class MLP(object):
def __init__(self, input, label, n_in, n_hidden, n_out, rng=None):
self.x = input
self.y = label
if rng is None:
rng = numpy.random.RandomState(1234)
# construct hidden_layer (tanh or sigmoid so far)
self.hidden_layer = HiddenLayer(input=self.x,
n_in=n_in,
n_out=n_hidden,
rng=rng,
activation=numpy.tanh)
# construct log_layer (softmax)
self.log_layer = LogisticRegression(input=self.hidden_layer.output,
label=self.y,
n_in=n_hidden,
n_out=n_out)
def train(self):
layer_input = self.hidden_layer.forward()
self.log_layer.train(input=layer_input)
self.hidden_layer.backward(prev_layer=self.log_layer)
def predict(self, x):
x = self.hidden_layer.output(x)
return self.log_layer.predict(x)
def tuneThreshold():
"""
Explore different values of threshold to see which one fits best
"""
thresholds = np.linspace(0.4,0.6, 10)
bestAcc = 0.0
bestModel = None
X_tr, y_tr, w_tr = loadData()
m, n = X_tr.shape
for th in thresholds:
model = LogisticRegression(features=['PRI_tau_eta',
'PRI_lep_eta',
'DER_deltar_tau_lep',
'PRI_met_sumet',
'DER_mass_transverse_met_lep'],
threshold=th)
model.train(X_tr, y_tr, w_tr)
p, r = model.predict(X_tr)
#calculate some accuracy on the same train set
acc = 100.0*(p.flatten() == y_tr.flatten()).sum()/m
print "%s %s%%"%(th, acc)
if acc > bestAcc:
bestAcc = acc
bestModel = model
#save the best model
bestModel.save('data/logisticRegression%.2f.txt'%acc)
def __init__(self, image_shape = [28, 12], filter_shape = [5, 5],
nkerns = [20, 50], batch_size = 500):
self.layers = []
rng = np.random.RandomState(23455)
# generate symbolic variables for input (x and y represent a
# minibatch)
self.x = T.matrix('x') # data, presented as rasterized images
self.y = T.ivector('y') # labels, presented as 1D vector of [int] labels
layer0_input = self.x.reshape((batch_size, 1, image_shape[0], image_shape[0]))
# Construct the first convolutional pooling layer:
# filtering reduces the image size to (28-5+1 , 28-5+1) = (24, 24)
# maxpooling reduces this further to (24/2, 24/2) = (12, 12)
# 4D output tensor is thus of shape (batch_size, nkerns[0], 12, 12)
layer0 = Layer(
rng,
input=layer0_input,
image_shape=(batch_size, 1, image_shape[0], image_shape[0]),
filter_shape=(nkerns[0], 1, filter_shape[0], filter_shape[0]),
poolsize=(2, 2)
)
self.layers.append(layer0)
# Construct the second convolutional pooling layer
# filtering reduces the image size to (12-5+1, 12-5+1) = (8, 8)
# maxpooling reduces this further to (8/2, 8/2) = (4, 4)
# 4D output tensor is thus of shape (batch_size, nkerns[1], 4, 4)
layer1 = Layer(
rng,
input=layer0.output,
image_shape=(batch_size, nkerns[0], image_shape[1], image_shape[1]),
filter_shape=(nkerns[1], nkerns[0], filter_shape[1], filter_shape[1]),
poolsize=(2, 2)
)
self.layers.append(layer1)
# the HiddenLayer being fully-connected, it operates on 2D matrices of
# shape (batch_size, num_pixels) (i.e matrix of rasterized images).
# This will generate a matrix of shape (batch_size, nkerns[1] * 4 * 4),
# or (500, 50 * 4 * 4) = (500, 800) with the default values.
layer2_input = layer1.output.flatten(2)
# construct a fully-connected sigmoidal layer
layer2 = HiddenLayer(
input=layer2_input,
rng = rng,
n_in=nkerns[1] * 4 * 4,
n_out=500,
activ=T.tanh
)
self.layers.append(layer2)
# classify the values of the fully-connected sigmoidal layer
layer3 = LogisticRegression(input=layer2.output, n_in=500, n_out=10)
self.layers.append(layer3)
# the cost we minimize during training is the NLL of the model
self.cost = layer3.negative_log_likelihood(self.y)
def test_classification(self, X, y):
logreg = LogisticRegression(lam_2=0.5)
logreg.train(X, y)
print("predict", logreg.predict(X[0]))
print("error:", sum((np.array([logreg.predict(x)
for x in X]) - np.array(y))**2))
print("F:", logreg.F(logreg.w, X, y))
print("w:", logreg.w)
print(logreg.fevals, logreg.gevals, logreg.adp)
def cross_validation(X,y,bsize, fold, eta, solver="SGD", wdecay=0):
from sklearn.cross_validation import StratifiedKFold
from LogisticRegression import LogisticRegression
scores=[]
skf = StratifiedKFold( y, fold)
for train_index, test_index in skf:
X_train, X_test, y_train, y_test = X[train_index,:], X[test_index,:], y[train_index], y[test_index]
lr = LogisticRegression(learning=solver,weight_decay=wdecay,eta_0=eta, batch_size=bsize)
lr.fit(X_train,y_train)
scores.append(lr.score(X_test,y_test))
return np.mean(scores)
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
#print self.sigmoid_layers[-1].sample_h_given_v().shape
self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def main():
#model = FakeModel() #TODO model parameters
model = LogisticRegression(features=['PRI_tau_eta',
'PRI_lep_eta',
'DER_deltar_tau_lep',
'PRI_met_sumet',
'DER_mass_transverse_met_lep'])
#load some previously saved model parameters
model.load('data/logisticRegression69.61.txt')
#load test data
data = np.loadtxt("data/test.csv", delimiter=',', skiprows=1)
ids = data[:,0].astype(int) #first column is id
X = data[:,1:31] #30 features
#make predictions (ranking and label)
r, p = model.predict(X)
#save to file
save(ids, r, p)
class NeuralNetwork:
def __init__(self, rng, n_in, n_out, hl):
# will contain basically a list of Hidden Layers objects.
self.layers = []
inp_size = n_in
for i in range(len(hl)):
HL = HiddenLayer(rng, inp_size, hl[i])
self.layers.append(HL)
inp_size = hl[i]
self.op = LogisticRegression(inp_size, n_out)
self.params = []
for l in self.layers:
self.params = self.params + l.params
self.params = self.params + self.op.params
# self.params = [l.params for l in self.layers]
# forward pass is here
def forward(self, x):
act = [x]
for i, l in enumerate(self.layers):
act.append(l.output(act[i]))
return act
def cost(self, x, y):
act = self.forward(x)
estimate = act[-1]
return self.op.cost(estimate, y)
def calcAccuracy(self, x, y):
act = self.forward(x)
ll = act[-1]
return self.op.calcAccuracy(ll, y)
def __init__(self, numpy_rng, theano_rng = None, n_ins=784,
hidden_layers_sizes = [500, 500], n_outs = 10, mode = 'dA'):
self.sigmoid_layers = []
self.ae_layers = []
self.params = []
self.n_layers = len(hidden_layers_sizes)
self.x = T.matrix('x')
self.y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
assert self.n_layers > 0
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(2 ** 30))
# allocate symbolic variables for the data
for i in range(self.n_layers):
if i==0:
input_size = n_ins
layer_input = self.x
else:
input_size = hidden_layers_sizes[i-1]
layer_input = self.sigmoid_layers[-1].output
sigmoid_layer = HiddenLayer(rng = numpy_rng, input = layer_input,
n_in = input_size,
n_out = hidden_layers_sizes[i],
activ = T.nnet.sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
self.params.extend(sigmoid_layer.params)
#initialize dA or sA
if mode == 'sA':
ae_layer = SparseAE(numpy_rng = numpy_rng, theano_rng = theano_rng,
input = layer_input, n_visible = input_size,
n_hidden = hidden_layers_sizes[i],
W = sigmoid_layer.W, bhid = sigmoid_layer.b)
else:
ae_layer = DenoiseAE(numpy_rng = numpy_rng, theano_rng = theano_rng,
input = layer_input, n_visible = input_size,
n_hidden = hidden_layers_sizes[i],
W = sigmoid_layer.W, bhid = sigmoid_layer.b)
self.ae_layers.append(ae_layer)
self.logLayer = LogisticRegression(input = self.sigmoid_layers[-1].output,
n_in = hidden_layers_sizes[-1],
n_out = n_outs)
self.params.extend(self.logLayer.params)
self.finetune_cost = self.logLayer.negative_log_likelihood(self.y)
self.errors = self.logLayer.errors(self.y)
def __init__(self, input, label,\
n_in, hidden_layer_sizes, n_out,\
rng=None, activation=ReLU):
self.x = input
self.y = label
self.hidden_layers = []
self.n_layers = len(hidden_layer_sizes)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_in
else:
input_size = hidden_layer_sizes[i-1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.hidden_layers[-1].output()
# construct hidden_layer
hidden_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=activation)
self.hidden_layers.append(hidden_layer)
# layer for ouput using Logistic Regression (softmax)
self.log_layer = LogisticRegression(input=self.hidden_layers[-1].output(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_out)
def testF(self, X, y):
logreg = LogisticRegression(lam_2=0.5)
logreg.train(X, y)
print("f complete")
print(logreg.f(logreg.w, X[0], y[0]))
print("f for first entry")
print(logreg.f(logreg.w, X[0], y[0]))
print("F")
print(logreg.F(logreg.w, X, y))
print("g ")
print(logreg.g(logreg.w, X[0], y[0]))
def __init__(self, rng, n_in, n_out, hl):
# will contain basically a list of Hidden Layers objects.
self.layers = []
inp_size = n_in
for i in range(len(hl)):
HL = HiddenLayer(rng, inp_size, hl[i])
self.layers.append(HL)
inp_size = hl[i]
self.op = LogisticRegression(inp_size, n_out)
self.params = []
for l in self.layers:
self.params = self.params + l.params
self.params = self.params + self.op.params
def __init__(self, input, label, n_in, n_hidden, n_out, rng=None):
self.x = input
self.y = label
if rng is None:
rng = numpy.random.RandomState(1234)
# construct hidden_layer (tanh or sigmoid so far)
self.hidden_layer = HiddenLayer(input=self.x,
n_in=n_in,
n_out=n_hidden,
rng=rng,
activation=numpy.tanh)
# construct log_layer (softmax)
self.log_layer = LogisticRegression(input=self.hidden_layer.output,
label=self.y,
n_in=n_hidden,
n_out=n_out)
def __init__(self, np_rng, theano_rng=None, n_ins=784, hidden_layer_sizes=[500, 500], n_outs=10):
self.sigmoid_layers = []
self.dA_layers = []
self.params = []
self.n_layers = len(hidden_layer_sizes)
assert self.n_layers > 0
if not theano_rng:
theano_rng = RandomStreams(np_rng.randint(2 ** 30))
self.x = T.matrix('x')
self.y = T.ivector('y')
for i in xrange(self.n_layers):
if i == 0:
n_in = n_ins
layer_input = self.x
else:
n_in = hidden_layer_sizes[i-1]
layer_input = self.sigmoid_layers[-1].output
n_out = hidden_layer_sizes[i]
sigmoid_layer = HiddenLayer(np_rng, layer_input, n_in, n_out, activation=T.nnet.sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
self.params.extend(sigmoid_layer.params)
dA_layer = AutoEncoder(np_rng, n_in, n_out, theano_rng=theano_rng, input=layer_input,
W=sigmoid_layer.W, b_hid=sigmoid_layer.b)
self.dA_layers.append(dA_layer)
self.log_layer = LogisticRegression(self.sigmoid_layers[-1].output, self.y, hidden_layer_sizes[-1], n_outs)
self.params.extend(self.log_layer.params)
self.finetune_cost = self.log_layer.negative_log_likelihood()
self.errors = self.log_layer.errors()
def modifyModel(self, batch_size, dataset):
print("Start to modify the model---------------------------")
dataset = dataset
self.batch_size = batch_size
"""
create Model
"""
datasets = YiWenData.load_data(dataset)
test_set_x, test_set_y = datasets[2]
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
# start-snippet-1
x = T.matrix('x') # the data is presented as rasterized images
# [int] labels
print('... building the model')
self.layer0_input = x.reshape((self.batch_size, 1, 28, 28))
self.layer0.modify(self.layer0_input, (self.batch_size, 1, 28, 28))
self.layer1.modify(self.layer0.output, (self.batch_size, self.nkerns[0], 12, 12))
self.layer2_input = self.layer1.output.flatten(2)
# construct a fully-connected sigmoidal layer
self.layer2 = self.layer2
# classify the values of the fully-connected sigmoidal layer
self.layer3 = LogisticRegression(input=self.layer2.output, n_in=500, n_out=7)
print("-------batch_size---------batch_size---------batch_size------------",self.layer0.image_shape)
def __init__(
self,
numpy_rng,
theano_rng=None,
n_ins=3600,
hidden_layers_sizes=[500, 500],
n_outs=6,
corruption_levels=[0.1, 0.1]
):
""" This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the sdA
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
:type corruption_levels: list of float
:param corruption_levels: amount of corruption to use for each
layer
"""
self.sigmoid_layers = []
self.dA_layers = []
self.params = []
self.n_layers = len(hidden_layers_sizes)
assert self.n_layers > 0
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(2 ** 30))
# allocate symbolic variables for the data
self.x = T.matrix('x') # the data is presented as rasterized images
self.y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
# The SdA is an MLP, for which all weights of intermediate layers
# are shared with a different denoising autoencoders
# We will first construct the SdA as a deep multilayer perceptron,
# and when constructing each sigmoidal layer we also construct a
# denoising autoencoder that shares weights with that layer
# During pretraining we will train these autoencoders (which will
# lead to chainging the weights of the MLP as well)
# During finetunining we will finish training the SdA by doing
# stochastich gradient descent on the MLP
for i in range(self.n_layers):
# construct the sigmoidal layer
# the size of the input is either the number of hidden units of
# the layer below or the input size if we are on the first layer
if i == 0:
input_size = n_ins
else:
input_size = hidden_layers_sizes[i - 1]
# the input to this layer is either the activation of the hidden
# layer below or the input of the SdA if you are on the first
# layer
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].output
sigmoid_layer = HiddenLayer(rng=numpy_rng,
input=layer_input,
n_in=input_size,
n_out=hidden_layers_sizes[i],
activation=T.nnet.sigmoid)
# add the layer to our list of layers
self.sigmoid_layers.append(sigmoid_layer)
# its arguably a philosophical question...
# but we are going to only declare that the parameters of the
# sigmoid_layers are parameters of the StackedDAA
# the visible biases in the dA are parameters of those
# dA, but not the SdA
self.params.extend(sigmoid_layer.params)
# Construct a denoising autoencoder that shared weights with this
# layer
dA_layer = dA(numpy_rng=numpy_rng,
theano_rng=theano_rng,
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layers_sizes[i],
W=sigmoid_layer.W,
bhid=sigmoid_layer.b)
self.dA_layers.append(dA_layer)
# We now need to add a logistic layer on top of the MLP
self.logLayer = LogisticRegression(
input=self.sigmoid_layers[-1].output,
n_in=hidden_layers_sizes[-1],
n_out=n_outs
)
self.params.extend(self.logLayer.params)
# construct a function that implements one step of finetunining
# compute the cost for second phase of training,
# defined as the negative log likelihood
self.finetune_cost = self.logLayer.negative_log_likelihood(self.y)
# compute the gradients with respect to the model parameters
# symbolic variable that points to the number of errors made on the
# minibatch given by self.x and self.y
self.errors = self.logLayer.errors(self.y)
def LogisticRegression_demo(learning_rate=0.13, n_epochs=1000, dataset='mnist.pkl.gz', batch_size=600):
datasets = load_multi()
train_set_x, train_set_y = datasets[0]
valid_set_x, valid_set_y = datasets[1]
test_set_x, test_set_y = datasets[2]
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
print '... building the model'
index = T.lscalar()
x = T.matrix('x')
y = T.ivector('y')
classifier = LogisticRegression(x, y, n_in=103, n_out=9)
test_model = theano.function(inputs=[index],
outputs=classifier.errors(),
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(),
givens={x: valid_set_x[index * batch_size:(index + 1) * batch_size],
y: valid_set_y[index * batch_size:(index + 1) * batch_size]})
cost, updates = classifier.get_cost_updates(learning_rate=learning_rate)
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]})
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):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
train_model(minibatch_index)
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
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 this_validation_loss < best_validation_loss:
if this_validation_loss < best_validation_loss * \
improvement_threshold:
patience = max(patience, iter * patience_increase)
best_validation_loss = this_validation_loss
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)))
## These are the hyperparameters to the classifiers. You may need to
# adjust these as you try to find the best fit for each classifier.
# Logistic Regression parameters
eta = .001
lambda_parameter = .1
# Do not change anything below this line!!
# -----------------------------------------------------------------
# Read from file and extract X and Y
df = pd.read_csv("fruit.csv")
X = df[['width', 'height']].values
Y = (df['fruit'] - 1).values
nb1 = GaussianGenerativeModel(isSharedCovariance=False)
nb1.fit(X,Y)
nb1.visualize("generative_result_separate_covariances.png")
nb2 = GaussianGenerativeModel(isSharedCovariance=True)
nb2.fit(X,Y)
nb2.visualize("generative_result_shared_covariances.png")
lr = LogisticRegression(eta=eta, lambda_parameter=lambda_parameter)
lr.fit(X,Y)
lr.visualize('logistic_regression_result.png')
def __init__(self, rng, input, n_in, n_hidden1, n_hidden2, n_hidden3,
n_out):
"""Initialize the parameters for the multilayer perceptron
:type rng: numpy.random.RandomState
:param rng: a random number generator used to initialize weights
:type input: theano.tensor.TensorType
:param input: symbolic variable that describes the input of the
architecture (one minibatch)
:type n_in: int
:param n_in: number of input units, the dimension of the space in
which the datapoints lie
:type n_hidden1: int
:param n_hidden1: number of hidden units for first layer
:type n_hidden2: int
:param n_hidden2: number of hidden units for second layer
:type n_out: int
:param n_out: number of output units, the dimension of the space in
which the labels lie
"""
# Since we are dealing with a one hidden layer MLP, this will translate
# into a HiddenLayer with a tanh activation function connected to the
# LogisticRegression layer; the activation function can be replaced by
# sigmoid or any other nonlinear function
self.First_hiddenLayer = HiddenLayer(rng=rng,
input=input,
n_in=n_in,
n_out=n_hidden1,
activation=relu)
self.Second_hiddenLayer = HiddenLayer(
rng=rng,
input=self.First_hiddenLayer.output,
n_in=n_hidden1,
n_out=n_hidden2,
activation=relu)
self.Third_hiddenLayer = HiddenLayer(
rng=rng,
input=self.Second_hiddenLayer.output,
n_in=n_hidden2,
n_out=n_hidden3,
activation=relu)
# The logistic regression layer gets as input the hidden units
# of the last hidden layer
self.logRegressionLayer = LogisticRegression(
input=self.Second_hiddenLayer.output, n_in=n_hidden2, n_out=n_out)
# end-snippet-2 start-snippet-3
# L1 norm ; one regularization option is to enforce L1 norm to
# be small
self.L1 = (abs(self.First_hiddenLayer.W).sum() +
abs(self.Second_hiddenLayer.W).sum() +
abs(self.Third_hiddenLayer.W).sum() +
abs(self.logRegressionLayer.W).sum())
# square of L2 norm ; one regularization option is to enforce
# square of L2 norm to be small
self.L2_sqr = ((self.First_hiddenLayer.W**2).sum() +
(self.Second_hiddenLayer.W**2).sum() +
(self.Third_hiddenLayer.W**2).sum() +
(self.logRegressionLayer.W**2).sum())
# negative log likelihood of the MLP is given by the negative
# log likelihood of the output of the model, computed in the
# logistic regression layer
self.negative_log_likelihood = (
self.logRegressionLayer.negative_log_likelihood)
# same holds for the function computing the number of errors
self.errors = self.logRegressionLayer.errors
# the parameters of the model are the parameters of the two layer it is
# made out of
self.params = self.First_hiddenLayer.params + self.Second_hiddenLayer.params + self.Third_hiddenLayer.params + self.logRegressionLayer.params
# end-snippet-3
# keep track of model input
self.input = input
class SdA(object):
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.dA_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct dA_layers
dA_layer = dA(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W,
hbias=sigmoid_layer.b)
self.dA_layers.append(dA_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, corruption_level=0.3, epochs=100):
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i - 1].sample_h_given_v(
layer_input)
da = self.dA_layers[i]
for epoch in xrange(epochs):
da.train(lr=lr,
corruption_level=corruption_level,
input=layer_input)
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
while epoch < epochs:
self.log_layer.train(lr=lr, input=layer_input)
# self.finetune_cost = self.log_layer.negative_log_likelihood()
# print >> sys.stderr, 'Training epoch %d, cost is ' % epoch, self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
return self.log_layer.predict(layer_input)
class SdA(object):
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.dA_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct dA_layers
dA_layer = dA(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W,
hbias=sigmoid_layer.b)
self.dA_layers.append(dA_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, corruption_level=0.3, epochs=100):
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i-1].sample_h_given_v(layer_input)
da = self.dA_layers[i]
for epoch in xrange(epochs):
da.train(lr=lr, corruption_level=corruption_level, input=layer_input)
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
while epoch < epochs:
self.log_layer.train(lr=lr, input=layer_input)
# self.finetune_cost = self.log_layer.negative_log_likelihood()
# print >> sys.stderr, 'Training epoch %d, cost is ' % epoch, self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
return self.log_layer.predict(layer_input)
from sklearn.model_selection import LeaveOneOut
#importing the logistic regression module from logisticRegression.py
from LogisticRegression import LogisticRegression
import numpy as np
irisdata = datasets.load_iris()
data = np.delete(irisdata['data'][50:], [0, 1], axis=1)
lv = LeaveOneOut()
lv.get_n_splits(data)
labels = irisdata.target[50:].ravel()
error = []
for train_index, test_index in lv.split(data):
#creating object for logistic regression
model = LogisticRegression()
train_data = data[train_index]
train_labels = labels[train_index]
test_data = data[test_index]
test_labels = labels[test_index]
#training the logistic regression object
model.train(train_data, train_labels)
error.append(1 - (test_labels == model.test(test_data, test_labels)[0]))
print(np.mean(error))
plt.yticks([0, 1], ytick, fontsize=14) #y軸の目盛りにラベルを表示
plt.xlabel('ある製品試験に不合格だった個数[個] ', fontsize=14) #x軸のラベル
plt.title('製品試験と工場（正常・異常）の関係', fontsize=16) #グラフのタイトル
plt.scatter(X[:11], y[:11], c='b') #散布図
plt.scatter(X[11:], y[11:], c='r') #散布図
plt.show() #グラフを表示
# 分類問題のデータセットXを作成
m = 22 # 不合格だった個数の最大数
X = np.arange(0, m, 1) # 0からm-1個の不合格だった個数を生成
# 分類問題のデータセット（正解ラベル）を作成
t = np.where(X > 10, 1, 0)
model = LogisticRegression()
iteration = 10000
cost = []
for i in range(iteration):
# 仮説の計算
y = model.predict(X)
# 目的関数の計算
J = model.cost_function(y, t)
cost.append(J)
# パラメータの更新
model.gradient_descent(X, y, t)
# 学習の経過をグラフ化
plt.plot(cost, c='b')
plt.xlabel('学習回数')
print('SEED:' + str(SEED))
# marginals_rand = np.random.multinomial(N, true_marginals.flatten(), size=1) / N
# marginals_rand = np.reshape(marginals_rand, [2, 2])
# while not (marginals_rand[1, 1] * marginals_rand[0, 1]):
# marginals_rand = np.random.multinomial(N, true_marginals.flatten(), size=1) / N
# marginals_rand = np.reshape(marginals_rand, [2, 2])
# marginals_rand = np.reshape(marginals_rand, [2, 2])
X_train, y_train, a_train = upload_data(ds=ds,
n_samples=n_train,
marginals=true_marginals)
X_test, y_test, a_test = upload_data(ds=ds,
n_samples=n_test,
marginals=true_marginals)
clf = LogisticRegression(fit_intercept=False, reg=0)
clf.fit(X_train, y_train)
# if ds == 'toy_correlated_for_most_fav_dist':
# clf.coef_ = np.array([0.25, 0.80])
# else:
# clf.coef_ = np.array([-.25, .8])
data_tuple = [X_test, a_test, y_test]
clf.coef_ = np.array([0.4, 1.12])
dist, optimum_ks, gamma_opt = calculate_distance_prob_eqopp_with_opt_params(
data_tuple=data_tuple,
function_of_gamma=f_gamma,
range_gamma=range_gamma,
k_opt_fcn=k_opt,
from LogisticRegression import LogisticRegression import numpy as np u = np.array([[0.5, 0, -0.3, -0.7, 0.5]]) v = np.array([[0.7, -0.4, 0.9, -0.5, 0.6]]) Y = np.random.randint(0, 2, (100, 1)) R = np.tile(Y, (1, 5)) E = np.random.rand(100, 1) X = u * R + (np.ones((100, 5)) - R) * v + E model1 = LogisticRegression() model1.fit(X, Y) print(model1.evaluate(X, Y)) model2 = LogisticRegression(stochastic=True, batch_size=50) model2.fit(X, Y) print(model2.evaluate(X, Y)) from sklearn.model_selection import train_test_split X, X_val, Y, Y_val = train_test_split(X, Y, test_size=0.2, random_state=42) model3 = LogisticRegression(stochastic=True, batch_size=50, epochs=10000) model3.fit(X, Y, X_val=X_val, Y_val=Y_val) print(model3.evaluate(X, Y))
# Do not change anything below this line!!
# -----------------------------------------------------------------
# Read from file and extract X and Y
df = pd.read_csv("fruit.csv")
X = df[['width', 'height']].values
Y = (df['fruit'] - 1).values
nb1 = GaussianGenerativeModel(isSharedCovariance=False)
nb1.fit(X,Y)
nb1.test_insample()
print "Gaussian model with separate covariance: in-sample error rate %.1f%%" % (nb1.insample_err * 100.0 )
nb1.visualize("generative_result_separate_covariances.png",show_charts=True)
nb2 = GaussianGenerativeModel(isSharedCovariance=True)
nb2.fit(X,Y)
nb2.test_insample()
print "Gaussian model with shared covariance: in-sample error rate %.1f%%" % (nb2.insample_err * 100.0 )
nb2.visualize("generative_result_shared_covariances.png",show_charts=True)
for idx,lamda in enumerate([ 0.0001, 0.001, 0.01, 0.1, 1, 0 ]):
lr = LogisticRegression(eta=eta, lambda_parameter=lamda)
lr.fit(X,Y)
lr.test_insample()
print "Logistic regression with lambda %.5f, in-sample error rate %.1f%%" % ( lamda, lr.insample_err * 100.0 )
lr.visualize('logistic_regression_result_%d.png' % idx, show_charts=True)
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
numpy_rng=None):
"""
documentation copied from:
http://www.cse.unsw.edu.au/~cs9444/Notes13/demo/DBN.py
This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if numpy_rng is None:
numpy_rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
#ORIG# for i in xrange(self.n_layers):
for i in range(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn import datasets
import matplotlib.pyplot as plt
from LogisticRegression import LogisticRegression
#from regression import LogisticRegression
def accuracy(y_true, y_pred):
accuracy = np.sum(y_true == y_pred) / len(y_true)
return accuracy
bc = datasets.load_breast_cancer()
X, y = bc.data, bc.target
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=1234)
regressor = LogisticRegression(learning_rate=0.0001, n_iters=1000)
regressor.fit(X_train, y_train)
predictions = regressor.predict(X_test)
print("LR classification accuracy:", accuracy(y_test, predictions))
def LogisticRegression_demo(learning_rate=0.13,
n_epochs=1000,
dataset='mnist.pkl.gz',
batch_size=600):
datasets = load_multi()
train_set_x, train_set_y = datasets[0]
valid_set_x, valid_set_y = datasets[1]
test_set_x, test_set_y = datasets[2]
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
print '... building the model'
index = T.lscalar()
x = T.matrix('x')
y = T.ivector('y')
classifier = LogisticRegression(x, y, n_in=103, n_out=9)
test_model = theano.function(
inputs=[index],
outputs=classifier.errors(),
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(),
givens={
x: valid_set_x[index * batch_size:(index + 1) * batch_size],
y: valid_set_y[index * batch_size:(index + 1) * batch_size]
})
cost, updates = classifier.get_cost_updates(learning_rate=learning_rate)
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]
})
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):
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches):
train_model(minibatch_index)
iter = (epoch - 1) * n_train_batches + minibatch_index
if (iter + 1) % validation_frequency == 0:
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 this_validation_loss < best_validation_loss:
if this_validation_loss < best_validation_loss * \
improvement_threshold:
patience = max(patience, iter * patience_increase)
best_validation_loss = this_validation_loss
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)))
class DBN(object):
"""Deep Belief Network
A deep belief network is obtained by stacking several RBMs on top of each
other. The hidden layer of the RBM at layer `i` becomes the input of the
RBM at layer `i+1`. The first layer RBM gets as input the input of the
network, and the hidden layer of the last RBM represents the output. When
used for classification, the DBN is treated as a MLP, by adding a logistic
regression layer on top.
"""
def __init__(self, numpy_rng, theano_rng=None, n_ins=3600,
hidden_layers_sizes=[500, 500], n_outs=6):
"""This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type hidden_layers_sizes: list of ints
:param hidden_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.sigmoid_layers = []
self.rbm_layers = []
self.params = []
self.n_layers = len(hidden_layers_sizes)
assert self.n_layers > 0
if not theano_rng:
theano_rng = MRG_RandomStreams(numpy_rng.randint(2 ** 30))
# allocate symbolic variables for the data
self.x = T.matrix('x') # the data is presented as rasterized images
self.y = T.ivector('y') # the labels are presented as 1D vector
# of [int] labels
# The DBN is an MLP, for which all weights of intermediate
# layers are shared with a different RBM. We will first
# construct the DBN as a deep multilayer perceptron, and when
# constructing each sigmoidal layer we also construct an RBM
# that shares weights with that layer. During pretraining we
# will train these RBMs (which will lead to chainging the
# weights of the MLP as well) During finetuning we will finish
# training the DBN by doing stochastic gradient descent on the
# MLP.
for i in range(self.n_layers):
# construct the sigmoidal layer
# the size of the input is either the number of hidden
# units of the layer below or the input size if we are on
# the first layer
if i == 0:
input_size = n_ins
else:
input_size = hidden_layers_sizes[i - 1]
# the input to this layer is either the activation of the
# hidden layer below or the input of the DBN if you are on
# the first layer
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].output
sigmoid_layer = HiddenLayer(rng=numpy_rng,
input=layer_input,
n_in=input_size,
n_out=hidden_layers_sizes[i],
activation=T.nnet.sigmoid)
# add the layer to our list of layers
self.sigmoid_layers.append(sigmoid_layer)
# its arguably a philosophical question... but we are
# going to only declare that the parameters of the
# sigmoid_layers are parameters of the DBN. The visible
# biases in the RBM are parameters of those RBMs, but not
# of the DBN.
self.params.extend(sigmoid_layer.params)
# Construct an RBM that shared weights with this layer
rbm_layer = RBM(numpy_rng=numpy_rng,
theano_rng=theano_rng,
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layers_sizes[i],
W=sigmoid_layer.W,
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# We now need to add a logistic layer on top of the MLP
self.logLayer = LogisticRegression(
input=self.sigmoid_layers[-1].output,
n_in=hidden_layers_sizes[-1],
n_out=n_outs)
self.params.extend(self.logLayer.params)
# compute the cost for second phase of training, defined as the
# negative log likelihood of the logistic regression (output) layer
self.finetune_cost = self.logLayer.negative_log_likelihood(self.y)
# compute the gradients with respect to the model parameters
# symbolic variable that points to the number of errors made on the
# minibatch given by self.x and self.y
self.errors = self.logLayer.errors(self.y)
def pretraining_functions(self, train_set_x, batch_size, k):
'''Generates a list of functions, for performing one step of
gradient descent at a given layer. The function will require
as input the minibatch index, and to train an RBM you just
need to iterate, calling the corresponding function on all
minibatch indexes.
:type train_set_x: theano.tensor.TensorType
:param train_set_x: Shared var. that contains all datapoints used
for training the RBM
:type batch_size: int
:param batch_size: size of a [mini]batch
:param k: number of Gibbs steps to do in CD-k / PCD-k
'''
# index to a [mini]batch
index = T.lscalar('index') # index to a minibatch
learning_rate = T.scalar('lr') # learning rate to use
# number of batches
n_batches = train_set_x.get_value(borrow=True).shape[0] / batch_size
# begining of a batch, given `index`
batch_begin = index * batch_size
# ending of a batch given `index`
batch_end = batch_begin + batch_size
pretrain_fns = []
for rbm in self.rbm_layers:
# get the cost and the updates list
# using CD-k here (persisent=None) for training each RBM.
# TODO: change cost function to reconstruction error
cost, updates = rbm.get_cost_updates(learning_rate,
persistent=None, k=k)
# compile the theano function
fn = theano.function(
inputs=[index,
theano.In(learning_rate, value=0.1)],
outputs=cost,
updates=updates,
givens={
self.x: train_set_x[batch_begin:batch_end]
}
)
# append `fn` to the list of functions
pretrain_fns.append(fn)
return pretrain_fns
def build_finetune_functions(self, datasets, batch_size, learning_rate):
'''Generates a function `train` that implements one step of
finetuning, a function `validate` that computes the error on a
batch from the validation set, and a function `test` that
computes the error on a batch from the testing set
:type datasets: list of pairs of theano.tensor.TensorType
:param datasets: It is a list that contain all the datasets;
the has to contain three pairs, `train`,
`valid`, `test` in this order, where each pair
is formed of two Theano variables, one for the
datapoints, the other for the labels
:type batch_size: int
:param batch_size: size of a minibatch
:type learning_rate: float
:param learning_rate: learning rate used during finetune stage
'''
(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_valid_batches = valid_set_x.get_value(borrow=True).shape[0]
n_valid_batches /= batch_size
n_test_batches = test_set_x.get_value(borrow=True).shape[0]
n_test_batches /= batch_size
index = T.lscalar('index') # index to a [mini]batch
# compute the gradients with respect to the model parameters
gparams = T.grad(self.finetune_cost, self.params)
# compute list of fine-tuning updates
updates = []
for param, gparam in zip(self.params, gparams):
updates.append((param, param - gparam * learning_rate))
train_fn = theano.function(
inputs=[index],
outputs=self.finetune_cost,
updates=updates,
givens={
self.x: train_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: train_set_y[
index * batch_size: (index + 1) * batch_size
]
}
)
test_score_i = theano.function(
[index],
self.errors,
givens={
self.x: test_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: test_set_y[
index * batch_size: (index + 1) * batch_size
]
}
)
valid_score_i = theano.function(
[index],
self.errors,
givens={
self.x: valid_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: valid_set_y[
index * batch_size: (index + 1) * batch_size
]
}
)
# Create a function that scans the entire validation set
def valid_score():
return [valid_score_i(i) for i in range(n_valid_batches)]
# Create a function that scans the entire test set
def test_score():
return [test_score_i(i) for i in range(n_test_batches)]
return train_fn, valid_score, test_score
simulated_separableish_features = np.vstack((x1, x2)).astype(np.float32)
simulated_labels = np.hstack((np.zeros(data_cnt), np.ones(data_cnt)))
return simulated_separableish_features, simulated_labels
train_data_cnt = 5000
train_x, train_y = generateData(train_data_cnt)
print train_x.shape, train_y.shape
test_data_cnt = 1000
test_x, test_y = generateData(test_data_cnt)
lr = LogisticRegression()
lr.fit(train_x, train_y)
model_name = 'lr.model'
lr.saveModel(model_name)
new_lr = LogisticRegression()
new_lr.loadModel(model_name)
pred_res = new_lr.predict(test_x)
print pred_res[:10]
correct_cnt = np.sum((pred_res == test_y).astype(int))
print correct_cnt
def __init__(self, rnn_size=[800], layer=[10]):
self.bidirectional_rnn = BidirectionalRNN('BidirectionalRNN', rnn_size)
self.logistic_regression = LogisticRegression('LogisticRegression',
rnn_size[-1], layer)
ax1.plot(smooth(Adamax_train_costs), color='#895CCC', label='Adamax')
ax1.legend()
ax2.plot(Adamax_val_errors, 'o-', color='#895CCC', label='Adamax')
ax2.legend()
plt.pause(1)
plt.show(block=False)
if __name__ == '__main__':
image_size = 28 * 28
classes = 10
# test on logistic regression
shapes = [(image_size, classes), (classes, )]
# construct the logistic regression class
classifier = lambda x: LogisticRegression(
input=x, n_in=image_size, n_out=classes)
print('start test on logistic regression......')
test_model(classifier, shapes, fig_num=1)
# test on mlp
n_hidden = 500
shapes = [(image_size, n_hidden), (n_hidden, ), (n_hidden, classes),
(classes, )]
rng = numpy.random.RandomState(1234)
# construct the mlp
classifier = lambda x: MLP(
rng=rng, input=x, n_in=image_size, n_hidden=n_hidden, n_out=classes)
print()
print()
print('start test on logistic regression......')
test_model(classifier, shapes, fig_num=2)
import pandas as pd
import numpy as np
from LogisticRegression import LogisticRegression
from Multinomial import Multinomial
def loadData(file):
data = pd.read_csv(file, header=None).fillna(0)
return data.drop_duplicates()
if __name__ == '__main__':
print("1 Spambase Logistic Regression")
LogisticRegression(loadData('./data/spambase.csv')).validate()
print("1 Breast Cancer Logistic Regression")
LogisticRegression(loadData('./data/breastcancer.csv')).validate()
print("1 Diabetes Logistic Regression")
LogisticRegression(loadData('./data/diabetes.csv')).validate()
print("2 Multivariate Bernoulli")
Multinomial(True).validate('./data/20NG_data/train_data.csv',
'./data/20NG_data/train_label.csv',
'./data/20NG_data/test_data.csv',
'./data/20NG_data/test_label.csv')
print("2 Multinomial")
Multinomial().validate('./data/20NG_data/train_data.csv',
'./data/20NG_data/train_label.csv',
filename = 'LogisticRegressionData1.txt'
def load_data(filename):
data = pd.read_csv(filename)
data=data.values
return data
data = load_data(filename)
dimensions = data.shape
x_train = data[0:50,0:dimensions[1]-1]
y_train = data[0:50,dimensions[1]-1:]
m = x_train.shape[0]
n = x_train.shape[1]
x_test = data[51:,0:dimensions[1]-1]
y_test = data[51:,dimensions[1]-1:]
tester = LogisticRegression()
tester.logistic_regression(x_train,y_train)
pred_probability = tester.predict_probability(x_test)
print "Probability of y being 1 for given testing samples:" + str(pred_probability)
pred_y = tester.predict_y(x_test)
print "Predicted value of y for given testing samples : " + str(pred_y)
plot_train = tester.plot_train(x_train,y_train)
plot_test = tester.plot_test(x_test,y_test)
acc = tester.accuracy(x_test,y_test)
print "Accuracy of regression algorithm = " + str(acc)
import numpy as np import matplotlib.pyplot as plt from sklearn import datasets iris = datasets.load_iris() X = iris.data y = iris.target X = X[y < 2, :2] y = y[y < 2] from model_selection import train_test_split X_train, X_test, y_train, y_test = train_test_split(X, y, seed=666) from LogisticRegression import LogisticRegression log_reg = LogisticRegression() log_reg.fit(X_train, y_train) # print(log_reg.score(X_test,y_test))#1.0 # # print(log_reg.predict_proba(X_test)) # #[0.92972035 0.98664939 0.14852024 0.01685947 0.0369836 0.0186637 # # 0.04936918 0.99669244 0.97993941 0.74524655 0.04473194 0.00339285 # # 0.26131273 0.0369836 0.84192923 0.79892262 0.82890209 0.32358166 # # 0.06535323 0.20735334] # # print(log_reg.coef_) #[ 3.01796521 -5.04447145] # print(log_reg.intercept_) #-0.6937719272911225 #因为就选了两个特征，可以观察x和y的关系对最终结果的影响范围
class CNN(object):
def __init__(self,
N,
label,
n_hidden,
n_out,
image_size,
channel,
n_kernels,
kernel_sizes,
pool_sizes,
rng=None,
activation=ReLU):
if rng is None:
rng = numpy.random.RandomState(1234)
self.N = N
self.n_hidden = n_hidden
self.n_kernels = n_kernels
self.pool_sizes = pool_sizes
self.conv_layers = []
self.conv_sizes = []
# construct 1st conv_layer
conv_layer0 = ConvPoolLayer(N, image_size, channel, n_kernels[0],
kernel_sizes[0], pool_sizes[0], rng,
activation)
self.conv_layers.append(conv_layer0)
conv_size = [
(image_size[0] - kernel_sizes[0][0] + 1) / pool_sizes[0][0],
(image_size[1] - kernel_sizes[0][1] + 1) / pool_sizes[0][1]
]
self.conv_sizes.append(conv_size)
# construct 2nd conv_layer
conv_layer1 = ConvPoolLayer(N, conv_size, n_kernels[0], n_kernels[1],
kernel_sizes[1], pool_sizes[1], rng,
activation)
self.conv_layers.append(conv_layer1)
conv_size = [
(conv_size[0] - kernel_sizes[1][0] + 1) / pool_sizes[1][0],
(conv_size[1] - kernel_sizes[1][0] + 1) / pool_sizes[1][1]
]
self.conv_sizes.append(conv_size)
# construct hidden_layer
self.hidden_layer = HiddenLayer(
None, n_kernels[-1] * conv_size[0] * conv_size[1], n_hidden, None,
None, rng, activation)
# construct log_layer
self.log_layer = LogisticRegression(None, label, n_hidden, n_out)
# def train(self, epochs, learning_rate, input=None):
def train(self, epochs, learning_rate, input, test_input=None):
for epoch in xrange(epochs):
if (epoch + 1) % 5 == 0:
print 'iter = %d/%d' % (epoch + 1, epochs)
print
if (test_input != None):
print '------------------'
print 'TEST PROCESSING...'
print self.predict(test_input)
print '------------------'
print
# forward first conv layer
pooled_X = self.conv_layers[0].forward(input=input)
# forward second conv layer
pooled_X = self.conv_layers[1].forward(input=pooled_X)
# flatten input
layer_input = self.flatten(pooled_X)
# forward hidden layer
layer_input = self.hidden_layer.forward(input=layer_input)
# forward & backward logistic layer
self.log_layer.train(lr=learning_rate, input=layer_input)
# backward hidden layer
self.hidden_layer.backward(prev_layer=self.log_layer,
lr=learning_rate)
flatten_size = self.n_kernels[-1] * self.conv_sizes[-1][
0] * self.conv_sizes[-1][1]
delta_flatten = numpy.zeros((self.N, flatten_size))
for n in xrange(self.N):
for i in xrange(flatten_size):
for j in xrange(self.n_hidden):
delta_flatten[n][i] += self.hidden_layer.W[i][
j] * self.hidden_layer.d_y[n][j]
# unflatten delta
delta = numpy.zeros(
(len(delta_flatten), self.n_kernels[-1],
self.conv_sizes[-1][0], self.conv_sizes[-1][1]))
for n in xrange(len(delta)):
index = 0
for k in xrange(self.n_kernels[-1]):
for i in xrange(self.conv_sizes[-1][0]):
for j in xrange(self.conv_sizes[-1][1]):
delta[n][k][i][j] = delta_flatten[n][index]
index += 1
# backward second conv layer
delta = self.conv_layers[1].backward(delta, self.conv_sizes[1],
learning_rate)
# backward first conv layer
self.conv_layers[0].backward(delta, self.conv_sizes[0],
learning_rate)
def flatten(self, input):
flatten_size = self.n_kernels[-1] * self.conv_sizes[-1][
0] * self.conv_sizes[-1][1]
flattened_input = numpy.zeros((len(input), flatten_size))
for n in xrange(len(flattened_input)):
index = 0
for k in xrange(self.n_kernels[-1]):
for i in xrange(self.conv_sizes[-1][0]):
for j in xrange(self.conv_sizes[-1][1]):
flattened_input[n][index] = input[n][k][i][j]
index += 1
# print flattened_input
return flattened_input
def predict(self, x):
pooled_X = self.conv_layers[0].forward(input=x)
pooled_X = self.conv_layers[1].forward(input=pooled_X)
layer_input = self.flatten(pooled_X)
x = self.hidden_layer.output(input=layer_input)
return self.log_layer.predict(x)
def PolynomialLogisticRegression(degree, C, penalty='l2'):
return Pipeline([('poly', PolynomialFeatures(degree=degree)),
('std_scaler', StandardScaler()),
('log_reg', LogisticRegression(C=C, penalty=penalty))])
reg.fit(X_train, Y_train)
predictions = reg.predict(X_test)
acc = accuracy(Y_test, predictions)
if acc > acc_max:
acc_max = acc
lr_max = lr_val
n_iter_max = iteration
return (lr_max, n_iter_max)
best_lr, best_n_iter = best_params()
print("Best Learning Rate:", best_lr)
print("Best Number Of Iterations:", best_n_iter)
# Best LR = 0.0001
# Best N_Iter = 1000
reg = LogisticRegression(lr=best_lr, n_iters=best_n_iter)
reg.fit(X_train, Y_train)
predictions = reg.predict(X_test)
print("Best Classification Accuracy", accuracy(Y_test, predictions))
# On Running the Code , The following warning will be shown:
# RuntimeWarning: overflow encountered in exp
# return 1 / (1 + np.exp(-X))
# This happens because X is very big which produces exp(-X) to be extremely small to be represented in 64bits hence 128bits required to represent it.
# Hence only selected number 'lr' value and 'n_iter' value is used.For small number of comparisions.
X[i][j] = (X[i][j] - MIN[j]) / (MAX[j] - MIN[j])
X = np.hstack((np.ones((len(X), 1)), X))
testing_X = np.array(X)
return training_X, training_Y, testing_X
def sigmoid(z):
return 1 / (1 + np.exp(-z))
if __name__ == "__main__":
training_X, training_y, testing_X = extract_features(normalization=True)
model = LogisticRegression(training_X, training_y)
weight = model.GradientDescent(optimizer="Adagrad")
testing_y = sigmoid(np.dot(testing_X, weight))
with open("output.csv", "w") as f:
print("id,label", file=f)
for i in range(testing_y.shape[0]):
if testing_y[i] >= 0.5:
print("{},1".format(i + 1), file=f)
else:
print("{},0".format(i + 1), file=f)
def __init__(self, numpy_rng, theano_rng=None, n_ins=3600,
hidden_layers_sizes=[500, 500], n_outs=6):
"""This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type hidden_layers_sizes: list of ints
:param hidden_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.sigmoid_layers = []
self.rbm_layers = []
self.params = []
self.n_layers = len(hidden_layers_sizes)
assert self.n_layers > 0
if not theano_rng:
theano_rng = MRG_RandomStreams(numpy_rng.randint(2 ** 30))
# allocate symbolic variables for the data
self.x = T.matrix('x') # the data is presented as rasterized images
self.y = T.ivector('y') # the labels are presented as 1D vector
# of [int] labels
# The DBN is an MLP, for which all weights of intermediate
# layers are shared with a different RBM. We will first
# construct the DBN as a deep multilayer perceptron, and when
# constructing each sigmoidal layer we also construct an RBM
# that shares weights with that layer. During pretraining we
# will train these RBMs (which will lead to chainging the
# weights of the MLP as well) During finetuning we will finish
# training the DBN by doing stochastic gradient descent on the
# MLP.
for i in range(self.n_layers):
# construct the sigmoidal layer
# the size of the input is either the number of hidden
# units of the layer below or the input size if we are on
# the first layer
if i == 0:
input_size = n_ins
else:
input_size = hidden_layers_sizes[i - 1]
# the input to this layer is either the activation of the
# hidden layer below or the input of the DBN if you are on
# the first layer
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].output
sigmoid_layer = HiddenLayer(rng=numpy_rng,
input=layer_input,
n_in=input_size,
n_out=hidden_layers_sizes[i],
activation=T.nnet.sigmoid)
# add the layer to our list of layers
self.sigmoid_layers.append(sigmoid_layer)
# its arguably a philosophical question... but we are
# going to only declare that the parameters of the
# sigmoid_layers are parameters of the DBN. The visible
# biases in the RBM are parameters of those RBMs, but not
# of the DBN.
self.params.extend(sigmoid_layer.params)
# Construct an RBM that shared weights with this layer
rbm_layer = RBM(numpy_rng=numpy_rng,
theano_rng=theano_rng,
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layers_sizes[i],
W=sigmoid_layer.W,
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# We now need to add a logistic layer on top of the MLP
self.logLayer = LogisticRegression(
input=self.sigmoid_layers[-1].output,
n_in=hidden_layers_sizes[-1],
n_out=n_outs)
self.params.extend(self.logLayer.params)
# compute the cost for second phase of training, defined as the
# negative log likelihood of the logistic regression (output) layer
self.finetune_cost = self.logLayer.negative_log_likelihood(self.y)
# compute the gradients with respect to the model parameters
# symbolic variable that points to the number of errors made on the
# minibatch given by self.x and self.y
self.errors = self.logLayer.errors(self.y)
from operator import imod
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn import datasets
import matplotlib.pyplot as plt
from LogisticRegression import LogisticRegression
bc = datasets.load_breast_cancer()
X, y = bc.data, bc.target
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=1234)
def accuracy(y_true, y_pred):
return np.sum(y_true == y_pred) / len(y_true)
regresor = LogisticRegression(lr=0.01, n_iters=10000)
regresor.fit(X_train, y_train)
predikcije = regresor.predict(X_test)
print("Preciznost: ", accuracy(y_test, predikcije))
print('Data sorted ...')
# Split data into training and test data - ignoring the critical data for now
X = np.concatenate((X_ordered, X_disordered))
Y = np.concatenate((Y_ordered, Y_disordered))
print(np.shape(X))
X_train, X_test, Y_train, Y_test = train_test_split(X, Y, train_size=0.20)
saveData = np.c_[X_train, Y_train]
np.save('test_set', saveData)
print('saved test set')
# Illustrate ordered vs disordered data
# L = 40
# fig = plt.figure()
# plt.subplot(121)
# plt.imshow(X_ordered[20000].reshape(L, L), cmap='plasma_r')
# plt.title('Ordered')
#
# plt.subplot(122)
# plt.imshow(X_disordered[20000].reshape(L, L), cmap='plasma_r')
# plt.title('Disordered')
# plt.show()
# Train on the training data
logreg = LogisticRegression(X_train, Y_train.reshape(len(Y_train), 1), X_test, Y_test.reshape(len(Y_test), 1))
logreg.fit_standard()
print(logreg.accuracy())
weight = logreg.getWeights()
np.save('weights_logreg.npy', weight)
class DBN(object):
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
numpy_rng=None):
"""
documentation copied from:
http://www.cse.unsw.edu.au/~cs9444/Notes13/demo/DBN.py
This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if numpy_rng is None:
numpy_rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
#ORIG# for i in xrange(self.n_layers):
for i in range(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, k=1, epochs=100):
# pre-train layer-wise
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i - 1].sample_h_given_v(
layer_input)
rbm = self.rbm_layers[i]
for epoch in xrange(epochs):
rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# cost = rbm.get_reconstruction_cross_entropy()
# print >> sys.stderr, \
# 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
# def pretrain(self, lr=0.1, k=1, epochs=100):
# # pre-train layer-wise
# for i in xrange(self.n_layers):
# rbm = self.rbm_layers[i]
# for epoch in xrange(epochs):
# layer_input = self.x
# for j in xrange(i):
# layer_input = self.sigmoid_layers[j].sample_h_given_v(layer_input)
# rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# # cost = rbm.get_reconstruction_cross_entropy()
# # print >> sys.stderr, \
# # 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
done_looping = False
while (epoch < epochs) and (not done_looping):
self.log_layer.train(lr=lr, input=layer_input)
# self.finetune_cost = self.log_layer.negative_log_likelihood()
# print >> sys.stderr, 'Training epoch %d, cost is ' % epoch, self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
out = self.log_layer.predict(layer_input)
return out
class DBN(object):
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
numpy_rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if numpy_rng is None:
numpy_rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
# print 'self.finetune_cost: ', self.finetune_cost
def pretrain(self, lr=0.1, k=1, epochs=1000, batch_size=-1):
pretaining_start_time = time.clock()
# pre-train layer-wise
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i - 1].sample_h_given_v(
layer_input)
rbm = self.rbm_layers[i]
# print 'layer_input', layer_input
for epoch in xrange(epochs):
batch_start = time.clock()
# rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# cost = rbm.get_reconstruction_cross_entropy()
# print >> sys.stderr, \
# 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
cost = 0.0
if batch_size == -1:
cost = rbm.contrastive_divergence(input=layer_input,
lr=lr,
k=k,
batch_size=-1)
else:
n_train_batches = len(
layer_input
) / batch_size # compute number of minibatches for training, validation and testing
mean_cost = []
for batch_index in xrange(n_train_batches):
mean_cost += [
rbm.contrastive_divergence(
input=layer_input[batch_index *
batch_size:(batch_index +
1) * batch_size],
lr=lr,
k=k,
batch_size=batch_size)
]
cost = numpy.mean(mean_cost)
batch_stop = time.clock()
batch_time = (batch_stop - batch_start)
print '\tPre-training layer [%d: %d X %d], epoch %d, cost %.7fm, entropy: %.2f, time is %.2f seconds' % (
i, rbm.n_visible, rbm.n_hidden, epoch, cost,
rbm.get_reconstruction_cross_entropy(), (batch_time))
# synchronous betwen rbm and sigmoid layer
self.sigmoid_layers[i].W = rbm.W
self.sigmoid_layers[i].b = rbm.hbias
# # Plot filters after each training epoch
# # Construct image from the weight matrix
# if layer == 0:
# if (epoch % 20 == 0):
# image = PIL.Image.fromarray(tile_raster_images(
# X = numpy.array(rbm.get_w().T),
# img_shape=(28, 28),
# tile_shape=(10, 10),
# tile_spacing=(1, 1)))
# image.save('result/filters_at_layer_%d_epoch_%d.png' % (layer, epoch))
# numpy.array(rbm.get_w().T).dump(('result/weight_at_layer_%d.txt' % layer))
# if layer == 0:
# image = PIL.Image.fromarray(tile_raster_images(
# X = numpy.array(rbm.get_w().T),
# img_shape=(28, rbm.n_visible / 28),
# tile_shape=(10, 10),
# tile_spacing=(1, 1)))
# image.save('result/filters_at_layer_%d.png' % layer)
pretaining_end_time = time.clock()
print('Total time for pretraining: ' + '%.2f seconds' %
((pretaining_end_time - pretaining_start_time)))
print self.sigmoid_layers[0].W
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
# label=self.y,
# n_in=hidden_layer_sizes[-1],
# n_out=n_outs)
# train log_layer
epoch = 0
done_looping = False
start_time = time.clock()
print layer_input
while (epoch < epochs) and (not done_looping):
self.log_layer.train(lr=lr, input=layer_input)
if (epoch % 20 == 0):
print('\tFine-tuning epoch %d, cost is ' % epoch
) #self.log_layer.negative_log_likelihood()
lr *= 0.95
epoch += 1
end_time = time.clock()
print('Total time for fine-tuning: ' + '%.2f seconds' %
((end_time - start_time)))
def predict(self, x=None, y=None):
input_x = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
input_x = sigmoid_layer.output(input=input_x)
out = self.log_layer.predict(input_x, y)
return out
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
numpy_rng=None):
"""
documentation copied from:
http://www.cse.unsw.edu.au/~cs9444/Notes13/demo/DBN.py
This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if numpy_rng is None:
numpy_rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
#ORIG# for i in xrange(self.n_layers):
for i in range(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def __init__(self, stateIn, deepOut = False):
global pickle
print(" Loading previous state ...")
if stateIn.endswith('gz'):
f = gzip.open(stateIn,'rb')
else:
f = open(stateIn, 'r')
state_name = pickle.load(f)
state = state_name[0]
self.names = state_name[1]
convValues = state.convValues
w0 = convValues[0][0]
b0 = convValues[0][1]
w1 = convValues[1][0]
b1 = convValues[1][1]
hiddenVals = state.hiddenValues
wHidden = hiddenVals[0]
bHidden = hiddenVals[1]
logRegValues = state.logRegValues
wLogReg = logRegValues[0]
bLogReg = logRegValues[1]
topo = state.topoplogy
nkerns = topo.nkerns
n_out = len(self.names)
assert(n_out == np.shape(wLogReg)[1])
print(" Some Values ...")
print(" Number of Kernels : " + str(nkerns))
print(" First Kernel w0[0][0] :\n" + str(w0[0][0]))
print(" bHidden :\n" + str(bHidden))
print(" bLogReg :\n" + str(bLogReg))
print(" Building the theano model")
batch_size = 1
x = T.matrix('x') # the data is presented as rasterized images
layer0_input = x.reshape((batch_size, 1, topo.ishape[0], topo.ishape[1]))
rng = np.random.RandomState(23455)
layer0 = LeNetConvPoolLayer(None, input=layer0_input,
image_shape=(batch_size, 1, topo.ishape[0], topo.ishape[0]),
filter_shape=(nkerns[0], 1, topo.filter_1, topo.filter_1),
poolsize=(topo.pool_1, topo.pool_1), wOld=w0, bOld=b0, deepOut=deepOut)
layer1 = LeNetConvPoolLayer(None, input=layer0.output,
image_shape=(batch_size, nkerns[0], topo.in_2, topo.in_2),
filter_shape=(nkerns[1], nkerns[0], topo.filter_2, topo.filter_2),
poolsize=(topo.pool_2, topo.pool_2), wOld=w1, bOld=b1, deepOut=deepOut)
layer2_input = layer1.output.flatten(2)
layer2 = HiddenLayer(None, input=layer2_input, n_in=nkerns[1] * topo.hidden_input,
n_out=topo.numLogisticInput, activation=T.tanh, Wold = wHidden, bOld = bHidden)
# classify the values of the fully-connected sigmoidal layer
layer3 = LogisticRegression(input=layer2.output, n_in=topo.numLogisticInput, n_out=n_out, Wold = wLogReg, bOld=bLogReg )
# create a function to compute the mistakes that are made by the model
# index = T.lscalar()
# test_model = theano.function([index], layer3.getProbs(),
# givens={x: test_set_x[index * batch_size: (index + 1) * batch_size]})
self.predict_model = theano.function([x], layer3.getProbs())
if (deepOut):
self.layer0_out = theano.function([x], layer0.output)
self.layer0_conv= theano.function([x], layer0.conv_out)
self.layer1_conv= theano.function([x], layer1.conv_out)
self.layer1_out = theano.function([x], layer1.output)
self.b0 = b0
self.b1 = b1
self.w0 = w0
self.w1 = w1
def evaluate_lenet5(topo,
loadPics,
learning_rate=0.005,
n_epochs=500,
stateIn=None,
stateOut=None):
rng = numpy.random.RandomState(23455)
theano_rng = RandomStreams(numpy.random.randint(2**30))
print "Loading the datasets for testing and validation..."
# Images
valid_set_x, valid_set_y = loadPics.getValidationData()
test_set_x, test_set_y = loadPics.getTestData()
print "... Loading the datasets"
n_out = loadPics.numberOfClassed
batch_size = 200 #TODO Check
print(" Learning rate " + str(learning_rate))
# compute number of minibatches for training, validation and testing
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0]
n_test_batches = test_set_x.get_value(borrow=True).shape[0]
n_valid_batches /= batch_size
n_test_batches /= batch_size
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
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
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
print 'Number of Kernels' + str(topo.nkerns)
in_2 = 14 #Input in second layer (layer1)
# Reshape matrix of rasterized images of shape (batch_size,28*28)
# to a 4D tensor, compatible with our LeNetConvPoolLayer
layer0_input = x.reshape((batch_size, 1, topo.ishape[0], topo.ishape[1]))
# Using presistent state from last run
w0 = w1 = b0 = b1 = wHidden = bHidden = wLogReg = bLogReg = None
if stateIn is not None:
print(" Loading previous state ...")
state_names = pickle.load(open(stateIn, "r"))
state = state_names[0]
convValues = state.convValues
w0 = convValues[0][0]
b0 = convValues[0][1]
w1 = convValues[1][0]
b1 = convValues[1][1]
hiddenVals = state.hiddenValues
wHidden = hiddenVals[0]
bHidden = hiddenVals[1]
logRegValues = state.logRegValues
wLogReg = logRegValues[0]
bLogReg = logRegValues[1]
print("Hallo Gallo")
# Construct the first convolutional pooling layer:
# filtering reduces the image size to (28-5+1,28-5+1)=(24,24)
# maxpooling reduces this further to (24/2,24/2) = (12,12)
# 4D output tensor is thus of shape (batch_size,nkerns[0],12,12)
layer0 = LeNetConvPoolLayer(rng,
input=layer0_input,
image_shape=(batch_size, 1, topo.ishape[0],
topo.ishape[0]),
filter_shape=(topo.nkerns[0], 1, topo.filter_1,
topo.filter_1),
poolsize=(topo.pool_1, topo.pool_1),
wOld=w0,
bOld=b0)
# Construct the second convolutional pooling layer
# filtering reduces the image size to (12-5+1,12-5+1)=(8,8)
# maxpooling reduces this further to (8/2,8/2) = (4,4)
# 4D output tensor is thus of shape (nkerns[0],nkerns[1],4,4)
layer1 = LeNetConvPoolLayer(rng,
input=layer0.output,
image_shape=(batch_size, topo.nkerns[0],
topo.in_2, topo.in_2),
filter_shape=(topo.nkerns[1], topo.nkerns[0],
topo.filter_2, topo.filter_2),
poolsize=(topo.pool_2, topo.pool_2),
wOld=w1,
bOld=b1)
# the HiddenLayer being fully-connected, it operates on 2D matrices of
# shape (batch_size,num_pixels) (i.e matrix of rasterized images).
# This will generate a matrix of shape (20,32*4*4) = (20,512)
layer2_input = layer1.output.flatten(2)
# Evt. some drop out for the fully connected layer
# Achtung p=1 entspricht keinem Dropout.
# layer2_input = theano_rng.binomial(size=layer2_input.shape, n=1, p=1 - 0.02) * layer2_input
# paper_6 no dropout
# paper_14 again 0.02 dropout
# paper_15 again no dropout
layer2 = HiddenLayer(rng,
input=layer2_input,
n_in=topo.nkerns[1] * topo.hidden_input,
n_out=topo.numLogisticInput,
activation=T.tanh,
Wold=wHidden,
bOld=bHidden)
# classify the values of the fully-connected sigmoidal layer
layer3 = LogisticRegression(input=layer2.output,
n_in=topo.numLogisticInput,
n_out=n_out,
Wold=wLogReg,
bOld=bLogReg)
# Some regularisation (not for the conv-Kernels)
L2_sqr = (layer2.W**2).sum() + (layer3.W**2).sum()
# the cost we minimize during training is the NLL of the model
cost = layer3.negative_log_likelihood(y) + 0.001 * L2_sqr
# create a function to compute the mistakes that are made by the model
test_model = theano.function(
[index],
layer3.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]
})
# Functions for statistics
test_logloss = theano.function(
[index],
cost,
givens={
x: test_set_x[index * batch_size:(index + 1) * batch_size],
y: test_set_y[index * batch_size:(index + 1) * batch_size]
})
validate_logloss = theano.function(
[index],
cost,
givens={
x: valid_set_x[index * batch_size:(index + 1) * batch_size],
y: valid_set_y[index * batch_size:(index + 1) * batch_size]
})
test_probs_fct = theano.function(
[index],
layer3.getProbs(),
givens={x: test_set_x[index * batch_size:(index + 1) * batch_size]})
validate_model = theano.function(
[index],
layer3.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]
})
# create a list of all model parameters to be fit by gradient descent
params = layer3.params + layer2.params + layer1.params + layer0.params
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
# train_model is a function that updates the model parameters by
# SGD Since this model has many parameters, it would be tedious to
# manually create an update rule for each model parameter. We thus
# create the updates list by automatically looping over all
# (params[i],grads[i]) pairs.
updates = []
for param_i, grad_i in zip(params, grads):
updates.append((param_i, param_i - learning_rate * grad_i))
###############
# 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
# go through this many
# minibatche before checking the network
# on the validation set; in this case we
# check every epoch
best_params = None
best_validation_loss = numpy.inf
best_iter = 0
test_score = 0.
start_time = time.clock()
epoch = 0
done_looping = False
epoch_fraction = 0.0
while (epoch < n_epochs) and (not done_looping):
# New epoch the training set is disturbed again
print(" Starting new training epoch")
print(" Manipulating the training set")
train_set_x, train_set_y = loadPics.giveMeNewTraining()
n_train_batches = train_set_x.get_value(borrow=True).shape[0]
n_train_batches /= batch_size
validation_frequency = min(n_train_batches, patience / 2)
print(" Compiling new function")
learning_rate *= 0.993 #See Paper from Cican
train_logloss = theano.function(
[index],
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]
})
print(" Finished compiling the training set")
epoch = epoch + 1
for minibatch_index in xrange(n_train_batches): #Alle einmal anfassen
iter = (epoch - 1) * n_train_batches + minibatch_index
epoch_fraction += 1.0 / float(n_train_batches)
cost_ij = train_logloss(minibatch_index)
if iter % 100 == 0:
print 'training @ iter = ', iter, ' epoch_fraction ', epoch_fraction, ' costs ' + str(
cost_ij)
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)
# compute zero-one loss on validation set
validation_log_loss = numpy.mean(
[validate_logloss(i) for i in xrange(n_valid_batches)])
test_log_loss = numpy.mean(
[test_logloss(i) for i in xrange(n_test_batches)])
# test it on the test set
test_start = time.clock()
test_losses = [test_model(i) for i in xrange(n_test_batches)]
train_costs = [
train_logloss(i) for i in xrange(n_test_batches)
]
dt = time.clock() - test_start
print 'Testing %i faces in %f msec image / sec %f', batch_size * n_test_batches, dt, dt / (
n_test_batches * batch_size)
test_score = numpy.mean(test_losses)
train_log_loss = numpy.mean(train_costs)
test_probs1 = [
test_probs_fct(i) for i in xrange(n_test_batches)
]
print('%i, %f, %f, %f, %f, %f, %f, 0.424242' %
(epoch, this_validation_loss * 100., test_score * 100.,
learning_rate, train_log_loss, validation_log_loss,
test_log_loss))
# 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)
# save best validation score and iteration number
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.))
# if (this_validation_loss < 0.02):
# learning_rate /= 2
# print("Decreased learning rate due to low xval error to " + str(learning_rate))
if patience <= iter:
print("--------- Finished Looping ----- earlier ")
done_looping = True
break
end_time = time.clock()
print('---------- Optimization complete -------------------------')
print('Res: ', str(topo.nkerns))
print('Res: ', learning_rate)
print('Res: Best validation score of %f %% obtained at iteration %i,' \
'with test performance %f %%' %
(best_validation_loss * 100., best_iter + 1, test_score * 100.))
print('Res: The code for file ' + os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
# Oliver
if not os.path.isdir("conv_images"):
os.makedirs("conv_images")
os.chdir("conv_images")
# d = layer0.W.get_value() #e.g. (20, 1, 5, 5) number of filter, num of incomming filters, dim filter
# for i in range(0, numpy.shape(d)[0]):
# dd = d[i][0]
# rescaled = (255.0 / dd.max() * (dd - dd.min())).astype(numpy.uint8)
# img = Image.fromarray(rescaled)
# img.save('filter_l0' + str(i) + '.png')
#
# d = layer1.W.get_value() #e.g. (20, 1, 5, 5) number of filter, num of incomming filters, dim filter
# for i in range(0, numpy.shape(d)[0]):
# dd = d[i][0]
# rescaled = (255.0 / dd.max() * (dd - dd.min())).astype(numpy.uint8)
# img = Image.fromarray(rescaled)
# img.save('filter_l1' + str(i) + '.png')
state = LeNet5State(topology=topo,
convValues=[
layer0.getParametersAsValues(),
layer1.getParametersAsValues()
],
hiddenValues=layer2.getParametersAsValues(),
logRegValues=layer3.getParametersAsValues())
print
if stateOut is not None:
pickle.dump([state, loadPics.getClasses()], open(stateOut, 'wb'))
print("Saved the pickeled data-set")
return learning_rate
class SdA(object):
"""Stacked denoising auto-encoder class (SdA)
A stacked denoising autoencoder model is obtained by stacking several
dAs. The hidden layer of the dA at layer `i` becomes the input of
the dA at layer `i+1`. The first layer dA gets as input the input of
the SdA, and the hidden layer of the last dA represents the output.
Note that after pretraining, the SdA is dealt with as a normal MLP,
the dAs are only used to initialize the weights.
"""
def __init__(
self,
numpy_rng,
theano_rng=None,
n_ins=3600,
hidden_layers_sizes=[500, 500],
n_outs=6,
corruption_levels=[0.1, 0.1]
):
""" This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the sdA
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
:type corruption_levels: list of float
:param corruption_levels: amount of corruption to use for each
layer
"""
self.sigmoid_layers = []
self.dA_layers = []
self.params = []
self.n_layers = len(hidden_layers_sizes)
assert self.n_layers > 0
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(2 ** 30))
# allocate symbolic variables for the data
self.x = T.matrix('x') # the data is presented as rasterized images
self.y = T.ivector('y') # the labels are presented as 1D vector of
# [int] labels
# The SdA is an MLP, for which all weights of intermediate layers
# are shared with a different denoising autoencoders
# We will first construct the SdA as a deep multilayer perceptron,
# and when constructing each sigmoidal layer we also construct a
# denoising autoencoder that shares weights with that layer
# During pretraining we will train these autoencoders (which will
# lead to chainging the weights of the MLP as well)
# During finetunining we will finish training the SdA by doing
# stochastich gradient descent on the MLP
for i in range(self.n_layers):
# construct the sigmoidal layer
# the size of the input is either the number of hidden units of
# the layer below or the input size if we are on the first layer
if i == 0:
input_size = n_ins
else:
input_size = hidden_layers_sizes[i - 1]
# the input to this layer is either the activation of the hidden
# layer below or the input of the SdA if you are on the first
# layer
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].output
sigmoid_layer = HiddenLayer(rng=numpy_rng,
input=layer_input,
n_in=input_size,
n_out=hidden_layers_sizes[i],
activation=T.nnet.sigmoid)
# add the layer to our list of layers
self.sigmoid_layers.append(sigmoid_layer)
# its arguably a philosophical question...
# but we are going to only declare that the parameters of the
# sigmoid_layers are parameters of the StackedDAA
# the visible biases in the dA are parameters of those
# dA, but not the SdA
self.params.extend(sigmoid_layer.params)
# Construct a denoising autoencoder that shared weights with this
# layer
dA_layer = dA(numpy_rng=numpy_rng,
theano_rng=theano_rng,
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layers_sizes[i],
W=sigmoid_layer.W,
bhid=sigmoid_layer.b)
self.dA_layers.append(dA_layer)
# We now need to add a logistic layer on top of the MLP
self.logLayer = LogisticRegression(
input=self.sigmoid_layers[-1].output,
n_in=hidden_layers_sizes[-1],
n_out=n_outs
)
self.params.extend(self.logLayer.params)
# construct a function that implements one step of finetunining
# compute the cost for second phase of training,
# defined as the negative log likelihood
self.finetune_cost = self.logLayer.negative_log_likelihood(self.y)
# compute the gradients with respect to the model parameters
# symbolic variable that points to the number of errors made on the
# minibatch given by self.x and self.y
self.errors = self.logLayer.errors(self.y)
def pretraining_functions(self, train_set_x, batch_size):
''' Generates a list of functions, each of them implementing one
step in trainnig the dA corresponding to the layer with same index.
The function will require as input the minibatch index, and to train
a dA you just need to iterate, calling the corresponding function on
all minibatch indexes.
:type train_set_x: theano.tensor.TensorType
:param train_set_x: Shared variable that contains all datapoints used
for training the dA
:type batch_size: int
:param batch_size: size of a [mini]batch
:type learning_rate: float
:param learning_rate: learning rate used during training for any of
the dA layers
'''
# index to a [mini]batch
index = T.lscalar('index') # index to a minibatch
corruption_level = T.scalar('corruption') # % of corruption to use
learning_rate = T.scalar('lr') # learning rate to use
# begining of a batch, given `index`
batch_begin = index * batch_size
# ending of a batch given `index`
batch_end = batch_begin + batch_size
pretrain_fns = []
for dA in self.dA_layers:
# get the cost and the updates list
cost, updates = dA.get_cost_updates(corruption_level,
learning_rate)
# compile the theano function
fn = theano.function(
inputs=[
index,
theano.In(corruption_level, value=0.2),
theano.In(learning_rate, value=0.1)
],
outputs=cost,
updates=updates,
givens={
self.x: train_set_x[batch_begin: batch_end]
}
)
# append `fn` to the list of functions
pretrain_fns.append(fn)
return pretrain_fns
def build_finetune_functions(self, datasets, batch_size, learning_rate):
'''Generates a function `train` that implements one step of
finetuning, a function `validate` that computes the error on
a batch from the validation set, and a function `test` that
computes the error on a batch from the testing set
:type datasets: list of pairs of theano.tensor.TensorType
:param datasets: It is a list that contain all the datasets;
the has to contain three pairs, `train`,
`valid`, `test` in this order, where each pair
is formed of two Theano variables, one for the
datapoints, the other for the labels
:type batch_size: int
:param batch_size: size of a minibatch
:type learning_rate: float
:param learning_rate: learning rate used during finetune stage
'''
(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_valid_batches = valid_set_x.get_value(borrow=True).shape[0]
n_valid_batches //= batch_size
n_test_batches = test_set_x.get_value(borrow=True).shape[0]
n_test_batches //= batch_size
index = T.lscalar('index') # index to a [mini]batch
# compute the gradients with respect to the model parameters
gparams = T.grad(self.finetune_cost, self.params)
# compute list of fine-tuning updates
updates = [
(param, param - gparam * learning_rate)
for param, gparam in zip(self.params, gparams)
]
train_fn = theano.function(
inputs=[index],
outputs=self.finetune_cost,
updates=updates,
givens={
self.x: train_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: train_set_y[
index * batch_size: (index + 1) * batch_size
]
},
name='train'
)
test_score_i = theano.function(
[index],
self.errors,
givens={
self.x: test_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: test_set_y[
index * batch_size: (index + 1) * batch_size
]
},
name='test'
)
valid_score_i = theano.function(
[index],
self.errors,
givens={
self.x: valid_set_x[
index * batch_size: (index + 1) * batch_size
],
self.y: valid_set_y[
index * batch_size: (index + 1) * batch_size
]
},
name='valid'
)
# Create a function that scans the entire validation set
def valid_score():
return [valid_score_i(i) for i in range(n_valid_batches)]
# Create a function that scans the entire test set
def test_score():
return [test_score_i(i) for i in range(n_test_batches)]
return train_fn, valid_score, test_score
# -----------------------------------------------------------------
# Read from file and extract X and Y
df = pd.read_csv("fruit.csv")
X = df[['width', 'height']].values
Y = (df['fruit'] - 1).values
nb1 = GaussianGenerativeModel(isSharedCovariance=False)
nb1.fit(X, Y)
nb1.visualize("generative_result_separate_covariances.png")
nb2 = GaussianGenerativeModel(isSharedCovariance=True)
nb2.fit(X, Y)
nb2.visualize("generative_result_shared_covariances.png")
lr = LogisticRegression(eta=eta, lambda_parameter=lambda_parameter)
lr.fit(X, Y)
lr.visualize('logistic_regression_result.png')
X_test = np.array([[4, 11], [8.5, 7]])
Y_nb1 = nb1.predict(X_test)
Y_nb2 = nb2.predict(X_test)
Y_lr = lr.predict(X_test)
print("Test fruit predictions for Gaussian Model:")
print("width 4 cm and height 11 cm: " + str(Y_nb1[0]))
print("width 8.5 cm and height 7 cm: " + str(Y_nb1[1]))
print("Test fruit predictions for Shared Covariance Gaussian Model:")
print("width 4 cm and height 11 cm: " + str(Y_nb2[0]))
print("width 8.5 cm and height 7 cm: " + str(Y_nb2[1]))
def sgd_optimization_mnist(learning_rate=0.13, n_epochs=1000,
dataset='mnist.pkl.gz',
batch_size=600):
"""
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
"""
datasets = load_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
# 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
# construct the logistic regression class
# Each MNIST image has size 28*28
classifier = LogisticRegression(input_data=x, n_in=28 * 28, n_out=10)
# the cost we minimize during training is the negative log likelihood of
# the model in symbolic format
cost = classifier.negative_log_likelihood(y)
# 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]
}
)
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]
}
)
# 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)
# start-snippet-3
# specify how to update the parameters of the model as a list of
# (variable, update expression) pairs.
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]
}
)
# 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 = numpy.inf
test_score = 0.
start_time = timeit.default_timer()
done_looping = False
epoch = 0
while (epoch < n_epochs) and (not done_looping):
epoch = epoch + 1
for minibatch_index in range(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 range(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 range(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.
)
)
# save the best model
with open('best_model.pkl', 'wb') as f:
pickle.dump(classifier, f)
if patience <= iter:
done_looping = True
break
end_time = timeit.default_timer()
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)))
# in order to run tests put in into the directiry prior to LogisticRegression
# directory
import pandas as pd
from LogisticRegression import LogisticRegression
df = pd.read_csv('iris.csv')
df[df.columns[4]] = df[df.columns[4]].map({
'Iris-setosa': 0,
'Iris-versicolor': 1,
'Iris-virginica': 2
})
print(df.head())
clf = LogisticRegression.LogisticRegression(n_iter=500)
print('\n Fitting...\n')
clf.fit(df[df.columns[:-1]].values, df[df.columns[-1]].values)
print('Predicting... \n\n')
prd = clf.predict(df[df.columns[:-1]].values)
for r, p in zip(df[df.columns[-1]].values, prd):
print(r, p)
class DBN(object):
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
numpy_rng=None):
"""
documentation copied from:
http://www.cse.unsw.edu.au/~cs9444/Notes13/demo/DBN.py
This class is made to support a variable number of layers.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: numpy random number generator used to draw initial
weights
:type theano_rng: theano.tensor.shared_randomstreams.RandomStreams
:param theano_rng: Theano random generator; if None is given one is
generated based on a seed drawn from `rng`
:type n_ins: int
:param n_ins: dimension of the input to the DBN
:type n_layers_sizes: list of ints
:param n_layers_sizes: intermediate layers size, must contain
at least one value
:type n_outs: int
:param n_outs: dimension of the output of the network
"""
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if numpy_rng is None:
numpy_rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
#ORIG# for i in xrange(self.n_layers):
for i in range(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, k=1, epochs=100):
# pre-train layer-wise
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i-1].sample_h_given_v(layer_input)
rbm = self.rbm_layers[i]
for epoch in xrange(epochs):
rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# cost = rbm.get_reconstruction_cross_entropy()
# print >> sys.stderr, \
# 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
# def pretrain(self, lr=0.1, k=1, epochs=100):
# # pre-train layer-wise
# for i in xrange(self.n_layers):
# rbm = self.rbm_layers[i]
# for epoch in xrange(epochs):
# layer_input = self.x
# for j in xrange(i):
# layer_input = self.sigmoid_layers[j].sample_h_given_v(layer_input)
# rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# # cost = rbm.get_reconstruction_cross_entropy()
# # print >> sys.stderr, \
# # 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
done_looping = False
while (epoch < epochs) and (not done_looping):
self.log_layer.train(lr=lr, input=layer_input)
# self.finetune_cost = self.log_layer.negative_log_likelihood()
# print >> sys.stderr, 'Training epoch %d, cost is ' % epoch, self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
out = self.log_layer.predict(layer_input)
return out
val_siamese_dataset = SiamesDataset(val_csv,
training_dir,
transform=transforms.Compose([transforms.Resize((224,224)),transforms.ToTensor()]))
val_dataloader = DataLoader(val_siamese_dataset,
shuffle=True,
num_workers=2,
batch_size=32)
model = models.vgg16(pretrained=True)
model.classifier[6] = nn.Linear(4096, 128)
print(model)
net = SiamesNet(model)
regresion = LogisticRegression(128,1)
if torch.cuda.is_available():
print('Cuda Disponible')
net.cuda()
regresion.cuda()
#criterion = ContrastiveLoss()
criterion = torch.nn.BCELoss()
#criterion =torch.nn.CrossEntropyLoss()
#optimizer = optim.RMSprop(regresion.parameters(), lr=1e-4, alpha=0.99, eps=1e-8, weight_decay=0.0005, momentum=0.9)
optimizer = torch.optim.Adam(regresion.parameters(), lr=0.0001)
#wandb.watch(regresion)
for epoch in range(0,1000):
class DBN(object):
def __init__(self, input=None, label=None, n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2, rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(
input=layer_input, n_in=input_size, n_out=hidden_layer_sizes[i], rng=rng, activation=sigmoid
)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b,
)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(), label=self.y, n_in=hidden_layer_sizes[-1], n_out=n_outs
)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, k=1, epochs=100):
# pre-train layer-wise
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i - 1].sample_h_given_v(layer_input)
rbm = self.rbm_layers[i]
for epoch in xrange(epochs):
rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# log pretraining as stderr every after 100 epochs
if (epoch + 1) % 100 == 0: # REMOVE this block for faster training
cost = rbm.get_reconstruction_cross_entropy()
print >> sys.stderr, "Pre-training layer %d, epoch %d, cost " % (i, epoch + 1), cost
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
done_looping = False
while (epoch < epochs) and (not done_looping):
self.log_layer.train(lr=lr, input=layer_input)
# log finetune training as stderr every 25 epochs
if (epoch + 1) % 25 == 0: # REMOVE this block for faster training
self.finetune_cost = self.log_layer.negative_log_likelihood()
print >> sys.stderr, "Training epoch %d, cost is " % (epoch + 1), self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
out = self.log_layer.predict(layer_input)
return out
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn import datasets
import matplotlib.pyplot as plt
from LogisticRegression import LogisticRegression
bc = datasets.load_breast_cancer()
X, y = bc.data, bc.target
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=1234)
def accuracy(y_true, y_pred):
accuracy = np.sum(y_true == y_pred) / len(y_true)
return accuracy
regressor = LogisticRegression(lr=0.001, nb_iters=1000)
regressor.fit(X_train, y_train)
predictions = regressor.predict(X_test)
print("Logistic Regression Accuracy : ", accuracy(y_test, predictions))
def evaluate_lenet5(learning_rate=0.15, n_epochs=200,
dataset='mnist.pkl.gz',
nkerns=[20, 20], batch_size=500):
""" Demonstrates lenet on CIFAR-10 dataset
: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 nkerns: list of ints
:param nkerns: number of kernels on each layer
"""
rng = numpy.random.RandomState(23455)
def shared_dataset(data_xy, borrow=True):
""" Function that loads the dataset into shared variables
The reason we store our dataset in shared variables is to allow
Theano to copy it into the GPU memory (when code is run on GPU).
Since copying data into the GPU is slow, copying a minibatch everytime
is needed (the default behaviour if the data is not in a shared
variable) would lead to a large decrease in performance.
"""
data_x, data_y = data_xy
shared_x = theano.shared(numpy.asarray(data_x,
dtype=theano.config.floatX),
borrow=borrow)
shared_y = theano.shared(numpy.asarray(data_y,
dtype=theano.config.floatX),
borrow=borrow)
# When storing data on the GPU it has to be stored as floats
# therefore we will store the labels as ``floatX`` as well
# (``shared_y`` does exactly that). But during our computations
# we need them as ints (we use labels as index, and if they are
# floats it doesn't make sense) therefore instead of returning
# ``shared_y`` we will have to cast it to int. This little hack
# lets ous get around this issue
return shared_x, T.cast(shared_y, 'int32')
data_batch_1 = unpickle('cifar-10-batches-py/data_batch_1')
data_batch_2 = unpickle('cifar-10-batches-py/data_batch_2')
data_batch_3 = unpickle('cifar-10-batches-py/data_batch_3')
data_batch_4 = unpickle('cifar-10-batches-py/data_batch_4')
data_batch_5 = unpickle('cifar-10-batches-py/data_batch_5')
test = unpickle('cifar-10-batches-py/test_batch')
train_set_1 = data_batch_1["data"]
train_set_2 = data_batch_2["data"]
train_set_3 = data_batch_3["data"]
train_set_4 = data_batch_4["data"]
train_set_5 = data_batch_5["data"]
X_train = numpy.concatenate((train_set_1, train_set_2, train_set_3, train_set_4, train_set_5), axis=0)
y_train = numpy.concatenate((data_batch_1["labels"], data_batch_2["labels"], data_batch_3["labels"],
data_batch_4["labels"], data_batch_5["labels"]))
test_set = test["data"]
Xte_rows = test_set.reshape(train_set_1.shape[0], 32 * 32 * 3)
Yte = numpy.asarray(test["labels"])
Xval_rows = X_train[:7500, :] # take first 1000 for validation
Yval = y_train[:7500]
Xtr_rows = X_train[7500:50000, :] # keep last 49,000 for train
Ytr = y_train[7500:50000]
mean_train = Xtr_rows.mean(axis=0)
stdv_train = Xte_rows.std(axis=0)
Xtr_rows = (Xtr_rows - mean_train) / stdv_train
Xval_rows = (Xval_rows - mean_train) / stdv_train
Xte_rows = (Xte_rows - mean_train) / stdv_train
learning_rate = theano.shared(learning_rate)
"""whitening"""
"""
Xtr_rows -= numpy.mean(Xtr_rows, axis=0) # zero-center the data (important)
cov = numpy.dot(Xtr_rows.T, Xtr_rows) / Xtr_rows.shape[0]
U,S,V = numpy.linalg.svd(cov)
Xrot = numpy.dot(Xtr_rows, U)# decorrelate the data
Xrot_reduced = numpy.dot(Xtr_rows, U[:,:100])
# whiten the data:
# divide by the eigenvalues (which are square roots of the singular values)
Xwhite = Xrot / numpy.sqrt(S + 1e-5)"""
"""whitening"""
#Xtr_rows = whiten(Xtr_rows)
# zero-center the data (important)
"""cov = numpy.dot(Xtr_rows.T, Xtr_rows) / Xtr_rows.shape[0]
U,S,V = numpy.linalg.svd(cov)
Xrot = numpy.dot(Xtr_rows, U)
Xtr_rows = Xrot / numpy.sqrt(S + 1e-5)
Xval_rot = numpy.dot(Xval_rows,U)
Xval_rows = Xval_rot / numpy.sqrt(S + 1e-5)
Xte_rot = numpy.dot(Xte_rows,U)
Xte_rows = Xte_rot / numpy.sqrt(S + 1e-5)
"""
train_set = (Xtr_rows, Ytr)
valid_set = (Xval_rows, Yval)
test_set = (Xte_rows, Yte)
test_set_x, test_set_y = shared_dataset(test_set)
valid_set_x, valid_set_y = shared_dataset(valid_set)
train_set_x, train_set_y = shared_dataset(train_set)
datasets = [(train_set_x, train_set_y), (valid_set_x, valid_set_y),
(test_set_x, test_set_y)]
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]
n_valid_batches = valid_set_x.get_value(borrow=True).shape[0]
n_test_batches = test_set_x.get_value(borrow=True).shape[0]
n_train_batches //= batch_size
n_valid_batches //= batch_size
n_test_batches //= batch_size
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
# start-snippet-1
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
######################
# BUILD ACTUAL MODEL #
######################
print('... building the model')
# Reshape matrix of rasterized images of shape (batch_size, 28 * 28)
# to a 4D tensor, compatible with our LeNetConvPoolLayer
# (28, 28) is the size of MNIST images.
layer0_input = x.reshape((batch_size, 3, 32, 32))
# Construct the first convolutional pooling layer:
# filtering reduces the image size to (32+4-5+1 , 32+4-5+1) = (32, 32)
# maxpooling reduces this further to (32/2, 32/2) = (16, 16)
# 4D output tensor is thus of shape (batch_size, nkerns[0], 16, 16)
layer0 = LeNetConvPoolLayer(
rng,
input=layer0_input,
image_shape=(batch_size, 3, 32, 32),
filter_shape=(nkerns[0], 3, 5, 5),
poolsize=(2, 2)
)
# Construct the second convolutional pooling layer
# filtering reduces the image size to (16+4-5+1, 16+4-5+1) = (16, 16)
# maxpooling reduces this further to (16/2, 16/2) = (8, 8)
# 4D output tensor is thus of shape (batch_size, nkerns[1], 8, 8)
layer1 = LeNetConvPoolLayer(
rng,
input=layer0.output,
image_shape=(batch_size, nkerns[0], 16, 16),
filter_shape=(nkerns[1], nkerns[0], 5, 5),
poolsize=(2, 2)
)
# the HiddenLayer being fully-connected, it operates on 2D matrices of
# shape (batch_size, num_pixels) (i.e matrix of rasterized images).
# This will generate a matrix of shape (batch_size, nkerns[1] * 4 * 4),
# or (500, 50 * 4 * 4) = (500, 800) with the default values.
layer2_input = layer1.output.flatten(2)
# construct a fully-connected sigmoidal layer
layer2 = HiddenLayer(
rng,
input=layer2_input,
n_in=nkerns[1] * 8 * 8,
n_out=500,
activation=relu
)
# classify the values of the fully-connected sigmoidal layer
layer3 = LogisticRegression(input=layer2.output, n_in=500, n_out=10)
# the cost we minimize during training is the NLL of the model
L2_reg = 0.001
L2_sqr = (
(layer2.W ** 2).sum()
+ (layer3.W ** 2).sum()
)
cost = layer3.negative_log_likelihood(y) + L2_reg * L2_sqr
# create a function to compute the mistakes that are made by the model
test_model = theano.function(
[index],
layer3.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(
[index],
layer3.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]
}
)
# create a list of all model parameters to be fit by gradient descent
params = layer3.params + layer2.params + layer1.params + layer0.params
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
# train_model is a function that updates the model parameters by
# SGD Since this model has many parameters, it would be tedious to
# manually create an update rule for each model parameter. We thus
# create the updates list by automatically looping over all
# (params[i], grads[i]) pairs.
updates = [
(param_i, param_i - learning_rate * grad_i)
for param_i, grad_i in zip(params, grads)
]
train_model = theano.function(
[index],
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-1
###############
# 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 = timeit.default_timer()
epoch = 0
done_looping = False
epoch_loss_list = []
epoch_val_list = []
while (epoch < n_epochs) and (not done_looping):
epoch += 1
if epoch == 10:
learning_rate.set_value(0.1)
# if epoch > 30:
# learning_rate.set_value(learning_rate.get_value()*0.9995)
if epoch > 3:
epoch_loss_np = numpy.reshape(epoch_loss_list, newshape=(len(epoch_loss_list), 3))
epoch_val_np = numpy.reshape(epoch_val_list, newshape=(len(epoch_val_list), 3))
numpy.savetxt(fname='epoc_cost.csv', X=epoch_loss_np,
fmt='%1.3f')
numpy.savetxt(fname='epoc_val_error.csv', X=epoch_val_np,
fmt='%1.3f')
for minibatch_index in range(n_train_batches):
iter = (epoch - 1) * n_train_batches + minibatch_index
if iter % 100 == 0:
print('training @ iter = ', iter)
cost_ij = train_model(minibatch_index)
epoch_loss_entry = [iter, epoch, float(cost_ij)]
epoch_loss_list.append(epoch_loss_entry)
if (iter + 1) % validation_frequency == 0:
# compute zero-one loss on validation set
validation_losses = [validate_model(i) for i
in range(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.))
epoch_val_entry = [iter, epoch, this_validation_loss]
epoch_val_list.append(epoch_val_entry)
# 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)
# save best validation score and iteration number
best_validation_loss = this_validation_loss
best_iter = iter
# test it on the test set
test_losses = [
test_model(i)
for i in range(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 = timeit.default_timer()
print('Optimization complete.')
print('Best validation score of %f %% obtained at iteration %i, '
'with test performance %f %%' %
(best_validation_loss * 100., best_iter + 1, test_score * 100.))
print(('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.)), file=sys.stderr)
epoch_loss_np = numpy.reshape(epoch_loss_list, newshape=(len(epoch_loss_list), 3))
epoch_val_np = numpy.reshape(epoch_val_list, newshape=(len(epoch_val_list), 3))
epoch_loss = pandas.DataFrame({"iter": epoch_loss_np[:, 0], "epoch": epoch_loss_np[:, 1],
"cost": epoch_loss_np[:, 2]})
epoch_vall = pandas.DataFrame({"iter": epoch_val_np[:, 0], "epoch": epoch_val_np[:, 1],
"val_error": epoch_val_np[:, 2]})
epoc_avg_loss = pandas.DataFrame(epoch_loss.groupby(['epoch']).mean()["cost"])
epoc_avg_val = pandas.DataFrame(epoch_vall.groupby(['epoch']).mean()["val_error"])
epoc_avg_loss = pandas.DataFrame({"epoch": epoc_avg_loss.index.values, "cost": epoc_avg_loss["cost"]})
epoc_avg_loss_val = pandas.DataFrame({"epoch": epoc_avg_val.index.values, "val_error": epoc_avg_val["val_error"]})
epoc_avg_loss.plot(kind="line", x="epoch", y="cost")
plt.show()
epoc_avg_loss_val.plot(kind='line', x="epoch", y="val_error")
plt.show()
class DBN(object):
def __init__(self, input=None, label=None,\
hidden_layer_sizes=[3, 3], num_layers=0, \
learning_rate=0.1):
self.x = input
self.y = label
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
assert self.num_layers >= 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
numpy_rng=numpy_rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
rbm_layer = RBM(
input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(
input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
def pretrain(self, lr=0.1, k=1, epochs=100):
# pre-train layer-wise
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[i - 1].sample_h_given_v(
layer_input)
rbm = self.rbm_layers[i]
for epoch in xrange(epochs):
rbm.contrastive_divergence(lr=lr, k=k, input=layer_input)
# cost = rbm.get_reconstruction_cross_entropy()
# print >> sys.stderr, \
# 'Pre-training layer %d, epoch %d, cost ' %(i, epoch), cost
def finetune(self, lr=0.1, epochs=100):
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# train log_layer
epoch = 0
done_looping = False
while (epoch < epochs) and (not done_looping):
self.log_layer.train(lr=lr, input=layer_input)
# self.finetune_cost = self.log_layer.negative_log_likelihood()
# print >> sys.stderr, 'Training epoch %d, cost is ' % epoch, self.finetune_cost
lr *= 0.95
epoch += 1
def predict(self, x):
layer_input = x
for i in xrange(self.n_layers):
sigmoid_layer = self.sigmoid_layers[i]
layer_input = sigmoid_layer.output(input=layer_input)
out = self.log_layer.predict(layer_input)
return out
class Dropout(object):
def __init__(self, input, label,\
n_in, hidden_layer_sizes, n_out,\
rng=None, activation=ReLU):
self.x = input
self.y = label
self.hidden_layers = []
self.n_layers = len(hidden_layer_sizes)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_in
else:
input_size = hidden_layer_sizes[i-1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.hidden_layers[-1].output()
# construct hidden_layer
hidden_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=activation)
self.hidden_layers.append(hidden_layer)
# layer for ouput using Logistic Regression (softmax)
self.log_layer = LogisticRegression(input=self.hidden_layers[-1].output(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_out)
def train(self, epochs=5000, dropout=True, p_dropout=0.5, rng=None):
for epoch in xrange(epochs):
dropout_masks = [] # create different masks in each training epoch
# forward hidden_layers
for i in xrange(self.n_layers):
if i == 0:
layer_input = self.x
layer_input = self.hidden_layers[i].forward(input=layer_input)
if dropout == True:
mask = self.hidden_layers[i].dropout(input=layer_input, p=p_dropout, rng=rng)
layer_input *= mask
dropout_masks.append(mask)
# forward & backward log_layer
self.log_layer.train(input=layer_input)
# backward hidden_layers
for i in reversed(xrange(0, self.n_layers)):
if i == self.n_layers-1:
prev_layer = self.log_layer
else:
prev_layer = self.hidden_layers[i+1]
if dropout == True:
self.hidden_layers[i].backward(prev_layer=prev_layer, dropout=True, mask=dropout_masks[i])
else:
self.hidden_layers[i].backward(prev_layer=prev_layer)
def predict(self, x, dropout=True, p_dropout=0.5):
layer_input = x
for i in xrange(self.n_layers):
if dropout == True:
self.hidden_layers[i].W = (1 - p_dropout) * self.hidden_layers[i].W
layer_input = self.hidden_layers[i].output(input=layer_input)
return self.log_layer.predict(layer_input)
def __init__(self, input=None, label=None,\
n_ins=2, hidden_layer_sizes=[3, 3], n_outs=2,\
rng=None):
self.x = input
self.y = label
self.sigmoid_layers = []
self.rbm_layers = []
self.n_layers = len(hidden_layer_sizes) # = len(self.rbm_layers)
if rng is None:
rng = numpy.random.RandomState(1234)
assert self.n_layers > 0
# construct multi-layer
for i in xrange(self.n_layers):
# layer_size
if i == 0:
input_size = n_ins
else:
input_size = hidden_layer_sizes[i - 1]
# layer_input
if i == 0:
layer_input = self.x
else:
layer_input = self.sigmoid_layers[-1].sample_h_given_v()
# construct sigmoid_layer
sigmoid_layer = HiddenLayer(input=layer_input,
n_in=input_size,
n_out=hidden_layer_sizes[i],
rng=rng,
activation=sigmoid)
self.sigmoid_layers.append(sigmoid_layer)
# construct rbm_layer
if i == 0:
rbm_layer = CRBM(input=layer_input, # continuous-valued inputs
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
else:
rbm_layer = RBM(input=layer_input,
n_visible=input_size,
n_hidden=hidden_layer_sizes[i],
W=sigmoid_layer.W, # W, b are shared
hbias=sigmoid_layer.b)
self.rbm_layers.append(rbm_layer)
# layer for output using Logistic Regression
self.log_layer = LogisticRegression(input=self.sigmoid_layers[-1].sample_h_given_v(),
label=self.y,
n_in=hidden_layer_sizes[-1],
n_out=n_outs)
# finetune cost: the negative log likelihood of the logistic regression layer
self.finetune_cost = self.log_layer.negative_log_likelihood()
