def svm_cva(dir, start=0, end=500, learning_rate=3e-4, n_epochs=10000,
dataset='./data/mnist.pkl.gz',
batch_size=500):
"""
Demonstrate stochastic gradient descent optimization of a log-linear
model
This is demonstrated on MNIST.
:type learning_rate: float
:param learning_rate: learning rate used (factor for the stochastic
gradient)
:type n_epochs: int
:param n_epochs: maximal number of epochs to run the optimizer
:type dataset: string
:param dataset: the path of the MNIST dataset file from
http://www.iro.umontreal.ca/~lisa/deep/data/mnist/mnist.pkl.gz
"""
'''
Difference
'''
print start, end, learning_rate, batch_size
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, train_set_y, train_y_matrix = datasets[0]
_, valid_set_y, valid_y_matrix = datasets[1]
_, test_set_y, test_y_matrix = datasets[2]
train_set_x, valid_set_x, test_set_x = datapy.load_feature_gpu(dir=dir, start=start,end=end)
print train_set_x.get_value().shape
print valid_set_x.get_value().shape
print test_set_x.get_value().shape
# compute number of minibatches for training, validation and testing
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
# generate symbolic variables for input (x and y represent a
# minibatch)
x = T.matrix('x') # data, presented as rasterized images
y = T.ivector('y') # labels, presented as 1D vector of [int] labels
'''
Differences
'''
y_matrix = T.imatrix('y_matrix') # labels, presented as 2D matrix of int labels
# construct the logistic regression class
# Each MNIST image has size 28*28
rng = np.random.RandomState(0)
n_in=end-start
classifier = Pegasos.Pegasos(input=x, rng=rng, n_in=n_in, n_out=10, weight_decay=1e-4, loss=1)
# the cost we minimize during training is the negative log likelihood of
# the model in symbolic format
cost = classifier.objective(10, y, y_matrix)
# compiling a Theano function that computes the mistakes that are made by
# the model on a minibatch
test_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x[index * batch_size: (index + 1) * batch_size],
y: test_set_y[index * batch_size: (index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size]
}
)
validate_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: valid_set_x[index * batch_size: (index + 1) * batch_size],
y: valid_set_y[index * batch_size: (index + 1) * batch_size],
#y_matrix: valid_y_matrix[index * batch_size: (index + 1) * batch_size]
}
)
# compute the gradient of cost with respect to theta = (W,b)
g_W = T.grad(cost=cost, wrt=classifier.W)
g_b = T.grad(cost=cost, wrt=classifier.b)
params = [classifier.W, classifier.b]
grads = [g_W, g_b]
# start-snippet-3
# specify how to update the parameters of the model as a list of
# (variable, update expression) pairs.
l_r = theano.shared(np.asarray(learning_rate, dtype=np.float32))
#get_optimizer = optimizer.get_simple_optimizer(learning_rate=learning_rate)
get_optimizer = optimizer.get_adam_optimizer_min(learning_rate=l_r, decay1 = 0.1, decay2 = 0.001)
updates = get_optimizer(params,grads)
# compiling a Theano function `train_model` that returns the cost, but in
# the same time updates the parameter of the model based on the rules
# defined in `updates`
train_model = theano.function(
inputs=[index],
outputs=[cost],
updates=updates,
givens={
x: train_set_x[index * batch_size: (index + 1) * batch_size],
y: train_set_y[index * batch_size: (index + 1) * batch_size],
y_matrix: train_y_matrix[index * batch_size: (index + 1) * batch_size]
}
)
# end-snippet-3
###############
# TRAIN MODEL #
###############
print '... training the model'
# early-stopping parameters
patience = 5000 # look as this many examples regardless
patience_increase = 2 # wait this much longer when a new best is
# found
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant
validation_frequency = min(n_train_batches, patience / 2)
# go through this many
# minibatche before checking the network
# on the validation set; in this case we
# check every epoch
best_validation_loss = np.inf
best_test_score = np.inf
test_score = 0.
start_time = time.clock()
logdir = dir + str(learning_rate)+'_c-'
done_looping = False
epoch = 0
while (epoch < n_epochs) and (not done_looping):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
minibatch_avg_cost = train_model(minibatch_index)
#print minibatch_avg_cost
# iteration number
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
# compute zero-one loss on validation set
validation_losses = [validate_model(i)
for i in xrange(n_valid_batches)]
this_validation_loss = np.mean(validation_losses)
this_test_losses = [test_model(i)
for i in xrange(n_test_batches)]
this_test_score = np.mean(this_test_losses)
if this_test_score < best_test_score:
best_test_score = this_test_score
with open(logdir+'hook.txt', 'a') as f:
print >>f, (
'epoch %i, minibatch %i/%i, validation error %f %%, test error %f %%' %
(
epoch,
minibatch_index + 1,
n_train_batches,
this_validation_loss * 100,
this_test_score *100.
)
)
print(
'epoch %i, minibatch %i/%i, validation error %f %%, test error %f %%' %
(
epoch,
minibatch_index + 1,
n_train_batches,
this_validation_loss * 100,
this_test_score *100.
)
)
# if we got the best validation score until now
if this_validation_loss < best_validation_loss:
#improve patience if loss improvement is good enough
if this_validation_loss < best_validation_loss * \
improvement_threshold:
patience = max(patience, iter * patience_increase)
best_validation_loss = this_validation_loss
# test it on the test set
test_losses = [test_model(i)
for i in xrange(n_test_batches)]
test_score = np.mean(test_losses)
with open(logdir+'hook.txt', 'a') as f:
print >>f,(
(
' epoch %i, minibatch %i/%i, test error of'
' best model %f %%'
) %
(
epoch,
minibatch_index + 1,
n_train_batches,
test_score * 100.
)
)
print(
(
' epoch %i, minibatch %i/%i, test error of'
' best model %f %%'
) %
(
epoch,
minibatch_index + 1,
n_train_batches,
test_score * 100.
)
)
if patience <= iter:
done_looping = True
break
end_time = time.clock()
with open(logdir+'hook.txt', 'a') as f:
print>>f,(
(
'Optimization complete with best validation score of %f %%,'
'with test performance %f %%'
)
% (best_validation_loss * 100., test_score * 100.)
)
print>>f, 'The code run for %d epochs, with %f epochs/sec' % (
epoch, 1. * epoch / (end_time - start_time))
print>>f, sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.1fs' % ((end_time - start_time)))
print>>f, best_test_score
print(
(
'Optimization complete with best validation score of %f %%,'
'with test performance %f %%'
)
% (best_validation_loss * 100., test_score * 100.)
)
print 'The code run for %d epochs, with %f epochs/sec' % (
epoch, 1. * epoch / (end_time - start_time))
print >> sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.1fs' % ((end_time - start_time)))
print best_test_score
def svm_cva(dir,
start=0,
end=500,
learning_rate=3e-4,
n_epochs=10000,
dataset='./data/mnist.pkl.gz',
batch_size=500):
"""
Demonstrate stochastic gradient descent optimization of a log-linear
model
This is demonstrated on MNIST.
:type learning_rate: float
:param learning_rate: learning rate used (factor for the stochastic
gradient)
:type n_epochs: int
:param n_epochs: maximal number of epochs to run the optimizer
:type dataset: string
:param dataset: the path of the MNIST dataset file from
http://www.iro.umontreal.ca/~lisa/deep/data/mnist/mnist.pkl.gz
"""
'''
Difference
'''
print start, end, learning_rate, batch_size
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, train_set_y, train_y_matrix = datasets[0]
_, valid_set_y, valid_y_matrix = datasets[1]
_, test_set_y, test_y_matrix = datasets[2]
train_set_x, valid_set_x, test_set_x = datapy.load_feature_gpu(dir=dir,
start=start,
end=end)
print train_set_x.get_value().shape
print valid_set_x.get_value().shape
print test_set_x.get_value().shape
# compute number of minibatches for training, validation and testing
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
# generate symbolic variables for input (x and y represent a
# minibatch)
x = T.matrix('x') # data, presented as rasterized images
y = T.ivector('y') # labels, presented as 1D vector of [int] labels
'''
Differences
'''
y_matrix = T.imatrix(
'y_matrix') # labels, presented as 2D matrix of int labels
# construct the logistic regression class
# Each MNIST image has size 28*28
rng = np.random.RandomState(0)
n_in = end - start
classifier = Pegasos.Pegasos(input=x,
rng=rng,
n_in=n_in,
n_out=10,
weight_decay=1e-4,
loss=1)
# the cost we minimize during training is the negative log likelihood of
# the model in symbolic format
cost = classifier.objective(10, y, y_matrix)
# compiling a Theano function that computes the mistakes that are made by
# the model on a minibatch
test_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x[index * batch_size:(index + 1) * batch_size],
y: test_set_y[index * batch_size:(index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size]
})
validate_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: valid_set_x[index * batch_size:(index + 1) * batch_size],
y: valid_set_y[index * batch_size:(index + 1) * batch_size],
#y_matrix: valid_y_matrix[index * batch_size: (index + 1) * batch_size]
})
# compute the gradient of cost with respect to theta = (W,b)
g_W = T.grad(cost=cost, wrt=classifier.W)
g_b = T.grad(cost=cost, wrt=classifier.b)
params = [classifier.W, classifier.b]
grads = [g_W, g_b]
# start-snippet-3
# specify how to update the parameters of the model as a list of
# (variable, update expression) pairs.
l_r = theano.shared(np.asarray(learning_rate, dtype=np.float32))
#get_optimizer = optimizer.get_simple_optimizer(learning_rate=learning_rate)
get_optimizer = optimizer.get_adam_optimizer_min(learning_rate=l_r,
decay1=0.1,
decay2=0.001)
updates = get_optimizer(params, grads)
# compiling a Theano function `train_model` that returns the cost, but in
# the same time updates the parameter of the model based on the rules
# defined in `updates`
train_model = theano.function(
inputs=[index],
outputs=[cost],
updates=updates,
givens={
x: train_set_x[index * batch_size:(index + 1) * batch_size],
y: train_set_y[index * batch_size:(index + 1) * batch_size],
y_matrix:
train_y_matrix[index * batch_size:(index + 1) * batch_size]
})
# end-snippet-3
###############
# TRAIN MODEL #
###############
print '... training the model'
# early-stopping parameters
patience = 5000 # look as this many examples regardless
patience_increase = 2 # wait this much longer when a new best is
# found
improvement_threshold = 0.995 # a relative improvement of this much is
# considered significant
validation_frequency = min(n_train_batches, patience / 2)
# go through this many
# minibatche before checking the network
# on the validation set; in this case we
# check every epoch
best_validation_loss = np.inf
best_test_score = np.inf
test_score = 0.
start_time = time.clock()
logdir = dir + str(learning_rate) + '_c-'
done_looping = False
epoch = 0
while (epoch < n_epochs) and (not done_looping):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
minibatch_avg_cost = train_model(minibatch_index)
#print minibatch_avg_cost
# iteration number
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
# compute zero-one loss on validation set
validation_losses = [
validate_model(i) for i in xrange(n_valid_batches)
]
this_validation_loss = np.mean(validation_losses)
this_test_losses = [
test_model(i) for i in xrange(n_test_batches)
]
this_test_score = np.mean(this_test_losses)
if this_test_score < best_test_score:
best_test_score = this_test_score
with open(logdir + 'hook.txt', 'a') as f:
print >> f, (
'epoch %i, minibatch %i/%i, validation error %f %%, test error %f %%'
% (epoch, minibatch_index + 1, n_train_batches,
this_validation_loss * 100, this_test_score * 100.))
print(
'epoch %i, minibatch %i/%i, validation error %f %%, test error %f %%'
% (epoch, minibatch_index + 1, n_train_batches,
this_validation_loss * 100, this_test_score * 100.))
# if we got the best validation score until now
if this_validation_loss < best_validation_loss:
#improve patience if loss improvement is good enough
if this_validation_loss < best_validation_loss * \
improvement_threshold:
patience = max(patience, iter * patience_increase)
best_validation_loss = this_validation_loss
# test it on the test set
test_losses = [
test_model(i) for i in xrange(n_test_batches)
]
test_score = np.mean(test_losses)
with open(logdir + 'hook.txt', 'a') as f:
print >> f, (
(' epoch %i, minibatch %i/%i, test error of'
' best model %f %%') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
print((' epoch %i, minibatch %i/%i, test error of'
' best model %f %%') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
if patience <= iter:
done_looping = True
break
end_time = time.clock()
with open(logdir + 'hook.txt', 'a') as f:
print >> f, (
('Optimization complete with best validation score of %f %%,'
'with test performance %f %%') %
(best_validation_loss * 100., test_score * 100.))
print >> f, 'The code run for %d epochs, with %f epochs/sec' % (
epoch, 1. * epoch / (end_time - start_time))
print >> f, sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.1fs' % ((end_time - start_time)))
print >> f, best_test_score
print(('Optimization complete with best validation score of %f %%,'
'with test performance %f %%') %
(best_validation_loss * 100., test_score * 100.))
print 'The code run for %d epochs, with %f epochs/sec' % (
epoch, 1. * epoch / (end_time - start_time))
print >> sys.stderr, ('The code for file ' + os.path.split(__file__)[1] +
' ran for %.1fs' % ((end_time - start_time)))
print best_test_score
def c_6layer_mnist_imputation(seed=0, ctype='cva',
pertub_type=3, pertub_prob=6, pertub_prob1=14, visualization_times=20,
denoise_times=200, predir=None, n_batch=144,
dataset='mnist.pkl.gz', batch_size=500):
"""
Missing data imputation
"""
#cp->cd->cpd->cd->c
nkerns=[32, 32, 64, 64, 64]
drops=[0, 0, 0, 0, 0, 1]
#skerns=[5, 3, 3, 3, 3]
#pools=[2, 1, 1, 2, 1]
#modes=['same']*5
n_hidden=[500, 50]
drop_inverses=[1,]
# 28->12->12->5->5/5*5*64->500->50->500->5*5*64/5->5->12->12->28
if dataset=='mnist.pkl.gz':
dim_input=(28, 28)
colorImg=False
logdir = 'results/imputation/'+ctype+'/mnist/'+ctype+'_6layer_mnist_'+str(pertub_type)+'_'+str(pertub_prob)+'_'+str(pertub_prob1)+'_'+str(denoise_times)+'_'
logdir += str(int(time.time()))+'/'
if not os.path.exists(logdir): os.makedirs(logdir)
print predir
with open(logdir+'hook.txt', 'a') as f:
print >>f, predir
train_set_x, test_set_x, test_set_x_pertub, pertub_label, pertub_number = datapy.load_pertub_data(dirs='data_imputation/', pertub_type=pertub_type, pertub_prob=pertub_prob,pertub_prob1=pertub_prob1)
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, _, _ = datasets[0]
valid_set_x, _, _ = datasets[1]
_, _, _ = datasets[2]
# compute number of minibatches for training, validation and testing
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
x = T.matrix('x')
x_pertub = T.matrix('x_pertub') # the data is presented as rasterized images
p_label = T.matrix('p_label')
random_z = T.matrix('random_z')
drop = T.iscalar('drop')
drop_inverse = T.iscalar('drop_inverse')
activation = nonlinearity.relu
rng = np.random.RandomState(seed)
rng_share = theano.tensor.shared_randomstreams.RandomStreams(0)
input_x = x_pertub.reshape((batch_size, 1, 28, 28))
recg_layer = []
cnn_output = []
#1
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, 1, 28, 28),
filter_shape=(nkerns[0], 1, 5, 5),
poolsize=(2, 2),
border_mode='valid',
activation=activation
))
if drops[0]==1:
cnn_output.append(recg_layer[-1].drop_output(input=input_x, drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(input=input_x))
#2
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[0], 12, 12),
filter_shape=(nkerns[1], nkerns[0], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[1]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#3
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[1], 12, 12),
filter_shape=(nkerns[2], nkerns[1], 3, 3),
poolsize=(2, 2),
border_mode='valid',
activation=activation
))
if drops[2]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#4
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[2], 5, 5),
filter_shape=(nkerns[3], nkerns[2], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[3]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#5
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[3], 5, 5),
filter_shape=(nkerns[4], nkerns[3], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[4]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
mlp_input_x = cnn_output[-1].flatten(2)
activations = []
#1
recg_layer.append(FullyConnected.FullyConnected(
rng=rng,
n_in= 5 * 5 * nkerns[-1],
n_out=n_hidden[0],
activation=activation
))
if drops[-1]==1:
activations.append(recg_layer[-1].drop_output(input=mlp_input_x, drop=drop, rng=rng_share))
else:
activations.append(recg_layer[-1].output(input=mlp_input_x))
#stochastic layer
recg_layer.append(GaussianHidden.GaussianHidden(
rng=rng,
input=activations[-1],
n_in=n_hidden[0],
n_out = n_hidden[1],
activation=None
))
z = recg_layer[-1].sample_z(rng_share)
gene_layer = []
z_output = []
random_z_output = []
#1
gene_layer.append(FullyConnected.FullyConnected(
rng=rng,
n_in=n_hidden[1],
n_out = n_hidden[0],
activation=activation
))
z_output.append(gene_layer[-1].output(input=z))
random_z_output.append(gene_layer[-1].output(input=random_z))
#2
gene_layer.append(FullyConnected.FullyConnected(
rng=rng,
n_in=n_hidden[0],
n_out = 5*5*nkerns[-1],
activation=activation
))
if drop_inverses[0]==1:
z_output.append(gene_layer[-1].drop_output(input=z_output[-1], drop=drop_inverse, rng=rng_share))
random_z_output.append(gene_layer[-1].drop_output(input=random_z_output[-1], drop=drop_inverse, rng=rng_share))
else:
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output(input=random_z_output[-1]))
input_z = z_output[-1].reshape((batch_size, nkerns[-1], 5, 5))
input_random_z = random_z_output[-1].reshape((n_batch, nkerns[-1], 5, 5))
#1
gene_layer.append(UnpoolConvNon.UnpoolConvNon(
rng,
image_shape=(batch_size, nkerns[-1], 5, 5),
filter_shape=(nkerns[-2], nkerns[-1], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
z_output.append(gene_layer[-1].output(input=input_z))
random_z_output.append(gene_layer[-1].output_random_generation(input=input_random_z, n_batch=n_batch))
#2
gene_layer.append(UnpoolConvNon.UnpoolConvNon(
rng,
image_shape=(batch_size, nkerns[-2], 5, 5),
filter_shape=(nkerns[-3], nkerns[-2], 3, 3),
poolsize=(2, 2),
border_mode='full',
activation=activation
))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(input=random_z_output[-1], n_batch=n_batch))
#3
gene_layer.append(UnpoolConvNon.UnpoolConvNon(
rng,
image_shape=(batch_size, nkerns[-3], 12, 12),
filter_shape=(nkerns[-4], nkerns[-3], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(input=random_z_output[-1], n_batch=n_batch))
#4
gene_layer.append(UnpoolConvNon.UnpoolConvNon(
rng,
image_shape=(batch_size, nkerns[-4], 12, 12),
filter_shape=(nkerns[-5], nkerns[-4], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(input=random_z_output[-1], n_batch=n_batch))
#5 stochastic layer
# for the last layer, the nonliearity should be sigmoid to achieve mean of Bernoulli
gene_layer.append(UnpoolConvNon.UnpoolConvNon(
rng,
image_shape=(batch_size, nkerns[-5], 12, 12),
filter_shape=(1, nkerns[-5], 5, 5),
poolsize=(2, 2),
border_mode='full',
activation=nonlinearity.sigmoid
))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(input=random_z_output[-1], n_batch=n_batch))
gene_layer.append(NoParamsBernoulliVisiable.NoParamsBernoulliVisiable(
#rng=rng,
#mean=z_output[-1],
#data=input_x,
))
logpx = gene_layer[-1].logpx(mean=z_output[-1], data=input_x)
# 4-D tensor of random generation
random_x_mean = random_z_output[-1]
random_x = gene_layer[-1].sample_x(rng_share, random_x_mean)
x_denoised = z_output[-1].flatten(2)
x_denoised = p_label*x+(1-p_label)*x_denoised
mse = ((x - x_denoised)**2).sum() / pertub_number
params=[]
for g in gene_layer:
params+=g.params
for r in recg_layer:
params+=r.params
train_activations = theano.function(
inputs=[index],
outputs=T.concatenate(activations, axis=1),
givens={
x_pertub: train_set_x[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
}
)
valid_activations = theano.function(
inputs=[index],
outputs=T.concatenate(activations, axis=1),
givens={
x_pertub: valid_set_x[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
}
)
test_activations = theano.function(
inputs=[x_pertub],
outputs=T.concatenate(activations, axis=1),
givens={
drop: np.cast['int32'](0)
}
)
imputation_model = theano.function(
inputs=[index, x_pertub],
outputs=[x_denoised, mse],
givens={
x: test_set_x[index * batch_size: (index + 1) * batch_size],
p_label:pertub_label[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0),
drop_inverse: np.cast['int32'](0)
}
)
##################
# Pretrain MODEL #
##################
model_epoch = 600
if os.environ.has_key('model_epoch'):
model_epoch = int(os.environ['model_epoch'])
if predir is not None:
color.printBlue('... setting parameters')
color.printBlue(predir)
if model_epoch == -1:
pre_train = np.load(predir+'best-model.npz')
else:
pre_train = np.load(predir+'model-'+str(model_epoch)+'.npz')
pre_train = pre_train['model']
if ctype == 'cva':
for (para, pre) in zip(params, pre_train):
para.set_value(pre)
elif ctype == 'cmmva':
for (para, pre) in zip(params, pre_train[:-2]):
para.set_value(pre)
else:
exit()
else:
exit()
###############
# TRAIN MODEL #
###############
print '... training'
epoch = 0
n_visualization = 100
output = np.ones((n_visualization, visualization_times+2, 784))
output[:,0,:] = test_set_x.get_value()[:n_visualization,:]
output[:,1,:] = test_set_x_pertub.get_value()[:n_visualization,:]
image = paramgraphics.mat_to_img(output[:,0,:].T, dim_input, colorImg=colorImg)
image.save(logdir+'data.png', 'PNG')
image = paramgraphics.mat_to_img(output[:,1,:].T, dim_input, colorImg=colorImg)
image.save(logdir+'data_pertub.png', 'PNG')
tmp = test_set_x_pertub.get_value()
while epoch < denoise_times:
epoch = epoch + 1
this_mse=0
for i in xrange(n_test_batches):
d, m = imputation_model(i, tmp[i * batch_size: (i + 1) * batch_size])
tmp[i * batch_size: (i + 1) * batch_size] = np.asarray(d)
this_mse+=m
if epoch<=visualization_times:
output[:,epoch+1,:] = tmp[:n_visualization,:]
print epoch, this_mse
with open(logdir+'hook.txt', 'a') as f:
print >>f, epoch, this_mse
image = paramgraphics.mat_to_img(tmp[:n_visualization,:].T, dim_input, colorImg=colorImg)
image.save(logdir+'procedure-'+str(epoch)+'.png', 'PNG')
np.savez(logdir+'procedure-'+str(epoch), tmp=tmp)
image = paramgraphics.mat_to_img((output.reshape(-1,784)).T, dim_input, colorImg=colorImg, tile_shape=(n_visualization,22))
image.save(logdir+'output.png', 'PNG')
np.savez(logdir+'output', output=output)
# save original train features and denoise test features
for i in xrange(n_train_batches):
if i == 0:
train_features = np.asarray(train_activations(i))
else:
train_features = np.vstack((train_features, np.asarray(train_activations(i))))
for i in xrange(n_valid_batches):
if i == 0:
valid_features = np.asarray(valid_activations(i))
else:
valid_features = np.vstack((valid_features, np.asarray(valid_activations(i))))
for i in xrange(n_test_batches):
if i == 0:
test_features = np.asarray(test_activations(tmp[i * batch_size: (i + 1) * batch_size]))
else:
test_features = np.vstack((test_features, np.asarray(test_activations(tmp[i * batch_size: (i + 1) * batch_size]))))
np.save(logdir+'train_features', train_features)
np.save(logdir+'valid_features', valid_features)
np.save(logdir+'test_features', test_features)
def c_6layer_mnist_imputation(seed=0,
pertub_type=3,
pertub_prob=6,
pertub_prob1=14,
predir=None,
n_batch=144,
dataset='mnist.pkl.gz',
batch_size=500):
"""
Missing data imputation
"""
#cp->cd->cpd->cd->c
nkerns = [32, 32, 64, 64, 64]
drops = [0, 0, 0, 0, 0, 1]
#skerns=[5, 3, 3, 3, 3]
#pools=[2, 1, 1, 2, 1]
#modes=['same']*5
n_hidden = [500, 50]
drop_inverses = [
1,
]
# 28->12->12->5->5/5*5*64->500->50->500->5*5*64/5->5->12->12->28
if dataset == 'mnist.pkl.gz':
dim_input = (28, 28)
colorImg = False
train_set_x, test_set_x, test_set_x_pertub, pertub_label, pertub_number = datapy.load_pertub_data(
dirs='data_imputation/',
pertub_type=pertub_type,
pertub_prob=pertub_prob,
pertub_prob1=pertub_prob1)
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, train_set_y, train_y_matrix = datasets[0]
valid_set_x, valid_set_y, valid_y_matrix = datasets[1]
_, test_set_y, test_y_matrix = datasets[2]
# compute number of minibatches for training, validation and testing
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
x = T.matrix('x')
#x_pertub = T.matrix('x_pertub') # the data is presented as rasterized images
#p_label = T.matrix('p_label')
y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
y_matrix = T.imatrix('y_matrix')
drop = T.iscalar('drop')
drop_inverse = T.iscalar('drop_inverse')
activation = nonlinearity.relu
rng = np.random.RandomState(seed)
rng_share = theano.tensor.shared_randomstreams.RandomStreams(0)
input_x = x.reshape((batch_size, 1, 28, 28))
recg_layer = []
cnn_output = []
#1
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, 1, 28, 28),
filter_shape=(nkerns[0], 1, 5, 5),
poolsize=(2, 2),
border_mode='valid',
activation=activation))
if drops[0] == 1:
cnn_output.append(recg_layer[-1].drop_output(input=input_x,
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(input=input_x))
#2
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[0], 12, 12),
filter_shape=(nkerns[1], nkerns[0], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[1] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#3
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[1], 12, 12),
filter_shape=(nkerns[2], nkerns[1], 3, 3),
poolsize=(2, 2),
border_mode='valid',
activation=activation))
if drops[2] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#4
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[2], 5, 5),
filter_shape=(nkerns[3], nkerns[2], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[3] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#5
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[3], 5, 5),
filter_shape=(nkerns[4], nkerns[3], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[4] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
mlp_input = cnn_output[-1].flatten(2)
recg_layer.append(
FullyConnected.FullyConnected(rng=rng,
n_in=nkerns[4] * 5 * 5,
n_out=500,
activation=activation))
feature = recg_layer[-1].drop_output(mlp_input, drop=drop, rng=rng_share)
# classify the values of the fully-connected sigmoidal layer
classifier = Pegasos.Pegasos(input=feature,
rng=rng,
n_in=500,
n_out=10,
weight_decay=0,
loss=1)
# the cost we minimize during training is the NLL of the model
cost = classifier.hinge_loss(10, y, y_matrix) * batch_size
weight_decay = 1.0 / n_train_batches
# create a list of all model parameters to be fit by gradient descent
params = []
for r in recg_layer:
params += r.params
params += classifier.params
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
learning_rate = 3e-4
l_r = theano.shared(np.asarray(learning_rate, dtype=np.float32))
get_optimizer = optimizer.get_adam_optimizer_min(learning_rate=l_r,
decay1=0.1,
decay2=0.001,
weight_decay=weight_decay)
updates = get_optimizer(params, grads)
'''
Save parameters and activations
'''
parameters = theano.function(
inputs=[],
outputs=params,
)
# create a function to compute the mistakes that are made by the model
test_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x[index * batch_size:(index + 1) * batch_size],
y: test_set_y[index * batch_size:(index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
})
test_pertub_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x_pertub[index * batch_size:(index + 1) * batch_size],
y: test_set_y[index * batch_size:(index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
})
validate_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: valid_set_x[index * batch_size:(index + 1) * batch_size],
#y_matrix: valid_y_matrix[index * batch_size: (index + 1) * batch_size],
y: valid_set_y[index * batch_size:(index + 1) * batch_size],
drop: np.cast['int32'](0)
})
##################
# Pretrain MODEL #
##################
model_epoch = 250
if os.environ.has_key('model_epoch'):
model_epoch = int(os.environ['model_epoch'])
if predir is not None:
color.printBlue('... setting parameters')
color.printBlue(predir)
if model_epoch == -1:
pre_train = np.load(predir + 'best-model.npz')
else:
pre_train = np.load(predir + 'model-' + str(model_epoch) + '.npz')
pre_train = pre_train['model']
for (para, pre) in zip(params, pre_train):
para.set_value(pre)
else:
exit()
###############
# TRAIN MODEL #
###############
valid_losses = [validate_model(i) for i in xrange(n_valid_batches)]
valid_score = np.mean(valid_losses)
test_losses = [test_model(i) for i in xrange(n_test_batches)]
test_score = np.mean(test_losses)
test_losses_pertub = [test_pertub_model(i) for i in xrange(n_test_batches)]
test_score_pertub = np.mean(test_losses_pertub)
print valid_score, test_score, test_score_pertub
def c_6layer_mnist_imputation(seed=0,
ctype='cva',
pertub_type=3,
pertub_prob=6,
pertub_prob1=14,
visualization_times=20,
denoise_times=200,
predir=None,
n_batch=144,
dataset='mnist.pkl.gz',
batch_size=500):
"""
Missing data imputation
"""
#cp->cd->cpd->cd->c
nkerns = [32, 32, 64, 64, 64]
drops = [0, 0, 0, 0, 0, 1]
#skerns=[5, 3, 3, 3, 3]
#pools=[2, 1, 1, 2, 1]
#modes=['same']*5
n_hidden = [500, 50]
drop_inverses = [
1,
]
# 28->12->12->5->5/5*5*64->500->50->500->5*5*64/5->5->12->12->28
if dataset == 'mnist.pkl.gz':
dim_input = (28, 28)
colorImg = False
logdir = 'results/imputation/' + ctype + '/mnist/' + ctype + '_6layer_mnist_' + str(
pertub_type) + '_' + str(pertub_prob) + '_' + str(
pertub_prob1) + '_' + str(denoise_times) + '_'
logdir += str(int(time.time())) + '/'
if not os.path.exists(logdir): os.makedirs(logdir)
print predir
with open(logdir + 'hook.txt', 'a') as f:
print >> f, predir
train_set_x, test_set_x, test_set_x_pertub, pertub_label, pertub_number = datapy.load_pertub_data(
dirs='data_imputation/',
pertub_type=pertub_type,
pertub_prob=pertub_prob,
pertub_prob1=pertub_prob1)
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, _, _ = datasets[0]
valid_set_x, _, _ = datasets[1]
_, _, _ = datasets[2]
# compute number of minibatches for training, validation and testing
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
x = T.matrix('x')
x_pertub = T.matrix(
'x_pertub') # the data is presented as rasterized images
p_label = T.matrix('p_label')
random_z = T.matrix('random_z')
drop = T.iscalar('drop')
drop_inverse = T.iscalar('drop_inverse')
activation = nonlinearity.relu
rng = np.random.RandomState(seed)
rng_share = theano.tensor.shared_randomstreams.RandomStreams(0)
input_x = x_pertub.reshape((batch_size, 1, 28, 28))
recg_layer = []
cnn_output = []
#1
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, 1, 28, 28),
filter_shape=(nkerns[0], 1, 5, 5),
poolsize=(2, 2),
border_mode='valid',
activation=activation))
if drops[0] == 1:
cnn_output.append(recg_layer[-1].drop_output(input=input_x,
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(input=input_x))
#2
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[0], 12, 12),
filter_shape=(nkerns[1], nkerns[0], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[1] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#3
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[1], 12, 12),
filter_shape=(nkerns[2], nkerns[1], 3, 3),
poolsize=(2, 2),
border_mode='valid',
activation=activation))
if drops[2] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#4
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[2], 5, 5),
filter_shape=(nkerns[3], nkerns[2], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[3] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#5
recg_layer.append(
ConvMaxPool.ConvMaxPool(rng,
image_shape=(batch_size, nkerns[3], 5, 5),
filter_shape=(nkerns[4], nkerns[3], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
if drops[4] == 1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1],
drop=drop,
rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
mlp_input_x = cnn_output[-1].flatten(2)
activations = []
#1
recg_layer.append(
FullyConnected.FullyConnected(rng=rng,
n_in=5 * 5 * nkerns[-1],
n_out=n_hidden[0],
activation=activation))
if drops[-1] == 1:
activations.append(recg_layer[-1].drop_output(input=mlp_input_x,
drop=drop,
rng=rng_share))
else:
activations.append(recg_layer[-1].output(input=mlp_input_x))
#stochastic layer
recg_layer.append(
GaussianHidden.GaussianHidden(rng=rng,
input=activations[-1],
n_in=n_hidden[0],
n_out=n_hidden[1],
activation=None))
z = recg_layer[-1].sample_z(rng_share)
gene_layer = []
z_output = []
random_z_output = []
#1
gene_layer.append(
FullyConnected.FullyConnected(rng=rng,
n_in=n_hidden[1],
n_out=n_hidden[0],
activation=activation))
z_output.append(gene_layer[-1].output(input=z))
random_z_output.append(gene_layer[-1].output(input=random_z))
#2
gene_layer.append(
FullyConnected.FullyConnected(rng=rng,
n_in=n_hidden[0],
n_out=5 * 5 * nkerns[-1],
activation=activation))
if drop_inverses[0] == 1:
z_output.append(gene_layer[-1].drop_output(input=z_output[-1],
drop=drop_inverse,
rng=rng_share))
random_z_output.append(gene_layer[-1].drop_output(
input=random_z_output[-1], drop=drop_inverse, rng=rng_share))
else:
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(
gene_layer[-1].output(input=random_z_output[-1]))
input_z = z_output[-1].reshape((batch_size, nkerns[-1], 5, 5))
input_random_z = random_z_output[-1].reshape((n_batch, nkerns[-1], 5, 5))
#1
gene_layer.append(
UnpoolConvNon.UnpoolConvNon(rng,
image_shape=(batch_size, nkerns[-1], 5, 5),
filter_shape=(nkerns[-2], nkerns[-1], 3,
3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
z_output.append(gene_layer[-1].output(input=input_z))
random_z_output.append(gene_layer[-1].output_random_generation(
input=input_random_z, n_batch=n_batch))
#2
gene_layer.append(
UnpoolConvNon.UnpoolConvNon(rng,
image_shape=(batch_size, nkerns[-2], 5, 5),
filter_shape=(nkerns[-3], nkerns[-2], 3,
3),
poolsize=(2, 2),
border_mode='full',
activation=activation))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(
input=random_z_output[-1], n_batch=n_batch))
#3
gene_layer.append(
UnpoolConvNon.UnpoolConvNon(rng,
image_shape=(batch_size, nkerns[-3], 12,
12),
filter_shape=(nkerns[-4], nkerns[-3], 3,
3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(
input=random_z_output[-1], n_batch=n_batch))
#4
gene_layer.append(
UnpoolConvNon.UnpoolConvNon(rng,
image_shape=(batch_size, nkerns[-4], 12,
12),
filter_shape=(nkerns[-5], nkerns[-4], 3,
3),
poolsize=(1, 1),
border_mode='same',
activation=activation))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(
input=random_z_output[-1], n_batch=n_batch))
#5 stochastic layer
# for the last layer, the nonliearity should be sigmoid to achieve mean of Bernoulli
gene_layer.append(
UnpoolConvNon.UnpoolConvNon(rng,
image_shape=(batch_size, nkerns[-5], 12,
12),
filter_shape=(1, nkerns[-5], 5, 5),
poolsize=(2, 2),
border_mode='full',
activation=nonlinearity.sigmoid))
z_output.append(gene_layer[-1].output(input=z_output[-1]))
random_z_output.append(gene_layer[-1].output_random_generation(
input=random_z_output[-1], n_batch=n_batch))
gene_layer.append(
NoParamsBernoulliVisiable.NoParamsBernoulliVisiable(
#rng=rng,
#mean=z_output[-1],
#data=input_x,
))
logpx = gene_layer[-1].logpx(mean=z_output[-1], data=input_x)
# 4-D tensor of random generation
random_x_mean = random_z_output[-1]
random_x = gene_layer[-1].sample_x(rng_share, random_x_mean)
x_denoised = z_output[-1].flatten(2)
x_denoised = p_label * x + (1 - p_label) * x_denoised
mse = ((x - x_denoised)**2).sum() / pertub_number
params = []
for g in gene_layer:
params += g.params
for r in recg_layer:
params += r.params
train_activations = theano.function(
inputs=[index],
outputs=T.concatenate(activations, axis=1),
givens={
x_pertub: train_set_x[index * batch_size:(index + 1) * batch_size],
drop: np.cast['int32'](0)
})
valid_activations = theano.function(
inputs=[index],
outputs=T.concatenate(activations, axis=1),
givens={
x_pertub: valid_set_x[index * batch_size:(index + 1) * batch_size],
drop: np.cast['int32'](0)
})
test_activations = theano.function(inputs=[x_pertub],
outputs=T.concatenate(activations,
axis=1),
givens={drop: np.cast['int32'](0)})
imputation_model = theano.function(
inputs=[index, x_pertub],
outputs=[x_denoised, mse],
givens={
x: test_set_x[index * batch_size:(index + 1) * batch_size],
p_label: pertub_label[index * batch_size:(index + 1) * batch_size],
drop: np.cast['int32'](0),
drop_inverse: np.cast['int32'](0)
})
##################
# Pretrain MODEL #
##################
model_epoch = 600
if os.environ.has_key('model_epoch'):
model_epoch = int(os.environ['model_epoch'])
if predir is not None:
color.printBlue('... setting parameters')
color.printBlue(predir)
if model_epoch == -1:
pre_train = np.load(predir + 'best-model.npz')
else:
pre_train = np.load(predir + 'model-' + str(model_epoch) + '.npz')
pre_train = pre_train['model']
if ctype == 'cva':
for (para, pre) in zip(params, pre_train):
para.set_value(pre)
elif ctype == 'cmmva':
for (para, pre) in zip(params, pre_train[:-2]):
para.set_value(pre)
else:
exit()
else:
exit()
###############
# TRAIN MODEL #
###############
print '... training'
epoch = 0
n_visualization = 100
output = np.ones((n_visualization, visualization_times + 2, 784))
output[:, 0, :] = test_set_x.get_value()[:n_visualization, :]
output[:, 1, :] = test_set_x_pertub.get_value()[:n_visualization, :]
image = paramgraphics.mat_to_img(output[:, 0, :].T,
dim_input,
colorImg=colorImg)
image.save(logdir + 'data.png', 'PNG')
image = paramgraphics.mat_to_img(output[:, 1, :].T,
dim_input,
colorImg=colorImg)
image.save(logdir + 'data_pertub.png', 'PNG')
tmp = test_set_x_pertub.get_value()
while epoch < denoise_times:
epoch = epoch + 1
this_mse = 0
for i in xrange(n_test_batches):
d, m = imputation_model(i,
tmp[i * batch_size:(i + 1) * batch_size])
tmp[i * batch_size:(i + 1) * batch_size] = np.asarray(d)
this_mse += m
if epoch <= visualization_times:
output[:, epoch + 1, :] = tmp[:n_visualization, :]
print epoch, this_mse
with open(logdir + 'hook.txt', 'a') as f:
print >> f, epoch, this_mse
image = paramgraphics.mat_to_img(tmp[:n_visualization, :].T,
dim_input,
colorImg=colorImg)
image.save(logdir + 'procedure-' + str(epoch) + '.png', 'PNG')
np.savez(logdir + 'procedure-' + str(epoch), tmp=tmp)
image = paramgraphics.mat_to_img((output.reshape(-1, 784)).T,
dim_input,
colorImg=colorImg,
tile_shape=(n_visualization, 22))
image.save(logdir + 'output.png', 'PNG')
np.savez(logdir + 'output', output=output)
# save original train features and denoise test features
for i in xrange(n_train_batches):
if i == 0:
train_features = np.asarray(train_activations(i))
else:
train_features = np.vstack(
(train_features, np.asarray(train_activations(i))))
for i in xrange(n_valid_batches):
if i == 0:
valid_features = np.asarray(valid_activations(i))
else:
valid_features = np.vstack(
(valid_features, np.asarray(valid_activations(i))))
for i in xrange(n_test_batches):
if i == 0:
test_features = np.asarray(
test_activations(tmp[i * batch_size:(i + 1) * batch_size]))
else:
test_features = np.vstack(
(test_features,
np.asarray(
test_activations(tmp[i * batch_size:(i + 1) *
batch_size]))))
np.save(logdir + 'train_features', train_features)
np.save(logdir + 'valid_features', valid_features)
np.save(logdir + 'test_features', test_features)
def c_6layer_mnist_imputation(seed=0,
pertub_type=3, pertub_prob=6, pertub_prob1=14,
predir=None, n_batch=144,
dataset='mnist.pkl.gz', batch_size=500):
"""
Missing data imputation
"""
#cp->cd->cpd->cd->c
nkerns=[32, 32, 64, 64, 64]
drops=[0, 0, 0, 0, 0, 1]
#skerns=[5, 3, 3, 3, 3]
#pools=[2, 1, 1, 2, 1]
#modes=['same']*5
n_hidden=[500, 50]
drop_inverses=[1,]
# 28->12->12->5->5/5*5*64->500->50->500->5*5*64/5->5->12->12->28
if dataset=='mnist.pkl.gz':
dim_input=(28, 28)
colorImg=False
train_set_x, test_set_x, test_set_x_pertub, pertub_label, pertub_number = datapy.load_pertub_data(dirs='data_imputation/', pertub_type=pertub_type, pertub_prob=pertub_prob,pertub_prob1=pertub_prob1)
datasets = datapy.load_data_gpu(dataset, have_matrix=True)
_, train_set_y, train_y_matrix = datasets[0]
valid_set_x, valid_set_y, valid_y_matrix = datasets[1]
_, test_set_y, test_y_matrix = datasets[2]
# compute number of minibatches for training, validation and testing
n_test_batches = test_set_x.get_value(borrow=True).shape[0] / batch_size
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0] / batch_size
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
x = T.matrix('x')
#x_pertub = T.matrix('x_pertub') # the data is presented as rasterized images
#p_label = T.matrix('p_label')
y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
y_matrix = T.imatrix('y_matrix')
drop = T.iscalar('drop')
drop_inverse = T.iscalar('drop_inverse')
activation = nonlinearity.relu
rng = np.random.RandomState(seed)
rng_share = theano.tensor.shared_randomstreams.RandomStreams(0)
input_x = x.reshape((batch_size, 1, 28, 28))
recg_layer = []
cnn_output = []
#1
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, 1, 28, 28),
filter_shape=(nkerns[0], 1, 5, 5),
poolsize=(2, 2),
border_mode='valid',
activation=activation
))
if drops[0]==1:
cnn_output.append(recg_layer[-1].drop_output(input=input_x, drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(input=input_x))
#2
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[0], 12, 12),
filter_shape=(nkerns[1], nkerns[0], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[1]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#3
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[1], 12, 12),
filter_shape=(nkerns[2], nkerns[1], 3, 3),
poolsize=(2, 2),
border_mode='valid',
activation=activation
))
if drops[2]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#4
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[2], 5, 5),
filter_shape=(nkerns[3], nkerns[2], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[3]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
#5
recg_layer.append(ConvMaxPool.ConvMaxPool(
rng,
image_shape=(batch_size, nkerns[3], 5, 5),
filter_shape=(nkerns[4], nkerns[3], 3, 3),
poolsize=(1, 1),
border_mode='same',
activation=activation
))
if drops[4]==1:
cnn_output.append(recg_layer[-1].drop_output(cnn_output[-1], drop=drop, rng=rng_share))
else:
cnn_output.append(recg_layer[-1].output(cnn_output[-1]))
mlp_input = cnn_output[-1].flatten(2)
recg_layer.append(FullyConnected.FullyConnected(
rng=rng,
n_in=nkerns[4] * 5 * 5,
n_out=500,
activation=activation
))
feature = recg_layer[-1].drop_output(mlp_input, drop=drop, rng=rng_share)
# classify the values of the fully-connected sigmoidal layer
classifier = Pegasos.Pegasos(input=feature, rng=rng, n_in=500, n_out=10, weight_decay=0, loss=1)
# the cost we minimize during training is the NLL of the model
cost = classifier.hinge_loss(10, y, y_matrix) * batch_size
weight_decay=1.0/n_train_batches
# create a list of all model parameters to be fit by gradient descent
params=[]
for r in recg_layer:
params+=r.params
params += classifier.params
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
learning_rate = 3e-4
l_r = theano.shared(np.asarray(learning_rate, dtype=np.float32))
get_optimizer = optimizer.get_adam_optimizer_min(learning_rate=l_r, decay1 = 0.1, decay2 = 0.001, weight_decay=weight_decay)
updates = get_optimizer(params,grads)
'''
Save parameters and activations
'''
parameters = theano.function(
inputs=[],
outputs=params,
)
# create a function to compute the mistakes that are made by the model
test_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x[index * batch_size: (index + 1) * batch_size],
y: test_set_y[index * batch_size: (index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
}
)
test_pertub_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: test_set_x_pertub[index * batch_size: (index + 1) * batch_size],
y: test_set_y[index * batch_size: (index + 1) * batch_size],
#y_matrix: test_y_matrix[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
}
)
validate_model = theano.function(
inputs=[index],
outputs=classifier.errors(y),
givens={
x: valid_set_x[index * batch_size: (index + 1) * batch_size],
#y_matrix: valid_y_matrix[index * batch_size: (index + 1) * batch_size],
y: valid_set_y[index * batch_size: (index + 1) * batch_size],
drop: np.cast['int32'](0)
}
)
##################
# Pretrain MODEL #
##################
model_epoch = 250
if os.environ.has_key('model_epoch'):
model_epoch = int(os.environ['model_epoch'])
if predir is not None:
color.printBlue('... setting parameters')
color.printBlue(predir)
if model_epoch == -1:
pre_train = np.load(predir+'best-model.npz')
else:
pre_train = np.load(predir+'model-'+str(model_epoch)+'.npz')
pre_train = pre_train['model']
for (para, pre) in zip(params, pre_train):
para.set_value(pre)
else:
exit()
###############
# TRAIN MODEL #
###############
valid_losses = [validate_model(i) for i in xrange(n_valid_batches)]
valid_score = np.mean(valid_losses)
test_losses = [test_model(i) for i in xrange(n_test_batches)]
test_score = np.mean(test_losses)
test_losses_pertub = [test_pertub_model(i) for i in xrange(n_test_batches)]
test_score_pertub = np.mean(test_losses_pertub)
print valid_score, test_score, test_score_pertub
