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ladder.py
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ladder.py
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import logging
import numpy as np
from collections import OrderedDict
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams as RandomStreams
from theano.tensor.nnet.conv import conv2d, ConvOp
from theano.sandbox.cuda.blas import GpuCorrMM
from theano.sandbox.cuda.basic_ops import gpu_contiguous
from blocks.bricks.cost import SquaredError
from blocks.bricks.cost import CategoricalCrossEntropy, MisclassificationRate
from blocks.graph import add_annotation, Annotation
from blocks.roles import add_role, PARAMETER, WEIGHT, BIAS
from utils import shared_param, AttributeDict
from nn import maxpool_2d, global_meanpool_2d, BNPARAM, softmax_n
logger = logging.getLogger('main.model')
floatX = theano.config.floatX
class LadderAE():
def __init__(self, p):
self.p = p
self.init_weights_transpose = False
self.default_lr = p.lr
self.shareds = OrderedDict()
self.rstream = RandomStreams(seed=p.seed)
self.rng = np.random.RandomState(seed=p.seed)
n_layers = len(p.encoder_layers)
assert n_layers > 1, "Need to define encoder layers"
assert n_layers == len(p.denoising_cost_x), (
"Number of denoising costs does not match with %d layers: %s" %
(n_layers, str(p.denoising_cost_x)))
def one_to_all(x):
""" (5.,) -> 5 -> (5., 5., 5.)
('relu',) -> 'relu' -> ('relu', 'relu', 'relu')
"""
if type(x) is tuple and len(x) == 1:
x = x[0]
if type(x) is float:
x = (np.float32(x),) * n_layers
if type(x) is str:
x = (x,) * n_layers
return x
p.decoder_spec = one_to_all(p.decoder_spec)
p.f_local_noise_std = one_to_all(p.f_local_noise_std)
acts = one_to_all(p.get('act', 'relu'))
assert n_layers == len(p.decoder_spec), "f and g need to match"
assert (n_layers == len(acts)), (
"Not enough activations given. Requires %d. Got: %s" %
(n_layers, str(acts)))
acts = acts[:-1] + ('softmax',)
def parse_layer(spec):
""" 'fc:5' -> ('fc', 5)
'5' -> ('fc', 5)
5 -> ('fc', 5)
'convv:3:2:2' -> ('convv', [3,2,2])
"""
if type(spec) is not str:
return "fc", spec
spec = spec.split(':')
l_type = spec.pop(0) if len(spec) >= 2 else "fc"
spec = map(int, spec)
spec = spec[0] if len(spec) == 1 else spec
return l_type, spec
enc = map(parse_layer, p.encoder_layers)
self.layers = list(enumerate(zip(enc, p.decoder_spec, acts)))
def weight(self, init, name, cast_float32=True, for_conv=False):
weight = self.shared(init, name, cast_float32, role=WEIGHT)
if for_conv:
return weight.dimshuffle('x', 0, 'x', 'x')
return weight
def bias(self, init, name, cast_float32=True, for_conv=False):
b = self.shared(init, name, cast_float32, role=BIAS)
if for_conv:
return b.dimshuffle('x', 0, 'x', 'x')
return b
def shared(self, init, name, cast_float32=True, role=PARAMETER, **kwargs):
p = self.shareds.get(name)
if p is None:
p = shared_param(init, name, cast_float32, role, **kwargs)
self.shareds[name] = p
return p
def counter(self):
name = 'counter'
p = self.shareds.get(name)
update = []
if p is None:
p_max_val = np.float32(10)
p = self.shared(np.float32(1), name, role=BNPARAM)
p_max = self.shared(p_max_val, name + '_max', role=BNPARAM)
update = [(p, T.clip(p + np.float32(1), np.float32(0), p_max)),
(p_max, p_max_val)]
return (p, update)
def noise_like(self, x):
noise = self.rstream.normal(size=x.shape, avg=0.0, std=1.0)
return T.cast(noise, dtype=floatX)
def rand_init(self, in_dim, out_dim):
""" Random initialization for fully connected layers """
W = self.rng.randn(in_dim, out_dim) / np.sqrt(in_dim)
return W
def rand_init_conv(self, dim):
""" Random initialization for convolution filters """
fan_in = np.prod(dtype=floatX, a=dim[1:])
bound = np.sqrt(3. / max(1.0, (fan_in)))
W = np.asarray(
self.rng.uniform(low=-bound, high=bound, size=dim), dtype=floatX)
return W
def new_activation_dict(self):
return AttributeDict({'z': {}, 'h': {}, 's': {}, 'm': {}})
def annotate_update(self, update, tag_to):
a = Annotation()
for (var, up) in update:
a.updates[var] = up
add_annotation(tag_to, a)
def apply(self, input_labeled, target_labeled, input_unlabeled):
self.layer_counter = 0
input_dim = self.p.encoder_layers[0]
# Store the dimension tuples in the same order as layers.
layers = self.layers
self.layer_dims = {0: input_dim}
self.lr = self.default_lr
self.costs = costs = AttributeDict()
self.costs.denois = AttributeDict()
self.act = AttributeDict()
self.error = AttributeDict()
top = len(layers) - 1
if input_labeled is None:
N = 0
else:
N = input_labeled.shape[0]
self.join = lambda l, u: T.concatenate([l, u], axis=0) if l else u
self.labeled = lambda x: x[:N] if x is not None else x
self.unlabeled = lambda x: x[N:] if x is not None else x
self.split_lu = lambda x: (self.labeled(x), self.unlabeled(x))
input_concat = self.join(input_labeled, input_unlabeled)
def encoder(input_, path_name, input_noise_std=0, noise_std=[]):
h = input_
logger.info(' 0: noise %g' % input_noise_std)
if input_noise_std > 0.:
h = h + self.noise_like(h) * input_noise_std
d = AttributeDict()
d.unlabeled = self.new_activation_dict()
d.labeled = self.new_activation_dict()
d.labeled.z[0] = self.labeled(h)
d.unlabeled.z[0] = self.unlabeled(h)
prev_dim = input_dim
for i, (spec, _, act_f) in layers[1:]:
d.labeled.h[i - 1], d.unlabeled.h[i - 1] = self.split_lu(h)
noise = noise_std[i] if i < len(noise_std) else 0.
curr_dim, z, m, s, h = self.f(h, prev_dim, spec, i, act_f,
path_name=path_name,
noise_std=noise)
assert self.layer_dims.get(i) in (None, curr_dim)
self.layer_dims[i] = curr_dim
d.labeled.z[i], d.unlabeled.z[i] = self.split_lu(z)
d.unlabeled.s[i] = s
d.unlabeled.m[i] = m
prev_dim = curr_dim
d.labeled.h[i], d.unlabeled.h[i] = self.split_lu(h)
return d
# Clean, supervised
logger.info('Encoder: clean, labeled')
clean = self.act.clean = encoder(input_concat, 'clean')
# Corrupted, supervised
logger.info('Encoder: corr, labeled')
corr = self.act.corr = encoder(input_concat, 'corr',
input_noise_std=self.p.super_noise_std,
noise_std=self.p.f_local_noise_std)
est = self.act.est = self.new_activation_dict()
# Decoder path in opposite order
logger.info('Decoder: z_corr -> z_est')
for i, ((_, spec), l_type, act_f) in layers[::-1]:
z_corr = corr.unlabeled.z[i]
z_clean = clean.unlabeled.z[i]
z_clean_s = clean.unlabeled.s.get(i)
z_clean_m = clean.unlabeled.m.get(i)
fspec = layers[i+1][1][0] if len(layers) > i+1 else (None, None)
if i == top:
ver = corr.unlabeled.h[i]
ver_dim = self.layer_dims[i]
top_g = True
else:
ver = est.z.get(i + 1)
ver_dim = self.layer_dims.get(i + 1)
top_g = False
z_est = self.g(z_lat=z_corr,
z_ver=ver,
in_dims=ver_dim,
out_dims=self.layer_dims[i],
l_type=l_type,
num=i,
fspec=fspec,
top_g=top_g)
if z_est is not None:
# Denoising cost
if z_clean_s and self.p.zestbn == 'bugfix':
z_est_norm = (z_est - z_clean_m) / T.sqrt(z_clean_s + np.float32(1e-10))
elif z_clean_s is None or self.p.zestbn == 'no':
z_est_norm = z_est
else:
assert False, 'Not supported path'
se = SquaredError('denois' + str(i))
costs.denois[i] = se.apply(z_est_norm.flatten(2),
z_clean.flatten(2)) \
/ np.prod(self.layer_dims[i], dtype=floatX)
costs.denois[i].name = 'denois' + str(i)
denois_print = 'denois %.2f' % self.p.denoising_cost_x[i]
else:
denois_print = ''
# Store references for later use
est.h[i] = self.apply_act(z_est, act_f)
est.z[i] = z_est
est.s[i] = None
est.m[i] = None
logger.info(' g%d: %10s, %s, dim %s -> %s' % (
i, l_type,
denois_print,
self.layer_dims.get(i+1),
self.layer_dims.get(i)
))
# Costs
y = target_labeled.flatten()
costs.class_clean = CategoricalCrossEntropy().apply(y, clean.labeled.h[top])
costs.class_clean.name = 'cost_class_clean'
costs.class_corr = CategoricalCrossEntropy().apply(y, corr.labeled.h[top])
costs.class_corr.name = 'cost_class_corr'
# This will be used for training
costs.total = costs.class_corr * 1.0
for i in range(top + 1):
if costs.denois.get(i) and self.p.denoising_cost_x[i] > 0:
costs.total += costs.denois[i] * self.p.denoising_cost_x[i]
costs.total.name = 'cost_total'
# Classification error
mr = MisclassificationRate()
self.error.clean = mr.apply(y, clean.labeled.h[top]) * np.float32(100.)
self.error.clean.name = 'error_rate_clean'
def apply_act(self, input, act_name):
if input is None:
return input
act = {
'relu': lambda x: T.maximum(0, x),
'leakyrelu': lambda x: T.switch(x > 0., x, 0.1 * x),
'linear': lambda x: x,
'softplus': lambda x: T.log(1. + T.exp(x)),
'sigmoid': lambda x: T.nnet.sigmoid(x),
'softmax': lambda x: softmax_n(x),
}.get(act_name)
assert act, 'unknown act %s' % act_name
if act_name == 'softmax':
input = input.flatten(2)
return act(input)
def annotate_bn(self, var, id, var_type, mb_size, size, norm_ax):
var_shape = np.array((1,) + size)
out_dim = np.prod(var_shape) / np.prod(var_shape[list(norm_ax)])
# Flatten the var - shared variable updating is not trivial otherwise,
# as theano seems to believe a row vector is a matrix and will complain
# about the updates
orig_shape = var.shape
var = var.flatten()
# Here we add the name and role, the variables will later be identified
# by these values
var.name = id + '_%s_clean' % var_type
add_role(var, BNPARAM)
shared_var = self.shared(np.zeros(out_dim),
name='shared_%s' % var.name, role=None)
# Update running average estimates. When the counter is reset to 1, it
# will clear its memory
cntr, c_up = self.counter()
one = np.float32(1)
run_avg = lambda new, old: one / cntr * new + (one - one / cntr) * old
if var_type == 'mean':
new_value = run_avg(var, shared_var)
elif var_type == 'var':
mb_size = T.cast(mb_size, 'float32')
new_value = run_avg(mb_size / (mb_size - one) * var, shared_var)
else:
raise NotImplemented('Unknown batch norm var %s' % var_type)
# Add the counter update to the annotated update if it is the first
# instance of a counter
self.annotate_update([(shared_var, new_value)] + c_up, var)
return var.reshape(orig_shape)
def f(self, h, in_dim, spec, num, act_f, path_name, noise_std=0):
# Generates identifiers used for referencing shared variables.
# E.g. clean and corrupted encoders will end up using the same
# variable name and hence sharing parameters
gen_id = lambda s: '_'.join(['f', str(num), s])
layer_type, _ = spec
# Pooling
if layer_type in ['maxpool', 'globalmeanpool']:
z, output_size = self.f_pool(h, spec, in_dim)
norm_ax = (0, -2, -1)
# after pooling, no activation func for now unless its softmax
act_f = "linear" if act_f != "softmax" else act_f
# Convolution
elif layer_type in ['convv', 'convf']:
z, output_size = self.f_conv(h, spec, in_dim, gen_id('W'))
norm_ax = (0, -2, -1)
# Fully connected
elif layer_type == "fc":
h = h.flatten(2) if h.ndim > 2 else h
_, dim = spec
W = self.weight(self.rand_init(np.prod(in_dim), dim), gen_id('W'))
z, output_size = T.dot(h, W), (dim,)
norm_ax = (0,)
else:
raise ValueError("Unknown layer spec: %s" % layer_type)
m = s = None
is_normalizing = True
if is_normalizing:
keep_dims = True
z_l = self.labeled(z)
z_u = self.unlabeled(z)
m = z_u.mean(norm_ax, keepdims=keep_dims)
s = z_u.var(norm_ax, keepdims=keep_dims)
m_l = z_l.mean(norm_ax, keepdims=keep_dims)
s_l = z_l.var(norm_ax, keepdims=keep_dims)
if path_name == 'clean':
# Batch normalization estimates the mean and variance of
# validation and test sets based on the training set
# statistics. The following annotates the computation of
# running average to the graph.
m_l = self.annotate_bn(m_l, gen_id('bn'), 'mean', z_l.shape[0],
output_size, norm_ax)
s_l = self.annotate_bn(s_l, gen_id('bn'), 'var', z_l.shape[0],
output_size, norm_ax)
z = self.join(
(z_l - m_l) / T.sqrt(s_l + np.float32(1e-10)),
(z_u - m) / T.sqrt(s + np.float32(1e-10)))
if noise_std > 0:
z += self.noise_like(z) * noise_std
# z for lateral connection
z_lat = z
b_init, c_init = 0.0, 1.0
b_c_size = output_size[0]
# Add bias
if act_f != 'linear':
z += self.bias(b_init * np.ones(b_c_size), gen_id('b'),
for_conv=len(output_size) > 1)
if is_normalizing:
# Add free parameter (gamma in original Batch Normalization paper)
# if needed by the activation. For instance ReLU does't need one
# and we only add it to softmax if hyperparameter top_c is set.
if (act_f not in ['relu', 'leakyrelu', 'linear', 'softmax'] or
(act_f == 'softmax' and self.p.top_c is True)):
c = self.weight(c_init * np.ones(b_c_size), gen_id('c'),
for_conv=len(output_size) > 1)
z *= c
h = self.apply_act(z, act_f)
logger.info(' f%d: %s, %s,%s noise %.2f, params %s, dim %s -> %s' % (
num, layer_type, act_f, ' BN,' if is_normalizing else '',
noise_std, spec[1], in_dim, output_size))
return output_size, z_lat, m, s, h
def f_pool(self, x, spec, in_dim):
layer_type, dims = spec
num_filters = in_dim[0]
if "globalmeanpool" == layer_type:
y, output_size = global_meanpool_2d(x, num_filters)
# scale the variance to match normal conv layers with xavier init
y = y * np.float32(in_dim[-1]) * np.float32(np.sqrt(3))
else:
assert dims[0] != 1 or dims[1] != 1
y, output_size = maxpool_2d(x, in_dim,
poolsize=(dims[1], dims[1]),
poolstride=(dims[0], dims[0]))
return y, output_size
def f_conv(self, x, spec, in_dim, weight_name):
layer_type, dims = spec
num_filters = dims[0]
filter_size = (dims[1], dims[1])
stride = (dims[2], dims[2])
bm = 'full' if 'convf' in layer_type else 'valid'
num_channels = in_dim[0]
W = self.weight(self.rand_init_conv(
(num_filters, num_channels) + filter_size), weight_name)
if stride != (1, 1):
f = GpuCorrMM(subsample=stride, border_mode=bm, pad=(0, 0))
y = f(gpu_contiguous(x), gpu_contiguous(W))
else:
assert self.p.batch_size == self.p.valid_batch_size
y = conv2d(x, W, image_shape=(2*self.p.batch_size, ) + in_dim,
filter_shape=((num_filters, num_channels) +
filter_size), border_mode=bm)
output_size = ((num_filters,) +
ConvOp.getOutputShape(in_dim[1:], filter_size,
stride, bm))
return y, output_size
def g(self, z_lat, z_ver, in_dims, out_dims, l_type, num, fspec, top_g):
f_layer_type, dims = fspec
is_conv = f_layer_type is not None and ('conv' in f_layer_type or
'pool' in f_layer_type)
gen_id = lambda s: '_'.join(['g', str(num), s])
in_dim = np.prod(dtype=floatX, a=in_dims)
out_dim = np.prod(dtype=floatX, a=out_dims)
num_filters = out_dims[0] if is_conv else out_dim
if l_type[-1] in ['0']:
g_type, u_type = l_type[:-1], l_type[-1]
else:
g_type, u_type = l_type, None
# Mapping from layer above: u
if u_type in ['0'] or z_ver is None:
if z_ver is None and u_type not in ['0']:
logger.warn('Decoder %d:%s without vertical input' %
(num, g_type))
u = None
else:
if top_g:
u = z_ver
elif is_conv:
u = self.g_deconv(z_ver, in_dims, out_dims, gen_id('W'), fspec)
else:
W = self.weight(self.rand_init(in_dim, out_dim), gen_id('W'))
u = T.dot(z_ver, W)
# Batch-normalize u
if u is not None:
norm_ax = (0,) if u.ndim <= 2 else (0, -2, -1)
keep_dims = True
u -= u.mean(norm_ax, keepdims=keep_dims)
u /= T.sqrt(u.var(norm_ax, keepdims=keep_dims) +
np.float32(1e-10))
# Define the g function
if not is_conv:
z_lat = z_lat.flatten(2)
bi = lambda inits, name: self.bias(inits * np.ones(num_filters),
gen_id(name), for_conv=is_conv)
wi = lambda inits, name: self.weight(inits * np.ones(num_filters),
gen_id(name), for_conv=is_conv)
if g_type == '':
z_est = None
elif g_type == 'i':
z_est = z_lat
elif g_type in ['sig']:
sigval = bi(0., 'c1') + wi(1., 'c2') * z_lat
if u is not None:
sigval += wi(0., 'c3') * u + wi(0., 'c4') * z_lat * u
sigval = T.nnet.sigmoid(sigval)
z_est = bi(0., 'a1') + wi(1., 'a2') * z_lat + wi(1., 'b1') * sigval
if u is not None:
z_est += wi(0., 'a3') * u + wi(0., 'a4') * z_lat * u
elif g_type in ['lin']:
a1 = wi(1.0, 'a1')
b = bi(0.0, 'b')
z_est = a1 * z_lat + b
elif g_type in ['relu']:
assert u is not None
b = bi(0., 'b')
x = u + b
z_est = self.apply_act(x, 'relu')
elif g_type in ['sigmoid']:
assert u is not None
b = bi(0., 'b')
c = wi(1., 'c')
z_est = self.apply_act((u + b) * c, 'sigmoid')
elif g_type in ['comparison_g2']:
# sig without the uz cross term
sigval = bi(0., 'c1') + wi(1., 'c2') * z_lat
if u is not None:
sigval += wi(0., 'c3') * u
sigval = T.nnet.sigmoid(sigval)
z_est = bi(0., 'a1') + wi(1., 'a2') * z_lat + wi(1., 'b1') * sigval
if u is not None:
z_est += wi(0., 'a3') * u
elif g_type in ['comparison_g3']:
# sig without the sigmoid nonlinearity
z_est = bi(0., 'a1') + wi(1., 'a2') * z_lat
if u is not None:
z_est += wi(0., 'a3') * u + wi(0., 'a4') * z_lat * u
elif g_type in ['comparison_g4']:
# No mixing between z_lat and u before final sum, otherwise similar
# to sig
def nonlin(inp, in_name='input', add_bias=True):
w1 = wi(1., 'w1_%s' % in_name)
b1 = bi(0., 'b1')
w2 = wi(1., 'w2_%s' % in_name)
b2 = bi(0., 'b2') if add_bias else 0
w3 = wi(0., 'w3_%s' % in_name)
return w2 * T.nnet.sigmoid(b1 + w1 * inp) + w3 * inp + b2
z_est = nonlin(z_lat, 'lat') if u is None else \
nonlin(z_lat, 'lat') + nonlin(u, 'ver', False)
elif g_type in ['comparison_g5', 'gauss']:
# Gaussian assumption on z: (z - mu) * v + mu
if u is None:
b1 = bi(0., 'b1')
w1 = wi(1., 'w1')
z_est = w1 * z_lat + b1
else:
a1 = bi(0., 'a1')
a2 = wi(1., 'a2')
a3 = bi(0., 'a3')
a4 = bi(0., 'a4')
a5 = bi(0., 'a5')
a6 = bi(0., 'a6')
a7 = wi(1., 'a7')
a8 = bi(0., 'a8')
a9 = bi(0., 'a9')
a10 = bi(0., 'a10')
mu = a1 * T.nnet.sigmoid(a2 * u + a3) + a4 * u + a5
v = a6 * T.nnet.sigmoid(a7 * u + a8) + a9 * u + a10
z_est = (z_lat - mu) * v + mu
elif 'gauss_stable_v' in g_type:
# Gaussian assumption on z: (z - mu) * v + mu
if u is None:
b1 = bi(0., 'b1')
w1 = wi(1., 'w1')
z_est = w1 * z_lat + b1
elif z_lat is None:
b1 = bi(0., 'b1')
w1 = wi(1., 'w1')
z_est = w1 * u + b1
else:
a1 = bi(0., 'a1')
a2 = wi(1., 'a2')
a3 = bi(0., 'a3')
a4 = bi(0., 'a4')
a5 = bi(0., 'a5')
a6 = bi(0., 'a6')
a7 = wi(1., 'a7')
a8 = bi(0., 'a8')
a9 = bi(0., 'a9')
a10 = bi(0., 'a10')
mu = a1 * T.nnet.sigmoid(a2 * u + a3) + a4 * u + a5
v = a6 * T.nnet.sigmoid(a7 * u + a8) + a9 * u + a10
v = T.nnet.sigmoid(v)
z_est = (z_lat - mu) * v + mu
else:
raise NotImplementedError("unknown g type: %s" % str(g_type))
# Reshape the output if z is for conv but u from fc layer
if (z_est is not None and type(out_dims) == tuple and
len(out_dims) > 1.0 and z_est.ndim < 4):
z_est = z_est.reshape((z_est.shape[0],) + out_dims)
return z_est
def g_deconv(self, z_ver, in_dims, out_dims, weight_name, fspec):
""" Inverse operation for each type of f used in convnets """
f_type, f_dims = fspec
assert z_ver is not None
num_channels = in_dims[0] if in_dims is not None else None
num_filters, width, height = out_dims[:3]
if f_type in ['globalmeanpool']:
u = T.addbroadcast(z_ver, 2, 3)
assert in_dims[1] == 1 and in_dims[2] == 1, \
"global pooling needs in_dims (1,1): %s" % str(in_dims)
elif f_type in ['maxpool']:
sh, str, size = z_ver.shape, f_dims[0], f_dims[1]
assert str == size, "depooling requires stride == size"
u = T.zeros((sh[0], sh[1], sh[2] * str, sh[3] * str),
dtype=z_ver.dtype)
for x in xrange(str):
for y in xrange(str):
u = T.set_subtensor(u[:, :, x::str, y::str], z_ver)
u = u[:, :, :width, :height]
elif f_type in ['convv', 'convf']:
filter_size, str = (f_dims[1], f_dims[1]), f_dims[2]
W_shape = (num_filters, num_channels) + filter_size
W = self.weight(self.rand_init_conv(W_shape), weight_name)
if str > 1:
# upsample if strided version
sh = z_ver.shape
u = T.zeros((sh[0], sh[1], sh[2] * str, sh[3] * str),
dtype=z_ver.dtype)
u = T.set_subtensor(u[:, :, ::str, ::str], z_ver)
else:
u = z_ver # no strides, only deconv
u = conv2d(u, W, filter_shape=W_shape,
border_mode='valid' if 'convf' in f_type else 'full')
u = u[:, :, :width, :height]
else:
raise NotImplementedError('Layer %s has no convolutional decoder'
% f_type)
return u