def __init__(self, model, type_model):
super(LatentTypeWithTuningCurve, self).__init__(model, type_model)
# Also initialize the tuning curves
self.mu = self.type_model['mu']
self.sigma = self.type_model['sigma']
# Create a basis for the stimulus response
self.spatial_basis = create_basis(self.type_model['spatial_basis'])
self.spatial_shape = self.type_model['spatial_shape']
self.spatial_ndim = len(self.spatial_shape)
(_,Bx) = self.spatial_basis.shape
self.temporal_basis = create_basis(self.type_model['temporal_basis'])
(_,Bt) = self.temporal_basis.shape
# Save the filter sizes
self.Bx = Bx
self.Bt = Bt
# Initialize interpolated bases
self.initialize_basis()
# Initialize RxBx and RxBt matrices for the per-type tuning curves
self.w_x = T.dmatrix('w_x')
self.w_t = T.dmatrix('w_t')
# Create function handles for the stimulus responses
self.stim_resp_t = T.dot(self.temporal_basis, self.w_t)
self.stim_resp_x = T.dot(self.spatial_basis, self.w_x)
# Add the probability of these tuning curves to the log probability
self.log_p += -0.5/self.sigma**2 *T.sum((self.w_x-self.mu)**2) + \
-0.5/self.sigma**2 *T.sum((self.w_t-self.mu)**2)
def test_pickle():
"""Test that a module can be pickled"""
M = Module()
M.x = (T.dmatrix())
M.y = (T.dmatrix())
a = T.dmatrix()
M.f = Method([a], a + M.x + M.y)
M.g = Method([a], a * M.x * M.y)
mode = get_mode()
m = M.make(x=numpy.zeros((4,5)), y=numpy.ones((2,3)), mode=mode)
m_dup = cPickle.loads(cPickle.dumps(m, protocol=-1))
assert numpy.all(m.x == m_dup.x) and numpy.all(m.y == m_dup.y)
m_dup.x[0,0] = 3.142
assert m_dup.f.input_storage[1].data[0,0] == 3.142
assert m.x[0,0] == 0.0 #ensure that m is not aliased to m_dup
#check that the unpickled version has the same argument/property aliasing
assert m_dup.x is m_dup.f.input_storage[1].data
assert m_dup.y is m_dup.f.input_storage[2].data
assert m_dup.x is m_dup.g.input_storage[1].data
assert m_dup.y is m_dup.g.input_storage[2].data
def make_functions(num_features):
W1_shape = (num_features/4, num_features)
b1_shape = num_features/4
W2_shape = (nb_classes, num_features/4)
b2_shape = nb_classes
W1 = shared(np.random.random(W1_shape) - 0.5, name = "W1")
b1 = shared(np.random.random(b1_shape) - 0.5, name = "b1")
W2 = shared(np.random.random(W2_shape) - 0.5, name = "W2")
b2 = shared(np.random.random(b2_shape) - 0.5, name = "b2")
x = T.dmatrix("x")
labels = T.dmatrix("labels")
hidden = T.nnet.sigmoid(x.dot(W1.transpose())+b1)
output = T.nnet.softmax(hidden.dot(W2.transpose()) + b2)
prediction = T.argmax(output, axis=1)
reg_lambda = 0.0001
regularization = reg_lambda * ((W1 * W1).sum() + (W2 * W2).sum() + (b1 * b1).sum() + (b2 * b2).sum())
cost = T.nnet.binary_crossentropy(output, labels).mean() + regularization
compute_prediction = function([x], prediction)
alpha = T.dscalar("alpha")
weights = [W1, W2, b1, b2]
updates = [(w, w-alpha * grad(cost, w)) for w in weights]
train_nn = function([x, labels, alpha],
cost,
updates = updates)
return train_nn, compute_prediction
def test_free_energy(self):
self.setUpAssociativeRBM()
rbm = self.rbm
w = rbm.W.get_value(borrow=True)
u = rbm.U.get_value(borrow=True)
v = T.dmatrix("v")
v2 = T.dmatrix("v2")
v_bias = rbm.v_bias.eval()
v_bias2 = rbm.v_bias2.eval()
h_bias = rbm.h_bias.eval()
res = rbm.free_energy(v, v2)
f = theano.function([v, v2], [res])
theano_res = f(self.x, self.y)
# Test for case only v1 is present
n1 = - np.dot(self.x, v_bias)
n2 = - np.dot(self.y, v_bias2)
n3 = - np.sum(np.log(1 + np.exp(h_bias + np.dot(self.x, w) + np.dot(self.y, u))))
np_res = n1 + n2 + n3
print theano_res
print np_res
diff = theano_res == np_res
self.assertTrue(np.all(diff))
def test_prop_up(self):
self.setUpSimpleRBM()
rbm = self.rbm
v1 = T.dmatrix("v1")
v2 = T.dmatrix("v2")
# Test Single
out = rbm.prop_up(v1)
out_fn = theano.function([], [out[0], out[1]], givens={v1: self.x1})
out_sum, out_sum_mapped = out_fn()
h_sum = np.dot(self.x1, rbm.W.get_value(borrow=True)) + rbm.h_bias.eval()
h_sum_mapped = 1 / (1 + np.exp(-h_sum))
self.assertTrue(np.all(out_sum == h_sum))
self.assertTrue((np.all(out_sum_mapped == h_sum_mapped)))
# Test Double
out = rbm.prop_up(v1, v2)
out_fn = theano.function([], [out[0], out[1]], givens={v1: self.x1, v2: self.x12})
out_sum, out_sum_mapped = out_fn()
h_sum = np.dot(self.x1, rbm.W.get_value(borrow=True)) + np.dot(self.x12, rbm.U.get_value(
borrow=True)) + rbm.h_bias.eval()
h_sum_mapped = 1 / (1 + np.exp(-h_sum))
# h_sum_mapped = theano.function([], [log_sig(h_sum)])()
self.assertTrue(np.all(out_sum == h_sum))
self.assertTrue((np.all(out_sum_mapped == h_sum_mapped)))
def test_prop_down(self):
self.setUpRBM()
self.assertTrue(self.rbm.h_n == 10)
rbm = self.rbm
W = rbm.W.get_value(borrow=True)
U = rbm.U.get_value(borrow=True)
v1 = T.dmatrix("v1")
v2 = T.dmatrix("v2")
h = np.array([[1, 2, 3, 4, 5, -1, -2, -3, -4, -5]])
# Single
x = T.dmatrix("x")
out = rbm.prop_down(x)
f = theano.function([x], out)
out_sum, out_sum_mapped = f(h)
h_sum = np.dot(h, W.T) + rbm.v_bias.eval()
h_sum_mapped = theano.function([], [log_sig(h_sum)])()
self.assertTrue(np.all(out_sum == h_sum))
self.assertTrue(np.all(out_sum_mapped == h_sum_mapped))
# Assoc
out = rbm.prop_down_assoc(x)
f = theano.function([x], out)
out_sum, out_sum_mapped = f(h)
h_sum2 = np.dot(h, U.T) + rbm.v_bias2.eval()
h_sum_mapped2 = theano.function([], [log_sig(h_sum2)])()
self.assertTrue(np.all(out_sum == h_sum2))
self.assertTrue(np.all(out_sum_mapped == h_sum_mapped2))
def test_validity2(self):
theano.config.on_unused_input = 'warn'
a0_var = T.dmatrix('a0')
r0_var = T.dmatrix('r0')
fri_var = T.dmatrix("fri")
out = T.dmatrix("out")
out_stale = T.dmatrix("out_stale")
f = theano.function([a0_var, r0_var, fri_var, out, out_stale],
dqn.build_loss(out, out_stale, a0_var, r0_var, fri_var, gamma=0.5))
sqr_mean, mean, y, q = f(np.array([[1, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 1]]),
np.array([[1],
[0],
[5]]),
np.array([[1],
[1],
[0]]),
np.array([[-5, 1, 2, 3, 4, 7],
[1, 4, 3, 4, 5, 9],
[0, 9, 0, 3, 2, 1]]),
np.array([[-5, 1, 2, 3, 4, 5],
[1, 2, 3, 4, 5, 6],
[8, 0, -1, -1, 2, 3]]))
print(y, q)
def createMLP(layers, s):
l_in = lasagne.layers.InputLayer(shape=(None, s))
prev_layer = l_in
Ws = []
for layer in layers:
enc = lasagne.layers.DenseLayer(prev_layer, num_units=layer, nonlinearity=rectify, W=init.Uniform(0.01))
Ws += [enc.W]
drop = lasagne.layers.DropoutLayer(enc, p=0.5)
prev_layer = drop
idx = 1
# creating mask
mask = lasagne.layers.InputLayer(shape=(None, layers[-1]))
prev_layer = lasagne.layers.ElemwiseMergeLayer([prev_layer, mask], merge_function=T.mul)
for layer in layers[-2::-1]:
print layer
dec = lasagne.layers.DenseLayer(prev_layer, num_units=layer, nonlinearity=rectify, W=Ws[-idx].T)
idx += 1
drop = lasagne.layers.DropoutLayer(dec, p=0.0)
prev_layer = drop
model = lasagne.layers.DenseLayer(prev_layer, num_units=s, nonlinearity=identity, W=Ws[0].T)
x_sym = T.dmatrix()
mask_sym = T.dmatrix()
all_params = lasagne.layers.get_all_params(model)
output = lasagne.layers.get_output(model, inputs={l_in: x_sym, mask: mask_sym})
loss_eval = lasagne.objectives.squared_error(output, x_sym).sum()
loss_eval /= (2.*batch_size)
updates = lasagne.updates.adam(loss_eval, all_params)
return l_in, mask, model, theano.function([x_sym, mask_sym], loss_eval, updates=updates)
def NNet(x=None, y=None, n_hid_layers=2):
# our points, one point per row
if x is None:
x = T.dmatrix()
# targets , one per row
if y is None:
y = T.dmatrix()
layers = []
_x = x
for i in xrange(n_hid_layers):
layers.append(Layer(x=_x))
_x = layers[-1].y
classif = LR(x=_x)
@symbolicmethod
def params():
rval = classif.params()
for l in layers:
rval.extend(l.params())
print([id(r) for r in rval])
return rval
if 0:
@symbolicmethod
def update(x, y):
pp = params()
gp = T.grad(classif.loss, pp)
return dict((p, p - 0.01*g) for p, g in zip(pp, gp))
return locals()
def LR(x=None, y=None, v=None, c=None, l2_coef=None):
# our points, one point per row
if x is None:
x = T.dmatrix()
# targets , one per row
if y is None:
y = T.dmatrix()
# first layer weights
if v is None:
v = T.dmatrix()
# first layer biases
if c is None:
c = T.dvector()
if l2_coef is None:
l2_coef = T.dscalar()
pred = T.dot(x, v) + c
sse = T.sum((pred - y) * (pred - y))
mse = sse / T.shape(y)[0]
v_l2 = T.sum(T.sum(v*v))
loss = mse + l2_coef * v_l2
@symbolicmethod
def params():
return [v, c]
return locals()
def __init__(self,N,Nsub,NRGC,prior=1):
self.N = N
self.Nsub = Nsub
self.NRGC = NRGC
U = Th.dmatrix() # SYMBOLIC variables #
V1 = Th.dvector() #
V2 = Th.dvector() #
STA = Th.dvector() #
STC = Th.dmatrix() #
theta = Th.dot( U.T , V1 ) #
UV1U = Th.dot( U , theta ) #
UV1V2U= Th.dot( V1 * U.T , (V2 * U.T).T ) #
posterior = -0.5 * Th.sum( V1 * V2 * U.T*U.T ) \
-0.25* Th.sum( UV1V2U.T * UV1V2U ) \
-0.5 * Th.sum( UV1U * UV1U * UV1U *V2 *V2 * V1 ) \
-0.5 * Th.sum( UV1U * UV1U * V2 * V1 ) \
-0.5 * Th.sum( theta * theta ) \
+ Th.dot( theta.T , STA ) \
+ Th.sum( Th.dot( V1* V2*U.T , U ) \
* (STC + STA.T*STA) )
dpost_dU = Th.grad( cost = posterior , #
wrt = U ) #
dpost_dV1 = Th.grad( cost = posterior , #
wrt = V1 ) #
dpost_dV2 = Th.grad( cost = posterior , #
wrt = V2 ) #
# self.posterior = function( [U,V2,V1,STA,STC], UV1V2U) #
self.posterior = function( [U,V2,V1,STA,STC], posterior) #
self.dpost_dU = function( [U,V2,V1,STA,STC], dpost_dU ) #
self.dpost_dV1 = function( [U,V2,V1,STA,STC], dpost_dV1 ) #
self.dpost_dV2 = function( [U,V2,V1,STA,STC], dpost_dV2 ) #
def make_theano_functions(self) :
x = T.dmatrix('x')
h1 = T.dot(x, self.w1.T) + self.b1
a1 = 1. / (1. + T.exp(-h1))
h2 = T.dot(a1,self.w2.T) + self.b2
a2 = T.nnet.softmax(h2)
f = theano.function([x], a2)
y = T.dmatrix('y')
loss = T.mean(T.sum(y*-T.log(a2), axis=1))
gradw1 = T.grad(loss, self.w1)
gradw2 = T.grad(loss, self.w2)
gradb1 = T.grad(loss, self.b1)
gradb2 = T.grad(loss, self.b2)
gradf = theano.function(
[x, y],
[loss, a2],
updates = [
(self.w1, self.w1-self.lr*gradw1),
(self.w2, self.w2-self.lr*gradw2),
(self.b1, self.b1-self.lr*gradb1),
(self.b2, self.b2-self.lr*gradb2)
]
)
return f, gradf
def UV12_input(V1=Th.dmatrix(),
STAs=Th.dmatrix(),
STCs=Th.dtensor3(),
N_spikes=Th.dvector(),
**other):
other.update(locals())
return named(**other)
def theano_sed():
"""
Function to create a theano function to compute the euclidian distances efficiently
Returns:
theano.compile.function_module.Function: Compiled function
"""
theano.config.compute_test_value = "ignore"
# Set symbolic variable as matrix (with the XYZ coords)
coord_T_x1 = T.dmatrix()
coord_T_x2 = T.dmatrix()
# Euclidian distances function
def squared_euclidean_distances(x_1, x_2):
sqd = T.sqrt(T.maximum(
(x_1 ** 2).sum(1).reshape((x_1.shape[0], 1)) +
(x_2 ** 2).sum(1).reshape((1, x_2.shape[0])) -
2 * x_1.dot(x_2.T), 0
))
return sqd
# Compiling function
f = theano.function([coord_T_x1, coord_T_x2],
squared_euclidean_distances(coord_T_x1, coord_T_x2),
allow_input_downcast=False)
return f
def test_infer_shape(self):
admat = dmatrix()
bdmat = dmatrix()
admat_val = numpy.random.rand(3, 4)
bdmat_val = numpy.random.rand(3, 4)
self._compile_and_check([admat, bdmat], [SoftmaxGrad()(admat, bdmat)],
[admat_val, bdmat_val], SoftmaxGrad)
def LQLEP_wBarrier( LQLEP = Th.dscalar(), ldet = Th.dscalar(), v1 = Th.dvector(),
N_spike = Th.dscalar(), ImM = Th.dmatrix(), U = Th.dmatrix(),
V2 = Th.dvector(), u = Th.dvector(), C = Th.dmatrix(),
**other):
'''
The actual Linear-Quadratic-Exponential-Poisson log-likelihood,
as a function of theta and M,
with a barrier on the log-det term and a prior.
'''
sq_nonlinearity = V2**2.*Th.sum( Th.dot(U,C)*U, axis=[1]) #Th.sum(U**2,axis=[1])
nonlinearity = V2 * Th.sqrt( Th.sum( Th.dot(U,C)*U, axis=[1])) #Th.sum(U**2,axis=[1]) )
if other.has_key('uc'):
LQLEP_wPrior = LQLEP + 0.5 * N_spike * ( 1./(ldet+250.)**2. \
- 0.000001 * Th.sum(Th.log(1.-4*sq_nonlinearity))) \
+ 10. * Th.sum( (u[2:]+u[:-2]-2*u[1:-1])**2. ) \
+ 10. * Th.sum( (other['uc'][2:]+other['uc'][:-2]-2*other['uc'][1:-1])**2. ) \
+ 0.000000001 * Th.sum( v1**2. )
# + 100. * Th.sum( v1 )
# + 0.0001*Th.sum( V2**2 )
else:
LQLEP_wPrior = LQLEP + 0.5 * N_spike * ( 1./(ldet+250.)**2. \
- 0.000001 * Th.sum(Th.log(1.-4*sq_nonlinearity))) \
+ 10. * Th.sum( (u[2:]+u[:-2]-2*u[1:-1])**2. ) \
+ 0.000000001 * Th.sum( v1**2. )
# + 100. * Th.sum( v1 )
# + 0.0001*Th.sum( V2**2 )
eigsImM,barrier = eig( ImM )
barrier = 1-(Th.sum(Th.log(eigsImM))>-250) * \
(Th.min(eigsImM)>0) * (Th.max(4*sq_nonlinearity)<1)
other.update(locals())
return named( **other )
def get_hidden_layers(dbn, layers):
print "... getting hidden layers"
test_data, test_label = get_test_set()
index = T.lscalar()
hidden_features = []
total_layers = len(layers)
w = T.dmatrix("w")
t = T.dmatrix("t")
b = T.vector("b")
z = T.dot(w,t)
# function for testing model
test_f = theano.function([w,t], z)
#loop through each layer
for i in xrange(total_layers):
weights = layers[i][0]
bias = layers[i][1]
if i == 0:
hidden_features.append( test_f(test_data,weights) )
else:
#use previous layer
prev_layer = hidden_features[i-1]
hidden_features.append( test_f(prev_layer,weights) )
# apply sigmoid
with open('hidden.pkl', 'w') as f:
cPickle.dump(hidden_features, f)
def test_validity(self):
theano.config.on_unused_input = 'warn'
a0_var = T.dmatrix('a0')
r0_var = T.dmatrix('r0')
fri_var = T.dmatrix("fri")
out = T.dmatrix("out")
out_stale = T.dmatrix("out_stale")
f = theano.function([a0_var, r0_var, fri_var, out, out_stale],
dqn.build_loss(out, out_stale, a0_var, r0_var, fri_var, gamma=0.5))
loss, not_loss, y, q = f(np.array([[1, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0]]),
np.array([[1],
[0]]),
np.array([[1],
[1]]),
np.array([[-5, 1, 2, 3, 4, 7],
[1, 4, 3, 4, 5, 9]]),
np.array([[-5, 1, 2, 3, 4, 5],
[1, 2, 3, 4, 5, 6]]))
self.assertTrue(np.all(y == [[3.5], [3]]))
self.assertTrue(np.all(q == [[-5], [4]]))
print(loss)
print(not_loss)
self.assertTrue(loss == 8.5)
def __init__(self, beta=0.1, n_in=1, n_out=1):
self.__beta = beta
self.__x = T.dmatrix('x')
self.__y = T.dmatrix('y')
self.__n_in = n_in
self.__n_out = n_out
self.__clf_model = _LogisticRegressionModel(d_input=self.__x,
n_in=self.__n_in,
n_out=self.__n_out)
self.__cost = self.__clf_model.negative_log_likelihood(self.__y)
# compute the gradient of cost with respect to theta = (W,b)
self.__g_W = T.grad(cost=self.__cost, wrt=self.__clf_model.W)
self.__g_b = T.grad(cost=self.__cost, wrt=self.__clf_model.b)
# start-snippet-3
# specify how to update the parameters of the model as a list of
# (variable, update expression) pairs.
self.__updates = [(self.__clf_model.W,
self.__clf_model.W - self.__beta * self.__g_W),
(self.__clf_model.b, self.__clf_model.b
- self.__beta * self.__g_b)]
self.__train_model = theano.function(
inputs=[self.__x, self.__y],
outputs=[self.__cost, self.__clf_model.y_pred, self.__g_W, self.__g_b],
updates=self.__updates,
)
self.__prediction_model = theano.function(
inputs=[self.__clf_model.input],
outputs=self.__clf_model.y_pred
)
def test_mixin_composition():
# Check composed expressions as parameters
a = theano.shared(0.0)
b = theano.shared(-1.0)
mu = a + b - 1.0
sigma = T.abs_(a * b)
p = Normal(mu=mu, sigma=sigma)
assert a in p.parameters_
assert b in p.parameters_
# Compose parameters with observed variables
a = theano.shared(1.0)
b = theano.shared(0.0)
y = T.dmatrix(name="y")
p = Normal(mu=a * y + b)
assert len(p.parameters_) == 3
assert a in p.parameters_
assert b in p.parameters_
assert p.sigma in p.parameters_
assert p.mu not in p.parameters_
assert len(p.observeds_) == 1
assert y in p.observeds_
# Check signatures
data_X = np.random.rand(10, 1)
data_y = np.random.rand(10, 1)
p.pdf(X=data_X, y=data_y)
p.cdf(X=data_X, y=data_y)
p.rvs(10, y=data_y)
# Check error
a = theano.shared(1.0)
b = theano.shared(0.0)
y = T.dmatrix() # y must be named
assert_raises(ValueError, Normal, mu=a * y + b)
def asho_test():
import theano.tensor as T
x = T.dmatrix('x')
w = T.dmatrix('w')
y = T.dot(x,w)
f = function([x,w],y)
def theano_setup(self):
W = T.dmatrix('W')
b = T.dvector('b')
c = T.dvector('c')
x = T.dmatrix('x')
s = T.dot(x, W) + c
# h = 1 / (1 + T.exp(-s))
# h = T.nnet.sigmoid(s)
h = T.tanh(s)
# r = T.dot(h,W.T) + b
# r = theano.printing.Print("r=")(2*T.tanh(T.dot(h,W.T) + b))
ract = T.dot(h,W.T) + b
r = self.output_scaling_factor * T.tanh(ract)
#g = function([W,b,c,x], h)
#f = function([W,b,c,h], r)
#fg = function([W,b,c,x], r)
# Another variable to be able to call a function
# with a noisy x and compare it to a reference x.
y = T.dmatrix('y')
all_losses = ((r - y)**2)
loss = T.sum(all_losses)
#loss = ((r - y)**2).sum()
self.theano_encode_decode = function([W,b,c,x], r)
self.theano_all_losses = function([W,b,c,x,y], [all_losses, T.abs_(s), T.abs_(ract)])
self.theano_gradients = function([W,b,c,x,y], [T.grad(loss, W), T.grad(loss, b), T.grad(loss, c)])
def __init__(self,
np_rng = np.random.RandomState(1234),
theano_rng = None,
n_in = 424 * 424 * 3,
n_out = 37, # galaxy classes
hidden_layer_sizes = [500, 500],
corruption_levels = [0.1, 0.2]):
self.np_rng = np_rng
if not theano_rng: theano_rng = RandomStreams(np_rng.randint(2 ** 30))
self.n_in = n_in
self.n_out = n_out
self.hidden_layer_sizes = hidden_layer_sizes
self.corruption_levels = corruption_levels
self.sigmoid_layers = []
self.da_layers = []
self.params = []
self.n_layers = len(hidden_layer_sizes)
assert self.n_layers > 0, 'must have some hidden layers'
self.x = T.dmatrix('x')
self.y = T.dmatrix('y')
self.build_layers()
def train( self, train_set, batch_size = 100 ):
for i in xrange(len(self.layers) - 1):
train_data = T.dmatrix('train_data')
x = T.dmatrix('x')
rng = numpy.random.RandomState(123)
theano_rng = RandomStreams(rng.randint(2 ** 10))
da = dA(
numpy_rng=rng,
theano_rng=theano_rng,
input=x,
n_visible=self.layers[i],
n_hidden=self.layers[i+1]
)
cost, updates = da.get_cost_updates(
corruption_level=0.,
learning_rate=0.4
)
train_da = theano.function(
[train_data],
cost,
updates=updates,
givens={
x: train_data
}
)
for epoch in xrange(200):
train_cost = []
for index in xrange(len(train_set)/batch_size):
train_cost.append(train_da(numpy.asarray(train_set[index * batch_size: (index + 1) * batch_size])))
print 'Training 1st ae epoch %d, cost ' % epoch, numpy.mean(train_cost)
train_set = da.get_hidden_values(train_set).eval()
self.dAs.append(da)
def neural_net(
x=T.dmatrix(), #our points, one point per row
y=T.dmatrix(), #our targets
w=T.dmatrix(), #first layer weights
b=T.dvector(), #first layer bias
v=T.dmatrix(), #second layer weights
c=T.dvector(), #second layer bias
step=T.dscalar(), #step size for gradient descent
l2_coef=T.dscalar() #l2 regularization amount
):
"""Idea A:
"""
hid = T.tanh(T.dot(x, w) + b)
pred = T.dot(hid, v) + c
sse = T.sum((pred - y) * (pred - y))
w_l2 = T.sum(T.sum(w*w))
v_l2 = T.sum(T.sum(v*v))
loss = sse + l2_coef * (w_l2 + v_l2)
def symbolic_params(cls):
return [cls.w, cls.b, cls.v, cls.c]
def update(cls, x, y, **kwargs):
params = cls.symbolic_params()
gp = T.grad(cls.loss, params)
return [], [In(p, update=p - cls.step * g) for p,g in zip(params, gp)]
def predict(cls, x, **kwargs):
return cls.pred, []
return locals()
def theano_setup(self):
# The matrices Wb and Wc were originally tied.
# Because of that, I decided to keep Wb and Wc with
# the same shape (instead of being transposed) to
# avoid disturbing the code as much as possible.
Wb = T.dmatrix('Wb')
Wc = T.dmatrix('Wc')
b = T.dvector('b')
c = T.dvector('c')
s = T.dscalar('s')
x = T.dmatrix('x')
h_act = T.dot(x, Wc) + c
if self.act_func[0] == 'tanh':
h = T.tanh(h_act)
elif self.act_func[0] == 'sigmoid':
h = T.nnet.sigmoid(h_act)
elif self.act_func[0] == 'id':
# bad idae
h = h_act
else:
raise("Invalid act_func[0]")
r_act = T.dot(h, Wb.T) + b
if self.act_func[1] == 'tanh':
r = s * T.tanh(r_act)
elif self.act_func[1] == 'sigmoid':
r = s * T.nnet.sigmoid(r_act)
elif self.act_func[1] == 'id':
r = s * r_act
else:
raise("Invalid act_func[1]")
# Another variable to be able to call a function
# with a noisy x and compare it to a reference x.
y = T.dmatrix('y')
loss = ((r - y)**2)
sum_loss = T.sum(loss)
# theano_encode_decode : vectorial function in argument X.
# theano_loss : vectorial function in argument X.
# theano_gradients : returns triplet of gradients, each of
# which involves the all data X summed
# so it's not a "vectorial" function.
self.theano_encode_decode = function([Wb,Wc,b,c,s,x], r)
self.theano_loss = function([Wb,Wc,b,c,s,x,y], loss)
self.theano_gradients = function([Wb,Wc,b,c,s,x,y],
[T.grad(sum_loss, Wb), T.grad(sum_loss, Wc),
T.grad(sum_loss, b), T.grad(sum_loss, c),
T.grad(sum_loss, s)])
# other useful theano functions for the experiments that involve
# adding noise to the hidden states
self.theano_encode = function([Wc,c,x], h)
self.theano_decode = function([Wb,b,s,h], r)
def test_argsort():
# Set up
rng = np.random.RandomState(seed=utt.fetch_seed())
m_val = rng.rand(3, 2)
v_val = rng.rand(4)
# Example 1
a = tensor.dmatrix()
w = argsort(a)
f = theano.function([a], w)
gv = f(m_val)
gt = np.argsort(m_val)
assert np.allclose(gv, gt)
# Example 2
a = tensor.dmatrix()
axis = tensor.lscalar()
w = argsort(a, axis)
f = theano.function([a, axis], w)
for axis_val in 0, 1:
gv = f(m_val, axis_val)
gt = np.argsort(m_val, axis_val)
assert np.allclose(gv, gt)
# Example 3
a = tensor.dvector()
w2 = argsort(a)
f = theano.function([a], w2)
gv = f(v_val)
gt = np.argsort(v_val)
assert np.allclose(gv, gt)
# Example 4
a = tensor.dmatrix()
axis = tensor.lscalar()
l = argsort(a, axis, "mergesort")
f = theano.function([a, axis], l)
for axis_val in 0, 1:
gv = f(m_val, axis_val)
gt = np.argsort(m_val, axis_val)
assert np.allclose(gv, gt)
# Example 5
a = tensor.dmatrix()
axis = tensor.lscalar()
a1 = ArgSortOp("mergesort", [])
a2 = ArgSortOp("quicksort", [])
# All the below should give true
assert a1 != a2
assert a1 == ArgSortOp("mergesort", [])
assert a2 == ArgSortOp("quicksort", [])
# Example 6: Testing axis=None
a = tensor.dmatrix()
w2 = argsort(a, None)
f = theano.function([a], w2)
gv = f(m_val)
gt = np.argsort(m_val, None)
assert np.allclose(gv, gt)
def test_infer_shape(self):
x = tensor.dmatrix()
y = tensor.dmatrix()
self._compile_and_check([x, y], [self.op_class()(x, y)],
[numpy.random.rand(5, 6),
numpy.random.rand(5, 6)],
self.op_class)
def eigs( theta = Th.dvector('theta'), M = Th.dmatrix('M') ,
STA = Th.dvector('STA') , STC = Th.dmatrix('STC'), **other):
'''
Return eigenvalues of I-sym(M), for display/debugging purposes.
'''
ImM = Th.identity_like(M)-(M+M.T)/2
w,v = eig( ImM )
return w
def ldet( theta = Th.dvector('theta'), M = Th.dmatrix('M') ,
STA = Th.dvector('STA'), STC = Th.dmatrix('STC'), **other):
'''
Return log-det of I-sym(M), for display/debugging purposes.
'''
ImM = Th.identity_like(M)-(M+M.T)/2
w, v = eig(ImM)
return Th.sum(Th.log(w))
def fit_rkl(data, log_p, max_epochs=20):
"""
Fit isotropic Gaussian by minimizing reverse Kullback-Leibler divergence.
"""
# data dimensionality
D = data.shape[0]
# data and hidden states
X = tt.dmatrix('X')
Z = tt.dmatrix('Z')
nr.seed(int(time() * 1000.) % 4294967295)
idx = nr.permutation(data.shape[1])[:100]
# initialize parameters
b = th.shared(np.mean(data[:, idx], 1)[:, None],
broadcastable=(False, True))
a = th.shared(np.std(data[:, idx] - b.get_value(), 1)[:, None],
broadcastable=[False, True])
# model density
q = lambda X: normal(X, b, a)
log_q = lambda X: -0.5 * tt.sum(tt.square(
(X - b) / a), 0) - D * tt.log(tt.abs_(a)) - D / 2. * np.log(np.pi)
G = lambda Z: a * Z + b
# geometric Jensen-Shannon divergence
RKL = tt.mean(tt.exp(log_p(X)) * (log_p(X) - log_q(X))) + tt.mean(0.0 * Z)
# function computing G-JSD and its gradient
f_rkl = th.function([Z, X], [RKL, th.grad(RKL, a), th.grad(RKL, b)])
# SGD hyperparameters
B = 200
mm = 0.8
lr = .5
da = 0.
db = 0.
try:
# display initial JSD
print('{0:>4} {1:.4f}'.format(
0, float(f_rkl(nr.randn(*data.shape), data)[0])))
for epoch in range(max_epochs):
values = []
# stochastic gradient descent
for t in range(0, data.shape[1], B):
Z = nr.randn(D, B)
Y = data[:, t:t + B]
v, ga, gb = f_rkl(Z, Y)
da = mm * da - lr * ga
db = mm * db - lr * gb
values.append(v)
a.set_value(a.get_value() + da)
b.set_value(b.get_value() + db)
# reduce learning rate
lr /= 2.
# display estimated JSD
print('{0:>4} {1:.4f}'.format(epoch + 1, np.mean(values)))
except KeyboardInterrupt:
pass
return a.get_value() * np.eye(D), b.get_value()
def evaluate_lenet5(learning_rate=0.05,
n_epochs=2000,
nkerns=[50],
batch_size=1,
window_width=4,
maxSentLength=64,
emb_size=300,
hidden_size=200,
margin=0.5,
L2_weight=0.0003,
update_freq=1,
norm_threshold=5.0,
max_truncate=40):
maxSentLength = max_truncate + 2 * (window_width - 1)
model_options = locals().copy()
print "model options", model_options
rootPath = '/mounts/data/proj/wenpeng/Dataset/WikiQACorpus/'
rng = numpy.random.RandomState(23455)
datasets, vocab_size = load_wikiQA_corpus(
rootPath + 'vocab.txt', rootPath + 'WikiQA-train.txt',
rootPath + 'test_filtered.txt', max_truncate,
maxSentLength) #vocab_size contain train, dev and test
#datasets, vocab_size=load_wikiQA_corpus(rootPath+'vocab_lower_in_word2vec.txt', rootPath+'WikiQA-train.txt', rootPath+'test_filtered.txt', maxSentLength)#vocab_size contain train, dev and test
mtPath = '/mounts/data/proj/wenpeng/Dataset/WikiQACorpus/MT/BLEU_NIST/'
mt_train, mt_test = load_mts_wikiQA(
mtPath + 'result_train/concate_2mt_train.txt',
mtPath + 'result_test/concate_2mt_test.txt')
wm_train, wm_test = load_wmf_wikiQA(
rootPath + 'train_word_matching_scores.txt',
rootPath + 'test_word_matching_scores.txt')
#wm_train, wm_test=load_wmf_wikiQA(rootPath+'train_word_matching_scores_normalized.txt', rootPath+'test_word_matching_scores_normalized.txt')
indices_train, trainY, trainLengths, normalized_train_length, trainLeftPad, trainRightPad = datasets[
0]
indices_train_l = indices_train[::2, :]
indices_train_r = indices_train[1::2, :]
trainLengths_l = trainLengths[::2]
trainLengths_r = trainLengths[1::2]
normalized_train_length_l = normalized_train_length[::2]
normalized_train_length_r = normalized_train_length[1::2]
trainLeftPad_l = trainLeftPad[::2]
trainLeftPad_r = trainLeftPad[1::2]
trainRightPad_l = trainRightPad[::2]
trainRightPad_r = trainRightPad[1::2]
indices_test, testY, testLengths, normalized_test_length, testLeftPad, testRightPad = datasets[
1]
indices_test_l = indices_test[::2, :]
indices_test_r = indices_test[1::2, :]
testLengths_l = testLengths[::2]
testLengths_r = testLengths[1::2]
normalized_test_length_l = normalized_test_length[::2]
normalized_test_length_r = normalized_test_length[1::2]
testLeftPad_l = testLeftPad[::2]
testLeftPad_r = testLeftPad[1::2]
testRightPad_l = testRightPad[::2]
testRightPad_r = testRightPad[1::2]
n_train_batches = indices_train_l.shape[0] / batch_size
n_test_batches = indices_test_l.shape[0] / batch_size
train_batch_start = list(numpy.arange(n_train_batches) * batch_size)
test_batch_start = list(numpy.arange(n_test_batches) * batch_size)
indices_train_l = theano.shared(numpy.asarray(indices_train_l,
dtype=theano.config.floatX),
borrow=True)
indices_train_r = theano.shared(numpy.asarray(indices_train_r,
dtype=theano.config.floatX),
borrow=True)
indices_test_l = theano.shared(numpy.asarray(indices_test_l,
dtype=theano.config.floatX),
borrow=True)
indices_test_r = theano.shared(numpy.asarray(indices_test_r,
dtype=theano.config.floatX),
borrow=True)
indices_train_l = T.cast(indices_train_l, 'int64')
indices_train_r = T.cast(indices_train_r, 'int64')
indices_test_l = T.cast(indices_test_l, 'int64')
indices_test_r = T.cast(indices_test_r, 'int64')
rand_values = random_value_normal((vocab_size + 1, emb_size),
theano.config.floatX,
numpy.random.RandomState(1234))
rand_values[0] = numpy.array(numpy.zeros(emb_size),
dtype=theano.config.floatX)
#rand_values[0]=numpy.array([1e-50]*emb_size)
rand_values = load_word2vec_to_init(rand_values,
rootPath + 'vocab_embs_300d.txt')
#rand_values=load_word2vec_to_init(rand_values, rootPath+'vocab_lower_in_word2vec_embs_300d.txt')
embeddings = theano.shared(value=rand_values, borrow=True)
#cost_tmp=0
error_sum = 0
# allocate symbolic variables for the data
index = T.lscalar()
x_index_l = T.lmatrix(
'x_index_l') # now, x is the index matrix, must be integer
x_index_r = T.lmatrix('x_index_r')
y = T.lvector('y')
left_l = T.lscalar()
right_l = T.lscalar()
left_r = T.lscalar()
right_r = T.lscalar()
length_l = T.lscalar()
length_r = T.lscalar()
norm_length_l = T.dscalar()
norm_length_r = T.dscalar()
mts = T.dmatrix()
wmf = T.dmatrix()
cost_tmp = T.dscalar()
#x=embeddings[x_index.flatten()].reshape(((batch_size*4),maxSentLength, emb_size)).transpose(0, 2, 1).flatten()
ishape = (emb_size, maxSentLength) # this is the size of MNIST images
filter_size = (emb_size, window_width)
#poolsize1=(1, ishape[1]-filter_size[1]+1) #?????????????????????????????
length_after_wideConv = ishape[1] + filter_size[1] - 1
######################
# 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
#layer0_input = x.reshape(((batch_size*4), 1, ishape[0], ishape[1]))
layer0_l_input = embeddings[x_index_l.flatten()].reshape(
(batch_size, maxSentLength,
emb_size)).transpose(0, 2, 1).dimshuffle(0, 'x', 1, 2)
layer0_r_input = embeddings[x_index_r.flatten()].reshape(
(batch_size, maxSentLength,
emb_size)).transpose(0, 2, 1).dimshuffle(0, 'x', 1, 2)
conv_W, conv_b = create_conv_para(rng,
filter_shape=(nkerns[0], 1,
filter_size[0],
filter_size[1]))
#layer0_output = debug_print(layer0.output, 'layer0.output')
layer0_l = Conv_with_input_para(rng,
input=layer0_l_input,
image_shape=(batch_size, 1, ishape[0],
ishape[1]),
filter_shape=(nkerns[0], 1, filter_size[0],
filter_size[1]),
W=conv_W,
b=conv_b)
layer0_r = Conv_with_input_para(rng,
input=layer0_r_input,
image_shape=(batch_size, 1, ishape[0],
ishape[1]),
filter_shape=(nkerns[0], 1, filter_size[0],
filter_size[1]),
W=conv_W,
b=conv_b)
layer0_l_output = debug_print(layer0_l.output, 'layer0_l.output')
layer0_r_output = debug_print(layer0_r.output, 'layer0_r.output')
layer1 = Average_Pooling_for_Top(rng,
input_l=layer0_l_output,
input_r=layer0_r_output,
kern=nkerns[0],
left_l=left_l,
right_l=right_l,
left_r=left_r,
right_r=right_r,
length_l=length_l + filter_size[1] - 1,
length_r=length_r + filter_size[1] - 1,
dim=maxSentLength + filter_size[1] - 1)
#layer2=HiddenLayer(rng, input=layer1_out, n_in=nkerns[0]*2, n_out=hidden_size, activation=T.tanh)
sum_uni_l = T.sum(layer0_l_input, axis=3).reshape((1, emb_size))
aver_uni_l = sum_uni_l / layer0_l_input.shape[3]
norm_uni_l = sum_uni_l / T.sqrt((sum_uni_l**2).sum())
sum_uni_r = T.sum(layer0_r_input, axis=3).reshape((1, emb_size))
aver_uni_r = sum_uni_r / layer0_r_input.shape[3]
norm_uni_r = sum_uni_r / T.sqrt((sum_uni_r**2).sum())
uni_cosine = cosine(sum_uni_l, sum_uni_r)
aver_uni_cosine = cosine(aver_uni_l, aver_uni_r)
uni_sigmoid_simi = debug_print(
T.nnet.sigmoid(T.dot(norm_uni_l, norm_uni_r.T)).reshape((1, 1)),
'uni_sigmoid_simi')
'''
linear=Linear(sum_uni_l, sum_uni_r)
poly=Poly(sum_uni_l, sum_uni_r)
sigmoid=Sigmoid(sum_uni_l, sum_uni_r)
rbf=RBF(sum_uni_l, sum_uni_r)
gesd=GESD(sum_uni_l, sum_uni_r)
'''
eucli_1 = 1.0 / (1.0 + EUCLID(sum_uni_l, sum_uni_r)) #25.2%
#eucli_1_exp=1.0/T.exp(EUCLID(sum_uni_l, sum_uni_r))
len_l = norm_length_l.reshape((1, 1))
len_r = norm_length_r.reshape((1, 1))
'''
len_l=length_l.reshape((1,1))
len_r=length_r.reshape((1,1))
'''
#length_gap=T.log(1+(T.sqrt((len_l-len_r)**2))).reshape((1,1))
#length_gap=T.sqrt((len_l-len_r)**2)
#layer3_input=mts
layer3_input = T.concatenate(
[ #mts,
uni_cosine, #eucli_1_exp,#uni_sigmoid_simi, #norm_uni_l-(norm_uni_l+norm_uni_r)/2,#uni_cosine, #
layer1.
output_cosine, #layer1.output_eucli_to_simi_exp,#layer1.output_sigmoid_simi,#layer1.output_vector_l-(layer1.output_vector_l+layer1.output_vector_r)/2,#layer1.output_cosine, #
len_l,
len_r,
wmf
],
axis=1) #, layer2.output, layer1.output_cosine], axis=1)
#layer3_input=T.concatenate([mts,eucli, uni_cosine, len_l, len_r, norm_uni_l-(norm_uni_l+norm_uni_r)/2], axis=1)
#layer3=LogisticRegression(rng, input=layer3_input, n_in=11, n_out=2)
layer3 = LogisticRegression(rng,
input=layer3_input,
n_in=(1) + (1) + 2 + 2,
n_out=2)
#L2_reg =(layer3.W** 2).sum()+(layer2.W** 2).sum()+(layer1.W** 2).sum()+(conv_W** 2).sum()
L2_reg = debug_print(
(layer3.W**2).sum() + (conv_W**2).sum(),
'L2_reg') #+(layer1.W** 2).sum()++(embeddings**2).sum()
cost_this = debug_print(layer3.negative_log_likelihood(y),
'cost_this') #+L2_weight*L2_reg
cost = debug_print(
(cost_this + cost_tmp) / update_freq + L2_weight * L2_reg, 'cost')
#cost=debug_print((cost_this+cost_tmp)/update_freq, 'cost')
test_model = theano.function(
[index], [layer3.prop_for_posi, layer3_input, y],
givens={
x_index_l: indices_test_l[index:index + batch_size],
x_index_r: indices_test_r[index:index + batch_size],
y: testY[index:index + batch_size],
left_l: testLeftPad_l[index],
right_l: testRightPad_l[index],
left_r: testLeftPad_r[index],
right_r: testRightPad_r[index],
length_l: testLengths_l[index],
length_r: testLengths_r[index],
norm_length_l: normalized_test_length_l[index],
norm_length_r: normalized_test_length_r[index],
mts: mt_test[index:index + batch_size],
wmf: wm_test[index:index + batch_size]
},
on_unused_input='ignore')
#params = layer3.params + layer2.params + layer1.params+ [conv_W, conv_b]
params = layer3.params + [conv_W, conv_b] #+[embeddings]# + layer1.params
params_conv = [conv_W, conv_b]
accumulator = []
for para_i in params:
eps_p = numpy.zeros_like(para_i.get_value(borrow=True),
dtype=theano.config.floatX)
accumulator.append(theano.shared(eps_p, borrow=True))
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
updates = []
for param_i, grad_i, acc_i in zip(params, grads, accumulator):
grad_i = debug_print(grad_i, 'grad_i')
acc = acc_i + T.sqr(grad_i)
updates.append(
(param_i,
param_i - learning_rate * grad_i / T.sqrt(acc))) #AdaGrad
updates.append((acc_i, acc))
train_model = theano.function(
[index, cost_tmp],
cost,
updates=updates,
givens={
x_index_l: indices_train_l[index:index + batch_size],
x_index_r: indices_train_r[index:index + batch_size],
y: trainY[index:index + batch_size],
left_l: trainLeftPad_l[index],
right_l: trainRightPad_l[index],
left_r: trainLeftPad_r[index],
right_r: trainRightPad_r[index],
length_l: trainLengths_l[index],
length_r: trainLengths_r[index],
norm_length_l: normalized_train_length_l[index],
norm_length_r: normalized_train_length_r[index],
mts: mt_train[index:index + batch_size],
wmf: wm_train[index:index + batch_size]
},
on_unused_input='ignore')
train_model_predict = theano.function(
[index], [cost_this, layer3.errors(y), layer3_input, y],
givens={
x_index_l: indices_train_l[index:index + batch_size],
x_index_r: indices_train_r[index:index + batch_size],
y: trainY[index:index + batch_size],
left_l: trainLeftPad_l[index],
right_l: trainRightPad_l[index],
left_r: trainLeftPad_r[index],
right_r: trainRightPad_r[index],
length_l: trainLengths_l[index],
length_r: trainLengths_r[index],
norm_length_l: normalized_train_length_l[index],
norm_length_r: normalized_train_length_r[index],
mts: mt_train[index:index + batch_size],
wmf: wm_train[index:index + batch_size]
},
on_unused_input='ignore')
###############
# TRAIN MODEL #
###############
print '... training'
# early-stopping parameters
patience = 500000000000000 # 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_params = None
best_validation_loss = numpy.inf
best_iter = 0
test_score = 0.
start_time = time.clock()
epoch = 0
done_looping = False
svm_max = 0.0
best_epoch = 0
while (epoch < n_epochs) and (not done_looping):
epoch = epoch + 1
#for minibatch_index in xrange(n_train_batches): # each batch
minibatch_index = 0
#shuffle(train_batch_start)#shuffle training data
cost_tmp = 0.0
for batch_start in train_batch_start:
# iter means how many batches have been runed, taking into loop
iter = (epoch - 1) * n_train_batches + minibatch_index + 1
minibatch_index = minibatch_index + 1
#if epoch %2 ==0:
# batch_start=batch_start+remain_train
#time.sleep(0.5)
#print batch_start
if iter % update_freq != 0:
cost_ij, error_ij, layer3_input, y = train_model_predict(
batch_start)
#print 'layer3_input', layer3_input
cost_tmp += cost_ij
error_sum += error_ij
#print 'cost_acc ',cost_acc
#print 'cost_ij ', cost_ij
#print 'cost_tmp before update',cost_tmp
else:
cost_average = train_model(batch_start, cost_tmp)
#print 'layer3_input', layer3_input
error_sum = 0
cost_tmp = 0.0 #reset for the next batch
#print 'cost_average ', cost_average
#print 'cost_this ',cost_this
#exit(0)
#exit(0)
if iter % n_train_batches == 0:
print 'training @ iter = ' + str(
iter) + ' average cost: ' + str(
cost_average) + ' error: ' + str(
error_sum) + '/' + str(
update_freq) + ' error rate: ' + str(
error_sum * 1.0 / update_freq)
#if iter ==1:
# exit(0)
if iter % validation_frequency == 0:
#write_file=open('log.txt', 'w')
test_probs = []
test_y = []
test_features = []
for i in test_batch_start:
prob_i, layer3_input, y = test_model(i)
#test_losses = [test_model(i) for i in test_batch_start]
test_probs.append(prob_i[0][0])
test_y.append(y[0])
test_features.append(layer3_input[0])
MAP, MRR = compute_map_mrr(rootPath + 'test_filtered.txt',
test_probs)
#now, check MAP and MRR
print(
('\t\t\t\t\t\tepoch %i, minibatch %i/%i, test MAP of best '
'model %f, MRR %f') %
(epoch, minibatch_index, n_train_batches, MAP, MRR))
#now, see the results of LR
#write_feature=open(rootPath+'feature_check.txt', 'w')
train_y = []
train_features = []
count = 0
for batch_start in train_batch_start:
cost_ij, error_ij, layer3_input, y = train_model_predict(
batch_start)
train_y.append(y[0])
train_features.append(layer3_input[0])
#write_feature.write(str(batch_start)+' '+' '.join(map(str,layer3_input[0]))+'\n')
#count+=1
#write_feature.close()
clf = svm.SVC(C=1.0, kernel='linear')
clf.fit(train_features, train_y)
results_svm = clf.decision_function(test_features)
MAP_svm, MRR_svm = compute_map_mrr(
rootPath + 'test_filtered.txt', results_svm)
lr = LinearRegression().fit(train_features, train_y)
results_lr = lr.predict(test_features)
MAP_lr, MRR_lr = compute_map_mrr(
rootPath + 'test_filtered.txt', results_lr)
print '\t\t\t\t\t\t\tSVM, MAP: ', MAP_svm, ' MRR: ', MRR_svm, ' LR: ', MAP_lr, ' MRR: ', MRR_lr
if patience <= iter:
done_looping = True
break
#after each epoch, increase the batch_size
if epoch % 2 == 1:
update_freq = update_freq * 1
else:
update_freq = update_freq / 1
#store the paras after epoch 15
if epoch == 15:
store_model_to_file(params_conv)
print 'Finished storing best conv params'
exit(0)
#print 'Batch_size: ', update_freq
end_time = time.clock()
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 >> sys.stderr, ('The code for file ' + os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
def evaluate_lenet5(self):
#def evaluate_lenet5(learning_rate=0.1, n_epochs=2000, nkerns=[6, 12], batch_size=70, useAllSamples=0, kmax=30, ktop=5, filter_size=[10,7],
# L2_weight=0.000005, dropout_p=0.5, useEmb=0, task=5, corpus=1):
rng = numpy.random.RandomState(23455)
n_train_batches=self.raw_data[0].shape[0]/self.batch_size
n_valid_batches=self.raw_data[1].shape[0]/self.batch_size
n_test_batches=self.raw_data[2].shape[0]/self.batch_size
train_batch_start=[]
dev_batch_start=[]
test_batch_start=[]
if self.useAllSamples:
train_batch_start=list(numpy.arange(n_train_batches)*self.batch_size)+[self.raw_data[0].shape[0]-self.batch_size]
dev_batch_start=list(numpy.arange(n_valid_batches)*self.batch_size)+[self.raw_data[1].shape[0]-self.batch_size]
test_batch_start=list(numpy.arange(n_test_batches)*self.batch_size)+[self.raw_data[2].shape[0]-self.batch_size]
n_train_batches=n_train_batches+1
n_valid_batches=n_valid_batches+1
n_test_batches=n_test_batches+1
else:
train_batch_start=list(numpy.arange(n_train_batches)*self.batch_size)
dev_batch_start=list(numpy.arange(n_valid_batches)*self.batch_size)
test_batch_start=list(numpy.arange(n_valid_batches)*self.batch_size)
'''
indices_train_theano=theano.shared(numpy.asarray(indices_train, dtype=theano.config.floatX), borrow=True)
indices_dev_theano=theano.shared(numpy.asarray(indices_dev, dtype=theano.config.floatX), borrow=True)
indices_train_theano=T.cast(indices_train_theano, 'int32')
indices_dev_theano=T.cast(indices_dev_theano, 'int32')
'''
# allocate symbolic variables for the data
index = T.lscalar() # index to a [mini]batch
x = T.dmatrix('x') # now, x is the index matrix, must be integer
y = T.dmatrix('y')
######################
# BUILD ACTUAL MODEL #
######################
print '... building the model'
inputs=debug_print(x, 'inputs')
labels=debug_print(y, 'labels')
layer2 = HiddenLayer(rng, input=inputs, n_in=self.source_embedding_size, n_out=self.target_embedding_size, activation=None)
layer2_output=debug_print(layer2.output, 'layer2_output')
#J= debug_print(- T.sum(labels * T.log(layer2_output) + (1 - labels) * T.log(1 - layer2_output), axis=1), 'J') # a vector of cross-entropy
J=T.sum((layer2_output - labels)**2, axis=1)
L2_reg = (layer2.W** 2).sum()
self.cost = T.mean(J) + self.L2_weight*L2_reg
validate_model = theano.function([index], self.cost,
givens={
x: self.dev_source[index: index + self.batch_size],
y: self.dev_target[index: index + self.batch_size]})
test_model = theano.function([index], layer2_output,
givens={
x: self.test_source[index: index + self.batch_size],
y: self.test_source[index: index + self.batch_size]})
# create a list of all model parameters to be fit by gradient descent
self.params = layer2.params
#params = layer3.params + layer2.params + layer0.params+[embeddings]
accumulator=[]
for para_i in self.params:
eps_p=numpy.zeros_like(para_i.get_value(borrow=True),dtype=theano.config.floatX)
accumulator.append(theano.shared(eps_p, borrow=True))
# create a list of gradients for all model parameters
grads = T.grad(self.cost, self.params)
updates = []
for param_i, grad_i, acc_i in zip(self.params, grads, accumulator):
acc = acc_i + T.sqr(grad_i)
updates.append((param_i, param_i - self.ini_learning_rate * grad_i / T.sqrt(acc))) #AdaGrad
updates.append((acc_i, acc))
train_model = theano.function([index], self.cost, updates=updates,
givens={
x: self.train_source[index: index + self.batch_size],
y: self.train_target[index: index + self.batch_size]})
###############
# TRAIN MODEL #
###############
print '... training'
# early-stopping parameters
patience = 500000 # 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_params = None
best_validation_loss = numpy.inf
best_iter = 0
test_score = 0.
start_time = time.clock()
epoch = 0
done_looping = False
vali_loss_list=[]
lowest_vali_loss=0
OOV_embs=numpy.zeros((len(self.OOV),self.target_embedding_size), dtype=theano.config.floatX)
while (epoch < self.n_epochs) and (not done_looping):
epoch = epoch + 1
#for minibatch_index in xrange(n_train_batches): # each batch
minibatch_index=0
for batch_start in train_batch_start:
# iter means how many batches have been runed, taking into loop
iter = (epoch - 1) * n_train_batches + minibatch_index +1
minibatch_index=minibatch_index+1
cost_of_each_iteration= train_model(batch_start)
#exit(0)
#print 'sentence embeddings:'
#print sentences_embs[:6,:]
#if iter ==1:
# exit(0)
if iter % validation_frequency == 0:
print 'training @ iter = '+str(iter)+' cost: '+str(cost_of_each_iteration)# +' error: '+str(error_ij)
if iter % validation_frequency == 0:
#print '\t iter: '+str(iter)
# compute zero-one loss on validation set
#validation_losses = [validate_model(i) for i in xrange(n_valid_batches)]
validation_losses=[]
for batch_start in dev_batch_start:
vali_loss_i=validate_model(batch_start)
validation_losses.append(vali_loss_i)
this_validation_loss = numpy.mean(validation_losses)
print('\t\tepoch %i, minibatch %i/%i, validation cost %f ' % \
(epoch, minibatch_index , n_train_batches, \
this_validation_loss))
if this_validation_loss < (minimal_of_list(vali_loss_list)-1.0): #is very small
#print str(minimal_of_list(vali_loss_list))+'-'+str(this_validation_loss)+'='+str(minimal_of_list(vali_loss_list)-this_validation_loss)
del vali_loss_list[:]
vali_loss_list.append(this_validation_loss)
lowest_vali_loss=this_validation_loss
#store params
self.best_params=self.params
for batch_start in test_batch_start:
predicted_embeddings=test_model(batch_start)
for row in range(batch_start, batch_start + self.batch_size):
OOV_embs[row]=predicted_embeddings[row-batch_start]
if len(vali_loss_list)==self.vali_cost_list_length: # only happen when self.vali_cost_list_length==1
print 'Training over, best model got at vali_cost:'+str(lowest_vali_loss)
return OOV_embs, self.OOV
elif len(vali_loss_list)<self.vali_cost_list_length:
if this_validation_loss < minimal_of_list(vali_loss_list): #if it's small, but not small enough
self.best_params=self.params
lowest_vali_loss=this_validation_loss
for batch_start in test_batch_start:
predicted_embeddings=test_model(batch_start)
for row in range(batch_start, batch_start + self.batch_size):
OOV_embs[row]=predicted_embeddings[row-batch_start]
vali_loss_list.append(this_validation_loss)
if len(vali_loss_list)==self.vali_cost_list_length:
print 'Training over, best model got at vali_cost:'+str(lowest_vali_loss)
return OOV_embs, self.OOV
#print vali_loss_list
if patience <= iter:
done_looping = True
break
end_time = time.clock()
'''
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 >> sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
return OOV_embs, self.OOV
###############################################
# EXAMPLE 2
###############################################
print('Building the model...')
x = T.dmatrix('x') # Symbolic input matrix
# Initializing the weight matrix and bias vector
W = theano.shared(value=np.zeros((28*28, 10),dtype=theano.config.floatX), name='W')
b = theano.shared(value=np.zeros((10,),dtype=theano.config.floatX), name='b')
p_y_given_x = T.exp(T.dot(x, W) + b)
p_y_given_x = p_y_given_x / T.sum(p_y_given_x,axis=1)[:,None]
# Symbolic description of how to compute prediction as class whose
# probability is maximal
def __init__(self, state_length, action_length, state_bounds, action_bounds, settings_):
super(NeuralNetwork,self).__init__(state_length, action_length, state_bounds, action_bounds, 0, settings_)
batch_size=32
# data types for model
State = T.dmatrix("State")
State.tag.test_value = np.random.rand(batch_size,self._state_length)
# ResultState = T.dmatrix("ResultState")
# ResultState.tag.test_value = np.random.rand(batch_size,self._state_length)
Action = T.dmatrix("Action")
Action.tag.test_value = np.random.rand(batch_size, self._action_length)
# create a small convolutional neural network
inputLayerState = lasagne.layers.InputLayer((None, self._state_length), input_var=State)
# inputLayerAction = lasagne.layers.InputLayer((None, self._action_length), Action)
# concatLayer = lasagne.layers.ConcatLayer([inputLayerState, inputLayerAction])
l_hid2ActA = lasagne.layers.DenseLayer(
inputLayerState, num_units=128,
nonlinearity=lasagne.nonlinearities.leaky_rectify,
W=lasagne.init.Uniform())
num_layers=1
"""
l_hid2ActA = lasagne.layers.DenseLayer(
inputLayerState, num_units=128,
nonlinearity=lasagne.nonlinearities.leaky_rectify)
l_hid2ActA = lasagne.layers.DenseLayer(
l_hid2ActA, num_units=64,
nonlinearity=lasagne.nonlinearities.leaky_rectify)
l_hid2ActA = lasagne.layers.DenseLayer(
l_hid2ActA, num_units=32,
nonlinearity=lasagne.nonlinearities.leaky_rectify)
"""
for i in range(num_layers):
l_hid2ActA = lasagne.layers.DenseLayer(
l_hid2ActA, num_units=64,
nonlinearity=lasagne.nonlinearities.leaky_rectify
# ,W=lasagne.init.Uniform()
)
self._l_out = lasagne.layers.DenseLayer(
l_hid2ActA, num_units=self._action_length,
nonlinearity=lasagne.nonlinearities.linear
# ,W=lasagne.init.Uniform()
)
# print "Initial W " + str(self._w_o.get_value())
self._learning_rate = 0.01
self._rho = 0.95
self._rms_epsilon = 0.001
self._updates=0
self._states_shared = theano.shared(
np.zeros((batch_size, self._state_length),
dtype=theano.config.floatX))
"""self._next_states_shared = theano.shared(
np.zeros((batch_size, self._state_length),
dtype=theano.config.floatX))
"""
self._actions_shared = theano.shared(
np.zeros((batch_size, self._action_length), dtype=theano.config.floatX),
)
inputs_ = {
State: State,
# Action: Action,
}
self._forward = lasagne.layers.get_output(self._l_out, inputs_, deterministic=True)
# self._target = (Reward + self._discount_factor * self._q_valsB)
self._diff = Action - self._forward
self._loss = 0.5 * self._diff ** 2
self._loss = T.mean(self._loss) + (1e-5 * lasagne.regularization.regularize_network_params(self._l_out, lasagne.regularization.l2))
self._loss2 = T.mean(self._loss)
self._params = lasagne.layers.helper.get_all_params(self._l_out)
self._givens_ = {
State: self._states_shared,
# ResultState: self._next_states_shared,
Action: self._actions_shared,
}
# SGD update
# self._updates_ = lasagne.updates.rmsprop(self._loss, self._params, self._learning_rate, self._rho,
# self._rms_epsilon)
self._all_grads = T.grad(self._loss, self._params)
# gself._all_grads = lasagne.updates.total_norm_constraint(self._all_grads, 0.5)
# self._params = lasagne.updates.norm_constraint(self._params, max_norm=0.4)
self._updates_ = lasagne.updates.momentum(self._all_grads, self._params, self._learning_rate, 0.9)
# self._updates_ = lasagne.updates.norm_constraint(self._updates_, self._params, max_norm=0.4)
# updates = lasagne.updates.nesterov(loss, params)
# updates = norm_constraint(updates, someparam, abs_max=15)
# TD update
# minimize Value function error
#self._updates_ = lasagne.updates.rmsprop(T.mean(self._q_func) + (1e-4 * lasagne.regularization.regularize_network_params(
#self._l_outA, lasagne.regularization.l2)), self._params,
# self._learning_rate * -T.mean(self._diff), self._rho, self._rms_epsilon)
# actDiff1 = (Action - self._q_valsActB) #TODO is this correct?
# actDiff = (actDiff1 - (Action - self._q_valsActA))
# actDiff = ((Action - self._q_valsActB2)) # Target network does not work well here?
#self._actDiff = ((Action - self._q_valsActA)) # Target network does not work well here?
#self._actLoss = 0.5 * self._actDiff ** 2 + (1e-4 * lasagne.regularization.regularize_network_params( self._l_outActA, lasagne.regularization.l2))
#self._actLoss = T.mean(self._actLoss)
self._train = theano.function([], [self._loss], updates=self._updates_, givens=self._givens_)
self._forwardDynamics = theano.function([], self._forward,
givens={State: self._states_shared,
# Action: self._actions_shared
})
inputs_ = [State,
# ResultState,
Action]
self._bellman_error = theano.function(inputs=inputs_, outputs=self._diff, allow_input_downcast=True)
# self._diffs = theano.function(input=[State])
# grad_params_ = [self._states_shared]
# grad_params_.extend(self._params)
self._get_grad = theano.function([], outputs=lasagne.updates.get_or_compute_grads(self._loss, [lasagne.layers.get_all_layers(self._l_out)[0].input_var] + self._params), allow_input_downcast=True, givens=self._givens_)
def __init__(self,
numpy_rng,
theano_rng=None,
input=None,
n_visible=300,
n_hidden=150,
W=None,
bhid=None,
bvis=None):
self.n_visible = n_visible
self.n_hidden = n_hidden
# create a Theano random generator that gives symbolic random values
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(2**30))
# note : W' was written as `W_prime` and b' as `b_prime`
if W == None:
# W is initialized with `initial_W` which is uniformely sampled
# from -4*sqrt(6./(n_visible+n_hidden)) and
# 4*sqrt(6./(n_hidden+n_visible))the output of uniform if
# converted using asarray to dtype
# theano.config.floatX so that the code is runable on GPU
print('这里W是空的')
initial_W = numpy.asarray(numpy_rng.uniform(
low=-4 * numpy.sqrt(6. / (n_hidden + n_visible)),
high=4 * numpy.sqrt(6. / (n_hidden + n_visible)),
size=(n_visible, n_hidden)),
dtype=theano.config.floatX)
W = theano.shared(value=initial_W, name='W', borrow=True)
if bvis == None:
print('这里bvis是空的')
bvis = theano.shared(value=numpy.zeros(n_visible,
dtype=theano.config.floatX),
name='bvis',
borrow=True)
if bhid == None:
print('这里bhid是空的')
bhid = theano.shared(value=numpy.zeros(n_hidden,
dtype=theano.config.floatX),
name='bhid',
borrow=True)
self.W = W
# b corresponds to the bias of the hidden
self.b = bhid
# b_prime corresponds to the bias of the visible
self.b_prime = bvis
# tied weights, therefore W_prime is W transpose
self.W_prime = self.W.T
self.theano_rng = theano_rng
# if no input is given, generate a variable representing the input
if input is None:
# we use a matrix because we expect a minibatch of several
# examples, each example being a row
self.x = T.dmatrix(name='input')
else:
self.x = input
self.params = [self.W, self.b, self.b_prime]
import gzip
import cPickle
f = gzip.open('C:/nnets/mnist.pkl.gz', 'rb')
train_set, valid_set, test_set = cPickle.load(f)
f.close()
n_train, n_test = map(lambda x: len(x[0]), [train_set, test_set])
dims = train_set[0].shape[1]
n_classes = len(set(train_set[1]))
import numpy
import theano
import theano.tensor as T
X = T.dmatrix()
y = T.ivector()
prepare_data = lambda x: (theano.shared(x[0].astype('float64')),
theano.shared(x[1].astype('int32')))
(training_x, training_y), (test_x, test_y), (validation_x, validation_y) = map(
prepare_data, [train_set, test_set, valid_set])
W = theano.shared(numpy.zeros([dims, n_classes]))
b = theano.shared(numpy.zeros(n_classes))
y_hat = T.nnet.softmax(T.dot(X, W) + b)
y_pred = T.argmax(y_hat, axis=1)
test_error = T.mean(T.neq(y_pred, y))
training_error = -T.mean(T.log(y_hat)[T.arange(y.shape[0]), y])
class Layer(object):
def __init__(self, inputs, in_size, out_size, activation_function=None):
self.W = theano.shared(numpy.random.normal(0, 1, (in_size, out_size)))
self.b = theano.shared(numpy.zeros(out_size) + 0.1)
self.Wx_plus_b = T.dot(inputs,self.W) + self.b
self.activation_function = activation_function
if activation_function is None:
self.out_puts = self.Wx_plus_b
else:
self.out_puts = self.activation_function(self.Wx_plus_b)
x_data = numpy.linspace(-1, 1, 300)[:, numpy.newaxis]
noise = numpy.random.normal(0, 0.05, x_data.shape)
y_data = numpy.square(x_data) - 0.5 + noise
x = T.dmatrix('x')
y = T.dmatrix('y')
l1 = Layer(x, 1, 10, T.nnet.relu)
l2 = Layer(l1.out_puts, 10, 1, None)
cost = T.mean(T.square(l2.out_puts - y))
gW1, gb1, gW2, gb2 = T.grad(cost, [l1.W, l1.b, l2.W, l2.b])
learning_rate = 0.05
train = theano.function(inputs=[x, y], outputs=cost, updates=[(l1.W, l1.W - learning_rate*gW1), \
(l1.b, l1.b - learning_rate*gb1), \
(l2.W, l2.W - learning_rate*gW2), \
(l2.b, l2.b - learning_rate*gb2)])
predict = theano.function(inputs=[x],outputs=l2.out_puts)
flg = plt.figure()
import theano
import theano.tensor as T
from math import sqrt
rng = numpy.random
N = 400 # training sample size
feats = 784 # number of input variables
hidden_layer = 100 # Número de capas ocultas
# generate a dataset: D = (input_values, target_class)
D = (rng.randn(N, feats), rng.randint(size=N, low=0, high=2))
training_steps = 10000
# Declare Theano symbolic variables
x = T.dmatrix("x")
y = T.dvector("y")
# initialize the weight vector w randomly
#
# this and the following bias variable b
# are shared so they keep their values
# between training iterations (updates)
w0 = theano.shared(rng.randn(feats, hidden_layer), name="w0")
w1 = theano.shared(rng.randn(hidden_layer) * sqrt(2.0/hidden_layer), name="w1")
# initialize the bias term
b0 = theano.shared(0., name="b0")
b1 = theano.shared(0., name="b1")
print("Initial model:")
def __init__(self,
numpy_rng,
theano_rng=None,
input=None,
n_visible=784,
n_hidden=500,
W=None,
bhid=None,
bvis=None):
self.n_hidden = n_hidden
self.n_visible = n_visible
#create a symbolic random variable:
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(23))
if not W:
W_values = numpy.asarray(numpy_rng.uniform(
low=12 * numpy.sqrt(6. / (n_hidden + n_visible)),
high=16 * numpy.sqrt(6. / (n_hidden + n_visible)),
size=(n_visible, n_hidden)),
dtype=theano.config.floatX)
W = theano.shared(value=W_values, name='W', borrow=True)
if not bvis:
bvis = theano.shared(
value=4 * numpy.zeros(n_visible, dtype=theano.config.floatX),
borrow=True)
if not bhid:
bhid = theano.shared(
value=4 * numpy.zeros(n_hidden, dtype=theano.config.floatX),
borrow=True)
# we are using tied weights, in which the output weights are just the
# transpose of the input ones.
self.W = W
self.W_prime = W.T
self.b = bhid
self.b_prime = bvis
# deltas = numpy.zeros(shape=(n_visible, n_hidden), dtype=theano.config.floatX)
self.deltaW = theano.shared(value=numpy.zeros(
shape=(n_visible, n_hidden), dtype=theano.config.floatX),
borrow=True)
self.deltaBvis = theano.shared(value=numpy.zeros(
n_visible, dtype=theano.config.floatX),
borrow=True)
self.deltaBhid = theano.shared(value=numpy.zeros(
n_hidden, dtype=theano.config.floatX),
borrow=True)
self.theano_rng = theano_rng
if input is None:
self.x = T.dmatrix(name='input')
else:
self.x = input
# bundle up all the params. No W_prime as is updated whenever W is updated.
self.params = [self.W, self.b, self.b_prime]
self.gparams = []
self.deltaParams = [self.deltaW, self.deltaBhid, self.deltaBvis]
def fit_mmd(data):
"""
Fit isotropic Gaussian by minimizing maximum mean discrepancy.
B{References:}
- A. Gretton et al., I{A Kernel Method for the Two-Sample-Problem}, NIPS, 2007
- Y. Li et al., I{Generative Moment Matching Networks}, ICML, 2015
"""
def gaussian_kernel(x, y, sigma=1.):
return tt.exp(-tt.sum(tt.square(x - y)) / sigma**2)
def mixed_kernel(x, y, sigma=[.5, 1., 2., 4., 8.]):
return tt.sum([gaussian_kernel(x, y, s) for s in sigma])
def gram_matrix(X, Y, kernel):
M = X.shape[0]
N = Y.shape[0]
G, _ = th.scan(
fn=lambda k: kernel(X[k // N], Y[k % N]),
sequences=[tt.arange(M * N)])
return G.reshape([M, N])
# hiddens
Z = tt.dmatrix('Z')
# parameters
b = th.shared(np.mean(data, 1)[None], broadcastable=[True, False])
A = th.shared(np.std(data - b.get_value().T))
# model samples
X = Z * A + b
# data
Y = tt.dmatrix('Y')
M = X.shape[0]
N = Y.shape[0]
Kyy = gram_matrix(Y, Y, mixed_kernel)
Kxy = gram_matrix(X, Y, mixed_kernel)
Kxx = gram_matrix(X, X, mixed_kernel)
MMDsq = tt.sum(Kxx) / M**2 - 2. / (N * M) * tt.sum(Kxy) + tt.sum(Kyy) / N**2
MMD = tt.sqrt(MMDsq)
f = th.function([Z, Y], [MMD, tt.grad(MMD, A), tt.grad(MMD, b)])
# batch size, momentum, learning rate schedule
B = 100
mm = 0.8
kappa = .7
tau = 1.
values = []
try:
for t in range(0, data.shape[1], B):
if t % 10000 == 0:
# reset momentum
dA = 0.
db = 0.
Z = nr.randn(B, data.shape[0])
Y = data.T[t:t + B]
lr = np.power(tau + (t + B) / B, -kappa)
v, gA, gb = f(Z, Y)
dA = mm * dA - lr * gA
db = mm * db - lr * gb
values.append(v)
A.set_value(A.get_value() + dA)
b.set_value(b.get_value() + db)
print('{0:>6} {1:.4f}'.format(t, np.mean(values[-100:])))
except KeyboardInterrupt:
pass
return A.get_value() * np.eye(data.shape[0]), b.get_value().T
import theano.tensor as T
from theano import function
from theano.tensor.shared_randomstreams import RandomStreams
import numpy
random = RandomStreams(seed=42)
a = random.normal((1, 3))
b = T.dmatrix('a')
f1 = a * b
g1 = function([b], f1)
print('numpy.ones((1,3)=', numpy.ones((1, 3)))
print('numpy.ones((1,3)=', numpy.ones((1, 3)))
print('numpy.ones((1,3)=', numpy.ones((1, 3)))
for i in range(50):
print("Invocation 1:", g1(numpy.ones((1, 3))))
def test_sparse():
print '\n\n*************************************************'
print ' TEST SPARSE'
print '*************************************************'
# fixed parameters
bsize = 10 # batch size
imshp = (28, 28)
kshp = (5, 5)
nkern = 1 # per output pixel
ssizes = ((1, 1), (2, 2))
convmodes = (
'full',
'valid',
)
# symbolic stuff
bias = T.dvector()
kerns = T.dvector()
input = T.dmatrix()
rng = N.random.RandomState(3423489)
import theano.gof as gof
#Mode(optimizer='fast_run', linker=gof.OpWiseCLinker(allow_gc=False)),):
ntot, ttot = 0, 0
for conv_mode in convmodes:
for ss in ssizes:
output, outshp = sp.applySparseFilter(kerns, kshp,\
nkern, input, imshp, ss, bias=bias, mode=conv_mode)
f = function([kerns, bias, input], output)
# build actual input images
img2d = N.arange(bsize * N.prod(imshp)).reshape((bsize, ) +
imshp)
img1d = img2d.reshape(bsize, -1)
zeropad_img = N.zeros((bsize,\
img2d.shape[1]+2*(kshp[0]-1),\
img2d.shape[2]+2*(kshp[1]-1)))
zeropad_img[:, kshp[0] - 1:kshp[0] - 1 + img2d.shape[1],
kshp[1] - 1:kshp[1] - 1 + img2d.shape[2]] = img2d
# build kernel matrix -- flatten it for theano stuff
filters = N.arange(N.prod(outshp)*N.prod(kshp)).\
reshape(nkern,N.prod(outshp[1:]),N.prod(kshp))
spfilt = filters.flatten()
biasvals = N.arange(N.prod(outshp))
# compute output by hand
ntime1 = time.time()
refout = N.zeros((bsize, nkern, outshp[1], outshp[2]))
patch = N.zeros((kshp[0], kshp[1]))
for b in xrange(bsize):
for k in xrange(nkern):
pixi = 0 # pixel index in raster order
for j in xrange(outshp[1]):
for i in xrange(outshp[2]):
n = j * ss[0]
m = i * ss[1]
patch = zeropad_img[b, n:n + kshp[0],
m:m + kshp[1]]
refout[b,k,j,i] = N.dot(filters[k,pixi,:],\
patch.flatten())
pixi += 1
refout = refout.reshape(bsize, -1) + biasvals
ntot += time.time() - ntime1
# need to flatten images
ttime1 = time.time()
out1 = f(spfilt, biasvals, img1d)
ttot += time.time() - ttime1
temp = refout - out1
assert (temp < 1e-10).all()
# test downward propagation
vis = T.grad(output, input, output)
downprop = function([kerns, output], vis)
temp1 = time.time()
for zz in range(100):
visval = downprop(spfilt, out1)
indices, indptr, spmat_shape, sptype, outshp, kmap = \
sp.convolution_indices.sparse_eval(imshp,kshp,nkern,ss,conv_mode)
spmat = sparse.csc_matrix((spfilt[kmap], indices, indptr),
spmat_shape)
visref = N.dot(out1, spmat.todense())
assert N.all(visref == visval)
print '**** Sparse Profiling Results ****'
print 'Numpy processing time: ', ntot
print 'Theano processing time: ', ttot
def mogaussian(D=2, K=10, N=100000, seed=2, D_max=100):
"""
Creates a random mixture of Gaussians and corresponding samples.
@rtype: C{tuple}
@return: a function representing the density and samples
"""
nr.seed(seed)
# mixture weights
p = nr.dirichlet([.5] * K)
# variances
v = 1. / np.square(nr.rand(K) + 1.)
# means; D_max makes sure that data only depends on seed and not on D
m = nr.randn(D_max, K) * 1.5
m = m[:D]
# density function
X = tt.dmatrix('X')
C = [np.eye(D) * _ for _ in v]
def log_p(X):
"""
@type X: C{ndarray}/C{TensorVariable}
@param X: data points stored column-wise
@rtype: C{ndarray}/C{TensorVariable}
"""
if isinstance(X, tt.TensorVariable):
return tt.log(
tt.sum(
[p[i] * normal(X, m[:, [i]], C[i]) for i in range(len(p))],
0))
else:
if log_p.f is None:
Y = tt.dmatrix('Y')
log_p.f = th.function([Y], log_p(Y))
return log_p.f(X)
log_p.f = None
def nonlog_p(X):
"""
@type X: C{ndarray}/C{TensorVariable}
@param X: data points stored column-wise
@rtype: C{ndarray}/C{TensorVariable}
"""
if isinstance(X, tt.TensorVariable):
return tt.sum(
[p[i] * normal(X, m[:, [i]], C[i]) for i in range(len(p))], 0)
else:
if nonlog_p.f is None:
Y = tt.dmatrix('Y')
nonlog_p.f = th.function([Y], nonlog_p(Y))
return nonlog_p.f(X)
nonlog_p.f = None
# sample data
M = nr.multinomial(N, p)
data = np.hstack(
nr.randn(D, M[i]) * np.sqrt(v[i]) + m[:, [i]] for i in range(len(p)))
data = data[:, nr.permutation(N)]
return nonlog_p, log_p, data
def test_searchsortedOp_on_no_1d_inp(self):
no_1d = tt.dmatrix("no_1d")
with pytest.raises(ValueError):
searchsorted(no_1d, self.v)
with pytest.raises(ValueError):
searchsorted(self.x, self.v, sorter=no_1d)
self.outputs = self.Wx_plus_b
else:
self.outputs = self.activation_function(self.Wx_plus_b)
# Make up some fake data
x_data = np.linspace(-1, 1, 300)[:, np.newaxis]
noise = np.random.normal(0, 0.05, x_data.shape)
y_data = np.square(x_data) - 0.5 + noise # y = x^2 - 0.5
# show the fake data
plt.scatter(x_data, y_data)
plt.show()
# determine the inputs dtype
x = T.dmatrix("x")
y = T.dmatrix("y")
# add layers
l1 = Layer(x, 1, 10, T.nnet.relu)
l2 = Layer(l1.outputs, 10, 1, None)
# compute the cost
cost = T.mean(T.square(l2.outputs - y))
# compute the gradients
gW1, gb1, gW2, gb2 = T.grad(cost, [l1.W, l1.b, l2.W, l2.b])
# apply gradient descent
learning_rate = 0.05
train = theano.function(inputs=[x, y],
def evaluate_lenet5(learning_rate=0.085, n_epochs=2000, nkerns=[50], batch_size=1, window_width=3,
maxSentLength=60, emb_size=300, hidden_size=200,
margin=0.5, L2_weight=0.0001, update_freq=1, norm_threshold=5.0):
model_options = locals().copy()
print "model options", model_options
rootPath='/mounts/data/proj/wenpeng/Dataset/MicrosoftParaphrase/tokenized_msr/';
rng = numpy.random.RandomState(23455)
datasets, vocab_size=load_msr_corpus(rootPath+'vocab.txt', rootPath+'tokenized_train.txt', rootPath+'tokenized_test.txt', maxSentLength)
mtPath='/mounts/data/proj/wenpeng/Dataset/paraphraseMT/'
mt_train, mt_test=load_mts(mtPath+'concate_15mt_train.txt', mtPath+'concate_15mt_test.txt')
wm_train, wm_test=load_wmf_wikiQA(rootPath+'train_word_matching_scores_normalized.txt', rootPath+'test_word_matching_scores_normalized.txt')
indices_train, trainY, trainLengths, normalized_train_length, trainLeftPad, trainRightPad= datasets[0]
indices_train_l=indices_train[::2,:]
indices_train_r=indices_train[1::2,:]
trainLengths_l=trainLengths[::2]
trainLengths_r=trainLengths[1::2]
normalized_train_length_l=normalized_train_length[::2]
normalized_train_length_r=normalized_train_length[1::2]
trainLeftPad_l=trainLeftPad[::2]
trainLeftPad_r=trainLeftPad[1::2]
trainRightPad_l=trainRightPad[::2]
trainRightPad_r=trainRightPad[1::2]
indices_test, testY, testLengths,normalized_test_length, testLeftPad, testRightPad= datasets[1]
indices_test_l=indices_test[::2,:]
indices_test_r=indices_test[1::2,:]
testLengths_l=testLengths[::2]
testLengths_r=testLengths[1::2]
normalized_test_length_l=normalized_test_length[::2]
normalized_test_length_r=normalized_test_length[1::2]
testLeftPad_l=testLeftPad[::2]
testLeftPad_r=testLeftPad[1::2]
testRightPad_l=testRightPad[::2]
testRightPad_r=testRightPad[1::2]
n_train_batches=indices_train_l.shape[0]/batch_size
n_test_batches=indices_test_l.shape[0]/batch_size
train_batch_start=list(numpy.arange(n_train_batches)*batch_size)
test_batch_start=list(numpy.arange(n_test_batches)*batch_size)
indices_train_l=theano.shared(numpy.asarray(indices_train_l, dtype=theano.config.floatX), borrow=True)
indices_train_r=theano.shared(numpy.asarray(indices_train_r, dtype=theano.config.floatX), borrow=True)
indices_test_l=theano.shared(numpy.asarray(indices_test_l, dtype=theano.config.floatX), borrow=True)
indices_test_r=theano.shared(numpy.asarray(indices_test_r, dtype=theano.config.floatX), borrow=True)
indices_train_l=T.cast(indices_train_l, 'int64')
indices_train_r=T.cast(indices_train_r, 'int64')
indices_test_l=T.cast(indices_test_l, 'int64')
indices_test_r=T.cast(indices_test_r, 'int64')
rand_values=random_value_normal((vocab_size+1, emb_size), theano.config.floatX, numpy.random.RandomState(1234))
rand_values[0]=numpy.array(numpy.zeros(emb_size))
#rand_values[0]=numpy.array([1e-50]*emb_size)
rand_values=load_word2vec_to_init(rand_values, rootPath+'vocab_embs_300d.txt')
embeddings=theano.shared(value=rand_values, borrow=True)
cost_tmp=0
error_sum=0
# allocate symbolic variables for the data
index = T.lscalar()
x_index_l = T.lmatrix('x_index_l') # now, x is the index matrix, must be integer
x_index_r = T.lmatrix('x_index_r')
y = T.lvector('y')
left_l=T.lscalar()
right_l=T.lscalar()
left_r=T.lscalar()
right_r=T.lscalar()
length_l=T.lscalar()
length_r=T.lscalar()
norm_length_l=T.dscalar()
norm_length_r=T.dscalar()
mts=T.dmatrix()
wmf=T.dmatrix()
cost_tmp=T.dscalar()
#x=embeddings[x_index.flatten()].reshape(((batch_size*4),maxSentLength, emb_size)).transpose(0, 2, 1).flatten()
ishape = (emb_size, maxSentLength) # this is the size of MNIST images
filter_size=(emb_size,window_width)
#poolsize1=(1, ishape[1]-filter_size[1]+1) #?????????????????????????????
length_after_wideConv=ishape[1]+filter_size[1]-1
######################
# 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
#layer0_input = x.reshape(((batch_size*4), 1, ishape[0], ishape[1]))
layer0_l_input = embeddings[x_index_l.flatten()].reshape((batch_size,maxSentLength, emb_size)).transpose(0, 2, 1).dimshuffle(0, 'x', 1, 2)
layer0_r_input = embeddings[x_index_r.flatten()].reshape((batch_size,maxSentLength, emb_size)).transpose(0, 2, 1).dimshuffle(0, 'x', 1, 2)
conv_W, conv_b=create_conv_para(rng, filter_shape=(nkerns[0], 1, filter_size[0], filter_size[1]))
#layer0_output = debug_print(layer0.output, 'layer0.output')
layer0_l = Conv_with_input_para(rng, input=layer0_l_input,
image_shape=(batch_size, 1, ishape[0], ishape[1]),
filter_shape=(nkerns[0], 1, filter_size[0], filter_size[1]), W=conv_W, b=conv_b)
layer0_r = Conv_with_input_para(rng, input=layer0_r_input,
image_shape=(batch_size, 1, ishape[0], ishape[1]),
filter_shape=(nkerns[0], 1, filter_size[0], filter_size[1]), W=conv_W, b=conv_b)
layer0_l_output=debug_print(layer0_l.output, 'layer0_l.output')
layer0_r_output=debug_print(layer0_r.output, 'layer0_r.output')
layer1=Average_Pooling_for_Top(rng, input_l=layer0_l_output, input_r=layer0_r_output, kern=nkerns[0],
left_l=left_l, right_l=right_l, left_r=left_r, right_r=right_r,
length_l=length_l+filter_size[1]-1, length_r=length_r+filter_size[1]-1,
dim=maxSentLength+filter_size[1]-1)
#layer2=HiddenLayer(rng, input=layer1_out, n_in=nkerns[0]*2, n_out=hidden_size, activation=T.tanh)
sum_uni_l=T.sum(layer0_l_input, axis=3).reshape((1, emb_size))
norm_uni_l=sum_uni_l/T.sqrt((sum_uni_l**2).sum())
sum_uni_r=T.sum(layer0_r_input, axis=3).reshape((1, emb_size))
norm_uni_r=sum_uni_r/T.sqrt((sum_uni_r**2).sum())
uni_cosine=cosine(sum_uni_l, sum_uni_r)
'''
linear=Linear(sum_uni_l, sum_uni_r)
poly=Poly(sum_uni_l, sum_uni_r)
sigmoid=Sigmoid(sum_uni_l, sum_uni_r)
rbf=RBF(sum_uni_l, sum_uni_r)
gesd=GESD(sum_uni_l, sum_uni_r)
'''
eucli_1=1.0/(1.0+EUCLID(sum_uni_l, sum_uni_r))#25.2%
#eucli_1=EUCLID(sum_uni_l, sum_uni_r)
len_l=norm_length_l.reshape((1,1))
len_r=norm_length_r.reshape((1,1))
'''
len_l=length_l.reshape((1,1))
len_r=length_r.reshape((1,1))
'''
#length_gap=T.log(1+(T.sqrt((len_l-len_r)**2))).reshape((1,1))
#length_gap=T.sqrt((len_l-len_r)**2)
#layer3_input=mts
layer3_input=T.concatenate([mts,
eucli_1, #uni_cosine,#norm_uni_l-(norm_uni_l+norm_uni_r)/2,#uni_cosine, #
layer1.output_eucli_to_simi, #layer1.output_cosine,#layer1.output_vector_l-(layer1.output_vector_l+layer1.output_vector_r)/2,#layer1.output_cosine, #
len_l, len_r,
#layer1.output_attentions,
#wmf,
], axis=1)#, layer2.output, layer1.output_cosine], axis=1)
#layer3_input=T.concatenate([mts,eucli, uni_cosine, len_l, len_r, norm_uni_l-(norm_uni_l+norm_uni_r)/2], axis=1)
#layer3=LogisticRegression(rng, input=layer3_input, n_in=11, n_out=2)
layer3=LogisticRegression(rng, input=layer3_input, n_in=15+(2)+(2)+2, n_out=2)
#L2_reg =(layer3.W** 2).sum()+(layer2.W** 2).sum()+(layer1.W** 2).sum()+(conv_W** 2).sum()
L2_reg =debug_print((layer3.W** 2).sum()+(conv_W** 2).sum(), 'L2_reg')#+(layer1.W** 2).sum()
cost_this =debug_print(layer3.negative_log_likelihood(y), 'cost_this')#+L2_weight*L2_reg
cost=debug_print((cost_this+cost_tmp)/update_freq+L2_weight*L2_reg, 'cost')
test_model = theano.function([index], [layer3.errors(y), layer3.y_pred, layer3_input, y],
givens={
x_index_l: indices_test_l[index: index + batch_size],
x_index_r: indices_test_r[index: index + batch_size],
y: testY[index: index + batch_size],
left_l: testLeftPad_l[index],
right_l: testRightPad_l[index],
left_r: testLeftPad_r[index],
right_r: testRightPad_r[index],
length_l: testLengths_l[index],
length_r: testLengths_r[index],
norm_length_l: normalized_test_length_l[index],
norm_length_r: normalized_test_length_r[index],
mts: mt_test[index: index + batch_size],
wmf: wm_test[index: index + batch_size]}, on_unused_input='ignore')
#params = layer3.params + layer2.params + layer1.params+ [conv_W, conv_b]
params = layer3.params+ [conv_W, conv_b]# + layer1.params
accumulator=[]
for para_i in params:
eps_p=numpy.zeros_like(para_i.get_value(borrow=True),dtype=theano.config.floatX)
accumulator.append(theano.shared(eps_p, borrow=True))
# create a list of gradients for all model parameters
grads = T.grad(cost, params)
updates = []
for param_i, grad_i, acc_i in zip(params, grads, accumulator):
#grad_i=debug_print(grad_i,'grad_i')
#norm=T.sqrt((grad_i**2).sum())
#if T.lt(norm_threshold, norm):
# print 'big norm'
# grad_i=grad_i*(norm_threshold/norm)
acc = acc_i + T.sqr(grad_i)
updates.append((param_i, param_i - learning_rate * grad_i / T.sqrt(acc))) #AdaGrad
updates.append((acc_i, acc))
train_model = theano.function([index,cost_tmp], [cost,layer3.errors(y), layer3_input], updates=updates,
givens={
x_index_l: indices_train_l[index: index + batch_size],
x_index_r: indices_train_r[index: index + batch_size],
y: trainY[index: index + batch_size],
left_l: trainLeftPad_l[index],
right_l: trainRightPad_l[index],
left_r: trainLeftPad_r[index],
right_r: trainRightPad_r[index],
length_l: trainLengths_l[index],
length_r: trainLengths_r[index],
norm_length_l: normalized_train_length_l[index],
norm_length_r: normalized_train_length_r[index],
mts: mt_train[index: index + batch_size],
wmf: wm_train[index: index + batch_size]}, on_unused_input='ignore')
train_model_predict = theano.function([index], [cost_this,layer3.errors(y), layer3_input, y , sum_uni_l, sum_uni_r, uni_cosine],
givens={
x_index_l: indices_train_l[index: index + batch_size],
x_index_r: indices_train_r[index: index + batch_size],
y: trainY[index: index + batch_size],
left_l: trainLeftPad_l[index],
right_l: trainRightPad_l[index],
left_r: trainLeftPad_r[index],
right_r: trainRightPad_r[index],
length_l: trainLengths_l[index],
length_r: trainLengths_r[index],
norm_length_l: normalized_train_length_l[index],
norm_length_r: normalized_train_length_r[index],
mts: mt_train[index: index + batch_size],
wmf: wm_train[index: index + batch_size]}, on_unused_input='ignore')
###############
# TRAIN MODEL #
###############
print '... training'
# early-stopping parameters
patience = 500000000000000 # 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/5, patience / 2)
# 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
max_acc=0.0
best_epoch=0
while (epoch < n_epochs) and (not done_looping):
epoch = epoch + 1
#for minibatch_index in xrange(n_train_batches): # each batch
minibatch_index=0
#shuffle(train_batch_start)#shuffle training data
cost_tmp=0.0
for batch_start in train_batch_start:
# iter means how many batches have been runed, taking into loop
iter = (epoch - 1) * n_train_batches + minibatch_index +1
minibatch_index=minibatch_index+1
#if epoch %2 ==0:
# batch_start=batch_start+remain_train
#time.sleep(0.5)
if iter%update_freq != 0:
cost_ij, error_ij, layer3_input, y, sum_uni_l, sum_uni_r, uni_cosine=train_model_predict(batch_start)
#print 'cost_ij: ', cost_ij
cost_tmp+=cost_ij
error_sum+=error_ij
else:
cost_average, error_ij, layer3_input= train_model(batch_start,cost_tmp)
#print 'training @ iter = '+str(iter)+' average cost: '+str(cost_average)+' sum error: '+str(error_sum)+'/'+str(update_freq)
error_sum=0
cost_tmp=0.0#reset for the next batch
#print layer3_input
#exit(0)
#exit(0)
if iter % n_train_batches == 0:
print 'training @ iter = '+str(iter)+' average cost: '+str(cost_average)+' error: '+str(error_sum)+'/'+str(update_freq)+' error rate: '+str(error_sum*1.0/update_freq)
#if iter ==1:
# exit(0)
if iter % validation_frequency == 0:
#write_file=open('log.txt', 'w')
test_losses=[]
for i in test_batch_start:
test_loss, pred_y, layer3_input, y=test_model(i)
#test_losses = [test_model(i) for i in test_batch_start]
test_losses.append(test_loss)
#write_file.write(str(pred_y[0])+'\n')#+'\t'+str(testY[i].eval())+
#write_file.close()
test_score = numpy.mean(test_losses)
print(('\t\t\t\t\t\tepoch %i, minibatch %i/%i, test acc of best '
'model %f %%') %
(epoch, minibatch_index, n_train_batches,
(1-test_score) * 100.))
#now, see the results of svm
write_feature=open('feature_check.txt', 'w')
train_y=[]
train_features=[]
for batch_start in train_batch_start:
cost_ij, error_ij, layer3_input, y, sum_uni_l, sum_uni_r, uni_cosine=train_model_predict(batch_start)
train_y.append(y[0])
train_features.append(layer3_input[0])
write_feature.write(' '.join(map(str,layer3_input[0]))+'\n')
write_feature.close()
test_y=[]
test_features=[]
for i in test_batch_start:
test_loss, pred_y, layer3_input, y=test_model(i)
test_y.append(y[0])
test_features.append(layer3_input[0])
clf = svm.SVC(kernel='linear')#OneVsRestClassifier(LinearSVC()) #linear 76.11%, poly 75.19, sigmoid 66.50, rbf 73.33
clf.fit(train_features, train_y)
results=clf.predict(test_features)
lr=LinearRegression().fit(train_features, train_y)
results_lr=lr.predict(test_features)
corr_count=0
corr_lr=0
test_size=len(test_y)
for i in range(test_size):
if results[i]==test_y[i]:
corr_count+=1
if numpy.absolute(results_lr[i]-test_y[i])<0.5:
corr_lr+=1
acc=corr_count*1.0/test_size
acc_lr=corr_lr*1.0/test_size
if acc > max_acc:
max_acc=acc
best_epoch=epoch
if acc_lr> max_acc:
max_acc=acc_lr
best_epoch=epoch
print '\t\t\t\t\t\t\t\t\t\t\tsvm acc: ', acc, 'LR acc: ', acc_lr, ' max acc: ', max_acc , ' at epoch: ', best_epoch
#exit(0)
if patience <= iter:
done_looping = True
break
#after each epoch, increase the batch_size
if epoch%2==1:
update_freq=update_freq*1
else:
update_freq=update_freq/1
#print 'Batch_size: ', update_freq
end_time = time.clock()
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 >> sys.stderr, ('The code for file ' +
os.path.split(__file__)[1] +
' ran for %.2fm' % ((end_time - start_time) / 60.))
def train(self, input_train, target_train=None, input_test=None,
target_test=None, epochs=100, epsilon=None,
summary_type='table'):
"""
Method train neural network.
Parameters
----------
input_train : array-like
target_train : array-like or None
input_test : array-like or None
target_test : array-like or None
epochs : int
Defaults to `100`.
epsilon : float or None
Defaults to ``None``.
"""
show_epoch = self.show_epoch
logs = self.logs
training = self.training = AttributeKeyDict()
if epochs <= 0:
raise ValueError("Number of epochs needs to be greater than 0.")
if epsilon is not None and epochs <= 2:
raise ValueError("Network should train at teast 3 epochs before "
"check the difference between errors")
if summary_type == 'table':
logging_info_about_the_data(self, input_train, input_test)
logging_info_about_training(self, epochs, epsilon)
logs.newline()
summary = SummaryTable(
table_builder=table.TableBuilder(
table.Column(name="Epoch #"),
table.NumberColumn(name="Train err"),
table.NumberColumn(name="Valid err"),
table.TimeColumn(name="Time", width=10),
stdout=logs.write
),
network=self,
delay_limit=1.,
delay_history_length=10,
)
elif summary_type == 'inline':
summary = InlineSummary(network=self)
else:
raise ValueError("`{}` is unknown summary type"
"".format(summary_type))
iterepochs = create_training_epochs_iterator(self, epochs, epsilon)
show_epoch = parse_show_epoch_property(self, epochs, epsilon)
training.show_epoch = show_epoch
# Storring attributes and methods in local variables we prevent
# useless __getattr__ call a lot of times in each loop.
# This variables speed up loop in case on huge amount of
# iterations.
training_errors = self.errors
validation_errors = self.validation_errors
shuffle_data = self.shuffle_data
train_epoch = self.train_epoch
epoch_end_signal = self.epoch_end_signal
train_end_signal = self.train_end_signal
on_epoch_start_update = self.on_epoch_start_update
is_first_iteration = True
can_compute_validation_error = (input_test is not None)
last_epoch_shown = 0
symMatrix = tt.dmatrix("symMatrix")
symEigenvalues, eigenvectors = tt.nlinalg.eig(symMatrix)
get_Eigen = theano.function([symMatrix], [symEigenvalues, eigenvectors] )
epsilon = []
alpha = []
alpha0 = []
with logs.disable_user_input():
for epoch in iterepochs:
validation_error = None
epoch_start_time = time.time()
on_epoch_start_update(epoch)
if shuffle_data:
input_train, target_train = shuffle(input_train,
target_train)
try:
train_error = train_epoch(input_train, target_train)
H = self.variables.hessian.get_value()
ev, _ = get_Eigen(H)
if can_compute_validation_error:
validation_error = self.prediction_error(input_test,
target_test)
epsilon.append(train_error)
alpha.append(numpy.sum(ev < 0))
alpha0.append(numpy.sum(ev == 0))
training_errors.append(train_error)
validation_errors.append(validation_error)
epoch_finish_time = time.time()
training.epoch_time = epoch_finish_time - epoch_start_time
if epoch % training.show_epoch == 0 or is_first_iteration:
summary.show_last()
last_epoch_shown = epoch
if epoch_end_signal is not None:
epoch_end_signal(self)
is_first_iteration = False
except StopNetworkTraining as err:
# TODO: This notification breaks table view in terminal.
# I need to show it in a different way.
logs.message("TRAIN", "Epoch #{} stopped. {}"
"".format(epoch, str(err)))
break
if epoch != last_epoch_shown:
summary.show_last()
if train_end_signal is not None:
train_end_signal(self)
summary.finish()
logs.newline()
plt.plot(alpha,epsilon,'r')
plt.plot(alpha0,epsilon,'b')
plt.xlabel('alpha')
plt.ylabel('epsilon')
# want to collect the output of stdout in a variable
capture = StringIO()
capture.truncate(0)
save_stdout = sys.stdout
sys.stdout = capture
print self.connection
sys.stdout=save_stdout
s = capture.getvalue()
s=s.split('\n')[0:][0]
str = self.class_name()
str1 = s+'---'+str+'-alpha-epsilon'+'.eps'
plt.savefig(str1,format='eps',dpi=1000)
plt.plot(iterepochs,epsilon)
plt.xlabel('iterepochs')
plt.ylabel('epsilon')
str2=s+'---'+str+'-epsilon-iterepochs'+'.eps'
plt.savefig(str2,format='eps',dpi=1000)
def train(num_epochs, batch_size, X_train, y_train, X_val, y_val, input_dim, output_dim, depth, num_units,
drop_input=None, drop_hidden=None, report=50):
"""
Train neural network.
:param num_epochs: training epochs count
:param batch_size: integer
:param X_train: numpy array with train data
:param y_train: numpy array with train targets
:param X_val: numpy array with validation data
:param y_val: numpy arrays with validation targets
:param input_dim: count of input units
:param output_dim: count of output units
:param depth: hidden layers count
:param num_units: count of units in hidden layers
:param drop_input: input dropout value
:param drop_hidden: hidden dropout value
:param report: report output frequency
:return: lasagne network
"""
input_var = T.dmatrix('inputs')
target_var = T.imatrix('targets')
network = build_mlp(input_dim, output_dim, depth, num_units, drop_input, drop_hidden, input_var)
# create a loss expression for training
prediction = lasagne.layers.get_output(network)
loss = lasagne.objectives.categorical_crossentropy(prediction, target_var)
loss = loss.mean()
# create update expressions for training
params = lasagne.layers.get_all_params(network, trainable=True)
updates = lasagne.updates.nesterov_momentum(loss, params, learning_rate=0.01, momentum=0.9)
# create a loss expression for validation with deterministic forward pass (disable dropout layers)
test_prediction = lasagne.layers.get_output(network, deterministic=True)
test_loss = lasagne.objectives.categorical_crossentropy(test_prediction, target_var)
test_loss = test_loss.mean()
# create an expression for the classification accuracy
test_acc = T.mean(T.eq(T.argmax(test_prediction, axis=1), T.argmax(target_var, axis=1)),
dtype=theano.config.floatX)
# compile a function performing a training step on a mini-batch
train_fn = theano.function([input_var, target_var], loss, updates=updates)
# compile a function computing the validation loss and accuracy
val_fn = theano.function([input_var, target_var], [test_loss, test_acc])
for epoch in range(num_epochs):
# full pass over the training data
train_err = 0
train_batches = 0
start_time = time.time()
for batch in iterate_minibatches(X_train, y_train, batch_size, shuffle=True):
inputs, targets = batch
train_err += train_fn(inputs, targets)
train_batches += 1
# full pass over the validation data
val_err = 0
val_acc = 0
val_batches = 0
for batch in iterate_minibatches(X_val, y_val, batch_size, shuffle=False):
inputs, targets = batch
err, acc = val_fn(inputs, targets)
val_err += err
val_acc += acc
val_batches += 1
if (epoch + 1) % report == 0:
print("Epoch {} of {} took {:.3f}s".format(epoch + 1, num_epochs, time.time() - start_time))
print("\ttraining loss:\t\t\t{:.6f}".format(train_err / train_batches))
print("\tvalidation loss:\t\t{:.6f}".format(val_err / val_batches))
print("\tvalidation accuracy:\t\t{:.2f} %".format(val_acc / val_batches * 100))
return network
def test_convolution(self):
# print '\n\n*************************************************'
# print ' TEST CONVOLUTION'
# print '*************************************************'
# fixed parameters
bsize = 10 # batch size
imshp = (28, 28)
kshp = (5, 5)
nkern = 5
ssizes = ((1, 1), (2, 2), (3, 3), (4, 4))
convmodes = ('full', 'valid')
# symbolic stuff
bias = tensor.dvector()
kerns = tensor.dmatrix()
input = tensor.dmatrix()
rng = numpy.random.RandomState(3423489)
filters = rng.randn(nkern, numpy.prod(kshp))
biasvals = rng.randn(nkern)
for mode in ('FAST_COMPILE', 'FAST_RUN'): # , profmode):
ttot, ntot = 0, 0
for conv_mode in convmodes:
for ss in ssizes:
output, outshp = sp.convolve(kerns, kshp, nkern, input,\
imshp, ss, bias=bias, mode=conv_mode)
f = function([kerns, bias, input], output, mode=mode)
# now test with real values
img2d = numpy.arange(bsize * numpy.prod(imshp)).reshape(( \
bsize,) + imshp)
img1d = img2d.reshape(bsize, -1)
# create filters (need to be flipped to use convolve2d)
filtersflipped = numpy.zeros((nkern, ) + kshp)
for k in range(nkern):
it = reversed(filters[k, :])
for i in range(kshp[0]):
for j in range(kshp[1]):
filtersflipped[k, i, j] = it.next()
# compute output with convolve2d
if conv_mode == 'valid':
fulloutshp = numpy.array(imshp) - numpy.array(kshp) + 1
else:
fulloutshp = numpy.array(imshp) + numpy.array(kshp) - 1
ntime1 = time.time()
refout = numpy.zeros((bsize, ) + tuple(fulloutshp) +
(nkern, ))
for b in range(bsize):
for n in range(nkern):
refout[b, ...,
n] = convolve2d(img2d[b, :, :],
filtersflipped[n, ...],
conv_mode)
ntot += time.time() - ntime1
# need to flatten images
bench1 = refout[:, 0::ss[0],
0::ss[1], :].reshape(bsize, -1, nkern)
bench1 += biasvals.reshape(1, 1, nkern)
# swap the last two dimensions (output needs to be nkern x outshp)
bench1 = numpy.swapaxes(bench1, 1, 2)
ttime1 = time.time()
out1 = f(filters, biasvals, img1d)
ttot += time.time() - ttime1
temp = bench1.flatten() - out1.flatten()
assert (temp < 1e-5).all()
def __init__(self,
theano_rng=None,
input=None,
n_visible=None,
n_hidden=None,
W=None,
bhid=None,
bvis=None,
activation=None,
firstlayer=1,
variance=None):
self.n_visible = n_visible
self.n_hidden = n_hidden
if not W:
initial_W = numpy.asarray(theano_rng.normal(0.0,
1.0 / numpy.sqrt(n_in),
size=(n_visible,
n_hidden)),
dtype=theano.config.floatX)
W = theano.shared(value=initial_W, name='W')
#initial_W = numpy.asarray( numpy_rng.uniform(
# low = -4*numpy.sqrt(6./(n_hidden+n_visible)),
# high = 4*numpy.sqrt(6./(n_hidden+n_visible)),
# size = (n_visible, n_hidden)),
# dtype = theano.config.floatX)
if not bvis:
bvis = theano.shared(
value=numpy.zeros(n_visible, dtype=theano.config.floatX))
if not bhid:
bhid = theano.shared(value=numpy.zeros(n_hidden,
dtype=theano.config.floatX),
name='b')
self.W = W
self.b = bhid
self.b_prime = bvis
self.W_prime = self.W.T
self.theano_rng = theano_rng
self.activation = activation
if input == None:
self.x = T.dmatrix(name='input')
else:
self.x = input
self.params = [self.W, self.b, self.b_prime]
# first layer, use Gaussian noise
self.firstlayer = firstlayer
if self.firstlayer == 1:
if variance == None:
self.var = T.vector(name='input')
else:
self.var = variance
else:
self.var = None
"eval()" takes a dictionary with names of variables and values to be assigned to them
eval() utimately imports a "function()", so we end up in the same situation, so it is
slower the first time we invoke this, subsequent invocations are faster since it saves
"function()" imported already
that way we don't need to import "function()", but importing and using it is more
flexible than relyin on "eval()" itself
'''
'''
Addition of two matrices is also very simple, the only difference is using
T.dmatrix instead of T.dscalar
'''
x = T.dmatrix('x')
y = T.dmatrix('y')
z = x + y
f2 = function([x, y], z)
'''
now we do not assign the matrices to x and y directly, but instead we pass matrices
to function as variables, invoking it like: "f2([matrix_nr_1], [matrix_nr_2])
here we add, elementwise, 2 2-dimensional matrices
'''
a1 = [[1, 2],
[3, 4]]
a2 = [[10, 20],
[30, 40]]
def exec_multilayer_conv_nnet_old(conv_mode,
ss,
bsize,
imshp,
kshps,
nkerns,
unroll_batch=0,
unroll_kern=0,
img=T.dmatrix(),
validate=True,
conv_op_py=False,
do_print=True,
repeat=1,
unroll_patch=False,
unroll_patch_size=False,
verbose=0):
# build actual input images
imgval = global_rng.rand(bsize, imshp[0], imshp[1], imshp[2])
a = T.dmatrix()
kerns = [a for i in nkerns]
inputs4 = dmatrix4()
kerns4 = dmatrix4()
# for each layer
ntot = 0
tctot = 0
tpytot = 0
for kshp, kern, nkern, n_layer in zip(kshps, kerns, nkerns,
range(len(nkerns))):
if do_print:
print '************* layer %i ***************' % n_layer
print conv_mode, ss, n_layer, kshp, nkern
# actual values
w = global_rng.random_sample(N.r_[nkern, imshp[0], kshp])
w_flip = flip(w, kshp).reshape(w.shape)
# manual implementation
# check first stage
padimg = imgval
if conv_mode == 'full':
padimg_shp = N.array(
imshp[1:]) + 2 * (N.array(kshp) - N.array([1, 1]))
padimg = N.zeros(N.r_[bsize, imshp[0], padimg_shp])
padimg[:, :, kshp[0] - 1:-kshp[0] + 1,
kshp[1] - 1:-kshp[1] + 1] = imgval
outshp = N.hstack(
(nkern, ConvOp.getOutputShape(imshp[1:], kshp, ss, conv_mode)))
time1 = time.time()
outval = N.zeros(N.r_[bsize, outshp])
if validate:
# causes an atexit problem
from scipy.signal.sigtools import _convolve2d
from scipy.signal.signaltools import _valfrommode, _bvalfromboundary
val = _valfrommode(conv_mode)
bval = _bvalfromboundary('fill')
for b in range(bsize): # loop over batches
for n in range(nkern): # loop over filters
for i in range(imshp[0]): # loop over input feature maps
outval[b, n, ...] += _convolve2d(\
imgval[b, i, ...], w_flip[n, i, ...], 1, val, bval, 0)[0::ss[0], 0::ss[1]]
ntot += time.time() - time1
# ConvOp
if unroll_patch and not unroll_patch_size:
conv_op = ConvOp(dx=ss[0],
dy=ss[1],
output_mode=conv_mode,
unroll_patch=unroll_patch,
verbose=verbose)(inputs4, kerns4)
else:
conv_op = ConvOp(imshp,
kshp,
nkern,
bsize,
ss[0],
ss[1],
conv_mode,
unroll_batch=unroll_batch,
unroll_kern=unroll_kern,
unroll_patch=unroll_patch,
verbose=verbose)(inputs4, kerns4)
l1shp = N.hstack(
(nkern, ConvOp.getOutputShape(imshp[1:], kshp, ss, conv_mode)))
propup2 = function([inputs4, kerns4], conv_op)
propup3 = function([inputs4, kerns4], conv_op, mode=Mode(linker="py"))
time1 = time.time()
for i in range(repeat):
hidval2_ = propup2(imgval, w_flip)
hidval2 = hidval2_ # [:,:,0::ss[0],0::ss[1]]
tctot += time.time() - time1
if conv_op_py:
time1 = time.time()
for i in range(repeat):
hidval3_ = propup3(imgval, w_flip)
hidval3 = hidval3_ # [:,:,0::ss[0],0::ss[1]]
tpytot += time.time() - time1
assert (N.abs(hidval2 - hidval3) < 1e-5).all()
else:
tpytot += 0
if validate:
temp = N.abs(outval - hidval2)
assert (temp < 1e-5).all()
if validate and conv_op_py:
temp = N.abs(outval - hidval3)
assert (temp < 1e-5).all()
imshp = tuple(outshp)
imgval = outval.reshape(bsize, outshp[0], outshp[1], outshp[2])
return tctot, tpytot, ntot
# View more python tutorials on my Youtube and Youku channel!!!
# Youtube video tutorial: https://www.youtube.com/channel/UCdyjiB5H8Pu7aDTNVXTTpcg
# Youku video tutorial: http://i.youku.com/pythontutorial
# 5 - theano.function
"""
Please note, this code is only for python 3+. If you are using python 2+, please modify the code accordingly.
"""
from __future__ import print_function
import numpy as np
import theano
import theano.tensor as T
# activation function example
x = T.dmatrix('x')
s = 1 / (1 + T.exp(-x)) # logistic or soft step
logistic = theano.function([x], s)
print(logistic([[0, 1],[-1, -2]]))
# multiply outputs for a function
a, b = T.dmatrices('a', 'b')
diff = a - b
abs_diff = abs(diff)
diff_squared = diff ** 2
f = theano.function([a, b], [diff, abs_diff, diff_squared])
print( f(np.ones((2, 2)), np.arange(4).reshape((2, 2))) )
# default value and name for a function
x, y, w = T.dscalars('x', 'y', 'w')
z = (x+y)*w
def exec_multilayer_conv_nnet(conv_mode,
ss,
bsize,
imshp,
kshps,
nkerns,
unroll_batch=0,
unroll_kern=0,
img=T.dmatrix(),
do_print=True,
repeat=1,
unroll_patch=False,
unroll_patch_size=False,
verbose=0):
# build actual input images
imgval = global_rng.rand(bsize, imshp[0], imshp[1], imshp[2])
a = T.dmatrix()
kerns = [a for i in nkerns]
inputs4 = dmatrix4()
kerns4 = dmatrix4()
# for each layer
ntot = 0
tctot = 0
tpytot = 0
for kshp, kern, nkern, n_layer in zip(kshps, kerns, nkerns,
range(len(nkerns))):
if do_print:
print '************* layer %i ***************' % n_layer
print conv_mode, ss, n_layer, kshp, nkern
# actual values
w = global_rng.random_sample(N.r_[nkern, imshp[0], kshp])
w_flip = flip(w, kshp).reshape(w.shape)
outshp = N.hstack(
(nkern, ConvOp.getOutputShape(imshp[1:], kshp, ss, conv_mode)))
time1 = time.time()
outval = N.zeros(N.r_[bsize, outshp])
# ConvOp
if unroll_patch and not unroll_patch_size:
conv_op = ConvOp(dx=ss[0],
dy=ss[1],
output_mode=conv_mode,
unroll_patch=unroll_patch,
verbose=verbose)(inputs4, kerns4)
else:
conv_op = ConvOp(imshp,
kshp,
nkern,
bsize,
ss[0],
ss[1],
conv_mode,
unroll_batch=unroll_batch,
unroll_kern=unroll_kern,
unroll_patch=unroll_patch,
verbose=verbose)(inputs4, kerns4)
l1shp = N.hstack(
(nkern, ConvOp.getOutputShape(imshp[1:], kshp, ss, conv_mode)))
propup2 = function([inputs4, kerns4], conv_op)
time1 = time.time()
for i in range(repeat):
hidval2_ = propup2(imgval, w_flip)
hidval2 = hidval2_ # [:,:,0::ss[0],0::ss[1]]
tctot += time.time() - time1
imshp = tuple(outshp)
imgval = outval.reshape(bsize, outshp[0], outshp[1], outshp[2])
return tctot, tpytot, ntot
def test1(self):
a = tensor.dmatrix()
w = sort(a)
f = theano.function([a], w)
utt.assert_allclose(f(self.m_val), np.sort(self.m_val))
def __init__(
self,
numpy_rng,
theano_rng=None,
input=None,
n_visible=784,
n_hidden=500,
W=None,
bhid=None,
bvis=None
):
"""
Initialize the dA class by specifying the number of visible units (the
dimension d of the input ), the number of hidden units ( the dimension
d' of the latent or hidden space ) and the corruption level. The
constructor also receives symbolic variables for the input, weights and
bias. Such a symbolic variables are useful when, for example the input
is the result of some computations, or when weights are shared between
the dA and an MLP layer. When dealing with SdAs this always happens,
the dA on layer 2 gets as input the output of the dA on layer 1,
and the weights of the dA are used in the second stage of training
to construct an MLP.
:type numpy_rng: numpy.random.RandomState
:param numpy_rng: number random generator used to generate 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 input: theano.tensor.TensorType
:param input: a symbolic description of the input or None for
standalone dA
:type n_visible: int
:param n_visible: number of visible units
:type n_hidden: int
:param n_hidden: number of hidden units
:type W: theano.tensor.TensorType
:param W: Theano variable pointing to a set of weights that should be
shared belong the dA and another architecture; if dA should
be standalone set this to None
:type bhid: theano.tensor.TensorType
:param bhid: Theano variable pointing to a set of biases values (for
hidden units) that should be shared belong dA and another
architecture; if dA should be standalone set this to None
:type bvis: theano.tensor.TensorType
:param bvis: Theano variable pointing to a set of biases values (for
visible units) that should be shared belong dA and another
architecture; if dA should be standalone set this to None
"""
self.n_visible = n_visible
self.n_hidden = n_hidden
# create a Theano random generator that gives symbolic random values
if not theano_rng:
theano_rng = RandomStreams(numpy_rng.randint(2 ** 30))
# note : W' was written as `W_prime` and b' as `b_prime`
if not W:
# W is initialized with `initial_W` which is uniformely sampled
# from -4*sqrt(6./(n_visible+n_hidden)) and
# 4*sqrt(6./(n_hidden+n_visible))the output of uniform if
# converted using asarray to dtype
# theano.config.floatX so that the code is runable on GPU
initial_W = numpy.asarray(
numpy_rng.uniform(
low=-4 * numpy.sqrt(6. / (n_hidden + n_visible)),
high=4 * numpy.sqrt(6. / (n_hidden + n_visible)),
size=(n_visible, n_hidden)
),
dtype=theano.config.floatX
)
W = theano.shared(value=initial_W, name='W', borrow=True)
if not bvis:
bvis = theano.shared(
value=numpy.zeros(
n_visible,
dtype=theano.config.floatX
),
borrow=True
)
if not bhid:
bhid = theano.shared(
value=numpy.zeros(
n_hidden,
dtype=theano.config.floatX
),
name='b',
borrow=True
)
self.W = W
# b corresponds to the bias of the hidden
self.b = bhid
# b_prime corresponds to the bias of the visible
self.b_prime = bvis
# tied weights, therefore W_prime is W transpose
self.W_prime = self.W.T
self.theano_rng = theano_rng
# if no input is given, generate a variable representing the input
if input is None:
# we use a matrix because we expect a minibatch of several
# examples, each example being a row
self.x = T.dmatrix(name='input')
else:
self.x = input
self.params = [self.W, self.b, self.b_prime]
def speed_multilayer_conv():
# calculate the speed up of different combination of unroll
# put the paramter to the same you will try.
validate = False # we don't validate the result to have it much faster!
repeat = 3
verbose = 1
unroll_batch = [1, 2, 3, 4, 5, 6, 10] # 15, 30, 60 always much slower
unroll_kern = [1, 2, 3, 4, 5, 6, 10] # 15, 30, 60 always much slower
#unroll_batch = [1,4,5]
#unroll_kern = [1,4,5]
#unroll_batch = [1,4]
#unroll_kern = [1,4]
unroll_patch = [True, False]
bsize = 60 # batch size
imshp_start = (1, 48, 48) # un square shape to test more corner case.
kshps = ([11, 12], ) # un square shape to test more corner case.
nkerns = [60] # per output pixel
ssizes = [
(1, 1),
] # (1,1)]#(2,2) bugged
convmodes = ['valid', 'full']
do_convolve2 = False
a = T.dmatrix()
kerns = [a for i in nkerns]
assert len(kshps) == len(nkerns) == len(kerns)
timing = N.zeros(
(len(unroll_batch), len(unroll_kern), 3, len(convmodes) * len(ssizes)))
t_b_k = []
# calculate the timing with unrolling
print 'time unroll batch kern'
best = []
worst = []
t_ = []
for unroll_b, n_b in zip(unroll_batch, range(len(unroll_batch))):
for unroll_k, n_k in zip(unroll_kern, range(len(unroll_kern))):
t_b_k.append(str(unroll_b) + "/" + str(unroll_k))
if not t_:
tctot, tpytot, ntot = [], [], []
for conv_mode, n_mode in zip(convmodes, range(len(convmodes))):
for ss, n_ss in zip(ssizes, range(len(ssizes))):
# tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet_old(conv_mode, ss, bsize, imshp_start, kshps, nkerns, unroll_batch=unroll_b, unroll_kern=unroll_k, validate=validate, verbose=verbose,do_print=False)
tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet(
conv_mode,
ss,
bsize,
imshp_start,
kshps,
nkerns,
unroll_batch=unroll_b,
unroll_kern=unroll_k,
verbose=verbose,
do_print=False,
repeat=repeat)
tctot += [tctot_]
tpytot += [tpytot_]
ntot += [ntot_]
if unroll_b == 4 and unroll_k == 4:
# print "unroll 4/4",tctot
best = tctot
if unroll_b == 1 and unroll_k == 1:
# print "unroll 1/1",tctot
worst = tctot
timing[n_b,
n_k] = [tctot, tpytot,
ntot] # [sum(tctot), sum(tpytot), sum(ntot)]
if not t_:
t = timing[:, :, 0, :] # We select only the c timing.
else:
t = t_
t = N.asarray(t)
# calculate the old timing
print 'time old version'
tctot, tpytot, ntot = [], [], []
tctot_ = []
if not tctot_:
for conv_mode, n_mode in zip(convmodes, range(len(convmodes))):
for ss, n_ss in zip(ssizes, range(len(ssizes))):
# tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet_old(conv_mode, ss, bsize, imshp_start, kshps, nkerns, unroll_batch=0, unroll_kern=0, validate=validate, verbose=verbose,do_print=False)
tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet(
conv_mode,
ss,
bsize,
imshp_start,
kshps,
nkerns,
unroll_batch=0,
unroll_kern=0,
verbose=verbose,
do_print=False,
repeat=repeat)
tctot += [tctot_]
tpytot += [tpytot_]
ntot += [ntot_]
else:
tctot = N.asarray(tctot_)
print "old code timing %.3fs" % sum(tctot), tctot
best = N.asarray(best)
worst = N.asarray(worst)
print "timing for unrolled version"
print "unroll_batch/unroll_kern valid_mode full_mode"
for n_b in range(len(unroll_batch)):
for n_k in range(len(unroll_kern)):
print(unroll_batch[n_b], unroll_kern[n_k]) + tuple(t[n_b,
n_k]), ','
t_detail = t
t = t.sum(axis=2)
print "max %.3fs" % t.max(
), "max param(batch unloop size/kernel unloop size)", t_b_k[t.argmax()]
print "min %.3fs" % t.min(
), "min param(batch unloop size/kernel unloop size)", t_b_k[t.argmin()]
print "speedup vs (1/1)%.3fx, vs old %.3fx" % (t.max() / t.min(),
sum(tctot) / t.min())
print worst / best, tctot / best
# calculate the timing of unroll_patch
print 'time unroll_patch'
tctot_patch = []
tctot_patch_size = []
for conv_mode, n_mode in zip(convmodes, range(len(convmodes))):
for ss, n_ss in zip(ssizes, range(len(ssizes))):
#tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet_old(conv_mode, ss, bsize, imshp_start, kshps, nkerns, unroll_batch=0, unroll_kern=0, validate=validate,unroll_patch=True,verbose=verbose,do_print=False)
tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet(
conv_mode,
ss,
bsize,
imshp_start,
kshps,
nkerns,
unroll_batch=0,
unroll_kern=0,
unroll_patch=True,
verbose=verbose,
do_print=False,
repeat=repeat)
tctot_patch += [tctot_]
#tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet_old(conv_mode, ss, bsize, imshp_start, kshps, nkerns, unroll_batch=0, unroll_kern=0, validate=validate,unroll_patch=True,verbose=verbose,do_print=False,unroll_patch_size=True)
tctot_, tpytot_, ntot_ = exec_multilayer_conv_nnet(
conv_mode,
ss,
bsize,
imshp_start,
kshps,
nkerns,
unroll_batch=0,
unroll_kern=0,
unroll_patch=True,
verbose=verbose,
do_print=False,
unroll_patch_size=True,
repeat=repeat)
tctot_patch_size += [tctot_]
t_patch = sum(tctot_patch)
print "unroll_patch without shape time", tctot_patch
print "speedup vs (1/1)%.3fx, vs old %.3fx" % (t.max() / t_patch,
sum(tctot) / t_patch)
print best / tctot_patch, worst / tctot_patch
t_patch_size = sum(tctot_patch_size)
print "unroll_patch with shape time", tctot_patch_size
print "speedup vs (1/1)%.3fx, vs old %.3fx" % (t.max() / t_patch_size,
sum(tctot) / t_patch_size)
print best / tctot_patch_size, worst / tctot_patch_size
return
class GaussianLikelihoodModel(LikelihoodModel):
def __init__(self, **parameters):
super(GaussianLikelihoodModel, self).__init__(**parameters)
self.sigma0inv = np.linalg.inv(self.sigma0)
self.D = self.sigma.shape[0]
self.compile()
def transition_probability(self, parent, child):
child_latent, child_time = child.get_state(
'latent_value'), child.get_state('time')
if parent is None:
return self.calculate_transition(child_latent, self.mu0,
child_time, -1)
parent_latent, parent_time = parent.get_state(
'latent_value'), parent.get_state('time')
assert parent_time < child_time, (parent_time, child_time)
return self.calculate_transition(child_latent, parent_latent,
child_time, parent_time)
@theanify(T.dvector('state'), T.dvector('parent'), T.dscalar('time'),
T.dscalar('parent_time'))
def calculate_transition(self, state, parent, time, parent_time):
sigma = (time - parent_time) * self.sigma
mu = parent
logdet = T.log(T.nlinalg.det(sigma))
delta = state - mu
pre = -(self.D / 2.0 * np.log(2 * np.pi) + 1 / 2.0 * logdet)
return pre + -0.5 * (T.dot(
delta, T.dot(T.nlinalg.matrix_inverse(sigma), delta)))
@theanify(T.dvector('mean'), T.dmatrix('cov'))
def sample(self, mean, cov):
e, v = T.nlinalg.eigh(cov)
x = RandomStreams().normal(size=(self.D, ))
x = T.dot(x, T.sqrt(e)[:, None] * v)
return x + mean
def sample_transition(self, node, parent):
children = node.children
time = node.get_state('time')
if parent is None:
mu0 = self.mu0
sigma0 = self.sigma0
sigma0inv = self.sigma0inv
else:
mu0 = parent.get_state('latent_value')
sigma0 = self.sigma * (time - parent.get_state('time'))
sigma0inv = np.linalg.inv(sigma0)
mus = [c.get_state('latent_value') for c in children]
sigmas = [self.sigma * (c.get_state('time') - time) for c in children]
sigmas_inv = [np.linalg.inv(s) for s in sigmas]
sigman = np.linalg.inv(sigma0inv + sum(sigmas_inv))
mun = np.dot(
sigman,
np.dot(sigma0inv, mu0) +
sum([np.dot(a, b) for a, b in zip(sigmas_inv, mus)]))
return self.sample(mun, sigman)
def get_parameters(self):
return {"sigma", "sigma0", "mu0"}
from blocks.serialization import load
from theano import tensor, function
# theano variables
features_car_cat = tensor.dmatrix('features_car_cat')
features_car_int = tensor.dmatrix('features_car_int')
features_nocar_cat = tensor.dmatrix('features_nocar_cat')
features_nocar_int = tensor.dmatrix('features_nocar_int')
features_cp = tensor.imatrix('codepostal')
features_hascar = tensor.imatrix('features_hascar')
main_loop = load(open("./model", "rb"))
model = main_loop.model
f = model.get_theano_function()
from fuel.datasets.hdf5 import H5PYDataset
submit_set = H5PYDataset('./data/data.hdf5',
which_sets=('submit', ),
load_in_memory=True)
print model.inputs
print submit_set.provides_sources
m = []
for i in model.inputs:
m.append(submit_set.provides_sources.index(i.name))
from fuel.schemes import SequentialScheme
from fuel.streams import DataStream