def analyze(cli_params):
p, _ = load_and_log_params(cli_params)
_, data, whiten, cnorm = setup_data(p, test_set=True)
ladder = setup_model(p)
# Analyze activations
dset, indices, calc_batchnorm = {
'train': (data.train, data.train_ind, False),
'valid': (data.valid, data.valid_ind, True),
'test': (data.test, data.test_ind, True),
}[p.data_type]
if calc_batchnorm:
logger.info('Calculating batch normalization for clean.labeled path')
main_loop = DummyLoop(
extensions=[
FinalTestMonitoring(
[ladder.costs.class_clean, ladder.error.clean]
+ ladder.costs.denois.values(),
make_datastream(data.train, data.train_ind,
# These need to match with the training
p.batch_size,
n_labeled=p.labeled_samples,
n_unlabeled=len(data.train_ind),
cnorm=cnorm,
whiten=whiten, scheme=ShuffledScheme),
make_datastream(data.valid, data.valid_ind,
p.valid_batch_size,
n_labeled=len(data.valid_ind),
n_unlabeled=len(data.valid_ind),
cnorm=cnorm,
whiten=whiten, scheme=ShuffledScheme),
prefix="valid_final", before_training=True),
ShortPrinting({
"valid_final": OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_C_de', [ladder.costs.denois.get(0),
ladder.costs.denois.get(1),
ladder.costs.denois.get(2),
ladder.costs.denois.get(3)]),
]),
}, after_training=True, use_log=False),
])
main_loop.run()
# Make a datastream that has all the indices in the labeled pathway
ds = make_datastream(dset, indices,
batch_size=p.get('batch_size'),
n_labeled=len(indices),
n_unlabeled=len(indices),
balanced_classes=False,
whiten=whiten,
cnorm=cnorm,
scheme=SequentialScheme)
# We want out the values after softmax
outputs = ladder.act.clean.labeled.h[len(ladder.layers) - 1]
# Replace the batch normalization paramameters with the shared variables
if calc_batchnorm:
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
inputs = {'features_labeled': [],
'targets_labeled': [],
'features_unlabeled': []}
# Loop over one epoch
for d in it:
# Store all inputs
for k, v in d.iteritems():
inputs[k] += [v]
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
inputs = {k: numpy.vstack(v) for k, v in inputs.iteritems()}
return inputs['targets_labeled'], res[0]
def analyze(cli_params):
p, _ = load_and_log_params(cli_params)
_, data = setup_data(p, test_set=True)
ladder = setup_model(p)
# Analyze activations
dset, indices, calc_batchnorm = {
'train': (data.train, data.train_ind, False),
'valid': (data.valid, data.valid_ind, True),
'test': (data.test, data.test_ind, True),
}[p.data_type]
if calc_batchnorm:
logger.info('Calculating batch normalization for clean.labeled path')
main_loop = DummyLoop(extensions=[
FinalTestMonitoring(
[ladder.costs.class_clean, ladder.error.clean] +
list(ladder.costs.denois.values()),
make_datastream(
data.train,
data.train_ind,
# These need to match with the training
p.batch_size,
n_labeled=p.labeled_samples,
n_unlabeled=len(data.train_ind),
scheme=ShuffledScheme),
make_datastream(data.valid,
data.valid_ind,
p.valid_batch_size,
n_labeled=len(data.valid_ind),
n_unlabeled=len(data.valid_ind),
scheme=ShuffledScheme),
prefix="valid_final",
before_training=True),
ShortPrinting(
{
"valid_final":
OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_C_de', [
ladder.costs.denois.get(0),
ladder.costs.denois.get(1),
ladder.costs.denois.get(2),
ladder.costs.denois.get(3)
]),
]),
},
after_training=True,
use_log=False),
])
main_loop.run()
# Make a datastream that has all the indices in the labeled pathway
ds = make_datastream(dset,
indices,
batch_size=p.get('batch_size'),
n_labeled=len(indices),
n_unlabeled=len(indices),
balanced_classes=False,
scheme=SequentialScheme)
# We want out the values after softmax
outputs = ladder.act.clean.labeled.h[len(ladder.layers) - 1]
# Replace the batch normalization paramameters with the shared variables
if calc_batchnorm:
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
inputs = {
'features_labeled': [],
'targets_labeled': [],
'features_unlabeled': []
}
# Loop over one epoch
for d in it:
# Store all inputs
for k, v in d.items():
inputs[k] += [v]
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
inputs = {k: numpy.vstack(v) for k, v in inputs.items()}
return inputs['targets_labeled'], res[0]
def dump_unlabeled_encoder(cli_params):
"""
called when dumping
:return: inputs, result
"""
p, _ = load_and_log_params(cli_params)
_, data, whiten, cnorm = setup_data(p, test_set=(p.data_type == 'test'))
ladder = setup_model(p)
# Analyze activations
if p.data_type == 'train':
dset, indices, calc_batchnorm = data.train, data.train_ind, False
elif p.data_type == 'valid':
dset, indices, calc_batchnorm = data.valid, data.valid_ind, True
elif p.data_type == 'test':
dset, indices, calc_batchnorm = data.test, data.test_ind, True
else:
raise Exception("Unknown data-type %s" % p.data_type)
if calc_batchnorm:
logger.info('Calculating batch normalization for clean.labeled path')
main_loop = DummyLoop(extensions=[
FinalTestMonitoring(
[
ladder.costs.class_clean, ladder.error.clean,
ladder.oos.clean
] + ladder.costs.denois.values(),
make_datastream(
data.train,
data.train_ind,
# These need to match with the training
p.batch_size,
n_labeled=p.labeled_samples,
n_unlabeled=len(data.train_ind),
balanced_classes=p.balanced_classes,
cnorm=cnorm,
whiten=whiten,
scheme=ShuffledScheme),
make_datastream(data.valid,
data.valid_ind,
p.valid_batch_size,
n_labeled=len(data.valid_ind),
n_unlabeled=len(data.valid_ind),
balanced_classes=p.balanced_classes,
cnorm=cnorm,
whiten=whiten,
scheme=ShuffledScheme),
prefix="valid_final",
before_training=True),
ShortPrinting(
{
"valid_final":
OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_O', ladder.oos.clean),
('VF_C_de', [
ladder.costs.denois.get(0),
ladder.costs.denois.get(1),
ladder.costs.denois.get(2),
ladder.costs.denois.get(3)
]),
]),
},
after_training=True,
use_log=False),
])
main_loop.run()
all_ind = numpy.arange(dset.num_examples)
# Make a datastream that has all the indices in the labeled pathway
ds = make_datastream(dset,
all_ind,
batch_size=p.get('batch_size'),
n_labeled=len(all_ind),
n_unlabeled=len(all_ind),
balanced_classes=False,
whiten=whiten,
cnorm=cnorm,
scheme=SequentialScheme)
# If layer=-1 we want out the values after softmax
if p.layer < 0:
# ladder.act.clean.unlabeled.h is a dict not a list
outputs = ladder.act.clean.labeled.h[len(ladder.layers) + p.layer]
else:
outputs = ladder.act.clean.labeled.h[p.layer]
# Replace the batch normalization paramameters with the shared variables
if calc_batchnorm:
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
# Loop over one epoch
for d in it:
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
return res[0]
def analyze(cli_params):
"""
called when evaluating
:return: inputs, result
"""
p, _ = load_and_log_params(cli_params)
_, data, whiten, cnorm = setup_data(p, test_set=(p.data_type == 'test'))
ladder = setup_model(p)
# Analyze activations
if p.data_type == 'train':
dset, indices, calc_batchnorm = data.train, data.train_ind, False
elif p.data_type == 'valid':
dset, indices, calc_batchnorm = data.valid, data.valid_ind, True
elif p.data_type == 'test':
dset, indices, calc_batchnorm = data.test, data.test_ind, True
else:
raise Exception("Unknown data-type %s" % p.data_type)
if calc_batchnorm:
logger.info('Calculating batch normalization for clean.labeled path')
main_loop = DummyLoop(extensions=[
FinalTestMonitoring(
[
ladder.costs.class_clean, ladder.error.clean,
ladder.oos.clean
] + ladder.costs.denois.values(),
make_datastream(
data.train,
data.train_ind,
# These need to match with the training
p.batch_size,
n_labeled=p.labeled_samples,
n_unlabeled=len(data.train_ind),
cnorm=cnorm,
balanced_classes=p.balanced_classes,
whiten=whiten,
scheme=ShuffledScheme),
make_datastream(data.valid,
data.valid_ind,
p.valid_batch_size,
n_labeled=len(data.valid_ind),
n_unlabeled=len(data.valid_ind),
balanced_classes=p.balanced_classes,
cnorm=cnorm,
whiten=whiten,
scheme=ShuffledScheme),
prefix="valid_final",
before_training=True),
ShortPrinting(
{
"valid_final":
OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_O', ladder.oos.clean),
('VF_C_de', [
ladder.costs.denois.get(0),
ladder.costs.denois.get(1),
ladder.costs.denois.get(2),
ladder.costs.denois.get(3)
]),
]),
},
after_training=True,
use_log=False),
])
main_loop.run()
# df = DataFrame.from_dict(main_loop.log, orient='index')
# col = 'valid_final_error_rate_clean'
# logger.info('%s %g' % (col, df[col].iloc[-1]))
# Make a datastream that has all the indices in the labeled pathway
ds = make_datastream(dset,
indices,
batch_size=p.get('batch_size'),
n_labeled=len(indices),
n_unlabeled=len(indices),
balanced_classes=False,
whiten=whiten,
cnorm=cnorm,
scheme=SequentialScheme)
# If layer=-1 we want out the values after softmax
outputs = ladder.act.clean.labeled.h[len(ladder.layers) - 1]
# Replace the batch normalization paramameters with the shared variables
if calc_batchnorm:
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
inputs = {
'features_labeled': [],
'targets_labeled': [],
'features_unlabeled': []
}
# Loop over one epoch
for d in it:
# Store all inputs
for k, v in d.iteritems():
inputs[k] += [v]
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
inputs = {k: numpy.concatenate(v) for k, v in inputs.iteritems()}
return inputs['targets_labeled'], res[0]
def dump_unlabeled_encoder(cli_params):
"""
called when dumping
:return: inputs, result
"""
p, _ = load_and_log_params(cli_params)
_, data, whiten, cnorm = setup_data(p, test_set=(p.data_type == 'test'))
ladder = setup_model(p)
# Analyze activations
if p.data_type == 'train':
dset, indices, calc_batchnorm = data.train, data.train_ind, False
elif p.data_type == 'valid':
dset, indices, calc_batchnorm = data.valid, data.valid_ind, True
elif p.data_type == 'test':
dset, indices, calc_batchnorm = data.test, data.test_ind, True
else:
raise Exception("Unknown data-type %s"%p.data_type)
if calc_batchnorm:
logger.info('Calculating batch normalization for clean.labeled path')
main_loop = DummyLoop(
extensions=[
FinalTestMonitoring(
[ladder.costs.class_clean, ladder.error.clean, ladder.oos.clean]
+ ladder.costs.denois.values(),
make_datastream(data.train, data.train_ind,
# These need to match with the training
p.batch_size,
n_labeled=p.labeled_samples,
n_unlabeled=len(data.train_ind),
balanced_classes=p.balanced_classes,
cnorm=cnorm,
whiten=whiten, scheme=ShuffledScheme),
make_datastream(data.valid, data.valid_ind,
p.valid_batch_size,
n_labeled=len(data.valid_ind),
n_unlabeled=len(data.valid_ind),
balanced_classes=p.balanced_classes,
cnorm=cnorm,
whiten=whiten, scheme=ShuffledScheme),
prefix="valid_final", before_training=True),
ShortPrinting({
"valid_final": OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_O', ladder.oos.clean),
('VF_C_de', [ladder.costs.denois.get(0),
ladder.costs.denois.get(1),
ladder.costs.denois.get(2),
ladder.costs.denois.get(3)]),
]),
}, after_training=True, use_log=False),
])
main_loop.run()
all_ind = numpy.arange(dset.num_examples)
# Make a datastream that has all the indices in the labeled pathway
ds = make_datastream(dset, all_ind,
batch_size=p.get('batch_size'),
n_labeled=len(all_ind),
n_unlabeled=len(all_ind),
balanced_classes=False,
whiten=whiten,
cnorm=cnorm,
scheme=SequentialScheme)
# If layer=-1 we want out the values after softmax
if p.layer < 0:
# ladder.act.clean.unlabeled.h is a dict not a list
outputs = ladder.act.clean.labeled.h[len(ladder.layers) + p.layer]
else:
outputs = ladder.act.clean.labeled.h[p.layer]
# Replace the batch normalization paramameters with the shared variables
if calc_batchnorm:
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
# Loop over one epoch
for d in it:
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
return res[0]
def train_ladder(cli_params, dataset=None, save_to='results/ova_all_full'):
cli_params['save_dir'] = prepare_dir(save_to)
logfile = os.path.join(cli_params['save_dir'], 'log.txt')
# Log also DEBUG to a file
fh = logging.FileHandler(filename=logfile)
fh.setLevel(logging.DEBUG)
logger.addHandler(fh)
logger.info('Logging into %s' % logfile)
p, loaded = load_and_log_params(cli_params)
ladder = setup_model(p)
# Training
all_params = ComputationGraph([ladder.costs.total]).parameters
logger.info('Found the following parameters: %s' % str(all_params))
# Fetch all batch normalization updates. They are in the clean path.
bn_updates = ComputationGraph([ladder.costs.class_clean]).updates
assert 'counter' in [u.name for u in bn_updates.keys()], \
'No batch norm params in graph - the graph has been cut?'
training_algorithm = GradientDescent(
cost=ladder.costs.total,
params=all_params,
step_rule=Adam(learning_rate=ladder.lr))
# In addition to actual training, also do BN variable approximations
training_algorithm.add_updates(bn_updates)
short_prints = {
"train": {
'T_C_class': ladder.costs.class_corr,
'T_C_de': ladder.costs.denois.values(),
},
"valid_approx":
OrderedDict([
('V_C_class', ladder.costs.class_clean),
('V_E', ladder.error.clean),
('V_C_de', ladder.costs.denois.values()),
]),
"valid_final":
OrderedDict([
('VF_C_class', ladder.costs.class_clean),
('VF_E', ladder.error.clean),
('VF_C_de', ladder.costs.denois.values()),
]),
}
ovadataset = dataset['ovadataset']
train_indexes = dataset['train_indexes']
val_indexes = dataset['val_indexes']
main_loop = MainLoop(
training_algorithm,
# Datastream used for training
make_datastream(ovadataset,
train_indexes,
p.batch_size,
scheme=ShuffledScheme),
model=Model(ladder.costs.total),
extensions=[
FinishAfter(after_n_epochs=p.num_epochs),
# This will estimate the validation error using
# running average estimates of the batch normalization
# parameters, mean and variance
ApproxTestMonitoring(
[ladder.costs.class_clean, ladder.error.clean] +
ladder.costs.denois.values(),
make_datastream(ovadataset, val_indexes, p.batch_size),
prefix="valid_approx"),
# This Monitor is slower, but more accurate since it will first
# estimate batch normalization parameters from training data and
# then do another pass to calculate the validation error.
FinalTestMonitoring(
[ladder.costs.class_clean, ladder.error.clean_mc] +
ladder.costs.denois.values(),
make_datastream(ovadataset, train_indexes, p.batch_size),
make_datastream(ovadataset, val_indexes, p.batch_size),
prefix="valid_final",
after_n_epochs=p.num_epochs),
TrainingDataMonitoring([
ladder.costs.total, ladder.costs.class_corr,
training_algorithm.total_gradient_norm
] + ladder.costs.denois.values(),
prefix="train",
after_epoch=True),
ShortPrinting(short_prints),
LRDecay(ladder.lr,
p.num_epochs * p.lrate_decay,
p.num_epochs,
after_epoch=True),
])
main_loop.run()
# Get results
df = main_loop.log.to_dataframe()
col = 'valid_final_error_matrix_cost'
logger.info('%s %g' % (col, df[col].iloc[-1]))
ds = make_datastream(ovadataset, val_indexes, p.batch_size)
outputs = ladder.act.clean.labeled.h[len(ladder.layers) - 1]
outputreplacer = TestMonitoring()
_, _, outputs = outputreplacer._get_bn_params(outputs)
cg = ComputationGraph(outputs)
f = cg.get_theano_function()
it = ds.get_epoch_iterator(as_dict=True)
res = []
inputs = {
'features_labeled': [],
'targets_labeled': [],
'features_unlabeled': []
}
# Loop over one epoch
for d in it:
# Store all inputs
for k, v in d.iteritems():
inputs[k] += [v]
# Store outputs
res += [f(*[d[str(inp)] for inp in cg.inputs])]
# Concatenate all minibatches
res = [numpy.vstack(minibatches) for minibatches in zip(*res)]
inputs = {k: numpy.vstack(v) for k, v in inputs.iteritems()}
if main_loop.log.status['epoch_interrupt_received']:
return None
return res[0], inputs
