_path' in kwargs:
with open(kwargs['load_path']) as f:
loaded = np.load(f)
model = Model(cost_train)
params_dicts = model.get_parameter_dict()
params_names = params_dicts.keys()
for param_name in params_names:
param = params_dicts[param_name]
# '/f_6_.W' --> 'f_6_.W'
slash_index = param_name.find('/')
param_name = param_name[slash_index + 1:]
if param.get_value().shape == loaded[param_name].shape:
print 'Found: ' + param_name
param.set_value(loaded[param_name])
else:
print 'Not found: ' + param_name
extensions = []
extensions.extend(
[FinishAfter(after_n_epochs=epochs), train_monitor, dev_monitor])
if test_cost:
test_inits = [p.clone() for p in init_updates]
cg_test = ComputationGraph([cost, bpc, perp] +
init_updates.values()).replace(
zip(init_updates.keys(), test_inits))
test_cost, test_bpc, test_perp = cg_test.outputs[:3]
test_init_updates = OrderedDict(zip(test_inits, cg_test.outputs[3:]))
test_monitor = DataStreamMonitoring(
variables=[test_cost, test_bpc, test_perp],
data_stream=test_stream,
prefix="test",
updates=test_init_updates)
extensions.extend([test_monitor])
if not os.path.exists(experiment_path):
os.makedirs(experiment_path)
log_path = os.path.join(experiment_path, 'log.txt')
fh = logging.FileHandler(filename=log_path)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
extensions.append(
SaveParams('dev_cost', model, experiment_path, every_n_epochs=1))
extensions.append(SaveLog(every_n_epochs=1))
extensions.append(ProgressBar())
extensions.append(Printing())
class RollsExtension(TrainingExtension):
""" rolls the cell and state activations between epochs so that first batch gets correct initial activations """
def __init__(self, shvars):
self.shvars = shvars
def before_epoch(self):
for v in self.shvars:
v.set_value(np.roll(v.get_value(), 1, 0))
extensions.append(
RollsExtension(init_updates.keys() + dev_init_updates.keys() +
(test_init_updates.keys() if test_cost else [])))
class LearningRateSchedule(TrainingExtension):
""" Lets you set a number to divide learning rate by each epoch + when to start doing that """
def __init__(self):
self.epoch_number = 0
def after_epoch(self):
self.epoch_number += 1
if self.epoch_number > decrease_lr_after_epoch:
learning_rate.set_value(learning_rate.get_value() / lr_decay)
if bool(lr_decay) != bool(decrease_lr_after_epoch):
raise ValueError(
'Need to define both lr_decay and decrease_lr_after_epoch')
if lr_decay and decrease_lr_after_epoch:
extensions.append(LearningRateSchedule())
main_loop = MainLoop(model=model,
data_stream=train_stream,
algorithm=algorithm,
extensions=extensions)
t1 = time.time()
print "Building time: %f" % (t1 - t0)
main_loop.run()
print "Execution time: %f" % (time.time() - t1)
########## hyper parameters###########################################
# We push initialization config to set different initialization schemes
convnet.push_initialization_config()
convnet.layers[0].weights_init = Uniform(width=0.2)
convnet.layers[1].weights_init = Uniform(width=0.2)
convnet.layers[2].weights_init = Uniform(width=0.2)
convnet.top_mlp.linear_transformations[0].weights_init = Uniform(width=0.2)
convnet.top_mlp.linear_transformations[1].weights_init = Uniform(width=0.2)
convnet.initialize()
#########################################################
#Generate output and error signal
predict = convnet.apply(x)
cost = CategoricalCrossEntropy().apply(y.flatten(), predict).copy(name='cost')
error = MisclassificationRate().apply(y.flatten(), predict)
#Little trick to plot the error rate in two different plots (We can't use two time the same data in the plot for a unknow reason)
error_rate = error.copy(name='error_rate')
error_rate2 = error.copy(name='error_rate2')
cg = ComputationGraph([cost, error_rate])
########### ALGORITHM of training#############
algorithm = GradientDescent(cost=cost,
parameters=cg.parameters,
step_rule=Adam(learning_rate=0.0005))
extensions = [
Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring([cost, error_rate, error_rate2],
stream_valid,
prefix="valid"),
def main(feature_maps=None, mlp_hiddens=None,
conv_sizes=None, pool_sizes=None, batch_size=None,
num_batches=None):
if feature_maps is None:
feature_maps = [32, 48, 64, 96, 96, 128]
if mlp_hiddens is None:
mlp_hiddens = [1000]
if conv_sizes is None:
conv_sizes = [9, 7, 5, 3, 2, 1]
if pool_sizes is None:
pool_sizes = [2, 2, 2, 2, 1, 1]
if batch_size is None:
batch_size = 64
conv_steps=[2, 1, 1, 1, 1, 1] #same as stride
image_size = (128, 128)
output_size = 2
learningRate = 0.001
drop_prob = 0.4
weight_noise = 0.75
num_epochs = 150
num_batches = None
host_plot='http://*****:*****@ %s' % (graph_name, datetime.datetime.now(), socket.gethostname()),
channels=[['train_error_rate', 'valid_error_rate'],
['train_total_gradient_norm']], after_epoch=True, server_url=host_plot))
PLOT_AVAILABLE = True
except ImportError:
PLOT_AVAILABLE = False
extensions.append(Checkpoint(save_to, after_epoch=True, after_training=True, save_separately=['log']))
logger.info("Building the model")
model = Model(cost)
########### Loading images #####################
main_loop = MainLoop(
algorithm,
stream_data_train,
model=model,
extensions=extensions)
main_loop.run()
def main(save_to, num_epochs,
regularization=0.0003, subset=None, num_batches=None,
histogram=None, resume=False):
batch_size = 500
output_size = 10
convnet = create_lenet_5()
layers = convnet.layers
x = tensor.tensor4('features')
y = tensor.lmatrix('targets')
# Normalize input and apply the convnet
probs = convnet.apply(x)
cost = (CategoricalCrossEntropy().apply(y.flatten(), probs)
.copy(name='cost'))
components = (ComponentwiseCrossEntropy().apply(y.flatten(), probs)
.copy(name='components'))
error_rate = (MisclassificationRate().apply(y.flatten(), probs)
.copy(name='error_rate'))
confusion = (ConfusionMatrix().apply(y.flatten(), probs)
.copy(name='confusion'))
confusion.tag.aggregation_scheme = Sum(confusion)
cg = ComputationGraph([cost, error_rate, components])
# Apply regularization to the cost
weights = VariableFilter(roles=[WEIGHT])(cg.variables)
l2_norm = sum([(W ** 2).sum() for W in weights])
l2_norm.name = 'l2_norm'
cost = cost + regularization * l2_norm
cost.name = 'cost_with_regularization'
if subset:
start = 30000 - subset // 2
mnist_train = MNIST(("train",), subset=slice(start, start+subset))
else:
mnist_train = MNIST(("train",))
mnist_train_stream = DataStream.default_stream(
mnist_train, iteration_scheme=ShuffledScheme(
mnist_train.num_examples, batch_size))
mnist_test = MNIST(("test",))
mnist_test_stream = DataStream.default_stream(
mnist_test,
iteration_scheme=ShuffledScheme(
mnist_test.num_examples, batch_size))
# Train with simple SGD
algorithm = GradientDescent(
cost=cost, parameters=cg.parameters,
step_rule=AdaDelta(decay_rate=0.99))
# `Timing` extension reports time for reading data, aggregating a batch
# and monitoring;
# `ProgressBar` displays a nice progress bar during training.
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs,
after_n_batches=num_batches),
DataStreamMonitoring(
[cost, error_rate, confusion],
mnist_test_stream,
prefix="test"),
TrainingDataMonitoring(
[cost, error_rate, l2_norm,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
ProgressBar(),
Printing()]
if histogram:
attribution = AttributionExtension(
components=components,
parameters=cg.parameters,
components_size=output_size,
after_batch=True)
extensions.insert(0, attribution)
if resume:
extensions.append(Load(save_to, True, True))
model = Model(cost)
main_loop = MainLoop(
algorithm,
mnist_train_stream,
model=model,
extensions=extensions)
main_loop.run()
if histogram:
save_attributions(attribution, filename=histogram)
with open('execution-log.json', 'w') as outfile:
json.dump(main_loop.log, outfile, cls=NumpyEncoder)
def main(save_to, num_epochs):
mlp = MLP([Tanh(), Softmax()], [784, 100, 10],
weights_init=IsotropicGaussian(0.01),
biases_init=Constant(0))
mlp.initialize()
x = tensor.matrix('features')
y = tensor.lmatrix('targets')
#attention --->
patch_shape = (16, 16);
image_shape = (784,100);
import numpy
import theano.tensor as T
n_spatial_dims = 2
cropper = SoftRectangularCropper(n_spatial_dims=n_spatial_dims,
patch_shape=patch_shape,
image_shape=image_shape,
kernel=Gaussian())
batch_size = 10
scales = 1.3**numpy.arange(-7, 6)
n_patches = len(scales)
locations = (numpy.ones((n_patches, batch_size, 2)) * image_shape/2).astype(numpy.float32)
scales = numpy.tile(scales[:, numpy.newaxis, numpy.newaxis], (1, batch_size, 2)).astype(numpy.float32)
Tpatches = T.stack(*[cropper.apply(x, T.constant(location), T.constant(scale))[0]
for location, scale in zip(locations, scales)])
patches = theano.function([x], Tpatches)(batch['features'])
import ipdb as pdb; pdb.set_trace()
probs = mlp.apply(tensor.flatten(patches, outdim=2))
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cg = ComputationGraph([cost])
W1, W2 = VariableFilter(roles=[WEIGHT])(cg.variables)
cost = cost + .00005 * (W1 ** 2).sum() + .00005 * (W2 ** 2).sum()
cost.name = 'final_cost'
mnist_train = MNIST(("train",))
mnist_test = MNIST(("test",))
algorithm = GradientDescent(
cost=cost, parameters=cg.parameters,
step_rule=Scale(learning_rate=0.1))
extensions = [Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(
[cost, error_rate],
Flatten(
DataStream.default_stream(
mnist_test,
iteration_scheme=SequentialScheme(
mnist_test.num_examples, 500)),
which_sources=('features',)),
prefix="test"),
TrainingDataMonitoring(
[cost, error_rate,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
Checkpoint(save_to),
Printing()]
if BLOCKS_EXTRAS_AVAILABLE:
extensions.append(Plot(
'MNIST example',
channels=[
['test_final_cost',
'test_misclassificationrate_apply_error_rate'],
['train_total_gradient_norm']]))
main_loop = MainLoop(
algorithm,
Flatten(
DataStream.default_stream(
mnist_train,
iteration_scheme=SequentialScheme(
mnist_train.num_examples, 50)),
which_sources=('features',)),
model=Model(cost),
extensions=extensions)
main_loop.run()
def main(save_to, num_epochs, flag, ksize):
batch_size = 128
dim = 100
n_steps = 20
i2h1 = MLP([Identity()], [784, dim], biases_init=Constant(0.), weights_init=IsotropicGaussian(.001))
h2o1 = MLP([Rectifier(), Softmax()], [dim, dim, 10], biases_init=Constant(0.), weights_init=IsotropicGaussian(.001))
rec1 = SimpleRecurrent(dim=dim, activation=Tanh(), weights_init=Orthogonal())
i2h1.initialize()
h2o1.initialize()
rec1.initialize()
x = tensor.tensor3('features')
y = tensor.lmatrix('targets')
preproc = i2h1.apply(x)
h1 = rec1.apply(preproc)
probs = tensor.flatten(h2o1.apply(h1[-1],), outdim=2)
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
error_rate = MisclassificationRate().apply(y.flatten(), probs)
cost.name = 'final_cost'
error_rate.name = 'error_rate'
cg = ComputationGraph([cost, error_rate])
mnist_train = MNIST("train", subset=slice(0, 50000))
mnist_valid = MNIST("train", subset=slice(50000, 60000))
mnist_test = MNIST("test")
trainstream = Mapping(Flatten(DataStream(mnist_train,
iteration_scheme=SequentialScheme(50000, batch_size))),
_meanize(n_steps, flag, ksize))
validstream = Mapping(Flatten(DataStream(mnist_valid,
iteration_scheme=SequentialScheme(10000,
batch_size))),
_meanize(n_steps, flag, ksize))
teststream = Mapping(Flatten(DataStream(mnist_test,
iteration_scheme=SequentialScheme(10000,
batch_size))),
_meanize(n_steps, flag, ksize))
algorithm = GradientDescent(
cost=cost, params=cg.parameters,
step_rule=CompositeRule([Adam(), StepClipping(100)]))
main_loop = MainLoop(
algorithm,
trainstream,
extensions=[Timing(),
FinishAfter(after_n_epochs=num_epochs),
DataStreamMonitoring(
[cost, error_rate],
validstream,
prefix="test"),
DataStreamMonitoringAndSaving(
[cost, error_rate],
teststream,
[i2h1, h2o1, rec1],
'best_'+save_to+'.pkl',
cost_name=error_rate.name,
after_epoch=True,
prefix='valid'
),
TrainingDataMonitoring(
[cost,
aggregation.mean(algorithm.total_gradient_norm)],
prefix="train",
after_epoch=True),
# Plot(
# save_to,
# channels=[
# ['test_final_cost',
# 'test_misclassificationrate_apply_error_rate'],
# ['train_total_gradient_norm']]),
Printing()])
main_loop.run()
def apply(self, input_labeled, target_labeled, input_unlabeled):
self.layer_counter = 0
input_dim = self.p.encoder_layers[0]
# Store the dimension tuples in the same order as layers.
layers = self.layers
self.layer_dims = {0: input_dim}
self.lr = self.shared(self.default_lr, 'learning_rate', role=None)
self.costs = costs = AttributeDict()
self.costs.denois = AttributeDict()
self.act = AttributeDict()
self.error = AttributeDict()
top = len(layers) - 1
N = input_labeled.shape[0]
self.join = lambda l, u: T.concatenate([l, u], axis=0)
self.labeled = lambda x: x[:N] if x is not None else x
self.unlabeled = lambda x: x[N:] if x is not None else x
self.split_lu = lambda x: (self.labeled(x), self.unlabeled(x))
input_concat = self.join(input_labeled, input_unlabeled)
def encoder(input_, path_name, input_noise_std=0, noise_std=[]):
h = input_
logger.info(' 0: noise %g' % input_noise_std)
if input_noise_std > 0.:
h = h + self.noise_like(h) * input_noise_std
d = AttributeDict()
d.unlabeled = self.new_activation_dict()
d.labeled = self.new_activation_dict()
d.labeled.z[0] = self.labeled(h)
d.unlabeled.z[0] = self.unlabeled(h)
prev_dim = input_dim
for i, (spec, _, act_f) in layers[1:]:
d.labeled.h[i - 1], d.unlabeled.h[i - 1] = self.split_lu(h)
noise = noise_std[i] if i < len(noise_std) else 0.
curr_dim, z, m, s, h = self.f(h,
prev_dim,
spec,
i,
act_f,
path_name=path_name,
noise_std=noise)
assert self.layer_dims.get(i) in (None, curr_dim)
self.layer_dims[i] = curr_dim
d.labeled.z[i], d.unlabeled.z[i] = self.split_lu(z)
d.unlabeled.s[i] = s
d.unlabeled.m[i] = m
prev_dim = curr_dim
d.labeled.h[i], d.unlabeled.h[i] = self.split_lu(h)
return d
# Clean, supervised
logger.info('Encoder: clean, labeled')
clean = self.act.clean = encoder(input_concat, 'clean')
# Corrupted, supervised
logger.info('Encoder: corr, labeled')
corr = self.act.corr = encoder(input_concat,
'corr',
input_noise_std=self.p.super_noise_std,
noise_std=self.p.f_local_noise_std)
est = self.act.est = self.new_activation_dict()
# Decoder path in opposite order
logger.info('Decoder: z_corr -> z_est')
for i, ((_, spec), l_type, act_f) in layers[::-1]:
z_corr = corr.unlabeled.z[i]
z_clean = clean.unlabeled.z[i]
z_clean_s = clean.unlabeled.s.get(i)
z_clean_m = clean.unlabeled.m.get(i)
fspec = layers[i + 1][1][0] if len(layers) > i + 1 else (None,
None)
if i == top:
ver = corr.unlabeled.h[i]
ver_dim = self.layer_dims[i]
top_g = True
else:
ver = est.z.get(i + 1)
ver_dim = self.layer_dims.get(i + 1)
top_g = False
z_est = self.g(z_lat=z_corr,
z_ver=ver,
in_dims=ver_dim,
out_dims=self.layer_dims[i],
l_type=l_type,
num=i,
fspec=fspec,
top_g=top_g)
if z_est is not None:
# Denoising cost
if z_clean_s:
z_est_norm = (z_est - z_clean_m) / z_clean_s
else:
z_est_norm = z_est
se = SquaredError('denois' + str(i))
costs.denois[i] = se.apply(z_est_norm.flatten(2),
z_clean.flatten(2)) \
/ np.prod(self.layer_dims[i], dtype=floatX)
costs.denois[i].name = 'denois' + str(i)
denois_print = 'denois %.2f' % self.p.denoising_cost_x[i]
else:
denois_print = ''
# Store references for later use
est.h[i] = self.apply_act(z_est, act_f)
est.z[i] = z_est
est.s[i] = None
est.m[i] = None
logger.info(' g%d: %10s, %s, dim %s -> %s' %
(i, l_type, denois_print, self.layer_dims.get(i + 1),
self.layer_dims.get(i)))
# Costs
y = target_labeled.flatten()
costs.class_clean = CategoricalCrossEntropy().apply(
y, clean.labeled.h[top])
costs.class_clean.name = 'cost_class_clean'
costs.class_corr = CategoricalCrossEntropy().apply(
y, corr.labeled.h[top])
costs.class_corr.name = 'cost_class_corr'
# This will be used for training
costs.total = costs.class_corr * 1.0
for i in range(top + 1):
if costs.denois.get(i) and self.p.denoising_cost_x[i] > 0:
costs.total += costs.denois[i] * self.p.denoising_cost_x[i]
costs.total.name = 'cost_total'
# Classification error
mr = MisclassificationRate()
self.error.clean = mr.apply(y, clean.labeled.h[top]) * np.float32(100.)
self.error.clean.name = 'error_rate_clean'
probs = Softmax().apply(n5)
statistics_list=[(M1,S1,a1), (M2,S2,a2), (M3,S3,a3), (M4,S4,a4), (M5,S5,a5)]
# initialize_variables
# for variable (M,S) in variables:
# compute M and S in the whole data.
if normalization == 'bn2':
for m,s,var in statistics_list:
var.tag.aggregation_scheme = MeanAndVariance(var, var.shape[0], axis = 0)
init_mn, init_var = DatasetEvaluator([var]).evaluate(stream_train)[var.name]
m.set_value(init_mn.astype(floatX))
s.set_value(sqrt(init_var).astype(floatX))
cost = CategoricalCrossEntropy().apply(y.flatten(), probs)
cost.name = 'cost'
error_rate = MisclassificationRate().apply(y.flatten(), probs)
error_rate.name = 'error_rate'
cg = ComputationGraph([cost])
parameters = cg.parameters
# add gradient descent to M,S
if normalization == 'bn2':
for m,s,var in statistics_list:
parameters.extend([m,s])
algorithm = GradientDescent(
cost=cost, parameters=parameters, step_rule=Adam(0.01))
def create_network(inputs=None, batch=batch_size):
if inputs is None:
inputs = T.tensor4('features')
x = T.cast(inputs,'float32')
x = x / 255. if dataset != 'binarized_mnist' else x
# GatedPixelCNN
gated = GatedPixelCNN(
name='gated_layer_0',
filter_size=7,
image_size=(img_dim,img_dim),
num_filters=h*n_channel,
num_channels=n_channel,
batch_size=batch,
weights_init=IsotropicGaussian(std=0.02, mean=0),
biases_init=Constant(0.02),
res=False
)
gated.initialize()
x_v, x_h = gated.apply(x, x)
for i in range(n_layer):
gated = GatedPixelCNN(
name='gated_layer_{}'.format(i+1),
filter_size=3,
image_size=(img_dim,img_dim),
num_channels=h*n_channel,
batch_size=batch,
weights_init=IsotropicGaussian(std=0.02, mean=0),
biases_init=Constant(0.02),
res=True
)
gated.initialize()
x_v, x_h = gated.apply(x_v, x_h)
conv_list = []
conv_list.extend([Rectifier(), ConvolutionalNoFlip((1,1), h*n_channel, mask_type='B', name='1x1_conv_1')])
#conv_list.extend([Rectifier(), ConvolutionalNoFlip((1,1), h*n_channel, mask='B', name='1x1_conv_2')])
conv_list.extend([Rectifier(), ConvolutionalNoFlip(*third_layer, mask_type='B', name='output_layer')])
sequence = ConvolutionalSequence(
conv_list,
num_channels=h*n_channel,
batch_size=batch,
image_size=(img_dim,img_dim),
border_mode='half',
weights_init=IsotropicGaussian(std=0.02, mean=0),
biases_init=Constant(0.02),
tied_biases=False
)
sequence.initialize()
x = sequence.apply(x_h)
if MODE == '256ary':
x = x.reshape((-1, 256, n_channel, img_dim, img_dim)).dimshuffle(0,2,3,4,1)
x = x.reshape((-1, 256))
x_hat = Softmax().apply(x)
inp = T.cast(inputs, 'int64').flatten()
cost = CategoricalCrossEntropy().apply(inp, x_hat) * img_dim * img_dim
cost_bits_dim = categorical_crossentropy(log_softmax(x), inp)
else:
x_hat = Logistic().apply(x)
cost = BinaryCrossEntropy().apply(inputs, x_hat) * img_dim * img_dim
#cost = T.nnet.binary_crossentropy(x_hat, inputs)
#cost = cost.sum() / inputs.shape[0]
cost_bits_dim = -(inputs * T.log2(x_hat) + (1.0 - inputs) * T.log2(1.0 - x_hat)).mean()
cost_bits_dim.name = "nnl_bits_dim"
cost.name = 'loglikelihood_nat'
return cost, cost_bits_dim