def setup_inference_procedure(self):
"""
Set the inference procedure for the model.
Default using `WeightDoubling`
"""
if not hasattr(self, 'inference_procedure') or \
self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_inference_procedure(self):
"""
.. todo::
WRITEME
"""
if not hasattr(self, 'inference_procedure') or \
self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_inference_procedure(self):
"""
Set the inference procedure for the model.
Default using `WeightDoubling`
"""
if not hasattr(self, "inference_procedure") or self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_inference_procedure(self):
"""
.. todo::
WRITEME
"""
if not hasattr(self, "inference_procedure") or self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
class DBM(Model):
"""
A deep Boltzmann machine.
See "Deep Boltzmann Machines" by Ruslan Salakhutdinov and Geoffrey Hinton
for details.
Parameters
----------
batch_size : int
The batch size the model should use. Some convolutional
LinearTransforms require a compile-time hardcoded batch size,
otherwise this would not be part of the model specification.
visible_layer : VisibleLayer
The visible layer of the DBM.
hidden_layers : list
The hidden layers. A list of HiddenLayer objects. The first
layer in the list is connected to the visible layer.
niter : int
Number of mean field iterations for variational inference
for the positive phase.
sampling_procedure : SamplingProcedure (optional)
An object that specifies how to draw samples from the model.
If not specified, some standard algorithm will be used.
inference_procedure : InferenceProcedure (optional)
An object that specifies how to perform mean field inference
in the model. If not specified, some standard algorithm will
be used.
"""
def __init__(self, batch_size, visible_layer, hidden_layers, niter,
sampling_procedure=None, inference_procedure=None):
super(DBM, self).__init__()
self.__dict__.update(locals())
del self.self
assert len(hidden_layers) >= 1
if len(hidden_layers) > 1 and niter <= 1:
raise ValueError("with more than one hidden layer, niter needs to "
"be greater than 1; otherwise mean field won't "
"work properly.")
self.setup_rng()
self.layer_names = set()
self.visible_layer.set_dbm(self)
for layer in hidden_layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
self._update_layer_input_spaces()
self.force_batch_size = batch_size
self.freeze_set = set([])
if inference_procedure is None:
self.setup_inference_procedure()
self.inference_procedure.set_dbm(self)
if sampling_procedure is None:
self.setup_sampling_procedure()
self.sampling_procedure.set_dbm(self)
def get_all_layers(self):
"""
Get all layers in this model.
Returns
-------
layers : list
"""
return [self.visible_layer] + self.hidden_layers
def energy(self, V, hidden):
"""
Compute the energy of current model with visible and hidden samples.
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not
mean field parameters)
hidden : list
List, one element per hidden layer, of batches of samples (must
be SAMPLES, not mean field parameters)
Returns
-------
rval : tensor_like
Vector containing the energy of each sample
Notes
-----
Applying this function to non-sample theano variables is not guaranteed
to give you an expected energy in general, so don't use this that way.
"""
terms = []
terms.append(self.visible_layer.expected_energy_term(state=V,
average=False))
# This condition could be relaxed, but current code assumes it
assert len(self.hidden_layers) > 0
terms.append(self.hidden_layers[0].expected_energy_term(
state_below=self.visible_layer.upward_state(V),
state=hidden[0], average_below=False, average=False))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
samples_below = hidden[i-1]
layer_below = self.hidden_layers[i-1]
samples_below = layer_below.upward_state(samples_below)
samples = hidden[i]
terms.append(layer.expected_energy_term(state_below=samples_below,
state=samples, average_below=False, average=False))
assert len(terms) > 0
rval = reduce(operator.add, terms)
assert rval.ndim == 1
return rval
def mf(self, *args, **kwargs):
"""
Perform mean field inference, using the model's inference procedure.
"""
self.setup_inference_procedure()
return self.inference_procedure.mf(*args, **kwargs)
def expected_energy(self, V, mf_hidden):
"""
Compute the energy of current model with the visible samples
and variational parameters.
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not
mean field parameters: the random variables in the expectation
are the hiddens only)
mf_hidden : list
List, one element per hidden layer, of batches of variational
parameters (must be VARIATIONAL PARAMETERS, not samples. Layers
with analytically determined variance parameters for their mean
field parameters will use those to integrate over the variational
distribution, so it's not generally the same thing as measuring
the energy at a point.)
Returns
-------
rval : tensor_like
Vector containing the expected energy of each example under the
corresponding variational distribution.
"""
self.visible_layer.space.validate(V)
assert isinstance(mf_hidden, (list, tuple))
assert len(mf_hidden) == len(self.hidden_layers)
terms = []
terms.append(self.visible_layer.expected_energy_term(state=V,
average=False))
# This condition could be relaxed, but current code assumes it
assert len(self.hidden_layers) > 0
terms.append(self.hidden_layers[0].expected_energy_term(
state_below=self.visible_layer.upward_state(V),
average_below=False, state=mf_hidden[0], average=True))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
layer_below = self.hidden_layers[i-1]
mf_below = mf_hidden[i-1]
mf_below = layer_below.upward_state(mf_below)
mf = mf_hidden[i]
terms.append(layer.expected_energy_term(state_below=mf_below,
state=mf, average_below=True, average=True))
assert len(terms) > 0
rval = reduce(operator.add, terms)
assert rval.ndim == 1
return rval
def setup_rng(self):
"""
Set the random number generator for the model.
"""
self.rng = make_np_rng(None, [2012, 10, 17], which_method="uniform")
def setup_inference_procedure(self):
"""
Set the inference procedure for the model.
Default using `WeightDoubling`
"""
if not hasattr(self, 'inference_procedure') or \
self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_sampling_procedure(self):
"""
Set the sampling procedure for the model.
Default using `GibbsEvenOdd`
"""
if not hasattr(self, 'sampling_procedure') or \
self.sampling_procedure is None:
self.sampling_procedure = GibbsEvenOdd()
self.sampling_procedure.set_dbm(self)
def get_output_space(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[-1].get_output_space()
def _update_layer_input_spaces(self):
"""
Tells each layer what its input space should be.
Notes
-----
This usually resets the layer's parameters!
"""
visible_layer = self.visible_layer
hidden_layers = self.hidden_layers
self.hidden_layers[0].set_input_space(visible_layer.space)
for i in xrange(1, len(hidden_layers)):
hidden_layers[i].set_input_space(
hidden_layers[i-1].get_output_space())
for layer in self.get_all_layers():
layer.finalize_initialization()
def add_layers(self, layers):
"""
Add new layers on top of the existing hidden layers
Parameters
----------
layers : list
layers to be added
"""
# Patch old pickle files
if not hasattr(self, 'rng'):
self.setup_rng()
hidden_layers = self.hidden_layers
assert len(hidden_layers) > 0
for layer in layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
layer.set_input_space(hidden_layers[-1].get_output_space())
hidden_layers.append(layer)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
def freeze(self, parameter_set):
"""
.. todo::
WRITEME
"""
# patch old pickle files
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
self.freeze_set = self.freeze_set.union(parameter_set)
def get_params(self):
"""
.. todo::
WRITEME
"""
rval = []
for param in self.visible_layer.get_params():
assert param.name is not None
rval = self.visible_layer.get_params()
for layer in self.hidden_layers:
for param in layer.get_params():
if param.name is None:
raise ValueError("All of your parameters should have "
"names, but one of " + layer.layer_name +
"'s doesn't")
layer_params = layer.get_params()
assert not isinstance(layer_params, set)
for param in layer_params:
if param not in rval:
rval.append(param)
# Patch pickle files that predate the freeze_set feature
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
rval = [elem for elem in rval if elem not in self.freeze_set]
assert all([elem.name is not None for elem in rval])
return rval
def set_batch_size(self, batch_size):
"""
.. todo::
WRITEME
"""
self.batch_size = batch_size
self.force_batch_size = batch_size
for layer in self.hidden_layers:
layer.set_batch_size(batch_size)
if not hasattr(self, 'inference_procedure'):
self.setup_inference_procedure()
self.inference_procedure.set_batch_size(batch_size)
@functools.wraps(Model._modify_updates)
def _modify_updates(self, updates):
self.visible_layer.modify_updates(updates)
for layer in self.hidden_layers:
layer.modify_updates(updates)
def get_input_space(self):
"""
.. todo::
WRITEME
"""
return self.visible_layer.space
def get_lr_scalers(self):
"""
.. todo::
WRITEME
"""
rval = OrderedDict()
params = self.get_params()
for layer in self.hidden_layers + [self.visible_layer]:
contrib = layer.get_lr_scalers()
# No two layers can contend to scale a parameter
assert not any([key in rval for key in contrib])
# Don't try to scale anything that's not a parameter
assert all([key in params for key in contrib])
rval.update(contrib)
assert all([isinstance(val, float) for val in rval.values()])
return rval
def get_weights(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights()
def get_weights_view_shape(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_view_shape()
def get_weights_format(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_format()
def get_weights_topo(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_topo()
def make_layer_to_state(self, num_examples, rng=None):
"""
Makes and returns a dictionary mapping layers to states.
By states, we mean here a real assignment, not a mean field
state. For example, for a layer containing binary random
variables, the state will be a shared variable containing
values in {0,1}, not [0,1]. The visible layer will be included.
Uses a dictionary so it is easy to unambiguously index a layer
without needing to remember rules like vis layer = 0, hiddens
start at 1, etc.
Parameters
----------
num_examples : int
Number of examples to make up the state
rng : MRG_RandomStreams
Random number generator, if None then use model's rng
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
if rng is None:
rng = self.rng
states = [layer.make_state(num_examples, rng) for layer in layers]
def recurse_check(layer, state):
if isinstance(state, (list, tuple)):
for elem in state:
recurse_check(layer, elem)
else:
val = state.get_value()
m = val.shape[0]
if m != num_examples:
raise ValueError(layer.layer_name + " gave state with " +
str(m) + " examples in some component."
"We requested " + str(num_examples))
for layer, state in safe_zip(layers, states):
recurse_check(layer, state)
rval = OrderedDict(safe_zip(layers, states))
return rval
def make_layer_to_symbolic_state(self, num_examples, rng=None):
"""
Makes and returns a dictionary mapping layers to states.
By states, we mean here a real assignment, not a mean field
state. For example, for a layer containing binary random
variables, the state will be a shared variable containing
values in {0,1}, not [0,1]. The visible layer will be included.
Uses a dictionary so it is easy to unambiguously index a layer
without needing to remember rules like vis layer = 0, hiddens
start at 1, etc.
Parameters
----------
num_examples : int
Number of examples to make up the state
rng : MRG_RandomStreams
Random number generator
Notes
-----
This method returns a symbolic expression of the state, while
`make_layer_to_state` returns a certain shared variable.
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
assert rng is not None
states = [layer.make_symbolic_state(num_examples, rng)
for layer in layers]
zipped = safe_zip(layers, states)
rval = OrderedDict(zipped)
return rval
def get_sampling_updates(self, layer_to_state, theano_rng,
layer_to_clamp=None, num_steps=1,
return_layer_to_updated=False):
"""
This method is for getting an updates dictionary for a theano function.
It thus implies that the samples are represented as shared variables.
If you want an expression for a sampling step applied to arbitrary
theano variables, use the `DBM.sampling_procedure.sample` method.
This is a wrapper around that method.
Parameters
----------
layer_to_state : dict
Dictionary mapping the SuperDBM_Layer instances contained in
self to shared variables representing batches of samples of them.
(you can allocate one by calling self.make_layer_to_state)
theano_rng : MRG_RandomStreams
Random number generator
layer_to_clamp : dict, optional
Dictionary mapping layers to bools. If a layer is not in the
dictionary, defaults to False. True indicates that this layer
should be clamped, so we are sampling from a conditional
distribution rather than the joint distribution
num_steps : int, optional
Steps of the sampling procedure. It samples for `num_steps`
times and use the last sample.
return_layer_to_updated : bool, optional
Whether returns the sample additionally
Returns
-------
rval : dict
Dictionary mapping each shared variable to an expression to
update it. Repeatedly applying these updates does MCMC sampling.
Notes
-----
The specific sampling schedule used by default is to sample all of the
even-idexed layers of model.hidden_layers, then the visible layer and
all the odd-indexed layers.
"""
updated = self.sampling_procedure.sample(layer_to_state, theano_rng,
layer_to_clamp, num_steps)
rval = OrderedDict()
def add_updates(old, new):
if isinstance(old, (list, tuple)):
for old_elem, new_elem in safe_izip(old, new):
add_updates(old_elem, new_elem)
else:
rval[old] = new
# Validate layer_to_clamp / make sure layer_to_clamp is a fully
# populated dictionary
if layer_to_clamp is None:
layer_to_clamp = OrderedDict()
for key in layer_to_clamp:
assert key is self.visible_layer or key in self.hidden_layers
for layer in [self.visible_layer] + self.hidden_layers:
if layer not in layer_to_clamp:
layer_to_clamp[layer] = False
# Translate update expressions into theano updates
for layer in layer_to_state:
old = layer_to_state[layer]
new = updated[layer]
if layer_to_clamp[layer]:
assert new is old
else:
add_updates(old, new)
assert isinstance(self.hidden_layers, list)
if return_layer_to_updated:
return rval, updated
return rval
def get_monitoring_channels(self, data):
"""
.. todo::
WRITEME
"""
space, source = self.get_monitoring_data_specs()
space.validate(data)
X = data
history = self.mf(X, return_history=True)
q = history[-1]
rval = OrderedDict()
ch = self.visible_layer.get_monitoring_channels()
for key in ch:
rval['vis_' + key] = ch[key]
for state, layer in safe_zip(q, self.hidden_layers):
ch = layer.get_monitoring_channels()
for key in ch:
rval[layer.layer_name + '_' + key] = ch[key]
ch = layer.get_monitoring_channels_from_state(state)
for key in ch:
rval['mf_' + layer.layer_name + '_' + key] = ch[key]
# Calculate mean squared reconstruction error
errs = (self.reconstruct(X)-X)**2
reconstr_err = errs.mean()
rval['reconstr_err'] = reconstr_err
if len(history) > 1:
prev_q = history[-2]
flat_q = flatten(q)
flat_prev_q = flatten(prev_q)
mx = None
for new, old in safe_zip(flat_q, flat_prev_q):
cur_mx = abs(new - old).max()
if new is old:
logger.error('{0} is {1}'.format(new, old))
assert False
if mx is None:
mx = cur_mx
else:
mx = T.maximum(mx, cur_mx)
rval['max_var_param_diff'] = mx
for layer, new, old in safe_zip(self.hidden_layers,
q, prev_q):
sum_diff = 0.
for sub_new, sub_old in safe_zip(flatten(new), flatten(old)):
sum_diff += abs(sub_new - sub_old).sum()
denom = self.batch_size * \
layer.get_total_state_space().get_total_dimension()
denom = np.cast[config.floatX](denom)
rval['mean_'+layer.layer_name+'_var_param_diff'] = \
sum_diff / denom
return rval
def get_monitoring_data_specs(self):
"""
Get the data_specs describing the data for get_monitoring_channel.
This implementation returns specification corresponding to unlabeled
inputs.
"""
return (self.get_input_space(), self.get_input_source())
def get_test_batch_size(self):
"""
.. todo::
WRITEME
"""
return self.batch_size
def reconstruct(self, V):
"""
Reconstruct the visible variables.
Returns
-------
recons : tensor_like
Unmasked reconstructed visible variables.
"""
H = self.mf(V)[0]
downward_state = self.hidden_layers[0].downward_state(H)
recons = self.visible_layer.inpaint_update(
layer_above=self.hidden_layers[0],
state_above=downward_state,
drop_mask=None, V=None)
return recons
def do_inpainting(self, *args, **kwargs):
"""
Does the inference required for multi-prediction training,
using the model's inference procedure.
"""
self.setup_inference_procedure()
return self.inference_procedure.do_inpainting(*args, **kwargs)
class DBM(Model):
"""
A deep Boltzmann machine.
See "Deep Boltzmann Machines" by Ruslan Salakhutdinov and Geoffrey Hinton
for details.
"""
def __init__(self, batch_size, visible_layer, hidden_layers, niter,
sampling_procedure=None, inference_procedure=None):
"""
Parameters
----------
batch_size : int
The batch size the model should use. Some convolutional \
LinearTransforms require a compile-time hardcoded batch size, \
otherwise this would not be part of the model specification.
visible_layer : WRITEME
The visible layer of the DBM.
hidden_layers : list
WRITEME
niter : int
WRITEME
sampling_procedure : WRITEME
inference_procedure : WRITEME
"""
self.__dict__.update(locals())
del self.self
assert len(hidden_layers) >= 1
self.setup_rng()
self.layer_names = set()
self.visible_layer.set_dbm(self)
for layer in hidden_layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
self._update_layer_input_spaces()
self.force_batch_size = batch_size
self.freeze_set = set([])
if inference_procedure is None:
self.setup_inference_procedure()
self.inference_procedure.set_dbm(self)
if sampling_procedure is None:
self.setup_sampling_procedure()
self.sampling_procedure.set_dbm(self)
def get_all_layers(self):
"""
.. todo::
WRITEME
"""
return [self.visible_layer] + self.hidden_layers
def energy(self, V, hidden):
"""
WRITEME
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not \
mean field parameters)
hidden : list
List, one element per hidden layer, of batches of samples (must \
be SAMPLES, not mean field parameters)
Returns
-------
rval : tensor_like
Vector containing the energy of each sample
Notes
-----
Applying this function to non-sample theano variables is not guaranteed
to give you an expected energy in general, so don't use this that way.
"""
terms = []
terms.append(self.visible_layer.expected_energy_term(state = V, average=False))
assert len(self.hidden_layers) > 0 # this could be relaxed, but current code assumes it
terms.append(self.hidden_layers[0].expected_energy_term(
state_below = self.visible_layer.upward_state(V),
state = hidden[0], average_below=False, average=False))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
samples_below = hidden[i-1]
layer_below = self.hidden_layers[i-1]
samples_below = layer_below.upward_state(samples_below)
samples = hidden[i]
terms.append(layer.expected_energy_term(state_below=samples_below, state=samples,
average_below=False, average=False))
assert len(terms) > 0
rval = reduce(lambda x, y: x + y, terms)
assert rval.ndim == 1
return rval
def mf(self, *args, **kwargs):
"""
.. todo::
WRITEME
"""
self.setup_inference_procedure()
return self.inference_procedure.mf(*args, **kwargs)
def expected_energy(self, V, mf_hidden):
"""
WRITEME
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not \
mean field parameters: the random variables in the expectation \
are the hiddens only)
mf_hidden : list
List, one element per hidden layer, of batches of variational \
parameters (must be VARIATIONAL PARAMETERS, not samples. Layers \
with analytically determined variance parameters for their mean \
field parameters will use those to integrate over the variational \
distribution, so it's not generally the same thing as measuring \
the energy at a point.)
Returns
-------
rval : tensor_like
Vector containing the expected energy of each example under the \
corresponding variational distribution.
"""
self.visible_layer.space.validate(V)
assert isinstance(mf_hidden, (list, tuple))
assert len(mf_hidden) == len(self.hidden_layers)
terms = []
terms.append(self.visible_layer.expected_energy_term(state = V, average=False))
assert len(self.hidden_layers) > 0 # this could be relaxed, but current code assumes it
terms.append(self.hidden_layers[0].expected_energy_term(
state_below=self.visible_layer.upward_state(V), average_below=False,
state=mf_hidden[0], average=True))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
layer_below = self.hidden_layers[i-1]
mf_below = mf_hidden[i-1]
mf_below = layer_below.upward_state(mf_below)
mf = mf_hidden[i]
terms.append(layer.expected_energy_term(state_below=mf_below, state=mf,
average_below=True, average=True))
assert len(terms) > 0
rval = reduce(lambda x, y: x + y, terms)
assert rval.ndim == 1
return rval
def setup_rng(self):
"""
.. todo::
WRITEME
"""
self.rng = np.random.RandomState([2012, 10, 17])
def setup_inference_procedure(self):
"""
.. todo::
WRITEME
"""
if not hasattr(self, 'inference_procedure') or \
self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_sampling_procedure(self):
"""
.. todo::
WRITEME
"""
if not hasattr(self, 'sampling_procedure') or \
self.sampling_procedure is None:
self.sampling_procedure = GibbsEvenOdd()
self.sampling_procedure.set_dbm(self)
def get_output_space(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[-1].get_output_space()
def _update_layer_input_spaces(self):
"""
Tells each layer what its input space should be.
Notes
-----
This usually resets the layer's parameters!
"""
visible_layer = self.visible_layer
hidden_layers = self.hidden_layers
self.hidden_layers[0].set_input_space(visible_layer.space)
for i in xrange(1,len(hidden_layers)):
hidden_layers[i].set_input_space(hidden_layers[i-1].get_output_space())
for layer in self.get_all_layers():
layer.finalize_initialization()
def add_layers(self, layers):
"""
Add new layers on top of the existing hidden layers
Parameters
----------
layers : WRITEME
"""
# Patch old pickle files
if not hasattr(self, 'rng'):
self.setup_rng()
hidden_layers = self.hidden_layers
assert len(hidden_layers) > 0
for layer in layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
layer.set_input_space(hidden_layers[-1].get_output_space())
hidden_layers.append(layer)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
def freeze(self, parameter_set):
"""
.. todo::
WRITEME
"""
# patch old pickle files
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
self.freeze_set = self.freeze_set.union(parameter_set)
def get_params(self):
"""
.. todo::
WRITEME
"""
rval = []
for param in self.visible_layer.get_params():
assert param.name is not None
rval = self.visible_layer.get_params()
for layer in self.hidden_layers:
for param in layer.get_params():
if param.name is None:
raise ValueError("All of your parameters should have names, but one of "+layer.layer_name+"'s doesn't")
layer_params = layer.get_params()
assert not isinstance(layer_params, set)
for param in layer_params:
if param not in rval:
rval.append(param)
# Patch pickle files that predate the freeze_set feature
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
rval = [elem for elem in rval if elem not in self.freeze_set]
assert all([elem.name is not None for elem in rval])
return rval
def set_batch_size(self, batch_size):
"""
.. todo::
WRITEME
"""
self.batch_size = batch_size
self.force_batch_size = batch_size
for layer in self.hidden_layers:
layer.set_batch_size(batch_size)
if not hasattr(self, 'inference_procedure'):
self.setup_inference_procedure()
self.inference_procedure.set_batch_size(batch_size)
def censor_updates(self, updates):
"""
.. todo::
WRITEME
"""
self.visible_layer.censor_updates(updates)
for layer in self.hidden_layers:
layer.censor_updates(updates)
def get_input_space(self):
"""
.. todo::
WRITEME
"""
return self.visible_layer.space
def get_lr_scalers(self):
"""
.. todo::
WRITEME
"""
rval = OrderedDict()
params = self.get_params()
for layer in self.hidden_layers + [ self.visible_layer ]:
contrib = layer.get_lr_scalers()
# No two layers can contend to scale a parameter
assert not any([key in rval for key in contrib])
# Don't try to scale anything that's not a parameter
assert all([key in params for key in contrib])
rval.update(contrib)
assert all([isinstance(val, float) for val in rval.values()])
return rval
def get_weights(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights()
def get_weights_view_shape(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_view_shape()
def get_weights_format(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_format()
def get_weights_topo(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_topo()
def make_layer_to_state(self, num_examples, rng=None):
"""
Makes and returns a dictionary mapping layers to states. By states, we
mean here a real assignment, not a mean field state. For example, for a
layer containing binary random variables, the state will be a shared
variable containing values in {0,1}, not [0,1]. The visible layer will
be included.
Uses a dictionary so it is easy to unambiguously index a layer without
needing to remember rules like vis layer = 0, hiddens start at 1, etc.
Parameters
----------
num_examples : int
WRITEME
rng : WRITEME
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
if rng is None:
rng = self.rng
states = [layer.make_state(num_examples, rng) for layer in layers]
zipped = safe_zip(layers, states)
def recurse_check(layer, state):
if isinstance(state, (list, tuple)):
for elem in state:
recurse_check(layer, elem)
else:
val = state.get_value()
m = val.shape[0]
if m != num_examples:
raise ValueError(layer.layer_name+" gave state with "+str(m)+ \
" examples in some component. We requested "+str(num_examples))
for layer, state in zipped:
recurse_check(layer, state)
rval = OrderedDict(zipped)
return rval
def make_layer_to_symbolic_state(self, num_examples, rng=None):
"""
.. todo::
Explain the difference with `make_layer_to_state`
Makes and returns a dictionary mapping layers to states. By states, we
mean here a real assignment, not a mean field state. For example, for a
layer containing binary random variables, the state will be a shared
variable containing values in {0,1}, not [0,1]. The visible layer will
be included.
Uses a dictionary so it is easy to unambiguously index a layer without
needing to remember rules like vis layer = 0, hiddens start at 1, etc.
Parameters
----------
num_examples : int
WRITEME
rng : WRITEME
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
assert rng is not None
states = [layer.make_symbolic_state(num_examples, rng) for layer in layers]
zipped = safe_zip(layers, states)
rval = OrderedDict(zipped)
return rval
def mcmc_steps(self, layer_to_state, theano_rng, layer_to_clamp=None,
num_steps=1):
"""
.. todo::
WRITEME
"""
warnings.warn("DBM.mcmc_steps is deprecated. You should instead " +
"call DBM.sampling_procedure.sample, which defaults " +
"to what DBM.mcmc_steps used to do. This method will " +
"be removed on or after July 31, 2014.")
return self.sampling_procedure.sample(layer_to_state, theano_rng,
layer_to_clamp, num_steps)
def get_sampling_updates(self, layer_to_state, theano_rng,
layer_to_clamp=None, num_steps=1,
return_layer_to_updated=False):
"""
This method is for getting an updates dictionary for a theano function.
It thus implies that the samples are represented as shared variables.
If you want an expression for a sampling step applied to arbitrary
theano variables, use the 'mcmc_steps' method. This is a wrapper around
that method.
Parameters
----------
layer_to_state: dict
Dictionary mapping the SuperDBM_Layer instances contained in \
self to shared variables representing batches of samples of them. \
(you can allocate one by calling self.make_layer_to_state)
theano_rng: MRG_RandomStreams
WRITEME
layer_to_clamp: dict, optional
Dictionary mapping layers to bools. If a layer is not in the \
dictionary, defaults to False. True indicates that this layer \
should be clamped, so we are sampling from a conditional \
distribution rather than the joint distribution
Returns
-------
rval : dict
Dictionary mapping each shared variable to an expression to \
update it. Repeatedly applying these updates does MCMC sampling.
Notes
-----
The specific sampling schedule used by default is to sample all of the
even-idexed layers of model.hidden_layers, then the visible layer and
all the odd-indexed layers.
"""
updated = self.sampling_procedure.sample(layer_to_state, theano_rng,
layer_to_clamp, num_steps)
rval = OrderedDict()
def add_updates(old, new):
if isinstance(old, (list, tuple)):
for old_elem, new_elem in safe_izip(old, new):
add_updates(old_elem, new_elem)
else:
rval[old] = new
# Validate layer_to_clamp / make sure layer_to_clamp is a fully
# populated dictionary
if layer_to_clamp is None:
layer_to_clamp = OrderedDict()
for key in layer_to_clamp:
assert key is self.visible_layer or key in self.hidden_layers
for layer in [self.visible_layer] + self.hidden_layers:
if layer not in layer_to_clamp:
layer_to_clamp[layer] = False
# Translate update expressions into theano updates
for layer in layer_to_state:
old = layer_to_state[layer]
new = updated[layer]
if layer_to_clamp[layer]:
assert new is old
else:
add_updates(old, new)
assert isinstance(self.hidden_layers, list)
if return_layer_to_updated:
return rval, updated
return rval
def get_monitoring_channels(self, data):
"""
.. todo::
WRITEME
"""
space, source = self.get_monitoring_data_specs()
space.validate(data)
X = data
history = self.mf(X, return_history = True)
q = history[-1]
rval = OrderedDict()
ch = self.visible_layer.get_monitoring_channels()
for key in ch:
rval['vis_'+key] = ch[key]
for state, layer in safe_zip(q, self.hidden_layers):
ch = layer.get_monitoring_channels()
for key in ch:
rval[layer.layer_name+'_'+key] = ch[key]
ch = layer.get_monitoring_channels_from_state(state)
for key in ch:
rval['mf_'+layer.layer_name+'_'+key] = ch[key]
if len(history) > 1:
prev_q = history[-2]
flat_q = flatten(q)
flat_prev_q = flatten(prev_q)
mx = None
for new, old in safe_zip(flat_q, flat_prev_q):
cur_mx = abs(new - old).max()
if new is old:
print new, 'is', old
assert False
if mx is None:
mx = cur_mx
else:
mx = T.maximum(mx, cur_mx)
rval['max_var_param_diff'] = mx
for layer, new, old in safe_zip(self.hidden_layers,
q, prev_q):
sum_diff = 0.
for sub_new, sub_old in safe_zip(flatten(new), flatten(old)):
sum_diff += abs(sub_new - sub_old).sum()
denom = self.batch_size * layer.get_total_state_space().get_total_dimension()
denom = np.cast[config.floatX](denom)
rval['mean_'+layer.layer_name+'_var_param_diff'] = sum_diff / denom
return rval
def get_monitoring_data_specs(self):
"""
Get the data_specs describing the data for get_monitoring_channel.
This implementation returns specification corresponding to unlabeled
inputs.
"""
return (self.get_input_space(), self.get_input_source())
def get_test_batch_size(self):
"""
.. todo::
WRITEME
"""
return self.batch_size
def reconstruct(self, V):
"""
.. todo::
WRITEME
"""
H = self.mf(V)[0]
downward_state = self.hidden_layers[0].downward_state(H)
recons = self.visible_layer.inpaint_update(
layer_above = self.hidden_layers[0],
state_above = downward_state,
drop_mask = None, V = None)
return recons
class DBM(Model):
"""
A deep Boltzmann machine.
See "Deep Boltzmann Machines" by Ruslan Salakhutdinov and Geoffrey Hinton
for details.
Parameters
----------
batch_size : int
The batch size the model should use. Some convolutional
LinearTransforms require a compile-time hardcoded batch size,
otherwise this would not be part of the model specification.
visible_layer : VisibleLayer
The visible layer of the DBM.
hidden_layers : list
The hidden layers. A list of HiddenLayer objects. The first
layer in the list is connected to the visible layer.
niter : int
Number of mean field iterations for variational inference
for the positive phase.
sampling_procedure : SamplingProcedure (optional)
An object that specifies how to draw samples from the model.
If not specified, some standard algorithm will be used.
inference_procedure : InferenceProcedure (optional)
An object that specifies how to perform mean field inference
in the model. If not specified, some standard algorithm will
be used.
"""
def __init__(self, batch_size, visible_layer, hidden_layers, niter,
sampling_procedure=None, inference_procedure=None):
super(DBM, self).__init__()
self.__dict__.update(locals())
del self.self
assert len(hidden_layers) >= 1
if len(hidden_layers) > 1 and niter <= 1:
raise ValueError("with more than one hidden layer, niter needs to "
"be greater than 1; otherwise mean field won't "
"work properly.")
self.setup_rng()
self.layer_names = set()
self.visible_layer.set_dbm(self)
for layer in hidden_layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
self._update_layer_input_spaces()
self.force_batch_size = batch_size
self.freeze_set = set([])
if inference_procedure is None:
self.setup_inference_procedure()
self.inference_procedure.set_dbm(self)
if sampling_procedure is None:
self.setup_sampling_procedure()
self.sampling_procedure.set_dbm(self)
def get_all_layers(self):
"""
Get all layers in this model.
Returns
-------
layers : list
"""
return [self.visible_layer] + self.hidden_layers
def energy(self, V, hidden):
"""
Compute the energy of current model with visible and hidden samples.
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not
mean field parameters)
hidden : list
List, one element per hidden layer, of batches of samples (must
be SAMPLES, not mean field parameters)
Returns
-------
rval : tensor_like
Vector containing the energy of each sample
Notes
-----
Applying this function to non-sample theano variables is not guaranteed
to give you an expected energy in general, so don't use this that way.
"""
terms = []
terms.append(self.visible_layer.expected_energy_term(state=V,
average=False))
# This condition could be relaxed, but current code assumes it
assert len(self.hidden_layers) > 0
"""
Here it doesn't matter whether to recalculate the D base on the samples from visible layer
or to use the initial D calculated from the raw data, because when we do the sampling on visible layer
we have included the information of D into the process. Therefore, Ds are guaranteed to be the same.
"""
D = None
if type(self.visible_layer) is ReplicatedSoftMaxLayer:
state_below,D = self.visible_layer.upward_state(V, D_is_initialized = True)
else:
state_below=self.visible_layer.upward_state(V)
terms.append(self.hidden_layers[0].expected_energy_term(
state_below=state_below,
state=hidden[0], average_below=False, average=False,D = D))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
samples_below = hidden[i-1]
layer_below = self.hidden_layers[i-1]
samples_below = layer_below.upward_state(samples_below)
samples = hidden[i]
terms.append(layer.expected_energy_term(state_below=samples_below,
state=samples, average_below=False, average=False))
assert len(terms) > 0
rval = reduce(operator.add, terms)
assert rval.ndim == 1
return rval
def mf(self, *args, **kwargs):
"""
Perform mean field inference, using the model's inference procedure.
"""
self.setup_inference_procedure()
return self.inference_procedure.mf(*args, **kwargs)
def expected_energy(self, V, mf_hidden):
"""
Compute the energy of current model with the visible samples
and variational parameters.
Parameters
----------
V : tensor_like
Theano batch of visible unit observations (must be SAMPLES, not
mean field parameters: the random variables in the expectation
are the hiddens only)
mf_hidden : list
List, one element per hidden layer, of batches of variational
parameters (must be VARIATIONAL PARAMETERS, not samples. Layers
with analytically determined variance parameters for their mean
field parameters will use those to integrate over the variational
distribution, so it's not generally the same thing as measuring
the energy at a point.)
Returns
-------
rval : tensor_like
Vector containing the expected energy of each example under the
corresponding variational distribution.
"""
self.visible_layer.space.validate(V)
assert isinstance(mf_hidden, (list, tuple))
assert len(mf_hidden) == len(self.hidden_layers)
terms = []
terms.append(self.visible_layer.expected_energy_term(state=V,
average=False))
# This condition could be relaxed, but current code assumes it
assert len(self.hidden_layers) > 0
D = None
if type(self.visible_layer) is ReplicatedSoftMaxLayer:
state_below, D =self.visible_layer.upward_state(V,D_is_initialized = True)
else:
state_below =self.visible_layer.upward_state(V)
terms.append(self.hidden_layers[0].expected_energy_term(
state_below=state_below,
average_below=False, state=mf_hidden[0], average=True, D = D))
for i in xrange(1, len(self.hidden_layers)):
layer = self.hidden_layers[i]
layer_below = self.hidden_layers[i-1]
mf_below = mf_hidden[i-1]
mf_below = layer_below.upward_state(mf_below)
mf = mf_hidden[i]
terms.append(layer.expected_energy_term(state_below=mf_below,
state=mf, average_below=True, average=True))
assert len(terms) > 0
rval = reduce(operator.add, terms)
assert rval.ndim == 1
return rval
def setup_rng(self):
"""
Set the random number generator for the model.
"""
self.rng = make_np_rng(None, [2012, 10, 17], which_method="uniform")
def setup_inference_procedure(self):
"""
Set the inference procedure for the model.
Default using `WeightDoubling`
"""
if not hasattr(self, 'inference_procedure') or \
self.inference_procedure is None:
self.inference_procedure = WeightDoubling()
self.inference_procedure.set_dbm(self)
def setup_sampling_procedure(self):
"""
Set the sampling procedure for the model.
Default using `GibbsEvenOdd`
"""
if not hasattr(self, 'sampling_procedure') or \
self.sampling_procedure is None:
self.sampling_procedure = GibbsEvenOdd()
self.sampling_procedure.set_dbm(self)
def get_output_space(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[-1].get_output_space()
def _update_layer_input_spaces(self):
"""
Tells each layer what its input space should be.
Notes
-----
This usually resets the layer's parameters!
"""
visible_layer = self.visible_layer
hidden_layers = self.hidden_layers
self.hidden_layers[0].set_input_space(visible_layer.space)
for i in xrange(1, len(hidden_layers)):
hidden_layers[i].set_input_space(
hidden_layers[i-1].get_output_space())
for layer in self.get_all_layers():
layer.finalize_initialization()
def add_layers(self, layers):
"""
Add new layers on top of the existing hidden layers
Parameters
----------
layers : list
layers to be added
"""
# Patch old pickle files
if not hasattr(self, 'rng'):
self.setup_rng()
hidden_layers = self.hidden_layers
assert len(hidden_layers) > 0
for layer in layers:
assert layer.get_dbm() is None
layer.set_dbm(self)
layer.set_input_space(hidden_layers[-1].get_output_space())
hidden_layers.append(layer)
assert layer.layer_name not in self.layer_names
self.layer_names.add(layer.layer_name)
def freeze(self, parameter_set):
"""
.. todo::
WRITEME
"""
# patch old pickle files
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
self.freeze_set = self.freeze_set.union(parameter_set)
def get_params(self):
"""
.. todo::
WRITEME
"""
rval = []
for param in self.visible_layer.get_params():
assert param.name is not None
rval = self.visible_layer.get_params()
for layer in self.hidden_layers:
for param in layer.get_params():
if param.name is None:
raise ValueError("All of your parameters should have "
"names, but one of " + layer.layer_name +
"'s doesn't")
layer_params = layer.get_params()
assert not isinstance(layer_params, set)
for param in layer_params:
if param not in rval:
rval.append(param)
# Patch pickle files that predate the freeze_set feature
if not hasattr(self, 'freeze_set'):
self.freeze_set = set([])
rval = [elem for elem in rval if elem not in self.freeze_set]
assert all([elem.name is not None for elem in rval])
return rval
def set_batch_size(self, batch_size):
"""
.. todo::
WRITEME
"""
self.batch_size = batch_size
self.force_batch_size = batch_size
for layer in self.hidden_layers:
layer.set_batch_size(batch_size)
if not hasattr(self, 'inference_procedure'):
self.setup_inference_procedure()
self.inference_procedure.set_batch_size(batch_size)
@functools.wraps(Model._modify_updates)
def _modify_updates(self, updates):
self.visible_layer.modify_updates(updates)
for layer in self.hidden_layers:
layer.modify_updates(updates)
def get_input_space(self):
"""
.. todo::
WRITEME
"""
return self.visible_layer.space
def get_lr_scalers(self):
"""
.. todo::
WRITEME
"""
rval = OrderedDict()
params = self.get_params()
for layer in self.hidden_layers + [self.visible_layer]:
contrib = layer.get_lr_scalers()
# No two layers can contend to scale a parameter
assert not any([key in rval for key in contrib])
# Don't try to scale anything that's not a parameter
assert all([key in params for key in contrib])
rval.update(contrib)
assert all([isinstance(val, float) for val in rval.values()])
return rval
def get_weights(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights()
def get_weights_view_shape(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_view_shape()
def get_weights_format(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_format()
def get_weights_topo(self):
"""
.. todo::
WRITEME
"""
return self.hidden_layers[0].get_weights_topo()
def make_layer_to_state(self, num_examples, rng=None):
"""
Makes and returns a dictionary mapping layers to states.
By states, we mean here a real assignment, not a mean field
state. For example, for a layer containing binary random
variables, the state will be a shared variable containing
values in {0,1}, not [0,1]. The visible layer will be included.
Uses a dictionary so it is easy to unambiguously index a layer
without needing to remember rules like vis layer = 0, hiddens
start at 1, etc.
Parameters
----------
num_examples : int
Number of examples to make up the state
rng : MRG_RandomStreams
Random number generator, if None then use model's rng
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
if rng is None:
rng = self.rng
states = [layer.make_state(num_examples, rng) for layer in layers]
def recurse_check(layer, state):
if isinstance(state, (list, tuple)):
for elem in state:
recurse_check(layer, elem)
else:
val = state.get_value()
m = val.shape[0]
if m != num_examples:
raise ValueError(layer.layer_name + " gave state with " +
str(m) + " examples in some component."
"We requested " + str(num_examples))
for layer, state in safe_zip(layers, states):
recurse_check(layer, state)
rval = OrderedDict(safe_zip(layers, states))
return rval
def make_layer_to_symbolic_state(self, num_examples, rng=None):
"""
Makes and returns a dictionary mapping layers to states.
By states, we mean here a real assignment, not a mean field
state. For example, for a layer containing binary random
variables, the state will be a shared variable containing
values in {0,1}, not [0,1]. The visible layer will be included.
Uses a dictionary so it is easy to unambiguously index a layer
without needing to remember rules like vis layer = 0, hiddens
start at 1, etc.
Parameters
----------
num_examples : int
Number of examples to make up the state
rng : MRG_RandomStreams
Random number generator
Notes
-----
This method returns a symbolic expression of the state, while
`make_layer_to_state` returns a certain shared variable.
"""
# Make a list of all layers
layers = [self.visible_layer] + self.hidden_layers
assert rng is not None
states = [layer.make_symbolic_state(num_examples, rng)
for layer in layers]
zipped = safe_zip(layers, states)
rval = OrderedDict(zipped)
return rval
def get_sampling_updates(self, layer_to_state, theano_rng,
layer_to_clamp=None, num_steps=1,
return_layer_to_updated=False):
"""
This method is for getting an updates dictionary for a theano function.
It thus implies that the samples are represented as shared variables.
If you want an expression for a sampling step applied to arbitrary
theano variables, use the `DBM.sampling_procedure.sample` method.
This is a wrapper around that method.
Parameters
----------
layer_to_state : dict
Dictionary mapping the SuperDBM_Layer instances contained in
self to shared variables representing batches of samples of them.
(you can allocate one by calling self.make_layer_to_state)
theano_rng : MRG_RandomStreams
Random number generator
layer_to_clamp : dict, optional
Dictionary mapping layers to bools. If a layer is not in the
dictionary, defaults to False. True indicates that this layer
should be clamped, so we are sampling from a conditional
distribution rather than the joint distribution
num_steps : int, optional
Steps of the sampling procedure. It samples for `num_steps`
times and use the last sample.
return_layer_to_updated : bool, optional
Whether returns the sample additionally
Returns
-------
rval : dict
Dictionary mapping each shared variable to an expression to
update it. Repeatedly applying these updates does MCMC sampling.
Notes
-----
The specific sampling schedule used by default is to sample all of the
even-idexed layers of model.hidden_layers, then the visible layer and
all the odd-indexed layers.
"""
updated = self.sampling_procedure.sample(layer_to_state, theano_rng,
layer_to_clamp, num_steps, D_is_initialized = True)
rval = OrderedDict()
def add_updates(old, new):
if isinstance(old, (list, tuple)):
for old_elem, new_elem in safe_izip(old, new):
add_updates(old_elem, new_elem)
else:
rval[old] = new
# Validate layer_to_clamp / make sure layer_to_clamp is a fully
# populated dictionary
if layer_to_clamp is None:
layer_to_clamp = OrderedDict()
for key in layer_to_clamp:
assert key is self.visible_layer or key in self.hidden_layers
for layer in [self.visible_layer] + self.hidden_layers:
if layer not in layer_to_clamp:
layer_to_clamp[layer] = False
# Translate update expressions into theano updates
for layer in layer_to_state:
old = layer_to_state[layer]
new = updated[layer]
if layer_to_clamp[layer]:
assert new is old
else:
add_updates(old, new)
assert isinstance(self.hidden_layers, list)
if return_layer_to_updated:
return rval, updated
return rval
def get_monitoring_channels(self, data):
"""
.. todo::
WRITEME
"""
space, source = self.get_monitoring_data_specs()
space.validate(data)
X = data
history = self.mf(X, return_history=True)
q = history[-1]
rval = OrderedDict()
ch = self.visible_layer.get_monitoring_channels()
for key in ch:
rval['vis_' + key] = ch[key]
for state, layer in safe_zip(q, self.hidden_layers):
ch = layer.get_monitoring_channels()
for key in ch:
rval[layer.layer_name + '_' + key] = ch[key]
ch = layer.get_monitoring_channels_from_state(state)
for key in ch:
rval['mf_' + layer.layer_name + '_' + key] = ch[key]
if len(history) > 1:
prev_q = history[-2]
flat_q = flatten(q)
flat_prev_q = flatten(prev_q)
mx = None
for new, old in safe_zip(flat_q, flat_prev_q):
cur_mx = abs(new - old).max()
if new is old:
logger.error('{0} is {1}'.format(new, old))
assert False
if mx is None:
mx = cur_mx
else:
mx = T.maximum(mx, cur_mx)
rval['max_var_param_diff'] = mx
for layer, new, old in safe_zip(self.hidden_layers,
q, prev_q):
sum_diff = 0.
for sub_new, sub_old in safe_zip(flatten(new), flatten(old)):
sum_diff += abs(sub_new - sub_old).sum()
denom = self.batch_size * \
layer.get_total_state_space().get_total_dimension()
denom = np.cast[config.floatX](denom)
rval['mean_'+layer.layer_name+'_var_param_diff'] = \
sum_diff / denom
return rval
def get_monitoring_data_specs(self):
"""
Get the data_specs describing the data for get_monitoring_channel.
This implementation returns specification corresponding to unlabeled
inputs.
"""
return (self.get_input_space(), self.get_input_source())
def get_test_batch_size(self):
"""
.. todo::
WRITEME
"""
return self.batch_size
def reconstruct(self, V):
"""
Reconstruct the visible variables.
Returns
-------
recons : tensor_like
Unmasked reconstructed visible variables.
"""
H = self.mf(V)[0]
downward_state = self.hidden_layers[0].downward_state(H)
recons = self.visible_layer.inpaint_update(
layer_above=self.hidden_layers[0],
state_above=downward_state,
drop_mask=None, V=None)
return recons
def do_inpainting(self, *args, **kwargs):
"""
Does the inference required for multi-prediction training,
using the model's inference procedure.
"""
self.setup_inference_procedure()
return self.inference_procedure.do_inpainting(*args, **kwargs)
def perform(self, X_raw, niter = None):
"""
Added by Ning Zhang
This method is used communicate with the Transformer.get_design_matrix()
Todo: save intermediate results to avoid repeating this step
Here X_raw is not the symbolic variable
"""
inputs = T.matrix()
if niter is None:
niter = self.niter
H_hat = self.inference_procedure.mf(V = inputs, niter = niter)
r_val = self.hidden_layers[-1].upward_state(H_hat[-1])
fn = theano.function([inputs], r_val,name='perform')
return fn(X_raw)
def __call__(self, X_raw, return_history = False, niter = None):
"""
Added by Ning Zhang
This method is used communicate with the StackedBlock.
It functionality is quite similar to perform.
Actually if one take a look at the code of TransformerDataset and StackedBlock
one can find the real content "perform" method is usually the "__call__" method
By implementing this method we easily stack multiple DBMs together.
X_raw: symbolic variable
return_history: return history of the all iterations
"""
if niter is None:
niter = self.niter
H_hat, history = self.inference_procedure.mf(V = X_raw, niter = niter, return_history = return_history)
if return_history:
output = []
for i in xrange(niter):
output.append(self.hidden_layers[-1].upward_state(history[i][-1]))
return output
else:
return self.hidden_layers[-1].upward_state(H_hat[-1])
def upward_pass(self, v, niter = None, double_bottom = False):
"""
Added by Ning Zhang.
This method is provided for making DBM as a MLP or a part of MLP
One thing should be noticed is that: if two layer DBM a.k.a. RBM is stacked together,
by directly using this mf method of inference_procedure, we actually derived a DBN because inside the inference_procedure would
treat all the intermediate models as itegral ones instead of intermediate layers.
Therefore, we modify the DoubleWeighting for this situation.
Todo: strictly speaking if DBMs are stacked and one want it do the exact Even-odd inference process
one should implement the downward_state and upward_state for DBM (not for its layers),
then the stacked DBMs can be function as a layer.
We leave it for the future.
"""
if niter is None:
niter = self.niter
H_hat = self.inference_procedure.mf(V = v, niter = self.niter, double_bottom = double_bottom)[-1]
return self.hidden_layers[-1].upward_state(H_hat[-1])
def downward_pass(self, input_state, niter = None, return_history = False, real_visible = False, double_weight_swicth = True):
"""
Added by Ning Zhang
This method is the reverse pass from top to bottom. One can take it as generalized version of reconstruction,
while involving all the hidden layers.
It would be used when a pre-trained RBM(DBM) being stacked together as a whole model by the newly defined pre_trained layer
in layer.py
It is the common case when we do the layer-wise training and fine-tuning.
Here double weighting MF approach is adopted when deal with the top and bottom layer case by case
based on the value of "real_visible".
Models contains "real" visible layer may not the case. By "real" we mean the visible layer directly
the raw training datasets not the intermediate representations derived from trained hidden layers.
real_visible: indicate if the visible layer in this model is the real one or the intermediate hidden one
double_weight: with False, this method is switched to serve for DBN not DBM
Todo: debugging and testing
"""
self.get_output_space().validate(input_state)
if niter is None:
niter = self.niter
if double_weight_swicth:
visible_input_factor = 1 if real_visible else 2
else:
visible_input_factor = 1
length = len(self.hidden_layers)
if length == 1:
return self.visible_layer.mf_update(state_above = input_state * visible_input_factor,
layer_above = self.hidden_layers[0]
)
else:
#do MF inference once
history = []
H_hat = []
for j in xrange(2,length+1):
i = length - j
if i == length - 2:
layer_below = self.hidden_layers[i-1]
state_below = layer_below.upward_state()
H_hat.append(self.hidden_layers[i].mf_update(state_above = input_state,
layer_above = self.hidden_layers[i + 1],
state_below = None,
double_weights = double_weight_swicth))
else:
H_hat.append(self.hidden_layers[i].mf_update(state_above = self.hidden_layers[i + 1].downward_state(H_hat[-1]),
layer_above = self.hidden_layers[i + 1],
state_below = None,
double_weights = double_weight_swicth))
# deal with visible layer
H_hat.append(self.visible_layer.mf_update(state_above = self.hidden_layers[0].downward_state(H_hat[-1]) * visible_input_factor,
layer_above = self.hidden_layers[0]
))
history.append(H_hat[-1])
# DBN style MF
if not double_weight_swicth:
for it in xrange(1, niter):
for j in xrange(2,length+1):
i = length - j
if i == length - 2:
H_hat[length-2-i] = self.hidden_layers[i].mf_update(state_above = input_state,
layer_above = self.hidden_layers[i + 1],
double_weights = False)
else:
H_hat.append(self.hidden_layers[i].mf_update(state_above = self.hidden_layers[i + 1].downward_state(H_hat[length-3-i]),
layer_above = self.hidden_layers[i + 1],
state_below = None,
double_weights = double_weight_swicth))
# deal with visible layer
H_hat[-1] = self.visible_layer.mf_update(state_above = self.hidden_layers[0].downward_state(H_hat[-2]),
layer_above = self.hidden_layers[0]
)
history.append(H_hat[-1])
else:
# recurrent MF inference, even-odd style (DBM)
for it in xrange(1, niter):
for j in xrange(2,length+1,2):
i = length - j
if i == length - 2:
# If there are only two hidden layers, we should add visual layer for the MF inference
if i == 0:
layer_below = self.visible_layer
state_below = layer_below.upward_state(H_hat[-1])
else:
layer_below = self.hidden_layers[i-1]
state_below = layer_below.upward_state(H_hat[length-1-i])
H_hat[length-2-i] = self.hidden_layers[i].mf_update(state_above = input_state,
layer_above = self.hidden_layers[i + 1],
state_below = state_below,
double_weights = False)
else:
layer_above = self.hidden_layers[i + 1]
state_above = layer_above.downward_state(H_hat[length-3-i])
if i == 0:
layer_below = self.visible_layer
state_below = layer_below.upward_state(H_hat[-1])
else:
layer_below = self.hidden_layers[i-1]
state_below = layer_below.upward_state(H_hat[length-1-i])
H_hat[length-2-i] = self.hidden_layers[i].mf_update(state_above = state_above,
layer_above = layer_above,
state_below = state_below,
layer_below = layer_below,
double_weights = False)
# deal with visible layer
if length % 2 == 1:
double_weights = 1 if real_visible else 2
H_hat[-1] = self.visible_layer.mf_update(state_above = self.hidden_layers[0].downward_state(H_hat[-2]) * double_weights,
layer_above = self.hidden_layers[0]
)
for j in xrange(3,length+1,2):
i = length - j
layer_above = self.hidden_layers[i + 1]
state_above = layer_above.downward_state(H_hat[length-3-i])
if i == 0:
layer_below = self.visible_layer
state_below = layer_below.upward_state(H_hat[-1])
else:
layer_below = self.hidden_layers[i-1]
state_below = layer_below.upward_state(H_hat[length-1-i])
H_hat[length-2-i] = self.hidden_layers[i].mf_update(state_above = state_above,
layer_above = layer_above,
state_below = state_below,
layer_below = layer_below,
double_weights = False)
if length % 2 == 0:
double_weights = 1 if real_visible else 2
H_hat[-1] = self.visible_layer.mf_update(state_above = self.hidden_layers[0].downward_state(H_hat[-2]) * double_weights,
layer_above = self.hidden_layers[0]
)
history.append(H_hat[-1])
# Run some checks on the output
for i in xrange(0, length -1):
down_state = self.hidden_layers[i].downward_state(H_hat[length - 2- i])
self.hidden_layers[i].get_input_space().validate(down_state)
self.visibile_layer.get_input_space().validate(self.hidden_layers[0].downward_state(H_hat[-2]))
if return_history:
return history
else:
return H_hat[-1]