def test_mlp(learning_rate=0.05, L1_reg=0.00, L2_reg=0.001, n_epochs=1000,
dataset='data/dataset_BioNlp2009_GE_95_all.pkl.gz', batch_size=32, n_hidden=2000):
"""
MLP参数
:type learning_rate: float
:param learning_rate: 学习率
:type L1_reg: float
:param L1_reg: L1正则化项权重
:type L2_reg: float
:param L2_reg: L2正则化项权重
:type n_epochs: int
:param n_epochs: 迭代最大次数
:type dataset: string
:param dataset: 数据集文件地址
"""
datasets = load_bionlp_data(dataset)
# 共享变量
train_set_x, train_set_y = datasets[0]
valid_set_x, valid_set_y = datasets[1]
test_set_x, test_set_y = datasets[2]
# 计算MiniBatch的个数
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
x = T.matrix('x') #
y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
rng = numpy.random.RandomState(1234)
# construct the MLP class
classifier = MLP(
rng=rng,
input=x,
n_in=2577,
n_hidden=n_hidden,
n_out=10
)
# 损失函数
cost = (
classifier.negative_log_likelihood(y)
+ L1_reg * classifier.L1
+ L2_reg * classifier.L2_sqr
)
# 在测试集上测试正确率
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]
}
)
# 在验证集上测试正确率
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]
}
)
# start-snippet-5
# compute the gradient of cost with respect to theta (sotred in params)
# the resulting gradients will be stored in a list gparams
# 计算梯度 w(1)\w(2)
gparams = [T.grad(cost, param) for param in classifier.params]
# specify how to update the parameters of the model as a list of
# (variable, update expression) pairs
# given two list the zip A = [a1, a2, a3, a4] and B = [b1, b2, b3, b4] of
# same length, zip generates a list C of same size, where each element
# is a pair formed from the two lists :
# C = [(a1, b1), (a2, b2), (a3, b3), (a4, b4)]
updates = [
(param, param - learning_rate * gparam)
for param, gparam in zip(classifier.params, gparams)
]
# 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]
}
)
# end-snippet-5
###############
# TRAIN MODEL #
###############
print '... training'
# early-stopping parameters
patience = 10000 # 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 = numpy.inf
best_iter = 0
test_score = 0.
start_time = time.clock()
epoch = 0
done_looping = False
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)
# 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 = numpy.mean(validation_losses)
print(
'epoch %i, minibatch %i/%i, validation error %f %%' %
(
epoch,
minibatch_index + 1,
n_train_batches,
this_validation_loss * 100.
)
)
'''
logger.info('epoch %i, minibatch %i/%i, validation error %f %% \r\n' %
(
epoch,
minibatch_index + 1,
n_train_batches,
this_validation_loss * 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
best_iter = iter
# test it on the test set
test_losses = [test_model(i) for i
in xrange(n_test_batches)]
test_score = numpy.mean(test_losses)
print((' epoch %i, minibatch %i/%i, test error of '
'best model %f %%') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
'''
logger.info((' epoch %i, minibatch %i/%i, test error of '
'best model %f %% \r\n') %
(epoch, minibatch_index + 1, n_train_batches,
test_score * 100.))
'''
if patience <= iter:
done_looping = True
break
end_time = time.clock()
print(('Optimization complete. Best validation score of %f %% '
'obtained at iteration %i, with test performance %f %%') %
(best_validation_loss * 100., best_iter + 1, test_score * 100.))
'''
def test_dA(learning_rate=0.2,
training_epochs=10,
dataset=['../train.txt ',None,'../test.txt'],
batch_size=1):
datasets = load_bionlp_data(dataset)
train_set_x, train_set_y = datasets[0]
# compute number of minibatches for training, validation and testing
n_train_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
# allocate symbolic variables for the data
index = T.lscalar('index') # index to a [mini]batch
x = T.matrix('x') # the data is presented as rasterized images
#####################################
# BUILDING THE MODEL CORRUPTION 30% #
#####################################
rng = numpy.random.RandomState(123)
theano_rng = RandomStreams(rng.randint(2 ** 30))
da = dA(
numpy_rng=rng,
theano_rng=theano_rng,
input=x,
n_hidden=4,
n_visible=4
)
cost, updates = da.get_cost_updates(
corruption_level=0.0,
learning_rate=learning_rate
)
train_da = theano.function(
[index],
cost,
updates=updates,
givens={
x: train_set_x[index * batch_size: (index + 1) * batch_size]
}
)
start_time = time.clock()
############
# TRAINING #
############
# go through training epochs
for epoch in xrange(training_epochs):
# go through trainng set
c = []
for batch_index in xrange(n_train_batches):
c.append(train_da(batch_index))
#print 'Training epoch %d, %fcost \n' % (epoch, numpy.mean(c))
print da.get_hidden_values(train_set_x).eval()
print da.get_restructed_error(train_set_x).eval()
end_time = time.clock()
print '耗时:%f'%(end_time-start_time)
def test_mlp(
initial_learning_rate,#learning rate
learning_rate_decay,
squared_filter_length_limit,
n_epochs,
batch_size,
mom_params,#momentum{'start':1,'end':2,'interval':3}
activations,
dropout,
dropout_rates,#
results_file_name,
layer_sizes,#structure
dataset,#[train,valid,test]
use_bias,#
random_seed=1234):
assert len(layer_sizes) - 1 == len(dropout_rates)
# extract the params for momentum
mom_start = mom_params["start"]
mom_end = mom_params["end"]
mom_epoch_interval = mom_params["interval"]
datasets = dm.load_bionlp_data(dataset)
train_set_x, train_set_y = datasets[0]
valid_set_x, valid_set_y = datasets[1]
test_set_x, test_set_y = datasets[2]
# 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
epoch = T.scalar()
x = T.matrix('x') # the data is presented as rasterized images
y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
learning_rate = theano.shared(np.asarray(initial_learning_rate,
dtype=theano.config.floatX))
rng = np.random.RandomState(random_seed)
# construct the MLP class
classifier = MLP(rng=rng, input=x,
layer_sizes=layer_sizes,
dropout_rates=dropout_rates,
activations=activations,
use_bias=use_bias)
# Build the expresson for the cost function.
cost = classifier.negative_log_likelihood(y)
dropout_cost = classifier.dropout_negative_log_likelihood(y)
# Compile theano function for testing.
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]})
#theano.printing.pydotprint(test_model, outfile="test_file.png",
# var_with_name_simple=True)
# Compile theano function for validation.
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]})
#theano.printing.pydotprint(validate_model, outfile="validate_file.png",
# var_with_name_simple=True)
# Compute gradients of the model wrt parameters
gparams = []
for param in classifier.params:
# Use the right cost function here to train with or without dropout.
gparam = T.grad(dropout_cost if dropout else cost, param)
gparams.append(gparam)
# ... and allocate mmeory for momentum'd versions of the gradient
gparams_mom = []
for param in classifier.params:
gparam_mom = theano.shared(np.zeros(param.get_value(borrow=True).shape,
dtype=theano.config.floatX))
gparams_mom.append(gparam_mom)
# Compute momentum for the current epoch
mom = ifelse(epoch < mom_epoch_interval,
mom_start*(1.0 - epoch/mom_epoch_interval) + mom_end*(epoch/mom_epoch_interval),
mom_end)
# Update the step direction using momentum
updates = OrderedDict()
for gparam_mom, gparam in zip(gparams_mom, gparams):
# Misha Denil's original version
#updates[gparam_mom] = mom * gparam_mom + (1. - mom) * gparam
# change the update rule to match Hinton's dropout paper
updates[gparam_mom] = mom * gparam_mom - (1. - mom) * learning_rate * gparam
# ... and take a step along that direction
for param, gparam_mom in zip(classifier.params, gparams_mom):
# Misha Denil's original version
#stepped_param = param - learning_rate * updates[gparam_mom]
# since we have included learning_rate in gparam_mom, we don't need it
# here
stepped_param = param + updates[gparam_mom]
# This is a silly hack to constrain the norms of the rows of the weight
# matrices. This just checks if there are two dimensions to the
# parameter and constrains it if so... maybe this is a bit silly but it
# should work for now.
if param.get_value(borrow=True).ndim == 2:
#squared_norms = T.sum(stepped_param**2, axis=1).reshape((stepped_param.shape[0],1))
#scale = T.clip(T.sqrt(squared_filter_length_limit / squared_norms), 0., 1.)
#updates[param] = stepped_param * scale
# constrain the norms of the COLUMNs of the weight, according to
# https://github.com/BVLC/caffe/issues/109
col_norms = T.sqrt(T.sum(T.sqr(stepped_param), axis=0))
desired_norms = T.clip(col_norms, 0, T.sqrt(squared_filter_length_limit))
scale = desired_norms / (1e-7 + col_norms)
updates[param] = stepped_param * scale
else:
updates[param] = stepped_param
# Compile theano function for training. This returns the training cost and
# updates the model parameters.
output = dropout_cost if dropout else cost
train_model = theano.function(inputs=[epoch, index], outputs=output,
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]})
#theano.printing.pydotprint(train_model, outfile="train_file.png",
# var_with_name_simple=True)
# Theano function to decay the learning rate, this is separate from the
# training function because we only want to do this once each epoch instead
# of after each minibatch.
decay_learning_rate = theano.function(inputs=[], outputs=learning_rate,
updates={learning_rate: learning_rate * learning_rate_decay})
###############
# TRAIN MODEL #
###############
print '... training'
best_params = None
best_validation_errors = np.inf
best_iter = 0
test_score = 0.
epoch_counter = 0
start_time = time.clock()
results_file = open(results_file_name, 'wb')
while epoch_counter < n_epochs:
# Train this epoch
epoch_counter = epoch_counter + 1
for minibatch_index in xrange(n_train_batches):
minibatch_avg_cost = train_model(epoch_counter, minibatch_index)
# Compute loss on validation set
validation_losses = [validate_model(i) for i in xrange(n_valid_batches)]
this_validation_errors = np.sum(validation_losses)
# Report and save progress.
print "epoch {}, test error {}, learning_rate={}{}".format(
epoch_counter, this_validation_errors,
learning_rate.get_value(borrow=True),
" **" if this_validation_errors < best_validation_errors else "")
best_validation_errors = min(best_validation_errors,
this_validation_errors)
results_file.write("{0}\n".format(this_validation_errors))
results_file.flush()
new_learning_rate = decay_learning_rate()
end_time = time.clock()
print(('Optimization complete. Best validation score of %f %% '
'obtained at iteration %i, with test performance %f %%') %
(best_validation_errors * 100., best_iter, test_score * 100.))
print >> sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
def sgd_optimization(learning_rate=0.13,
n_epochs=1000,
dataset=['../train.txt',None,'../test.txt'],
batch_size=1):
datasets = dm.load_bionlp_data(dataset)
train_set_x, train_set_y = datasets[0]
if datasets[1]!=None:
valid_set_x, valid_set_y = datasets[1]
test_set_x, test_set_y = datasets[2]
# 计算MiniBatch的个数；每个minibatch，更新一次参数
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
# 通过索引获取数据
index = T.lscalar() # index to a [mini]batch
# x,y : minibatch
x = T.matrix('x') # data
y = T.ivector('y') # labels,一维向量
# construct the logistic regression class
classifier = LogisticRegression(input=x, n_in=28 * 28, n_out=10)
# 负对数自然函数，损失函数
cost = classifier.negative_log_likelihood(y)
# compiling a Theano function that computes the mistakes that are made by
# the model on a minibatch
# 计算模型在验证集与测试集的误差..
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]
}
)
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]
}
)
# 梯度计算
g_W = T.grad(cost=cost, wrt=classifier.W)
g_b = T.grad(cost=cost, wrt=classifier.b)
# 更新参数
updates = [(classifier.W, classifier.W - learning_rate * g_W),
(classifier.b, classifier.b - learning_rate * g_b)]
# 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]
}
)
###############
# TRAIN MODEL #
###############
print '... training the model'
patience = 5000
patience_increase = 2
improvement_threshold = 0.995
validation_frequency = min(n_train_batches, patience / 2)
best_validation_loss = numpy.inf
test_score = 0.
start_time = time.clock()
done_looping = False
epoch = 0
while (epoch < n_epochs) and (not done_looping):
# 每一次迭代...
epoch = epoch + 1
#对于每次迭代；遍历一遍训练集
for minibatch_index in xrange(n_train_batches):
# 在一个MiniBatch中的平均损失
minibatch_avg_cost = train_model(minibatch_index)
#
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
# 在验证集上计算平均损失
validation_losses = [validate_model(i)
for i in xrange(n_valid_batches)]
this_validation_loss = numpy.mean(validation_losses)
print(
'epoch %i, minibatch %i/%i, validation error %f %%' %
(
epoch,
minibatch_index + 1,
n_train_batches,
this_validation_loss * 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 = numpy.mean(test_losses)
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()
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)))
