class TensorGraph(Model):
def __init__(self,
tensorboard=False,
tensorboard_log_frequency=100,
batch_size=100,
random_seed=None,
use_queue=True,
graph=None,
learning_rate=0.001,
**kwargs):
"""
Parameters
----------
tensorboard: bool
Should we log to model_dir data for tensorboard?
tensorboard_log_frequency: int
How many training batches before logging tensorboard?
batch_size: int
default batch size for training and evaluating
use_queue: boolean
if True when building we will create a tf.FIFO queue, which will hold
all features, weights, and labels. We will feed the inputs into this
queue in batches of self.batch_size in a separate thread from the
thread training the model. You cannot use a queue when
batches are not of consistent size
graph: tensorflow.Graph
the Graph in which to create Tensorflow objects. If None, a new Graph
is created.
learning_rate: float or LearningRateSchedule
the learning rate to use for optimization
kwargs
"""
# Layer Management
self.layers = dict()
self.features = list()
self.labels = list()
self.outputs = list()
self.task_weights = list()
self.submodels = list()
self.loss = Constant(0)
self.built = False
self.queue_installed = False
self.optimizer = Adam(learning_rate=learning_rate,
beta1=0.9,
beta2=0.999,
epsilon=1e-7)
# Singular place to hold Tensor objects which don't serialize
# These have to be reconstructed on restoring from pickle
# See TensorGraph._get_tf() for more details on lazy construction
self.tensor_objects = {
"FileWriter": None,
"Graph": graph,
"train_op": None,
"summary_op": None,
}
self.tensorboard = tensorboard
self.tensorboard_log_frequency = tensorboard_log_frequency
self.tensorboard_step = 0
self.global_step = 0
self.use_queue = use_queue
self.batch_size = batch_size
self.random_seed = random_seed
super(TensorGraph, self).__init__(**kwargs)
self.save_file = "%s/%s" % (self.model_dir, "model")
self.model_class = None
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
if self.use_queue and self.tensorboard:
raise ValueError(
"Currently TensorGraph cannot both use_queue and tensorboard at the same time"
)
def _add_layer(self, layer):
if layer.name is None:
layer.name = "%s_%s" % (layer.__class__.__name__,
len(self.layers) + 1)
if layer.name in self.layers:
return
if isinstance(layer, Feature):
self.features.append(layer)
if isinstance(layer, Label):
self.labels.append(layer)
if isinstance(layer, Weights):
self.task_weights.append(layer)
self.layers[layer.name] = layer
for in_layer in layer.in_layers:
self._add_layer(in_layer)
def fit(self,
dataset,
nb_epoch=10,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
deterministic=False,
restore=False,
submodel=None):
"""Train this model on a dataset.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
deterministic: bool
if True, the samples are processed in order. If False, a different random
order is used for each epoch.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
"""
return self.fit_generator(
self.default_generator(dataset,
epochs=nb_epoch,
deterministic=deterministic),
max_checkpoints_to_keep, checkpoint_interval, restore, submodel)
def fit_generator(self,
feed_dict_generator,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
restore=False,
submodel=None):
"""Train this model on data from a generator.
Parameters
----------
feed_dict_generator: generator
this should generate batches, each represented as a dict that maps
Layers to values.
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
Returns
-------
the average loss over the most recent checkpoint interval
"""
def create_feed_dict():
if self.use_queue:
while True:
yield {self._training_placeholder: 1.0}
for d in feed_dict_generator:
feed_dict = dict(d)
feed_dict[self._training_placeholder] = 1.0
yield feed_dict
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
time1 = time.time()
loss = self.loss
if submodel is None:
train_op = self._get_tf('train_op')
else:
train_op = submodel.get_train_op()
if submodel.loss is not None:
loss = submodel.loss
if checkpoint_interval > 0:
saver = tf.train.Saver(max_to_keep=max_checkpoints_to_keep)
if restore:
self.restore()
avg_loss, n_averaged_batches = 0.0, 0.0
n_samples = 0
n_enqueued = [0]
final_sample = [None]
if self.use_queue:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, feed_dict_generator, self._get_tf("Graph"),
self.session, n_enqueued, final_sample))
enqueue_thread.start()
for feed_dict in create_feed_dict():
if self.use_queue:
# Don't let this thread get ahead of the enqueue thread, since if
# we try to read more batches than the total number that get queued,
# this thread will hang indefinitely.
while n_enqueued[0] <= n_samples:
if n_samples == final_sample[0]:
break
time.sleep(0)
if n_samples == final_sample[0]:
break
n_samples += 1
should_log = (self.tensorboard and
n_samples % self.tensorboard_log_frequency == 0)
fetches = [train_op, loss.out_tensor]
if should_log:
fetches.append(self._get_tf("summary_op"))
fetched_values = self.session.run(fetches, feed_dict=feed_dict)
if should_log:
self._log_tensorboard(fetches[2])
avg_loss += fetched_values[1]
n_averaged_batches += 1
self.global_step += 1
if checkpoint_interval > 0 and self.global_step % checkpoint_interval == checkpoint_interval - 1:
saver.save(self.session,
self.save_file,
global_step=self.global_step)
avg_loss = float(avg_loss) / n_averaged_batches
print('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
avg_loss, n_averaged_batches = 0.0, 0.0
if n_averaged_batches > 0:
avg_loss = float(avg_loss) / n_averaged_batches
if checkpoint_interval > 0:
if n_averaged_batches > 0:
print('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
saver.save(self.session,
self.save_file,
global_step=self.global_step)
time2 = time.time()
print("TIMING: model fitting took %0.3f s" % (time2 - time1))
return avg_loss
def _log_tensorboard(self, summary):
"""
TODO(LESWING) set epoch
Parameters
----------
Returns
-------
"""
global_step = int(self.global_step)
writer = self._get_tf("FileWriter")
writer.reopen()
writer.add_summary(summary, global_step=global_step)
writer.close()
def fit_on_batch(self, X, y, w, submodel=None):
if not self.built:
self.build()
dataset = NumpyDataset(X, y)
return self.fit(dataset, nb_epoch=1, submodel=submodel)
def default_generator(self,
dataset,
epochs=1,
predict=False,
deterministic=True,
pad_batches=True):
if len(self.features) > 1:
raise ValueError("More than one Feature, must use generator")
if len(self.labels) > 1:
raise ValueError("More than one Label, must use generator")
if len(self.task_weights) > 1:
raise ValueError("More than one Weights, must use generator")
for epoch in range(epochs):
for (X_b, y_b, w_b,
ids_b) in dataset.iterbatches(batch_size=self.batch_size,
deterministic=deterministic,
pad_batches=pad_batches):
feed_dict = dict()
if len(self.labels) == 1 and y_b is not None and not predict:
feed_dict[self.labels[0]] = y_b
if len(self.features) == 1 and X_b is not None:
feed_dict[self.features[0]] = X_b
if len(self.task_weights
) == 1 and w_b is not None and not predict:
feed_dict[self.task_weights[0]] = w_b
for (initial_state, zero_state) in zip(self.rnn_initial_states,
self.rnn_zero_states):
feed_dict[initial_state] = zero_state
yield feed_dict
def predict_on_generator(self, generator, transformers=[], outputs=None):
"""
Parameters
----------
generator: Generator
Generator that constructs feed dictionaries for TensorGraph.
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs.
If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
if not self.built:
self.build()
if outputs is None:
outputs = self.outputs
elif not isinstance(outputs, collections.Sequence):
outputs = [outputs]
with self._get_tf("Graph").as_default():
# Gather results for each output
results = [[] for out in outputs]
for feed_dict in generator:
feed_dict = {
self.layers[k.name].out_tensor: v
for k, v in six.iteritems(feed_dict)
}
feed_dict[self._training_placeholder] = 0.0
feed_results = self.session.run(outputs, feed_dict=feed_dict)
if len(feed_results) > 1:
if len(transformers):
raise ValueError("Does not support transformations "
"for multiple outputs.")
elif len(feed_results) == 1:
result = undo_transforms(feed_results[0], transformers)
feed_results = [result]
for ind, result in enumerate(feed_results):
results[ind].append(result)
final_results = []
for result_list in results:
final_results.append(np.concatenate(result_list, axis=0))
# If only one output, just return array
if len(final_results) == 1:
return final_results[0]
else:
return final_results
def predict_proba_on_generator(self,
generator,
transformers=[],
outputs=None):
"""
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
return self.predict_on_generator(generator, transformers, outputs)
def predict_on_batch(self, X, transformers=[], outputs=None):
"""Generates predictions for input samples, processing samples in a batch.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
transformers: List
List of dc.trans.Transformers
Returns
-------
A Numpy array of predictions.
"""
dataset = NumpyDataset(X=X, y=None)
generator = self.default_generator(dataset,
predict=True,
pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_proba_on_batch(self, X, transformers=[], outputs=None):
"""Generates predictions for input samples, processing samples in a batch.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
transformers: List
List of dc.trans.Transformers
Returns
-------
A Numpy array of predictions.
"""
return self.predict_on_batch(X, transformers, outputs)
def predict(self, dataset, transformers=[], outputs=None):
"""
Uses self to make predictions on provided Dataset object.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs[0] (single
output). If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
Returns
-------
results: numpy ndarray or list of numpy ndarrays
"""
generator = self.default_generator(dataset,
predict=True,
pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_proba(self, dataset, transformers=[], outputs=None):
"""
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs[0] (single
output). If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
Returns
-------
y_pred: numpy ndarray or list of numpy ndarrays
"""
generator = self.default_generator(dataset,
predict=True,
pad_batches=False)
return self.predict_proba_on_generator(generator, transformers,
outputs)
def topsort(self):
def add_layers_to_list(layer, sorted_layers):
if layer in sorted_layers:
return
for in_layer in layer.in_layers:
add_layers_to_list(in_layer, sorted_layers)
sorted_layers.append(layer)
sorted_layers = []
for l in self.features + self.labels + self.task_weights + self.outputs:
add_layers_to_list(l, sorted_layers)
add_layers_to_list(self.loss, sorted_layers)
for submodel in self.submodels:
if submodel.loss is not None:
add_layers_to_list(submodel.loss, sorted_layers)
return sorted_layers
def build(self):
if self.built:
return
with self._get_tf("Graph").as_default():
self._training_placeholder = tf.placeholder(dtype=tf.float32,
shape=())
if self.random_seed is not None:
tf.set_random_seed(self.random_seed)
self._install_queue()
for layer in self.topsort():
with tf.name_scope(layer.name):
layer.create_tensor(training=self._training_placeholder)
self.rnn_initial_states += layer.rnn_initial_states
self.rnn_final_states += layer.rnn_final_states
self.rnn_zero_states += layer.rnn_zero_states
layer.add_summary_to_tg()
self.session = tf.Session()
self.built = True
# Ensure all training operators have been created.
self._get_tf('train_op')
for submodel in self.submodels:
train_op = submodel.get_train_op()
# Initialize variables.
self.session.run(tf.global_variables_initializer())
for layer in self.layers.values():
if layer.variable_values is not None:
variables = self.get_layer_variables(layer)
for var, val in zip(variables, layer.variable_values):
self.session.run(var.assign(val))
for layer in self.layers.values():
if layer.tensorboard:
self.tensorboard = True
tf.summary.scalar("loss", self.loss.out_tensor)
for layer in self.layers.values():
if layer.tensorboard:
tf.summary.tensor_summary(layer.name, layer.out_tensor)
if self.tensorboard:
writer = self._get_tf("FileWriter")
writer.add_graph(self._get_tf("Graph"))
writer.close()
# As a sanity check, make sure all tensors have the correct shape.
for layer in self.layers.values():
try:
assert list(layer.shape) == layer.out_tensor.get_shape(
).as_list(
), '%s: Expected shape %s does not match actual shape %s' % (
layer.name, layer.shape,
layer.out_tensor.get_shape().as_list())
except NotImplementedError:
pass
def _install_queue(self):
"""
"""
if not self.use_queue or self.queue_installed:
for layer in self.features + self.labels + self.task_weights:
layer.pre_queue = True
return
names = []
shapes = []
pre_q_inputs = []
q = InputFifoQueue(shapes, names, in_layers=pre_q_inputs)
q.name = "%s_%s" % (q.__class__.__name__, len(self.layers) + 1)
for layer in self.features + self.labels + self.task_weights:
pre_q_input = layer.create_pre_q(self.batch_size)
shapes.append(pre_q_input.shape)
names.append(pre_q_input.name)
pre_q_inputs.append(pre_q_input)
layer.in_layers.append(q)
self._add_layer(q)
self.input_queue = q
self.queue_installed = True
def set_loss(self, layer):
self._add_layer(layer)
self.loss = layer
def add_output(self, layer):
self._add_layer(layer)
self.outputs.append(layer)
def set_optimizer(self, optimizer):
"""Set the optimizer to use for fitting."""
self.optimizer = optimizer
def create_submodel(self, layers=None, loss=None, optimizer=None):
"""Create an alternate objective for training one piece of a TensorGraph.
A TensorGraph consists of a set of layers, and specifies a loss function and
optimizer to use for training those layers. Usually this is sufficient, but
there are cases where you want to train different parts of a model separately.
For example, a GAN consists of a generator and a discriminator. They are
trained separately, and they use different loss functions.
A submodel defines an alternate objective to use in cases like this. It may
optionally specify any of the following: a subset of layers in the model to
train; a different loss function; and a different optimizer to use. This
method creates a submodel, which you can then pass to fit() to use it for
training.
Parameters
----------
layers: list
the list of layers to train. If None, all layers in the model will be
trained.
loss: Layer
the loss function to optimize. If None, the model's main loss function
will be used.
optimizer: Optimizer
the optimizer to use for training. If None, the model's main optimizer
will be used.
Returns
-------
the newly created submodel, which can be passed to any of the fitting
methods.
"""
if self.built:
raise ValueError(
'Submodels must be created before build() is called.')
submodel = Submodel(self, layers, loss, optimizer)
self.submodels.append(submodel)
if loss is not None:
self._add_layer(loss)
return submodel
def get_pickling_errors(self, obj, seen=None):
if seen == None:
seen = []
try:
state = obj.__getstate__()
except AttributeError:
return
if state == None:
return
if isinstance(state, tuple):
if not isinstance(state[0], dict):
state = state[1]
else:
state = state[0].update(state[1])
result = {}
for i in state:
try:
pickle.dumps(state[i], protocol=2)
except pickle.PicklingError:
if not state[i] in seen:
seen.append(state[i])
result[i] = self.get_pickling_errors(state[i], seen)
return result
def save(self):
# Remove out_tensor from the object to be pickled
must_restore = False
tensor_objects = self.tensor_objects
rnn_initial_states = self.rnn_initial_states
rnn_final_states = self.rnn_final_states
rnn_zero_states = self.rnn_zero_states
session = self.session
self.tensor_objects = {}
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
self.session = None
out_tensors = []
if self.built:
must_restore = True
for layer in self.topsort():
out_tensors.append(layer.none_tensors())
training_placeholder = self._training_placeholder
self._training_placeholder = None
self.built = False
# Pickle itself
pickle_name = os.path.join(self.model_dir, "model.pickle")
with open(pickle_name, 'wb') as fout:
try:
pickle.dump(self, fout)
except Exception as e:
print(self.get_pickling_errors(self))
raise e
# add out_tensor back to everyone
if must_restore:
for index, layer in enumerate(self.topsort()):
layer.set_tensors(out_tensors[index])
self._training_placeholder = training_placeholder
self.built = True
self.tensor_objects = tensor_objects
self.rnn_initial_states = rnn_initial_states
self.rnn_final_states = rnn_final_states
self.rnn_zero_states = rnn_zero_states
self.session = session
def evaluate_generator(self,
feed_dict_generator,
metrics,
transformers=[],
labels=None,
outputs=None,
weights=[],
per_task_metrics=False):
if labels is None:
raise ValueError
n_tasks = len(self.outputs)
n_classes = self.outputs[0].out_tensor.get_shape()[-1].value
evaluator = GeneratorEvaluator(self,
feed_dict_generator,
transformers,
labels=labels,
outputs=outputs,
weights=weights,
n_tasks=n_tasks,
n_classes=n_classes)
if not per_task_metrics:
scores = evaluator.compute_model_performance(metrics)
return scores
else:
scores, per_task_scores = evaluator.compute_model_performance(
metrics, per_task_metrics=per_task_metrics)
return scores, per_task_scores
def get_layer_variables(self, layer):
"""Get the list of trainable variables in a layer of the graph."""
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
if layer.variable_scope == '':
return []
return tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES,
scope=layer.variable_scope)
def get_global_step(self):
return self._get_tf("GlobalStep")
def _get_tf(self, obj):
"""Fetches underlying TensorFlow primitives.
Parameters
----------
obj: str
If "Graph", returns tf.Graph instance. If "FileWriter", returns
tf.summary.FileWriter. If "Optimizer", returns the optimizer. If
"train_op", returns the train operation. If "summary_op", returns the
merged summary. If "GlobalStep" returns the global step.
Returns
-------
TensorFlow Object
"""
if obj in self.tensor_objects and self.tensor_objects[obj] is not None:
return self.tensor_objects[obj]
if obj == "Graph":
self.tensor_objects['Graph'] = tf.Graph()
elif obj == "FileWriter":
self.tensor_objects['FileWriter'] = tf.summary.FileWriter(
self.model_dir)
elif obj == 'Optimizer':
self.tensor_objects[
'Optimizer'] = self.optimizer._create_optimizer(
self._get_tf('GlobalStep'))
elif obj == 'train_op':
opt = self._get_tf('Optimizer')
global_step = self._get_tf('GlobalStep')
try:
self.tensor_objects['train_op'] = opt.minimize(
self.loss.out_tensor, global_step=global_step)
except ValueError:
# The loss doesn't depend on any variables.
self.tensor_objects['train_op'] = 0
elif obj == 'summary_op':
self.tensor_objects['summary_op'] = tf.summary.merge_all(
key=tf.GraphKeys.SUMMARIES)
elif obj == 'GlobalStep':
with self._get_tf("Graph").as_default():
self.tensor_objects['GlobalStep'] = tf.Variable(
0, trainable=False)
return self._get_tf(obj)
def save_checkpoint(self, max_checkpoints_to_keep=5):
"""Save a checkpoint to disk.
Usually you do not need to call this method, since fit() saves checkpoints
automatically. If you have disabled automatic checkpointing during fitting,
this can be called to manually write checkpoints.
Parameters
----------
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
"""
saver = tf.train.Saver(max_to_keep=max_checkpoints_to_keep)
saver.save(self.session, self.save_file, global_step=self.global_step)
def restore(self):
"""Reload the values of all variables from the most recent checkpoint file."""
if not self.built:
self.build()
last_checkpoint = tf.train.latest_checkpoint(self.model_dir)
if last_checkpoint is None:
raise ValueError('No checkpoint found')
with self._get_tf("Graph").as_default():
saver = tf.train.Saver()
saver.restore(self.session, last_checkpoint)
def get_num_tasks(self):
return len(self.outputs)
def get_pre_q_input(self, input_layer):
layer_name = input_layer.name
pre_q_name = "%s_pre_q" % layer_name
return self.layers[pre_q_name]
@staticmethod
def load_from_dir(model_dir):
pickle_name = os.path.join(model_dir, "model.pickle")
with open(pickle_name, 'rb') as fout:
tensorgraph = pickle.load(fout)
tensorgraph.built = False
tensorgraph.model_dir = model_dir
try:
tensorgraph.restore()
except ValueError:
pass # No checkpoint to load
return tensorgraph
def __del__(self):
pass
class TensorGraph(Model):
def __init__(self,
tensorboard=False,
tensorboard_log_frequency=100,
batch_size=100,
random_seed=None,
use_queue=True,
mode="regression",
graph=None,
learning_rate=0.001,
**kwargs):
"""
TODO(LESWING) allow a model to change its learning rate
Parameters
----------
tensorboard: bool
Should we log to model_dir data for tensorboard?
tensorboard_log_frequency: int
How many training batches before logging tensorboard?
batch_size: int
default batch size for training and evaluating
use_queue: boolean
if True when building we will create a tf.FIFO queue, which will hold
all features, weights, and labels. We will feed the inputs into this
queue in batches of self.batch_size in a separate thread from the
thread training the model. You cannot use a queue when
batches are not of consistent size
mode: str
"regression" or "classification". "classification" models on
predict will do an argmax(axis=2) to determine the class of the
prediction.
graph: tensorflow.Graph
the Graph in which to create Tensorflow objects. If None, a new Graph
is created.
learning_rate: float or LearningRateSchedule
the learning rate to use for optimization
kwargs
"""
# Layer Management
self.nxgraph = nx.DiGraph()
self.layers = dict()
self.features = list()
self.labels = list()
self.outputs = list()
self.task_weights = list()
self.loss = None
self.built = False
self.queue_installed = False
self.optimizer = Adam(
learning_rate=learning_rate, beta1=0.9, beta2=0.999, epsilon=1e-7)
# Singular place to hold Tensor objects which don't serialize
# These have to be reconstructed on restoring from pickle
# See TensorGraph._get_tf() for more details on lazy construction
self.tensor_objects = {
"FileWriter": None,
"Graph": graph,
"train_op": None,
"summary_op": None,
}
self.tensorboard = tensorboard
self.tensorboard_log_frequency = tensorboard_log_frequency
self.tensorboard_step = 0
self.mode = mode
self.global_step = 0
self.last_checkpoint = None
self.use_queue = use_queue
self.batch_size = batch_size
self.random_seed = random_seed
super(TensorGraph, self).__init__(**kwargs)
self.save_file = "%s/%s" % (self.model_dir, "model")
self.model_class = None
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
def _add_layer(self, layer):
if layer.name is None:
layer.name = "%s_%s" % (layer.__class__.__name__, len(self.layers) + 1)
if layer.name in self.layers:
return
if isinstance(layer, Feature):
self.features.append(layer)
if isinstance(layer, Label):
self.labels.append(layer)
if isinstance(layer, Weights):
self.task_weights.append(layer)
self.nxgraph.add_node(layer.name)
self.layers[layer.name] = layer
for in_layer in layer.in_layers:
self._add_layer(in_layer)
self.nxgraph.add_edge(in_layer.name, layer.name)
def fit(self,
dataset,
nb_epoch=10,
max_checkpoints_to_keep=5,
checkpoint_interval=1000):
return self.fit_generator(
self.default_generator(dataset, epochs=nb_epoch),
max_checkpoints_to_keep, checkpoint_interval)
def fit_generator(self,
feed_dict_generator,
max_checkpoints_to_keep=5,
checkpoint_interval=1000):
def create_feed_dict():
if self.use_queue:
while True:
yield {self._training_placeholder: 1.0}
for d in feed_dict_generator:
feed_dict = {k.out_tensor: v for k, v in six.iteritems(d)}
feed_dict[self._training_placeholder] = 1.0
yield feed_dict
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
time1 = time.time()
train_op = self._get_tf('train_op')
saver = tf.train.Saver(max_to_keep=max_checkpoints_to_keep)
with tf.Session() as sess:
self._initialize_weights(sess, saver)
avg_loss, n_batches = 0.0, 0.0
coord = tf.train.Coordinator()
n_samples = 0
if self.use_queue:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, feed_dict_generator, self._get_tf("Graph"), sess,
coord))
enqueue_thread.start()
output_tensors = [x.out_tensor for x in self.outputs]
fetches = output_tensors + [train_op, self.loss.out_tensor]
for feed_dict in create_feed_dict():
try:
fetched_values = sess.run(fetches, feed_dict=feed_dict)
loss = fetched_values[-1]
avg_loss += loss
n_batches += 1
self.global_step += 1
n_samples += 1
if self.tensorboard and n_samples % self.tensorboard_log_frequency == 0:
summary = sess.run(
self._get_tf("summary_op"), feed_dict=feed_dict)
self._log_tensorboard(summary)
except OutOfRangeError:
break
if self.global_step % checkpoint_interval == checkpoint_interval - 1:
saver.save(sess, self.save_file, global_step=self.global_step)
self.last_checkpoint = saver.last_checkpoints[-1]
avg_loss = float(avg_loss) / n_batches
print('Ending global_step %d: Average loss %g' % (self.global_step,
avg_loss))
avg_loss, n_batches = 0.0, 0.0
avg_loss = float(avg_loss) / n_batches
print('Ending global_step %d: Average loss %g' % (self.global_step,
avg_loss))
saver.save(sess, self.save_file, global_step=self.global_step)
self.last_checkpoint = saver.last_checkpoints[-1]
############################################################## TIMING
time2 = time.time()
print("TIMING: model fitting took %0.3f s" % (time2 - time1))
############################################################## TIMING
def _log_tensorboard(self, summary):
"""
TODO(LESWING) set epoch
Parameters
----------
Returns
-------
"""
global_step = int(self.global_step)
writer = self._get_tf("FileWriter")
writer.reopen()
writer.add_summary(summary, global_step=global_step)
writer.close()
def fit_on_batch(self, X, y, w):
if not self.built:
self.build()
dataset = NumpyDataset(X, y)
return self.fit(dataset, nb_epoch=1)
def default_generator(self,
dataset,
epochs=1,
predict=False,
pad_batches=True):
if len(self.features) > 1:
raise ValueError("More than one Feature, must use generator")
if len(self.labels) > 1:
raise ValueError("More than one Label, must use generator")
if len(self.task_weights) > 1:
raise ValueError("More than one Weights, must use generator")
for epoch in range(epochs):
for (X_b, y_b, w_b, ids_b) in dataset.iterbatches(
batch_size=self.batch_size,
deterministic=True,
pad_batches=pad_batches):
feed_dict = dict()
if len(self.labels) == 1 and y_b is not None and not predict:
feed_dict[self.labels[0]] = y_b
if len(self.features) == 1 and X_b is not None:
feed_dict[self.features[0]] = X_b
if len(self.task_weights) == 1 and w_b is not None and not predict:
feed_dict[self.task_weights[0]] = w_b
for (initial_state, zero_state) in zip(self.rnn_initial_states,
self.rnn_zero_states):
feed_dict[initial_state] = zero_state
yield feed_dict
def predict_on_generator(self, generator, transformers=[]):
"""Generates output predictions for the input samples,
processing the samples in a batched way.
# Arguments
x: the input data, as a Numpy array.
batch_size: integer.
verbose: verbosity mode, 0 or 1.
# Returns
A Numpy array of predictions.
"""
retval = self.predict_proba_on_generator(generator, transformers)
if self.mode == 'classification':
retval = np.expand_dims(from_one_hot(retval, axis=2), axis=1)
return retval
def predict_proba_on_generator(self, generator, transformers=[]):
"""
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
with tf.Session() as sess:
saver = tf.train.Saver()
self._initialize_weights(sess, saver)
out_tensors = [x.out_tensor for x in self.outputs]
results = []
for feed_dict in generator:
feed_dict = {
self.layers[k.name].out_tensor: v
for k, v in six.iteritems(feed_dict)
}
feed_dict[self._training_placeholder] = 0.0
result = np.array(sess.run(out_tensors, feed_dict=feed_dict))
if len(result.shape) == 3:
result = np.transpose(result, axes=[1, 0, 2])
result = undo_transforms(result, transformers)
results.append(result)
return np.concatenate(results, axis=0)
def bayesian_predict_on_batch(self, X, transformers=[], n_passes=4):
"""
Returns:
mu: numpy ndarray of shape (n_samples, n_tasks)
sigma: numpy ndarray of shape (n_samples, n_tasks)
"""
dataset = NumpyDataset(X=X, y=None, n_tasks=len(self.outputs))
y_ = []
for i in range(n_passes):
generator = self.default_generator(
dataset, predict=True, pad_batches=True)
y_.append(self.predict_on_generator(generator, transformers))
y_ = np.concatenate(y_, axis=2)
mu = np.mean(y_, axis=2)
sigma = np.std(y_, axis=2)
return mu, sigma
def predict_on_smiles_batch(self,
smiles,
featurizer,
n_tasks,
transformers=[]):
"""
# Returns:
A numpy ndarray of shape (n_samples, n_tasks)
"""
convmols = featurize_smiles_np(smiles, featurizer)
dataset = NumpyDataset(X=convmols, y=None, n_tasks=len(self.outputs))
generator = self.default_generator(dataset, predict=True, pad_batches=True)
return self.predict_on_generator(generator, transformers)
def predict_on_batch(self, X, sess=None, transformers=[]):
"""Generates output predictions for the input samples,
processing the samples in a batched way.
# Arguments
x: the input data, as a Numpy array.
batch_size: integer.
verbose: verbosity mode, 0 or 1.
# Returns
A Numpy array of predictions.
"""
dataset = NumpyDataset(X=X, y=None)
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers)
def predict_proba_on_batch(self, X, sess=None, transformers=[]):
dataset = NumpyDataset(X=X, y=None)
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_proba_on_generator(generator, transformers)
def predict(self, dataset, transformers=[], batch_size=None):
"""
Uses self to make predictions on provided Dataset object.
Returns:
y_pred: numpy ndarray of shape (n_samples,)
"""
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers)
def predict_proba(self, dataset, transformers=[], batch_size=None):
"""
TODO: Do transformers even make sense here?
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_proba_on_generator(generator, transformers)
def topsort(self):
return nx.topological_sort(self.nxgraph)
def build(self):
if self.built:
return
with self._get_tf("Graph").as_default():
self._training_placeholder = tf.placeholder(dtype=tf.float32, shape=())
if self.random_seed is not None:
tf.set_random_seed(self.random_seed)
self._install_queue()
order = self.topsort()
for node in order:
with tf.name_scope(node):
node_layer = self.layers[node]
node_layer.create_tensor(training=self._training_placeholder)
self.rnn_initial_states += node_layer.rnn_initial_states
self.rnn_final_states += node_layer.rnn_final_states
self.rnn_zero_states += node_layer.rnn_zero_states
node_layer.add_summary_to_tg()
self.built = True
for layer in self.layers.values():
if layer.tensorboard:
self.tensorboard = True
tf.summary.scalar("loss", self.loss.out_tensor)
for layer in self.layers.values():
if layer.tensorboard:
tf.summary.tensor_summary(layer.name, layer.out_tensor)
if self.tensorboard:
writer = self._get_tf("FileWriter")
writer.add_graph(self._get_tf("Graph"))
writer.close()
# As a sanity check, make sure all tensors have the correct shape.
for layer in self.layers.values():
try:
assert list(layer.shape) == layer.out_tensor.get_shape().as_list(
), '%s: Expected shape %s does not match actual shape %s' % (
layer.name, layer.shape, layer.out_tensor.get_shape().as_list())
except NotImplementedError:
pass
def _install_queue(self):
"""
"""
if not self.use_queue or self.queue_installed:
for layer in self.features + self.labels + self.task_weights:
layer.pre_queue = True
return
names = []
shapes = []
pre_q_inputs = []
q = InputFifoQueue(shapes, names, in_layers=pre_q_inputs)
q.name = "%s_%s" % (q.__class__.__name__, len(self.layers) + 1)
for layer in self.features + self.labels + self.task_weights:
pre_q_input = layer.create_pre_q(self.batch_size)
shapes.append(pre_q_input.shape)
names.append(pre_q_input.name)
pre_q_inputs.append(pre_q_input)
layer.in_layers.append(q)
self.nxgraph.add_edge(q.name, layer.name)
self._add_layer(q)
self.input_queue = q
self.queue_installed = True
def set_loss(self, layer):
self._add_layer(layer)
self.loss = layer
def add_output(self, layer):
self._add_layer(layer)
self.outputs.append(layer)
def set_optimizer(self, optimizer):
"""Set the optimizer to use for fitting."""
self.optimizer = optimizer
def get_pickling_errors(self, obj, seen=None):
if seen == None:
seen = []
try:
state = obj.__getstate__()
except AttributeError:
return
if state == None:
return
if isinstance(state, tuple):
if not isinstance(state[0], dict):
state = state[1]
else:
state = state[0].update(state[1])
result = {}
for i in state:
try:
pickle.dumps(state[i], protocol=2)
except pickle.PicklingError:
if not state[i] in seen:
seen.append(state[i])
result[i] = self.get_pickling_errors(state[i], seen)
return result
def save(self):
# Remove out_tensor from the object to be pickled
must_restore = False
tensor_objects = self.tensor_objects
rnn_initial_states = self.rnn_initial_states
rnn_final_states = self.rnn_final_states
rnn_zero_states = self.rnn_zero_states
self.tensor_objects = {}
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
out_tensors = []
if self.built:
must_restore = True
for node in self.topsort():
node_layer = self.layers[node]
out_tensors.append(node_layer.none_tensors())
optimizer = self.optimizer
self.optimizer = None
training_placeholder = self._training_placeholder
self._training_placeholder = None
self.built = False
# Pickle itself
pickle_name = os.path.join(self.model_dir, "model.pickle")
with open(pickle_name, 'wb') as fout:
try:
pickle.dump(self, fout)
except Exception as e:
print(self.get_pickling_errors(self))
raise e
# add out_tensor back to everyone
if must_restore:
for index, node in enumerate(self.topsort()):
node_layer = self.layers[node]
node_layer.set_tensors(out_tensors[index])
self._training_placeholder = training_placeholder
self.optimizer = optimizer
self.built = True
self.tensor_objects = tensor_objects
self.rnn_initial_states = rnn_initial_states
self.rnn_final_states = rnn_final_states
self.rnn_zero_states = rnn_zero_states
def evaluate_generator(self,
feed_dict_generator,
metrics,
transformers=[],
labels=None,
outputs=None,
weights=[],
per_task_metrics=False):
if labels is None:
raise ValueError
n_tasks = len(self.outputs)
n_classes = self.outputs[0].out_tensor.get_shape()[-1].value
evaluator = GeneratorEvaluator(
self,
feed_dict_generator,
transformers,
labels=labels,
outputs=outputs,
weights=weights,
n_tasks=n_tasks,
n_classes=n_classes)
if not per_task_metrics:
scores = evaluator.compute_model_performance(metrics)
return scores
else:
scores, per_task_scores = evaluator.compute_model_performance(
metrics, per_task_metrics=per_task_metrics)
return scores, per_task_scores
def get_layer_variables(self, layer):
"""Get the list of trainable variables in a layer of the graph."""
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
return tf.get_collection(
tf.GraphKeys.GLOBAL_VARIABLES, scope=layer.variable_scope)
def get_global_step(self):
return self._get_tf("GlobalStep")
def _get_tf(self, obj):
"""
TODO(LESWING) REALLY NEED TO DOCUMENT THIS
Parameters
----------
obj
Returns
-------
TensorFlow Object
"""
if obj in self.tensor_objects and self.tensor_objects[obj] is not None:
return self.tensor_objects[obj]
if obj == "Graph":
self.tensor_objects['Graph'] = tf.Graph()
elif obj == "FileWriter":
self.tensor_objects['FileWriter'] = tf.summary.FileWriter(self.model_dir)
elif obj == 'Optimizer':
self.tensor_objects['Optimizer'] = self.optimizer._create_optimizer(
self._get_tf('GlobalStep'))
elif obj == 'train_op':
self.tensor_objects['train_op'] = self._get_tf('Optimizer').minimize(
self.loss.out_tensor, global_step=self._get_tf('GlobalStep'))
elif obj == 'summary_op':
self.tensor_objects['summary_op'] = tf.summary.merge_all(
key=tf.GraphKeys.SUMMARIES)
elif obj == 'GlobalStep':
with self._get_tf("Graph").as_default():
self.tensor_objects['GlobalStep'] = tf.Variable(0, trainable=False)
return self._get_tf(obj)
def _initialize_weights(self, sess, saver):
"""
Parameters
----------
sess: tf.Session
The Session must be open
saver: tf.train.Saver
A saver object to save/restore checkpoints
Returns
-------
"""
if self.last_checkpoint is None:
sess.run(tf.global_variables_initializer())
saver.save(sess, self.save_file, global_step=self.global_step)
self.last_checkpoint = saver.last_checkpoints[-1]
else:
saver.restore(sess, self.last_checkpoint)
def get_num_tasks(self):
return len(self.outputs)
def get_pre_q_input(self, input_layer):
layer_name = input_layer.name
pre_q_name = "%s_pre_q" % layer_name
return self.layers[pre_q_name]
@staticmethod
def load_from_dir(model_dir):
pickle_name = os.path.join(model_dir, "model.pickle")
with open(pickle_name, 'rb') as fout:
tensorgraph = pickle.load(fout)
tensorgraph.built = False
return tensorgraph
def __del__(self):
pass
class TensorGraph(Model):
def __init__(self,
tensorboard=False,
tensorboard_log_frequency=100,
batch_size=100,
random_seed=None,
use_queue=True,
graph=None,
learning_rate=0.001,
configproto=None,
**kwargs):
"""
Parameters
----------
tensorboard: bool
Should we log to model_dir data for tensorboard?
tensorboard_log_frequency: int
How many training batches before logging tensorboard?
batch_size: int
default batch size for training and evaluating
use_queue: boolean
if True when building we will create a tf.FIFO queue, which will hold
all features, weights, and labels. We will feed the inputs into this
queue in batches of self.batch_size in a separate thread from the
thread training the model. You cannot use a queue when
batches are not of consistent size
graph: tensorflow.Graph
the Graph in which to create Tensorflow objects. If None, a new Graph
is created.
learning_rate: float or LearningRateSchedule
the learning rate to use for optimization
configproto: a tf.ConfigProto() object used to create tf.Session()
"""
# Layer Management
self.layers = dict()
self.features = list()
self.labels = list()
self.outputs = list()
self.variances = list()
self.task_weights = list()
self.submodels = list()
self.loss = Constant(0)
self.built = False
self.queue_installed = False
self.optimizer = Adam(
learning_rate=learning_rate, beta1=0.9, beta2=0.999, epsilon=1e-7)
self.configproto = configproto
# Singular place to hold Tensor objects which don't serialize
# These have to be reconstructed on restoring from pickle
# See TensorGraph._get_tf() for more details on lazy construction
self.tensor_objects = {
"FileWriter": None,
"Graph": graph,
"train_op": None,
"summary_op": None,
}
self.tensorboard = tensorboard
self.tensorboard_log_frequency = tensorboard_log_frequency
self.tensorboard_step = 0
self.global_step = 0
self.use_queue = use_queue
self.batch_size = batch_size
self.random_seed = random_seed
super(TensorGraph, self).__init__(**kwargs)
self.save_file = "%s/%s" % (self.model_dir, "model")
self.model_class = None
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
if self.use_queue and self.tensorboard:
raise ValueError(
"Currently TensorGraph cannot both use_queue and tensorboard at the same time"
)
def _add_layer(self, layer):
if layer.name is None:
layer.name = "%s_%s" % (layer.__class__.__name__, len(self.layers) + 1)
if layer.name in self.layers:
return
if isinstance(layer, Feature):
self.features.append(layer)
if isinstance(layer, Label):
self.labels.append(layer)
if isinstance(layer, Weights):
self.task_weights.append(layer)
self.layers[layer.name] = layer
for in_layer in layer.in_layers:
self._add_layer(in_layer)
def fit(self,
dataset,
nb_epoch=10,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
deterministic=False,
restore=False,
submodel=None,
**kwargs):
"""Train this model on a dataset.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
deterministic: bool
if True, the samples are processed in order. If False, a different random
order is used for each epoch.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
"""
return self.fit_generator(
self.default_generator(
dataset, epochs=nb_epoch, deterministic=deterministic),
max_checkpoints_to_keep, checkpoint_interval, restore, submodel)
def fit_generator(self,
feed_dict_generator,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
restore=False,
submodel=None):
"""Train this model on data from a generator.
Parameters
----------
feed_dict_generator: generator
this should generate batches, each represented as a dict that maps
Layers to values.
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
Returns
-------
the average loss over the most recent checkpoint interval
"""
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
time1 = time.time()
loss = self.loss
if submodel is not None and submodel.loss is not None:
loss = submodel.loss
if tfe.in_eager_mode():
# In eager mode we want an optimizer and a function to compute the
# gradient of the loss.
submodel_vars = None
if submodel is None:
optimizer = self._get_tf("Optimizer")
else:
optimizer = submodel.create_optimizer()
if submodel.layers is not None:
submodel_vars = set()
for layer in submodel.layers:
for var in layer.variables:
submodel_vars.add(var)
val_grad_fn = tfe.implicit_value_and_gradients(
lambda x: self._run_graph([loss], x, True)[0])
else:
# In graph mode we want a training operation.
if submodel is None:
train_op = self._get_tf('train_op')
else:
train_op = submodel.get_train_op()
if checkpoint_interval > 0:
saver = tf.train.Saver(
self.get_variables(),
max_to_keep=max_checkpoints_to_keep,
save_relative_paths=True)
if restore:
self.restore()
avg_loss, n_averaged_batches = 0.0, 0.0
n_samples = 0
n_enqueued = [0]
final_sample = [None]
if self.queue_installed:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, feed_dict_generator, self._get_tf("Graph"),
self.session, n_enqueued, final_sample))
enqueue_thread.start()
for feed_dict in self._create_feed_dicts(feed_dict_generator, True):
if self.queue_installed:
# Don't let this thread get ahead of the enqueue thread, since if
# we try to read more batches than the total number that get queued,
# this thread will hang indefinitely.
while n_enqueued[0] <= n_samples:
if n_samples == final_sample[0]:
break
time.sleep(0)
if n_samples == final_sample[0]:
break
n_samples += 1
should_log = (self.tensorboard and
n_samples % self.tensorboard_log_frequency == 0)
if tfe.in_eager_mode():
value, grads_and_vars = val_grad_fn(feed_dict)
if submodel_vars is not None:
grads_and_vars = [
x for x in grads_and_vars if x[1] in submodel_vars
]
optimizer.apply_gradients(grads_and_vars)
avg_loss += value
else:
fetches = [train_op, loss.out_tensor]
if should_log:
fetches.append(self._get_tf("summary_op"))
fetched_values = self.session.run(fetches, feed_dict=feed_dict)
if should_log:
self._log_tensorboard(fetched_values[2])
avg_loss += fetched_values[1]
n_averaged_batches += 1
self.global_step += 1
if checkpoint_interval > 0 and self.global_step % checkpoint_interval == checkpoint_interval - 1:
saver.save(self.session, self.save_file, global_step=self.global_step)
avg_loss = float(avg_loss) / n_averaged_batches
logger.info('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
avg_loss, n_averaged_batches = 0.0, 0.0
if n_averaged_batches > 0:
avg_loss = float(avg_loss) / n_averaged_batches
if checkpoint_interval > 0:
if n_averaged_batches > 0:
logger.info('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
saver.save(self.session, self.save_file, global_step=self.global_step)
time2 = time.time()
logger.info("TIMING: model fitting took %0.3f s" % (time2 - time1))
return avg_loss
def _log_tensorboard(self, summary):
"""
TODO(LESWING) set epoch
Parameters
----------
Returns
-------
"""
global_step = int(self.global_step)
writer = self._get_tf("FileWriter")
writer.reopen()
writer.add_summary(summary, global_step=global_step)
writer.close()
def fit_on_batch(self, X, y, w, submodel=None):
if not self.built:
self.build()
dataset = NumpyDataset(X, y)
return self.fit(dataset, nb_epoch=1, submodel=submodel)
def default_generator(self,
dataset,
epochs=1,
predict=False,
deterministic=True,
pad_batches=True):
if len(self.features) > 1:
raise ValueError("More than one Feature, must use generator")
if len(self.labels) > 1:
raise ValueError("More than one Label, must use generator")
if len(self.task_weights) > 1:
raise ValueError("More than one Weights, must use generator")
for epoch in range(epochs):
for (X_b, y_b, w_b, ids_b) in dataset.iterbatches(
batch_size=self.batch_size,
deterministic=deterministic,
pad_batches=pad_batches):
feed_dict = dict()
if len(self.labels) == 1 and y_b is not None and not predict:
feed_dict[self.labels[0]] = y_b
if len(self.features) == 1 and X_b is not None:
feed_dict[self.features[0]] = X_b
if len(self.task_weights) == 1 and w_b is not None and not predict:
feed_dict[self.task_weights[0]] = w_b
for (initial_state, zero_state) in zip(self.rnn_initial_states,
self.rnn_zero_states):
feed_dict[initial_state] = zero_state
yield feed_dict
def __call__(self, *inputs, **kwargs):
"""Execute the model in eager mode to compute outputs as a function of inputs.
This is very similar to predict_on_batch(), except that it returns the outputs
as tensors rather than numpy arrays. That means you can compute the graph's
outputs, then do additional calculations based on them, and gradients will
be tracked correctly through the whole process.
Parameters
----------
inputs: tensors
the values to use for the model's features. The number of inputs must
exactly match the length of the model's `features` property. The values
may be tensors, numpy arrays, or anything else that can be converted to
tensors of the correct shape.
outputs: list of Layers
the output layers to compute. If this is omitted, self.outputs is used
(that is, all outputs that have been added by calling add_output()).
Returns
-------
The output tensors, or a list of tensors if multiple outputs were requested.
"""
if len(inputs) != len(self.features):
raise ValueError('Expected %d inputs, received %d' % len(self.features),
len(inputs))
# TODO Once we drop Python 2 support, turn outputs into a proper keyword arg
# instead of using the **kwargs hack.
if 'outputs' in kwargs:
outputs = kwargs['outputs']
else:
outputs = self.outputs
feed_dict = dict(zip(self.features, inputs))
results = self._run_graph(outputs, feed_dict, False)
if len(results) == 1:
return results[0]
return results
def _predict(self, generator, transformers, outputs, uncertainty):
"""
Predict outputs for data provided by a generator.
This is the private implementation of prediction. Do not call it directly.
Instead call one of the public prediction methods.
Parameters
----------
generator: Generator
Generator that constructs feed dictionaries for TensorGraph.
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs.
If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
uncertainty: bool
specifies whether this is being called as part of estimating uncertainty.
If True, it sets the training flag so that dropout will be enabled, and
returns the values of the uncertainty outputs.
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
if not self.built:
self.build()
if outputs is None:
outputs = self.outputs
elif not isinstance(outputs, collections.Sequence):
outputs = [outputs]
if uncertainty:
if len(self.variances) == 0:
raise ValueError('This model cannot compute uncertainties')
if len(self.variances) != len(outputs):
raise ValueError(
'The number of variances must exactly match the number of outputs')
tensors = outputs + self.variances
else:
tensors = outputs
with self._get_tf("Graph").as_default():
# Gather results for each output
results = [[] for out in tensors]
n_samples = 0
n_enqueued = [0]
final_sample = [None]
if self.queue_installed:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, generator, self._get_tf("Graph"), self.session,
n_enqueued, final_sample))
enqueue_thread.start()
for feed_dict in self._create_feed_dicts(generator, uncertainty):
if self.queue_installed:
# Don't let this thread get ahead of the enqueue thread, since if
# we try to read more batches than the total number that get queued,
# this thread will hang indefinitely.
while n_enqueued[0] <= n_samples:
if n_samples == final_sample[0]:
break
time.sleep(0)
if n_samples == final_sample[0]:
break
n_samples += 1
feed_results = self._run_graph(tensors, feed_dict, uncertainty)
if tfe.in_eager_mode():
feed_results = [f.numpy() for f in feed_results]
if len(feed_results) > 1:
if len(transformers):
raise ValueError("Does not support transformations "
"for multiple outputs.")
elif len(feed_results) == 1:
result = undo_transforms(feed_results[0], transformers)
feed_results = [result]
for ind, result in enumerate(feed_results):
results[ind].append(result)
final_results = []
for result_list in results:
final_results.append(np.concatenate(result_list, axis=0))
# If only one output, just return array
if len(final_results) == 1:
return final_results[0]
elif uncertainty:
return zip(final_results[:len(outputs)], final_results[len(outputs):])
else:
return final_results
def predict_on_generator(self, generator, transformers=[], outputs=None):
"""
Parameters
----------
generator: Generator
Generator that constructs feed dictionaries for TensorGraph.
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs.
If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
return self._predict(generator, transformers, outputs, False)
def predict_on_batch(self, X, transformers=[], outputs=None):
"""Generates predictions for input samples, processing samples in a batch.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
transformers: List
List of dc.trans.Transformers
Returns
-------
A Numpy array of predictions.
"""
dataset = NumpyDataset(X=X, y=None)
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_uncertainty_on_batch(self, X, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
dataset = NumpyDataset(X=X, y=None)
return self.predict_uncertainty(dataset, masks)
def predict(self, dataset, transformers=[], outputs=None):
"""
Uses self to make predictions on provided Dataset object.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs=self.outputs. If outputs is
a Layer/Tensor, then will evaluate and return as a single ndarray. If
outputs is a list of Layers/Tensors, will return a list of ndarrays.
Returns
-------
results: numpy ndarray or list of numpy ndarrays
"""
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_uncertainty(self, dataset, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
sum_pred = []
sum_sq_pred = []
sum_var = []
for i in range(masks):
generator = self.default_generator(
dataset, predict=True, pad_batches=False)
results = self._predict(generator, [], self.outputs, True)
if len(sum_pred) == 0:
for p, v in results:
sum_pred.append(p)
sum_sq_pred.append(p * p)
sum_var.append(v)
else:
for j, (p, v) in enumerate(results):
sum_pred[j] += p
sum_sq_pred[j] += p * p
sum_var[j] += v
output = []
std = []
for i in range(len(sum_pred)):
p = sum_pred[i] / masks
output.append(p)
std.append(np.sqrt(sum_sq_pred[i] / masks - p * p + sum_var[i] / masks))
if len(output) == 1:
return (output[0], std[0])
else:
return zip(output, std)
def topsort(self):
def add_layers_to_list(layer, sorted_layers):
if layer in sorted_layers:
return
for in_layer in layer.in_layers:
add_layers_to_list(in_layer, sorted_layers)
sorted_layers.append(layer)
sorted_layers = []
for l in self.features + self.labels + self.task_weights + self.outputs + self.variances:
add_layers_to_list(l, sorted_layers)
add_layers_to_list(self.loss, sorted_layers)
for submodel in self.submodels:
if submodel.loss is not None:
add_layers_to_list(submodel.loss, sorted_layers)
return sorted_layers
def build(self):
if self.built:
return
if tfe.in_eager_mode():
# In eager mode, we need to execute every layer once to ensure its variables
# have been created.
def build_layers(layer, tensors):
if layer in tensors:
return tensors[layer]
inputs = [build_layers(input, tensors) for input in layer.in_layers]
if isinstance(layer, Input):
# We can't execute Input layers in eager mode, since they would try
# to create placeholders. Instead create a tensor of the correct
# size and type.
shape = [1 if s is None else s for s in layer.shape]
tensor = tf.zeros(shape, layer.dtype)
else:
with tf.name_scope(layer.name):
tensor = layer.create_tensor(in_layers=inputs, set_tensors=False)
tensors[layer] = tensor
return tensor
tensors = {}
with self._get_tf("Graph").as_default():
# Build the layers.
build_layers(self.loss, tensors)
for output in self.outputs:
build_layers(output, tensors)
for variance in self.variances:
build_layers(variance, tensors)
for submodel in self.submodels:
build_layers(submodel.loss, tensors)
# Initialize variables.
for layer in self.layers.values():
if layer.variable_values is not None:
for var, val in zip(layer.variables, layer.variable_values):
var.assign(val)
self.session = None
self._training_placeholder = None
self.built = True
return
# In graph mode we need to create the computation graph.
with self._get_tf("Graph").as_default():
self._training_placeholder = tf.placeholder(dtype=tf.float32, shape=())
if self.random_seed is not None:
tf.set_random_seed(self.random_seed)
self._install_queue()
for layer in self.topsort():
with tf.name_scope(layer.name):
layer.create_tensor(training=self._training_placeholder)
self.rnn_initial_states += layer.rnn_initial_states
self.rnn_final_states += layer.rnn_final_states
self.rnn_zero_states += layer.rnn_zero_states
layer.add_summary_to_tg()
self.session = tf.Session(config=self.configproto)
self.built = True
# Ensure all training operators have been created.
self._get_tf('train_op')
for submodel in self.submodels:
train_op = submodel.get_train_op()
# Initialize variables.
self.session.run(tf.global_variables_initializer())
for layer in self.layers.values():
if layer.variable_values is not None:
variables = self.get_layer_variables(layer)
for var, val in zip(variables, layer.variable_values):
self.session.run(var.assign(val))
for layer in self.layers.values():
if layer.tensorboard:
self.tensorboard = True
tf.summary.scalar("loss", self.loss.out_tensor)
for layer in self.layers.values():
if layer.tensorboard:
tf.summary.tensor_summary(layer.name, layer.out_tensor)
if self.tensorboard:
writer = self._get_tf("FileWriter")
writer.add_graph(self._get_tf("Graph"))
writer.close()
# As a sanity check, make sure all tensors have the correct shape.
for layer in self.layers.values():
try:
assert list(layer.shape) == layer.out_tensor.get_shape().as_list(
), '%s: Expected shape %s does not match actual shape %s' % (
layer.name, layer.shape, layer.out_tensor.get_shape().as_list())
except NotImplementedError:
pass
def _install_queue(self):
"""
"""
if not self.use_queue or self.queue_installed:
for layer in self.features + self.labels + self.task_weights:
layer.pre_queue = True
return
inputs = self.features + self.labels + self.task_weights
if len(inputs) == 0:
return
names = []
shapes = []
pre_q_inputs = []
q = InputFifoQueue(shapes, names, in_layers=pre_q_inputs)
q.name = "%s_%s" % (q.__class__.__name__, len(self.layers) + 1)
for layer in inputs:
pre_q_input = layer.create_pre_q()
shapes.append(pre_q_input.shape)
names.append(pre_q_input.name)
pre_q_inputs.append(pre_q_input)
layer.in_layers.append(q)
self._add_layer(q)
self.input_queue = q
self.queue_installed = True
def set_loss(self, layer):
self._add_layer(layer)
self.loss = layer
def add_output(self, layer):
"""Add an output layer that can be computed by predict()"""
self._add_layer(layer)
self.outputs.append(layer)
def add_variance(self, layer):
"""Add a layer that computes the variance in an output.
If a model supports uncertainty, it must call add_variance() once for every
output. Each variance layer has the same shape as the corresponding output,
and each element computes an estimate of the variance from aleatoric
uncertainty in the corresponding element of the output.
In addition, if a model supports uncertainty it MUST use dropout on every
layer. Otherwise, the uncertainties it computes will be inaccurate.
"""
self._add_layer(layer)
self.variances.append(layer)
def set_optimizer(self, optimizer):
"""Set the optimizer to use for fitting."""
self.optimizer = optimizer
def create_submodel(self, layers=None, loss=None, optimizer=None):
"""Create an alternate objective for training one piece of a TensorGraph.
A TensorGraph consists of a set of layers, and specifies a loss function and
optimizer to use for training those layers. Usually this is sufficient, but
there are cases where you want to train different parts of a model separately.
For example, a GAN consists of a generator and a discriminator. They are
trained separately, and they use different loss functions.
A submodel defines an alternate objective to use in cases like this. It may
optionally specify any of the following: a subset of layers in the model to
train; a different loss function; and a different optimizer to use. This
method creates a submodel, which you can then pass to fit() to use it for
training.
Parameters
----------
layers: list
the list of layers to train. If None, all layers in the model will be
trained.
loss: Layer
the loss function to optimize. If None, the model's main loss function
will be used.
optimizer: Optimizer
the optimizer to use for training. If None, the model's main optimizer
will be used.
Returns
-------
the newly created submodel, which can be passed to any of the fitting
methods.
"""
if self.built:
raise ValueError('Submodels must be created before build() is called.')
submodel = Submodel(self, layers, loss, optimizer)
self.submodels.append(submodel)
if loss is not None:
self._add_layer(loss)
return submodel
def get_pickling_errors(self, obj, seen=None):
if seen == None:
seen = []
try:
state = obj.__getstate__()
except AttributeError:
return
if state == None:
return
if isinstance(state, tuple):
if not isinstance(state[0], dict):
state = state[1]
else:
state = state[0].update(state[1])
result = {}
for i in state:
try:
pickle.dumps(state[i], protocol=2)
except pickle.PicklingError:
if not state[i] in seen:
seen.append(state[i])
result[i] = self.get_pickling_errors(state[i], seen)
return result
def save(self):
# Remove out_tensor from the object to be pickled
must_restore = False
tensor_objects = self.tensor_objects
rnn_initial_states = self.rnn_initial_states
rnn_final_states = self.rnn_final_states
rnn_zero_states = self.rnn_zero_states
session = self.session
self.tensor_objects = {}
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
self.session = None
out_tensors = []
submodel_ops = []
if self.built:
must_restore = True
for layer in self.topsort():
out_tensors.append(layer.none_tensors())
for submodel in self.submodels:
submodel_ops.append(submodel._train_op)
submodel._train_op = None
training_placeholder = self._training_placeholder
self._training_placeholder = None
self.built = False
# Pickle itself
pickle_name = os.path.join(self.model_dir, "model.pickle")
with open(pickle_name, 'wb') as fout:
try:
pickle.dump(self, fout)
except Exception as e:
logger.info(self.get_pickling_errors(self))
raise e
# add out_tensor back to everyone
if must_restore:
for index, layer in enumerate(self.topsort()):
layer.set_tensors(out_tensors[index])
for submodel, op in zip(self.submodels, submodel_ops):
submodel._train_op = op
self._training_placeholder = training_placeholder
self.built = True
self.tensor_objects = tensor_objects
self.rnn_initial_states = rnn_initial_states
self.rnn_final_states = rnn_final_states
self.rnn_zero_states = rnn_zero_states
self.session = session
def evaluate_generator(self,
feed_dict_generator,
metrics,
transformers=[],
labels=None,
outputs=None,
weights=[],
per_task_metrics=False):
if labels is None:
raise ValueError
n_tasks = len(self.outputs)
n_classes = self.outputs[0].out_tensor.get_shape()[-1].value
evaluator = GeneratorEvaluator(
self,
feed_dict_generator,
transformers,
labels=labels,
outputs=outputs,
weights=weights,
n_tasks=n_tasks,
n_classes=n_classes)
if not per_task_metrics:
scores = evaluator.compute_model_performance(metrics)
return scores
else:
scores, per_task_scores = evaluator.compute_model_performance(
metrics, per_task_metrics=per_task_metrics)
return scores, per_task_scores
def get_layer_variables(self, layer):
"""Get the list of trainable variables in a layer of the graph."""
if tfe.in_eager_mode():
return layer.variables
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
if layer.variable_scope == '':
return []
return tf.get_collection(
tf.GraphKeys.TRAINABLE_VARIABLES, scope=layer.variable_scope)
def get_variables(self):
"""Get the list of all trainable variables in the graph."""
if not self.built:
self.build()
if tfe.in_eager_mode():
variables = []
for layer in self.layers.values():
variables += layer.variables
return variables
else:
with self._get_tf("Graph").as_default():
return tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)
def get_global_step(self):
return self._get_tf("GlobalStep")
def _get_tf(self, obj):
"""Fetches underlying TensorFlow primitives.
Parameters
----------
obj: str
If "Graph", returns tf.Graph instance. If "FileWriter", returns
tf.summary.FileWriter. If "Optimizer", returns the optimizer. If
"train_op", returns the train operation. If "summary_op", returns the
merged summary. If "GlobalStep" returns the global step.
Returns
-------
TensorFlow Object
"""
if obj in self.tensor_objects and self.tensor_objects[obj] is not None:
return self.tensor_objects[obj]
if obj == "Graph":
self.tensor_objects['Graph'] = tf.Graph()
elif obj == "FileWriter":
self.tensor_objects['FileWriter'] = tf.summary.FileWriter(self.model_dir)
elif obj == 'Optimizer':
self.tensor_objects['Optimizer'] = self.optimizer._create_optimizer(
self._get_tf('GlobalStep'))
elif obj == 'train_op':
opt = self._get_tf('Optimizer')
global_step = self._get_tf('GlobalStep')
try:
self.tensor_objects['train_op'] = opt.minimize(
self.loss.out_tensor, global_step=global_step)
except ValueError:
# The loss doesn't depend on any variables.
self.tensor_objects['train_op'] = 0
elif obj == 'summary_op':
self.tensor_objects['summary_op'] = tf.summary.merge_all(
key=tf.GraphKeys.SUMMARIES)
elif obj == 'GlobalStep':
with self._get_tf("Graph").as_default():
self.tensor_objects['GlobalStep'] = create_variable(0, trainable=False)
return self._get_tf(obj)
def save_checkpoint(self, max_checkpoints_to_keep=5):
"""Save a checkpoint to disk.
Usually you do not need to call this method, since fit() saves checkpoints
automatically. If you have disabled automatic checkpointing during fitting,
this can be called to manually write checkpoints.
Parameters
----------
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
"""
saver = tf.train.Saver(
self.get_variables(), max_to_keep=max_checkpoints_to_keep)
saver.save(self.session, self.save_file, global_step=self.global_step)
def get_checkpoints(self):
"""Get a list of all available checkpoint files."""
return tf.train.get_checkpoint_state(
self.model_dir).all_model_checkpoint_paths
def restore(self, checkpoint=None):
"""Reload the values of all variables from a checkpoint file.
Parameters
----------
checkpoint: str
the path to the checkpoint file to load. If this is None, the most recent
checkpoint will be chosen automatically. Call get_checkpoints() to get a
list of all available checkpoints.
"""
if not self.built:
self.build()
if checkpoint is None:
checkpoint = tf.train.latest_checkpoint(self.model_dir)
if checkpoint is None:
raise ValueError('No checkpoint found')
with self._get_tf("Graph").as_default():
reader = NewCheckpointReader(checkpoint)
var_names = set([x for x in reader.get_variable_to_shape_map()])
var_list = []
for var in self.get_variables():
name = var.name
if ':' in name:
name = name[:name.rfind(':')]
if name in var_names:
var_list.append(var)
saver = tf.train.Saver(var_list=var_list)
saver.restore(self.session, checkpoint)
def get_num_tasks(self):
return len(self.outputs)
def get_pre_q_input(self, input_layer):
layer_name = input_layer.name
pre_q_name = "%s_pre_q" % layer_name
return self.layers[pre_q_name]
@staticmethod
def load_from_dir(model_dir, restore=True):
pickle_name = os.path.join(model_dir, "model.pickle")
with open(pickle_name, 'rb') as fout:
tensorgraph = pickle.load(fout)
tensorgraph.built = False
tensorgraph.model_dir = model_dir
if restore:
try:
tensorgraph.restore()
except ValueError:
pass # No checkpoint to load
return tensorgraph
def __del__(self):
pass
def _create_feed_dicts(self, generator, training):
"""Create feed dicts for use in fitting or prediction.
Parameters
----------
generator: Generator
the feed dict generator that was passed to fit_generator() or predict_on_generator()
training: bool
True during training, False during prediction
"""
train_value = 1.0 if training else 0.0
if self.queue_installed:
while True:
yield {self._training_placeholder: train_value}
else:
for d in generator:
feed_dict = {}
for key, value in d.items():
if isinstance(key, Input):
value = _ensure_value_shape(value, key)
if tfe.in_eager_mode():
value = tf.cast(value, key.dtype)
feed_dict[key] = value
else:
feed_dict[key] = value
if not tfe.in_eager_mode():
feed_dict[self._training_placeholder] = train_value
yield feed_dict
def _run_graph(self, outputs, feed_dict, training):
"""Run the calculations in the graph to compute some outputs.
In graph mode, this just calls session.run(). In eager mode, it executes
all required layers to compute the output.
Parameters
----------
outputs: list of Layers
the output layers to compute
feed_dict: dict
maps input layers to values
training: bool
whether this is being executed in training mode
"""
if not tfe.in_eager_mode():
return self.session.run(outputs, feed_dict)
def run_layers(layer, tensors):
if layer in tensors:
return tensors[layer]
inputs = [run_layers(input, tensors) for input in layer.in_layers]
tensor = layer.create_tensor(
in_layers=inputs, set_tensors=False, training=training)
tensors[layer] = tensor
return tensor
tensors = feed_dict.copy()
return [run_layers(o, tensors) for o in outputs]
def make_estimator(self,
feature_columns,
weight_column=None,
metrics={},
model_dir=None,
config=None):
"""Construct a Tensorflow Estimator from this model.
tf.estimator.Estimator is the standard Tensorflow API for representing models.
This method provides interoperability between DeepChem and other Tensorflow
based tools by allowing any model to be used an Estimator.
Once this method returns, the Estimator it created is independent of the model
it was created from. They do not share tensors, variables, save files, or any
other resources. The Estimator is a self contained object with its own methods
for training, evaluation, prediction, checkpointing, etc.
Parameters
----------
feature_columns: list of tf.feature_column objects
this describes the input features to the models. There must be one entry
for each Feature layer in this model's features field.
weight_column: tf.feature_column or None
if this model includes a Weights layer, this describes the input weights.
Otherwise, this should be None.
metrics: map
metrics that should be computed in calls to evaluate(). For each entry,
the key is the name to report for the metric, and the value is a function
of the form f(labels, predictions, weights) that returns the tensors for
computing the metric. Any of the functions in tf.metrics can be used, as
can other functions that satisfy the same interface.
model_dir: str
the directory in which the Estimator should save files. If None, this
defaults to the model's model_dir.
config: RunConfig
configuration options for the Estimator
"""
# Check the inputs.
if tfe.in_eager_mode():
raise ValueError('make_estimator() is not supported in eager mode')
if len(feature_columns) != len(self.features):
raise ValueError(
'This model requires %d feature column(s)' % len(self.features))
if len(self.labels) != 1:
raise ValueError(
'Can only create an Estimator from a model with exactly one Label input'
)
if len(self.task_weights) > 1:
raise ValueError(
'Cannot create an Estimator from a model with multiple Weight inputs')
if weight_column is None:
if len(self.task_weights) > 0:
raise ValueError('This model requires a weight column')
else:
if len(self.task_weights) == 0:
raise ValueError(
'Cannot specify weight_column for a model with no Weight inputs')
if model_dir is None:
model_dir = self.model_dir
# Define a function that recursively creates tensors from layers.
def create_tensors(layer, tensors, training):
if layer in tensors:
return tensors[layer]
inputs = [
create_tensors(in_layer, tensors, training)
for in_layer in layer.in_layers
]
tensor = layer.create_tensor(
in_layers=inputs, set_tensors=False, training=training)
tensors[layer] = tensor
layer.add_summary_to_tg(tensor)
return tensor
# Define the model function.
def model_fn(features, labels, mode):
# Define the inputs.
tensors = self.create_estimator_inputs(feature_columns, weight_column,
features, labels, mode)
for layer, tensor in tensors.items():
layer.add_summary_to_tg(tensor)
# Create the correct outputs, based on the mode.
if mode == tf.estimator.ModeKeys.PREDICT:
predictions = {}
for i, output in enumerate(self.outputs):
predictions[i] = create_tensors(output, tensors, 0)
return tf.estimator.EstimatorSpec(mode, predictions=predictions)
if mode == tf.estimator.ModeKeys.EVAL:
loss = create_tensors(self.loss, tensors, 0)
predictions = create_tensors(self.outputs[0], tensors, 0)
if len(self.task_weights) == 0:
weights = None
else:
weights = tensors[self.task_weights[0]]
eval_metric_ops = {}
for name, function in metrics.items():
eval_metric_ops[name] = function(tensors[self.labels[0]], predictions,
weights)
return tf.estimator.EstimatorSpec(
mode, loss=loss, eval_metric_ops=eval_metric_ops)
if mode == tf.estimator.ModeKeys.TRAIN:
loss = create_tensors(self.loss, tensors, 1)
global_step = tf.train.get_global_step()
optimizer = self.optimizer._create_optimizer(global_step)
train_op = optimizer.minimize(loss, global_step=global_step)
return tf.estimator.EstimatorSpec(mode, loss=loss, train_op=train_op)
raise ValueError('Unknown mode')
# Create the Estimator.
return tf.estimator.Estimator(
model_fn=model_fn, model_dir=model_dir, config=config)
def create_estimator_inputs(self, feature_columns, weight_column, features,
labels, mode):
"""This is called by make_estimator() to create tensors for the inputs.
feature_columns and weight_column are the arguments passed to
make_estimator(). features, labels, and mode are the arguments passed to
the estimator's model function. This method creates and returns a dict with
one entry for every Feature, Label, or Weights layer in the graph. The keys
are the layers, and the values are the tensors that correspond to them.
Any subclass that overrides default_generator() must also override this
method.
"""
if self.__class__.default_generator != TensorGraph.default_generator:
raise ValueError(
"Class overrides default_generator() but not create_estimator_inputs()"
)
tensors = {}
for layer, column in zip(self.features, feature_columns):
tensors[layer] = tf.feature_column.input_layer(features, [column])
if weight_column is not None:
tensors[self.task_weights[0]] = tf.feature_column.input_layer(
features, [weight_column])
if labels is not None:
tensors[self.labels[0]] = tf.cast(labels, self.labels[0].dtype)
return tensors
class KerasModel(Model):
"""This is a DeepChem model implemented by a Keras model.
This class provides several advantages over using the Keras model's fitting
and prediction methods directly.
1. It provides better integration with the rest of DeepChem, such as direct
support for Datasets and Transformers.
2. It defines the loss in a more flexible way. In particular, Keras does not
support multidimensional weight matrices, which makes it impossible to
implement most multitask models with Keras.
3. It provides various additional features not found in the Keras Model class,
such as uncertainty prediction and saliency mapping.
The loss function for a model can be defined in two different ways. For
models that have only a single output and use a standard loss function, you
can simply provide a dc.models.losses.Loss object. This defines the loss for
each sample or sample/task pair. The result is automatically multiplied by
the weights and averaged over the batch. Any additional losses computed by
model layers, such as weight decay penalties, are also added.
For more complicated cases, you can instead provide a function that directly
computes the total loss. It must be of the form f(outputs, labels, weights),
taking the list of outputs from the model, the expected values, and any weight
matrices. It should return a scalar equal to the value of the loss function
for the batch. No additional processing is done to the result; it is up to
you to do any weighting, averaging, adding of penalty terms, etc.
You can optionally provide an output_types argument, which describes how to
interpret the model's outputs. This should be a list of strings, one for each
output. Each entry must have one of the following values:
- 'prediction': This is a normal output, and will be returned by predict().
If output types are not specified, all outputs are assumed to be of this
type.
- 'loss': This output will be used in place of the normal outputs for
computing the loss function. For example, models that output probability
distributions usually do it by computing unbounded numbers (the logits),
then passing them through a softmax function to turn them into
probabilities. When computing the cross entropy, it is more numerically
stable to use the logits directly rather than the probabilities. You can
do this by having the model produce both probabilities and logits as
outputs, then specifying output_types=['prediction', 'loss']. When
predict() is called, only the first output (the probabilities) will be
returned. But during training, it is the second output (the logits) that
will be passed to the loss function.
- 'variance': This output is used for estimating the uncertainty in another
output. To create a model that can estimate uncertainty, there must be the
same number of 'prediction' and 'variance' outputs. Each variance output
must have the same shape as the corresponding prediction output, and each
element is an estimate of the variance in the corresponding prediction.
Also be aware that if a model supports uncertainty, it MUST use dropout on
every layer. Otherwise, the uncertainties it computes will be inaccurate.
"""
def __init__(self,
model,
loss,
output_types=None,
batch_size=100,
model_dir=None,
learning_rate=0.001,
optimizer=None,
tensorboard=False,
tensorboard_log_frequency=100,
**kwargs):
"""Create a new KerasModel.
Parameters
----------
model: tf.keras.Model
the Keras model implementing the calculation
loss: dc.models.losses.Loss or function
a Loss or function defining how to compute the training loss for each
batch, as described above
output_types: list of strings
the type of each output from the model, as described above
batch_size: int
default batch size for training and evaluating
model_dir: str
the directory on disk where the model will be stored. If this is None,
a temporary directory is created.
learning_rate: float or LearningRateSchedule
the learning rate to use for fitting. If optimizer is specified, this is
ignored.
optimizer: Optimizer
the optimizer to use for fitting. If this is specified, learning_rate is
ignored.
tensorboard: bool
whether to log progress to TensorBoard during training
tensorboard_log_frequency: int
the frequency at which to log data to TensorBoard, measured in batches
"""
super(KerasModel, self).__init__(
model_instance=model, model_dir=model_dir, **kwargs)
self.model = model
if isinstance(loss, Loss):
self._loss_fn = _StandardLoss(model, loss)
else:
self._loss_fn = loss
self.batch_size = batch_size
if optimizer is None:
self.optimizer = Adam(learning_rate=learning_rate)
else:
self.optimizer = optimizer
self.tensorboard = tensorboard
self.tensorboard_log_frequency = tensorboard_log_frequency
self._tensorboard_step = 0
if tensorboard and tf.executing_eagerly():
raise ValueError(
"Logging to TensorBoard is not currently supported in eager mode")
if output_types is None:
self._prediction_outputs = None
self._loss_outputs = None
self._variance_outputs = None
else:
self._prediction_outputs = []
self._loss_outputs = []
self._variance_outputs = []
for i, type in enumerate(output_types):
if type == 'prediction':
self._prediction_outputs.append(i)
elif type == 'loss':
self._loss_outputs.append(i)
elif type == 'variance':
self._variance_outputs.append(i)
else:
raise ValueError('Unknown output type "%s"' % type)
self._built = False
self._inputs_built = False
self._training_ops_built = False
self._initialized_vars = set()
def _ensure_built(self):
"""The first time this is called, create internal data structures."""
if self._built:
return
self._built = True
if not tf.executing_eagerly():
self.session = tf.Session()
self._global_step = tf.Variable(0, trainable=False)
self._tf_optimizer = self.optimizer._create_optimizer(self._global_step)
self._checkpoint = tf.train.Checkpoint(
optimizer=self._tf_optimizer, model=self.model)
self._init_new_vars()
def _create_inputs(self, example_inputs):
"""The first time this is called, create tensors representing the inputs and outputs."""
if self._inputs_built:
return
self._ensure_built()
self._inputs_built = True
if len(self.model.inputs) > 0:
self._input_dtypes = [t.dtype.as_numpy_dtype for t in self.model.inputs]
else:
self._input_dtypes = [
np.float32 if x.dtype == np.float64 else x.dtype
for x in example_inputs
]
if tf.executing_eagerly():
return
if len(self.model.inputs) > 0:
self._input_placeholders = self.model.inputs
else:
# The model doesn't specify inputs, so guess the input shapes based on the
# example batch.
input_shapes = [(None,) + i.shape[1:] for i in example_inputs]
self._input_placeholders = [
tf.placeholder(dtype=tf.as_dtype(t), shape=s)
for s, t in zip(input_shapes, self._input_dtypes)
]
if len(input_shapes) == 1:
self.model.build(input_shapes[0])
else:
self.model.build(input_shapes)
if len(self._input_placeholders) == 1:
self._output_tensors = self.model(
self._input_placeholders[0], training=False)
self._uncertainty_tensors = self.model(
self._input_placeholders[0], training=True)
else:
self._output_tensors = self.model(
self._input_placeholders, training=False)
self._uncertainty_tensors = self.model(
self._input_placeholders, training=True)
if isinstance(self._output_tensors, tf.Tensor):
self._output_tensors = [self._output_tensors]
if self._prediction_outputs is None:
self._prediction_outputs = list(range(len(self._output_tensors)))
self._loss_outputs = list(range(len(self._output_tensors)))
self._init_new_vars()
def _create_training_ops(self, example_batch):
"""The first time this is called, create tensors used in optimization."""
if self._training_ops_built:
return
self._create_inputs(example_batch[0])
self._training_ops_built = True
self._label_dtypes = [
np.float32 if x.dtype == np.float64 else x.dtype
for x in example_batch[1]
]
self._weights_dtypes = [
np.float32 if x.dtype == np.float64 else x.dtype
for x in example_batch[2]
]
if tf.executing_eagerly():
return
self._label_placeholders = [
tf.placeholder(dtype=tf.as_dtype(t), shape=x.shape)
for x, t in zip(example_batch[1], self._label_dtypes)
]
self._weights_placeholders = [
tf.placeholder(dtype=tf.as_dtype(t), shape=x.shape)
for x, t in zip(example_batch[2], self._weights_dtypes)
]
self._loss_tensor = self._loss_fn(
[self._output_tensors[i] for i in self._loss_outputs],
self._label_placeholders, self._weights_placeholders)
try:
self._train_op = self._tf_optimizer.minimize(
self._loss_tensor, global_step=self._global_step)
except ValueError:
# The loss doesn't depend on any variables.
self._train_op = 0
if self.tensorboard:
self._summary_ops = tf.summary.scalar('loss', self._loss_tensor)
self._summary_writer = tf.summary.FileWriter(self.model_dir)
self._init_new_vars()
def _init_new_vars(self):
"""Initialize any new variables created since the last call to this method."""
if not tf.executing_eagerly():
vars = set(tf.global_variables())
new_vars = vars.difference(self._initialized_vars)
self.session.run(tf.variables_initializer(new_vars))
self._initialized_vars = vars
def fit(self,
dataset,
nb_epoch=10,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
deterministic=False,
restore=False):
"""Train this model on a dataset.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
deterministic: bool
if True, the samples are processed in order. If False, a different random
order is used for each epoch.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
"""
return self.fit_generator(
self.default_generator(
dataset, epochs=nb_epoch, deterministic=deterministic),
max_checkpoints_to_keep, checkpoint_interval, restore)
def fit_generator(self,
generator,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
restore=False):
"""Train this model on data from a generator.
Parameters
----------
generator: generator
this should generate batches, each represented as a tuple of the form
(inputs, labels, weights).
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
Returns
-------
the average loss over the most recent checkpoint interval
"""
self._ensure_built()
if restore:
self.restore()
if checkpoint_interval > 0:
manager = tf.train.CheckpointManager(self._checkpoint, self.model_dir,
max_checkpoints_to_keep)
avg_loss = 0.0
averaged_batches = 0
time1 = time.time()
# Main training loop.
for batch in generator:
self._create_training_ops(batch)
inputs, labels, weights = self._prepare_batch(batch)
self._tensorboard_step += 1
should_log = (
self.tensorboard and
self._tensorboard_step % self.tensorboard_log_frequency == 0)
if tf.executing_eagerly():
# In eager mode we execute the loss function, accumulating the gradients.
with tf.GradientTape() as tape:
outputs = self.model(inputs[0])
if isinstance(outputs, tf.Tensor):
outputs = [outputs]
if self._loss_outputs is not None:
outputs = [outputs[i] for i in self._loss_outputs]
loss = self._loss_fn(outputs, labels, weights)
avg_loss += loss
grads = tape.gradient(loss, self.model.trainable_variables)
self._tf_optimizer.apply_gradients(
zip(grads, self.model.trainable_variables))
tf.assign_add(self._global_step, 1)
current_step = self._global_step.numpy()
else:
# In graph mode we execute the training op.
fetches = [self._train_op, self._loss_tensor, self._global_step]
if should_log:
fetches.append(self._summary_ops)
feed_dict = dict(zip(self._input_placeholders, inputs))
feed_dict.update(dict(zip(self._label_placeholders, labels)))
feed_dict.update(dict(zip(self._weights_placeholders, weights)))
fetched_values = self.session.run(fetches, feed_dict=feed_dict)
avg_loss += fetched_values[1]
current_step = fetched_values[2]
if should_log:
self._summary_writer.reopen()
self._summary_writer.add_summary(
fetched_values[3], global_step=current_step)
self._summary_writer.close()
# Report progress and write checkpoints.
averaged_batches += 1
if checkpoint_interval > 0 and current_step % checkpoint_interval == checkpoint_interval - 1:
self._exec_with_session(lambda: manager.save())
avg_loss = float(avg_loss) / averaged_batches
print(
'Ending global_step %d: Average loss %g' % (current_step, avg_loss))
avg_loss = 0.0
averaged_batches = 0
# Report final results.
if checkpoint_interval > 0:
if averaged_batches > 0:
avg_loss = float(avg_loss) / averaged_batches
print(
'Ending global_step %d: Average loss %g' % (current_step, avg_loss))
self._exec_with_session(lambda: manager.save())
time2 = time.time()
print("TIMING: model fitting took %0.3f s" % (time2 - time1))
return avg_loss
def fit_on_batch(self, X, y, w):
"""Perform a single step of training.
Parameters
----------
X: ndarray
the inputs for the batch
y: ndarray
the labels for the batch
w: ndarray
the weights for the batch
"""
if not self.built:
self.build()
dataset = NumpyDataset(X, y, w)
return self.fit(dataset, nb_epoch=1)
def _predict(self, generator, transformers, uncertainty):
"""
Predict outputs for data provided by a generator.
This is the private implementation of prediction. Do not call it directly.
Instead call one of the public prediction methods.
Parameters
----------
generator: generator
this should generate batches, each represented as a tuple of the form
(inputs, labels, weights).
transformers: list of dc.trans.Transformers
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
uncertainty: bool
specifies whether this is being called as part of estimating uncertainty.
If True, it sets the training flag so that dropout will be enabled, and
returns the values of the uncertainty outputs.
Returns:
a NumPy array of the model produces a single output, or a list of arrays
if it produces multiple outputs
"""
results = None
variances = None
if uncertainty:
if self._variance_outputs is None or len(self._variance_outputs) == 0:
raise ValueError('This model cannot compute uncertainties')
if len(self._variance_outputs) != len(self._prediction_outputs):
raise ValueError(
'The number of variances must exactly match the number of outputs')
for batch in generator:
inputs, labels, weights = batch
self._create_inputs(inputs)
inputs, _, _ = self._prepare_batch((inputs, None, None))
if tf.executing_eagerly():
# In eager mode we invoke the model directly.
if len(inputs) == 1:
inputs = inputs[0]
outputs = self.model(inputs, training=uncertainty)
outputs = [t.numpy() for t in outputs]
else:
# In graph mode we execute the output tensors.
if uncertainty:
fetches = self._uncertainty_tensors
else:
fetches = self._output_tensors
feed_dict = dict(zip(self._input_placeholders, inputs))
outputs = self.session.run(fetches, feed_dict=feed_dict)
# Apply tranformers and record results.
if uncertainty:
var = [outputs[i] for i in self._variance_outputs]
if variances is None:
variances = var
else:
for i, t in enumerate(var):
variances[i].append(t)
if self._prediction_outputs is not None:
outputs = [outputs[i] for i in self._prediction_outputs]
if len(transformers) > 0:
if len(outputs) > 1:
raise ValueError(
"predict() does not support Transformers for models with multiple outputs."
)
elif len(outputs) == 1:
outputs = [undo_transforms(outputs[0], transformers)]
if results is None:
results = [outputs]
else:
for i, t in enumerate(outputs):
results[i].append(t)
# Concatenate arrays to create the final results.
final_results = []
final_variances = []
for r in results:
final_results.append(np.concatenate(r, axis=0))
if uncertainty:
for v in variances:
final_variances.append(np.concatenate(v, axis=0))
return zip(final_results, final_variances)
# If only one output, just return array
if len(final_results) == 1:
return final_results[0]
else:
return final_results
def predict_on_generator(self, generator, transformers=[]):
"""
Parameters
----------
generator: generator
this should generate batches, each represented as a tuple of the form
(inputs, labels, weights).
transformers: list of dc.trans.Transformers
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
Returns:
a NumPy array of the model produces a single output, or a list of arrays
if it produces multiple outputs
"""
return self._predict(generator, transformers, False)
def predict_on_batch(self, X, transformers=[]):
"""Generates predictions for input samples, processing samples in a batch.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
transformers: list of dc.trans.Transformers
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
Returns
-------
a NumPy array of the model produces a single output, or a list of arrays
if it produces multiple outputs
"""
dataset = NumpyDataset(X=X, y=None)
return self.predict(dataset, transformers)
def predict_uncertainty_on_batch(self, X, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
dataset = NumpyDataset(X=X, y=None)
return self.predict_uncertainty(dataset, masks)
def predict(self, dataset, transformers=[]):
"""
Uses self to make predictions on provided Dataset object.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
transformers: list of dc.trans.Transformers
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
Returns
-------
a NumPy array of the model produces a single output, or a list of arrays
if it produces multiple outputs
"""
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers)
def predict_uncertainty(self, dataset, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
sum_pred = []
sum_sq_pred = []
sum_var = []
for i in range(masks):
generator = self.default_generator(
dataset, predict=True, pad_batches=False)
results = self._predict(generator, [], True)
if len(sum_pred) == 0:
for p, v in results:
sum_pred.append(p)
sum_sq_pred.append(p * p)
sum_var.append(v)
else:
for j, (p, v) in enumerate(results):
sum_pred[j] += p
sum_sq_pred[j] += p * p
sum_var[j] += v
output = []
std = []
for i in range(len(sum_pred)):
p = sum_pred[i] / masks
output.append(p)
std.append(np.sqrt(sum_sq_pred[i] / masks - p * p + sum_var[i] / masks))
if len(output) == 1:
return (output[0], std[0])
else:
return zip(output, std)
def evaluate_generator(self,
generator,
metrics,
transformers=[],
per_task_metrics=False):
"""Evaluate the performance of this model on the data produced by a generator.
Parameters
----------
generator: generator
this should generate batches, each represented as a tuple of the form
(inputs, labels, weights).
metric: deepchem.metrics.Metric
Evaluation metric
transformers: list of dc.trans.Transformers
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
per_task_metrics: bool
If True, return per-task scores.
Returns
-------
dict
Maps tasks to scores under metric.
"""
evaluator = GeneratorEvaluator(self, generator, transformers)
return evaluator.compute_model_performance(metrics, per_task_metrics)
def compute_saliency(self, X):
"""Compute the saliency map for an input sample.
This computes the Jacobian matrix with the derivative of each output element
with respect to each input element. More precisely,
- If this model has a single output, it returns a matrix of shape
(output_shape, input_shape) with the derivatives.
- If this model has multiple outputs, it returns a list of matrices, one
for each output.
This method cannot be used on models that take multiple inputs.
Parameters
----------
X: ndarray
the input data for a single sample
Returns
-------
the Jacobian matrix, or a list of matrices
"""
input_shape = X.shape
X = np.reshape(X, [1] + list(X.shape))
self._create_inputs([X])
X, _, _ = self._prepare_batch((X, None, None))
if tf.executing_eagerly():
# In eager mode we use a GradientTape to compute gradients.
X = tf.constant(X)
with tf.GradientTape(
persistent=True, watch_accessed_variables=False) as tape:
tape.watch(X)
outputs = self.model(X)
if isinstance(outputs, tf.Tensor):
outputs = [outputs]
final_result = []
for output in outputs:
output_shape = tuple(output.shape.as_list()[1:])
output = tf.reshape(output, [-1])
result = []
for i in range(output.shape[0]):
result.append(tape.gradient(output[i], X))
final_result.append(
tf.reshape(tf.stack(result), output_shape + input_shape).numpy())
else:
# In graph mode we use tf.gradients().
def jacobian(y, x):
# Adapted from https://github.com/tensorflow/tensorflow/issues/675#issuecomment-319891923.
y = tf.reshape(tf.convert_to_tensor(y)[0], [-1])
n = y.shape[0]
loop_vars = [
tf.constant(0, tf.int32),
tf.TensorArray(tf.float32, size=n)
]
_, jacobian = tf.while_loop(
lambda j, _: j < n,
lambda j, result: (j + 1, result.write(j, tf.gradients(y[j], x))),
loop_vars)
return jacobian.stack()
grads = [
jacobian(self._output_tensors[i], self._input_placeholders[0])
for i in self._prediction_outputs
]
feed_dict = {self._input_placeholders[0]: X}
result = self.session.run(grads, feed_dict=feed_dict)
output_shapes = [
tuple(o.shape.as_list()[1:]) for o in self._output_tensors
]
final_result = [
x.reshape(s + input_shape) for x, s in zip(result, output_shapes)
]
if len(final_result) == 1:
return final_result[0]
return final_result
def _prepare_batch(self, batch):
inputs, labels, weights = batch
inputs = [
x if x.dtype == t else x.astype(t)
for x, t in zip(inputs, self._input_dtypes)
]
if labels is not None:
labels = [
x if x.dtype == t else x.astype(t)
for x, t in zip(labels, self._label_dtypes)
]
if weights is not None:
weights = [
x if x.dtype == t else x.astype(t)
for x, t in zip(weights, self._weights_dtypes)
]
return (inputs, labels, weights)
def default_generator(self,
dataset,
epochs=1,
predict=False,
deterministic=True,
pad_batches=True):
for epoch in range(epochs):
for (X_b, y_b, w_b, ids_b) in dataset.iterbatches(
batch_size=self.batch_size,
deterministic=deterministic,
pad_batches=pad_batches):
yield ([X_b], [y_b], [w_b])
def save_checkpoint(self, max_checkpoints_to_keep=5):
"""Save a checkpoint to disk.
Usually you do not need to call this method, since fit() saves checkpoints
automatically. If you have disabled automatic checkpointing during fitting,
this can be called to manually write checkpoints.
Parameters
----------
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
"""
self._ensure_built()
manager = tf.train.CheckpointManager(self._checkpoint, self.model_dir,
max_checkpoints_to_keep)
self._exec_with_session(lambda: manager.save())
def _exec_with_session(self, f):
if tf.executing_eagerly():
f()
else:
with self.session.as_default():
f()
def get_checkpoints(self):
"""Get a list of all available checkpoint files."""
return tf.train.get_checkpoint_state(
self.model_dir).all_model_checkpoint_paths
def restore(self, checkpoint=None):
"""Reload the values of all variables from a checkpoint file.
Parameters
----------
checkpoint: str
the path to the checkpoint file to load. If this is None, the most recent
checkpoint will be chosen automatically. Call get_checkpoints() to get a
list of all available checkpoints.
"""
if checkpoint is None:
checkpoint = tf.train.latest_checkpoint(self.model_dir)
if checkpoint is None:
raise ValueError('No checkpoint found')
if tf.executing_eagerly():
self._checkpoint.restore(checkpoint)
else:
self._checkpoint.restore(checkpoint).run_restore_ops(self.session)
class TensorGraph(Model):
def __init__(self,
tensorboard=False,
tensorboard_log_frequency=100,
batch_size=100,
random_seed=None,
use_queue=True,
graph=None,
learning_rate=0.001,
configproto=None,
**kwargs):
"""
Parameters
----------
tensorboard: bool
Should we log to model_dir data for tensorboard?
tensorboard_log_frequency: int
How many training batches before logging tensorboard?
batch_size: int
default batch size for training and evaluating
use_queue: boolean
if True when building we will create a tf.FIFO queue, which will hold
all features, weights, and labels. We will feed the inputs into this
queue in batches of self.batch_size in a separate thread from the
thread training the model. You cannot use a queue when
batches are not of consistent size
graph: tensorflow.Graph
the Graph in which to create Tensorflow objects. If None, a new Graph
is created.
learning_rate: float or LearningRateSchedule
the learning rate to use for optimization
configproto: a tf.ConfigProto() object used to create tf.Session()
"""
# Layer Management
self.layers = dict()
self.features = list()
self.labels = list()
self.outputs = list()
self.variances = list()
self.task_weights = list()
self.submodels = list()
self.loss = Constant(0)
self.built = False
self.queue_installed = False
self.optimizer = Adam(
learning_rate=learning_rate, beta1=0.9, beta2=0.999, epsilon=1e-7)
self.configproto = configproto
# Singular place to hold Tensor objects which don't serialize
# These have to be reconstructed on restoring from pickle
# See TensorGraph._get_tf() for more details on lazy construction
self.tensor_objects = {
"FileWriter": None,
"Graph": graph,
"train_op": None,
"summary_op": None,
}
self.tensorboard = tensorboard
self.tensorboard_log_frequency = tensorboard_log_frequency
self.tensorboard_step = 0
self.global_step = 0
self.use_queue = use_queue
self.batch_size = batch_size
self.random_seed = random_seed
super(TensorGraph, self).__init__(**kwargs)
self.save_file = "%s/%s" % (self.model_dir, "model")
self.model_class = None
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
if self.use_queue and self.tensorboard:
raise ValueError(
"Currently TensorGraph cannot both use_queue and tensorboard at the same time"
)
def _add_layer(self, layer):
if layer.name is None:
layer.name = "%s_%s" % (layer.__class__.__name__, len(self.layers) + 1)
if layer.name in self.layers:
return
if isinstance(layer, Feature):
self.features.append(layer)
if isinstance(layer, Label):
self.labels.append(layer)
if isinstance(layer, Weights):
self.task_weights.append(layer)
self.layers[layer.name] = layer
for in_layer in layer.in_layers:
self._add_layer(in_layer)
def fit(self,
dataset,
nb_epoch=10,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
deterministic=False,
restore=False,
submodel=None,
**kwargs):
"""Train this model on a dataset.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
deterministic: bool
if True, the samples are processed in order. If False, a different random
order is used for each epoch.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
"""
return self.fit_generator(
self.default_generator(
dataset, epochs=nb_epoch, deterministic=deterministic),
max_checkpoints_to_keep, checkpoint_interval, restore, submodel)
def fit_generator(self,
feed_dict_generator,
max_checkpoints_to_keep=5,
checkpoint_interval=1000,
restore=False,
submodel=None):
"""Train this model on data from a generator.
Parameters
----------
feed_dict_generator: generator
this should generate batches, each represented as a dict that maps
Layers to values.
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
checkpoint_interval: int
the frequency at which to write checkpoints, measured in training steps.
Set this to 0 to disable automatic checkpointing.
restore: bool
if True, restore the model from the most recent checkpoint and continue training
from there. If False, retrain the model from scratch.
submodel: Submodel
an alternate training objective to use. This should have been created by
calling create_submodel().
Returns
-------
the average loss over the most recent checkpoint interval
"""
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
time1 = time.time()
loss = self.loss
if submodel is not None and submodel.loss is not None:
loss = submodel.loss
if tfe.in_eager_mode():
# In eager mode we want an optimizer and a function to compute the
# gradient of the loss.
submodel_vars = None
if submodel is None:
optimizer = self._get_tf("Optimizer")
else:
optimizer = submodel.create_optimizer()
if submodel.layers is not None:
submodel_vars = set()
for layer in submodel.layers:
for var in layer.variables:
submodel_vars.add(var)
val_grad_fn = tfe.implicit_value_and_gradients(
lambda x: self._run_graph([loss], x, True)[0])
else:
# In graph mode we want a training operation.
if submodel is None:
train_op = self._get_tf('train_op')
else:
train_op = submodel.get_train_op()
if checkpoint_interval > 0:
saver = tf.train.Saver(
self.get_variables(),
max_to_keep=max_checkpoints_to_keep,
save_relative_paths=True)
if restore:
self.restore()
avg_loss, n_averaged_batches = 0.0, 0.0
n_samples = 0
n_enqueued = [0]
final_sample = [None]
if self.queue_installed:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, feed_dict_generator, self._get_tf("Graph"),
self.session, n_enqueued, final_sample))
enqueue_thread.start()
for feed_dict in self._create_feed_dicts(feed_dict_generator, True):
if self.queue_installed:
# Don't let this thread get ahead of the enqueue thread, since if
# we try to read more batches than the total number that get queued,
# this thread will hang indefinitely.
while n_enqueued[0] <= n_samples:
if n_samples == final_sample[0]:
break
time.sleep(0)
if n_samples == final_sample[0]:
break
n_samples += 1
should_log = (self.tensorboard and
n_samples % self.tensorboard_log_frequency == 0)
if tfe.in_eager_mode():
value, grads_and_vars = val_grad_fn(feed_dict)
if submodel_vars is not None:
grads_and_vars = [
x for x in grads_and_vars if x[1] in submodel_vars
]
optimizer.apply_gradients(grads_and_vars)
avg_loss += value
else:
fetches = [train_op, loss.out_tensor]
if should_log:
fetches.append(self._get_tf("summary_op"))
fetched_values = self.session.run(fetches, feed_dict=feed_dict)
if should_log:
self._log_tensorboard(fetched_values[2])
avg_loss += fetched_values[1]
n_averaged_batches += 1
self.global_step += 1
if checkpoint_interval > 0 and self.global_step % checkpoint_interval == checkpoint_interval - 1:
saver.save(self.session, self.save_file, global_step=self.global_step)
avg_loss = float(avg_loss) / n_averaged_batches
logger.info('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
avg_loss, n_averaged_batches = 0.0, 0.0
if n_averaged_batches > 0:
avg_loss = float(avg_loss) / n_averaged_batches
if checkpoint_interval > 0:
if n_averaged_batches > 0:
logger.info('Ending global_step %d: Average loss %g' %
(self.global_step, avg_loss))
saver.save(self.session, self.save_file, global_step=self.global_step)
time2 = time.time()
logger.info("TIMING: model fitting took %0.3f s" % (time2 - time1))
return avg_loss
def _log_tensorboard(self, summary):
"""
TODO(LESWING) set epoch
Parameters
----------
Returns
-------
"""
global_step = int(self.global_step)
writer = self._get_tf("FileWriter")
writer.reopen()
writer.add_summary(summary, global_step=global_step)
writer.close()
def fit_on_batch(self, X, y, w, submodel=None):
if not self.built:
self.build()
dataset = NumpyDataset(X, y)
return self.fit(dataset, nb_epoch=1, submodel=submodel)
def default_generator(self,
dataset,
epochs=1,
predict=False,
deterministic=True,
pad_batches=True):
if len(self.features) > 1:
raise ValueError("More than one Feature, must use generator")
if len(self.labels) > 1:
raise ValueError("More than one Label, must use generator")
if len(self.task_weights) > 1:
raise ValueError("More than one Weights, must use generator")
for epoch in range(epochs):
for (X_b, y_b, w_b, ids_b) in dataset.iterbatches(
batch_size=self.batch_size,
deterministic=deterministic,
pad_batches=pad_batches):
feed_dict = dict()
if len(self.labels) == 1 and y_b is not None and not predict:
feed_dict[self.labels[0]] = y_b
if len(self.features) == 1 and X_b is not None:
feed_dict[self.features[0]] = X_b
if len(self.task_weights) == 1 and w_b is not None and not predict:
feed_dict[self.task_weights[0]] = w_b
for (initial_state, zero_state) in zip(self.rnn_initial_states,
self.rnn_zero_states):
feed_dict[initial_state] = zero_state
yield feed_dict
def __call__(self, *inputs, **kwargs):
"""Execute the model in eager mode to compute outputs as a function of inputs.
This is very similar to predict_on_batch(), except that it returns the outputs
as tensors rather than numpy arrays. That means you can compute the graph's
outputs, then do additional calculations based on them, and gradients will
be tracked correctly through the whole process.
Parameters
----------
inputs: tensors
the values to use for the model's features. The number of inputs must
exactly match the length of the model's `features` property. The values
may be tensors, numpy arrays, or anything else that can be converted to
tensors of the correct shape.
outputs: list of Layers
the output layers to compute. If this is omitted, self.outputs is used
(that is, all outputs that have been added by calling add_output()).
Returns
-------
The output tensors, or a list of tensors if multiple outputs were requested.
"""
if len(inputs) != len(self.features):
raise ValueError('Expected %d inputs, received %d' % len(self.features),
len(inputs))
# TODO Once we drop Python 2 support, turn outputs into a proper keyword arg
# instead of using the **kwargs hack.
if 'outputs' in kwargs:
outputs = kwargs['outputs']
else:
outputs = self.outputs
feed_dict = dict(zip(self.features, inputs))
results = self._run_graph(outputs, feed_dict, False)
if len(results) == 1:
return results[0]
return results
def _predict(self, generator, transformers, outputs, uncertainty):
"""
Predict outputs for data provided by a generator.
This is the private implementation of prediction. Do not call it directly.
Instead call one of the public prediction methods.
Parameters
----------
generator: Generator
Generator that constructs feed dictionaries for TensorGraph.
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs.
If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
uncertainty: bool
specifies whether this is being called as part of estimating uncertainty.
If True, it sets the training flag so that dropout will be enabled, and
returns the values of the uncertainty outputs.
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
if not self.built:
self.build()
if outputs is None:
outputs = self.outputs
elif not isinstance(outputs, collections.Sequence):
outputs = [outputs]
if uncertainty:
if len(self.variances) == 0:
raise ValueError('This model cannot compute uncertainties')
if len(self.variances) != len(outputs):
raise ValueError(
'The number of variances must exactly match the number of outputs')
tensors = outputs + self.variances
else:
tensors = outputs
with self._get_tf("Graph").as_default():
# Gather results for each output
results = [[] for out in tensors]
n_samples = 0
n_enqueued = [0]
final_sample = [None]
if self.queue_installed:
enqueue_thread = threading.Thread(
target=_enqueue_batch,
args=(self, generator, self._get_tf("Graph"), self.session,
n_enqueued, final_sample))
enqueue_thread.start()
for feed_dict in self._create_feed_dicts(generator, uncertainty):
if self.queue_installed:
# Don't let this thread get ahead of the enqueue thread, since if
# we try to read more batches than the total number that get queued,
# this thread will hang indefinitely.
while n_enqueued[0] <= n_samples:
if n_samples == final_sample[0]:
break
time.sleep(0)
if n_samples == final_sample[0]:
break
n_samples += 1
feed_results = self._run_graph(tensors, feed_dict, uncertainty)
if tfe.in_eager_mode():
feed_results = [f.numpy() for f in feed_results]
if len(feed_results) > 1:
if len(transformers):
raise ValueError("Does not support transformations "
"for multiple outputs.")
elif len(feed_results) == 1:
result = undo_transforms(feed_results[0], transformers)
feed_results = [result]
for ind, result in enumerate(feed_results):
results[ind].append(result)
final_results = []
for result_list in results:
final_results.append(np.concatenate(result_list, axis=0))
# If only one output, just return array
if len(final_results) == 1:
return final_results[0]
elif uncertainty:
return zip(final_results[:len(outputs)], final_results[len(outputs):])
else:
return final_results
def predict_on_generator(self, generator, transformers=[], outputs=None):
"""
Parameters
----------
generator: Generator
Generator that constructs feed dictionaries for TensorGraph.
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs = self.outputs.
If outputs is a Layer/Tensor, then will evaluate and return as a
single ndarray. If outputs is a list of Layers/Tensors, will return a list
of ndarrays.
Returns:
y_pred: numpy ndarray of shape (n_samples, n_classes*n_tasks)
"""
return self._predict(generator, transformers, outputs, False)
def predict_on_batch(self, X, transformers=[], outputs=None):
"""Generates predictions for input samples, processing samples in a batch.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
transformers: List
List of dc.trans.Transformers
Returns
-------
A Numpy array of predictions.
"""
dataset = NumpyDataset(X=X, y=None)
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_uncertainty_on_batch(self, X, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
X: ndarray
the input data, as a Numpy array.
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
dataset = NumpyDataset(X=X, y=None)
return self.predict_uncertainty(dataset, masks)
def predict(self, dataset, transformers=[], outputs=None):
"""
Uses self to make predictions on provided Dataset object.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
transformers: list
List of dc.trans.Transformers.
outputs: object
If outputs is None, then will assume outputs=self.outputs. If outputs is
a Layer/Tensor, then will evaluate and return as a single ndarray. If
outputs is a list of Layers/Tensors, will return a list of ndarrays.
Returns
-------
results: numpy ndarray or list of numpy ndarrays
"""
generator = self.default_generator(dataset, predict=True, pad_batches=False)
return self.predict_on_generator(generator, transformers, outputs)
def predict_uncertainty(self, dataset, masks=50):
"""
Predict the model's outputs, along with the uncertainty in each one.
The uncertainty is computed as described in https://arxiv.org/abs/1703.04977.
It involves repeating the prediction many times with different dropout masks.
The prediction is computed as the average over all the predictions. The
uncertainty includes both the variation among the predicted values (epistemic
uncertainty) and the model's own estimates for how well it fits the data
(aleatoric uncertainty). Not all models support uncertainty prediction.
Parameters
----------
dataset: dc.data.Dataset
Dataset to make prediction on
masks: int
the number of dropout masks to average over
Returns
-------
for each output, a tuple (y_pred, y_std) where y_pred is the predicted
value of the output, and each element of y_std estimates the standard
deviation of the corresponding element of y_pred
"""
sum_pred = []
sum_sq_pred = []
sum_var = []
for i in range(masks):
generator = self.default_generator(
dataset, predict=True, pad_batches=False)
results = self._predict(generator, [], self.outputs, True)
if len(sum_pred) == 0:
for p, v in results:
sum_pred.append(p)
sum_sq_pred.append(p * p)
sum_var.append(v)
else:
for j, (p, v) in enumerate(results):
sum_pred[j] += p
sum_sq_pred[j] += p * p
sum_var[j] += v
output = []
std = []
for i in range(len(sum_pred)):
p = sum_pred[i] / masks
output.append(p)
std.append(np.sqrt(sum_sq_pred[i] / masks - p * p + sum_var[i] / masks))
if len(output) == 1:
return (output[0], std[0])
else:
return zip(output, std)
def topsort(self):
def add_layers_to_list(layer, sorted_layers):
if layer in sorted_layers:
return
for in_layer in layer.in_layers:
add_layers_to_list(in_layer, sorted_layers)
sorted_layers.append(layer)
sorted_layers = []
for l in self.features + self.labels + self.task_weights + self.outputs + self.variances:
add_layers_to_list(l, sorted_layers)
add_layers_to_list(self.loss, sorted_layers)
for submodel in self.submodels:
if submodel.loss is not None:
add_layers_to_list(submodel.loss, sorted_layers)
return sorted_layers
def build(self):
if self.built:
return
if tfe.in_eager_mode():
# In eager mode, we need to execute every layer once to ensure its variables
# have been created.
def build_layers(layer, tensors):
if layer in tensors:
return tensors[layer]
inputs = [build_layers(input, tensors) for input in layer.in_layers]
if isinstance(layer, Input):
# We can't execute Input layers in eager mode, since they would try
# to create placeholders. Instead create a tensor of the correct
# size and type.
shape = [1 if s is None else s for s in layer.shape]
tensor = tf.zeros(shape, layer.dtype)
else:
with tf.name_scope(layer.name):
tensor = layer.create_tensor(in_layers=inputs, set_tensors=False)
tensors[layer] = tensor
return tensor
tensors = {}
with self._get_tf("Graph").as_default():
# Build the layers.
build_layers(self.loss, tensors)
for output in self.outputs:
build_layers(output, tensors)
for variance in self.variances:
build_layers(variance, tensors)
for submodel in self.submodels:
build_layers(submodel.loss, tensors)
# Initialize variables.
for layer in self.layers.values():
if layer.variable_values is not None:
for var, val in zip(layer.variables, layer.variable_values):
var.assign(val)
self.session = None
self._training_placeholder = None
self.built = True
return
# In graph mode we need to create the computation graph.
with self._get_tf("Graph").as_default():
self._training_placeholder = tf.placeholder(dtype=tf.float32, shape=())
if self.random_seed is not None:
tf.set_random_seed(self.random_seed)
self._install_queue()
self.built = True
for layer in self.topsort():
with tf.name_scope(layer.name):
layer.create_tensor(training=self._training_placeholder)
self.rnn_initial_states += layer.rnn_initial_states
self.rnn_final_states += layer.rnn_final_states
self.rnn_zero_states += layer.rnn_zero_states
layer.add_summary_to_tg(layer.out_tensor,
self.get_layer_variables(layer))
self.session = tf.Session(config=self.configproto)
# Ensure all training operators have been created.
self._get_tf('train_op')
for submodel in self.submodels:
train_op = submodel.get_train_op()
# Initialize variables.
self.session.run(tf.global_variables_initializer())
for layer in self.layers.values():
if layer.variable_values is not None:
variables = self.get_layer_variables(layer)
for var, val in zip(variables, layer.variable_values):
self.session.run(var.assign(val))
for layer in self.layers.values():
if layer.tensorboard:
self.tensorboard = True
tf.summary.scalar("loss", self.loss.out_tensor)
for layer in self.layers.values():
if layer.tensorboard:
tf.summary.tensor_summary(layer.name, layer.out_tensor)
if self.tensorboard:
writer = self._get_tf("FileWriter")
writer.add_graph(self._get_tf("Graph"))
writer.close()
# As a sanity check, make sure all tensors have the correct shape.
for layer in self.layers.values():
try:
assert list(layer.shape) == layer.out_tensor.get_shape().as_list(
), '%s: Expected shape %s does not match actual shape %s' % (
layer.name, layer.shape, layer.out_tensor.get_shape().as_list())
except NotImplementedError:
pass
def _install_queue(self):
"""
"""
if not self.use_queue or self.queue_installed:
for layer in self.features + self.labels + self.task_weights:
layer.pre_queue = True
return
inputs = self.features + self.labels + self.task_weights
if len(inputs) == 0:
return
names = []
shapes = []
pre_q_inputs = []
q = InputFifoQueue(shapes, names, in_layers=pre_q_inputs)
q.name = "%s_%s" % (q.__class__.__name__, len(self.layers) + 1)
for layer in inputs:
pre_q_input = layer.create_pre_q()
shapes.append(pre_q_input.shape)
names.append(pre_q_input.name)
pre_q_inputs.append(pre_q_input)
layer.in_layers.append(q)
self._add_layer(q)
self.input_queue = q
self.queue_installed = True
def set_loss(self, layer):
self._add_layer(layer)
self.loss = layer
def add_output(self, layer):
"""Add an output layer that can be computed by predict()"""
self._add_layer(layer)
self.outputs.append(layer)
def add_variance(self, layer):
"""Add a layer that computes the variance in an output.
If a model supports uncertainty, it must call add_variance() once for every
output. Each variance layer has the same shape as the corresponding output,
and each element computes an estimate of the variance from aleatoric
uncertainty in the corresponding element of the output.
In addition, if a model supports uncertainty it MUST use dropout on every
layer. Otherwise, the uncertainties it computes will be inaccurate.
"""
self._add_layer(layer)
self.variances.append(layer)
def set_optimizer(self, optimizer):
"""Set the optimizer to use for fitting."""
self.optimizer = optimizer
def create_submodel(self, layers=None, loss=None, optimizer=None):
"""Create an alternate objective for training one piece of a TensorGraph.
A TensorGraph consists of a set of layers, and specifies a loss function and
optimizer to use for training those layers. Usually this is sufficient, but
there are cases where you want to train different parts of a model separately.
For example, a GAN consists of a generator and a discriminator. They are
trained separately, and they use different loss functions.
A submodel defines an alternate objective to use in cases like this. It may
optionally specify any of the following: a subset of layers in the model to
train; a different loss function; and a different optimizer to use. This
method creates a submodel, which you can then pass to fit() to use it for
training.
Parameters
----------
layers: list
the list of layers to train. If None, all layers in the model will be
trained.
loss: Layer
the loss function to optimize. If None, the model's main loss function
will be used.
optimizer: Optimizer
the optimizer to use for training. If None, the model's main optimizer
will be used.
Returns
-------
the newly created submodel, which can be passed to any of the fitting
methods.
"""
if self.built:
raise ValueError('Submodels must be created before build() is called.')
submodel = Submodel(self, layers, loss, optimizer)
self.submodels.append(submodel)
if loss is not None:
self._add_layer(loss)
return submodel
def get_pickling_errors(self, obj, seen=None):
if seen == None:
seen = []
try:
state = obj.__getstate__()
except AttributeError:
return
if state == None:
return
if isinstance(state, tuple):
if not isinstance(state[0], dict):
state = state[1]
else:
state = state[0].update(state[1])
result = {}
for i in state:
try:
pickle.dumps(state[i], protocol=2)
except pickle.PicklingError:
if not state[i] in seen:
seen.append(state[i])
result[i] = self.get_pickling_errors(state[i], seen)
return result
def save(self):
# Remove out_tensor from the object to be pickled
must_restore = False
tensor_objects = self.tensor_objects
rnn_initial_states = self.rnn_initial_states
rnn_final_states = self.rnn_final_states
rnn_zero_states = self.rnn_zero_states
session = self.session
self.tensor_objects = {}
self.rnn_initial_states = []
self.rnn_final_states = []
self.rnn_zero_states = []
self.session = None
out_tensors = []
submodel_ops = []
if self.built:
must_restore = True
for layer in self.topsort():
out_tensors.append(layer.none_tensors())
for submodel in self.submodels:
submodel_ops.append(submodel._train_op)
submodel._train_op = None
training_placeholder = self._training_placeholder
self._training_placeholder = None
self.built = False
# Pickle itself
pickle_name = os.path.join(self.model_dir, "model.pickle")
with open(pickle_name, 'wb') as fout:
try:
pickle.dump(self, fout)
except Exception as e:
logger.info(self.get_pickling_errors(self))
raise e
# add out_tensor back to everyone
if must_restore:
for index, layer in enumerate(self.topsort()):
layer.set_tensors(out_tensors[index])
for submodel, op in zip(self.submodels, submodel_ops):
submodel._train_op = op
self._training_placeholder = training_placeholder
self.built = True
self.tensor_objects = tensor_objects
self.rnn_initial_states = rnn_initial_states
self.rnn_final_states = rnn_final_states
self.rnn_zero_states = rnn_zero_states
self.session = session
def evaluate_generator(self,
feed_dict_generator,
metrics,
transformers=[],
labels=None,
outputs=None,
weights=[],
per_task_metrics=False):
if labels is None:
raise ValueError
n_tasks = len(self.outputs)
n_classes = self.outputs[0].out_tensor.get_shape()[-1].value
evaluator = GeneratorEvaluator(
self,
feed_dict_generator,
transformers,
labels=labels,
outputs=outputs,
weights=weights,
n_tasks=n_tasks,
n_classes=n_classes)
if not per_task_metrics:
scores = evaluator.compute_model_performance(metrics)
return scores
else:
scores, per_task_scores = evaluator.compute_model_performance(
metrics, per_task_metrics=per_task_metrics)
return scores, per_task_scores
def get_layer_variables(self, layer):
"""Get the list of trainable variables in a layer of the graph."""
if tfe.in_eager_mode():
return layer.variables
if not self.built:
self.build()
with self._get_tf("Graph").as_default():
if layer.variable_scope == '':
return []
return tf.get_collection(
tf.GraphKeys.TRAINABLE_VARIABLES, scope=layer.variable_scope)
def get_variables(self):
"""Get the list of all trainable variables in the graph."""
if not self.built:
self.build()
if tfe.in_eager_mode():
variables = []
for layer in self.layers.values():
variables += layer.variables
return variables
else:
with self._get_tf("Graph").as_default():
return tf.get_collection(tf.GraphKeys.TRAINABLE_VARIABLES)
def get_global_step(self):
return self._get_tf("GlobalStep")
def _get_tf(self, obj):
"""Fetches underlying TensorFlow primitives.
Parameters
----------
obj: str
If "Graph", returns tf.Graph instance. If "FileWriter", returns
tf.summary.FileWriter. If "Optimizer", returns the optimizer. If
"train_op", returns the train operation. If "summary_op", returns the
merged summary. If "GlobalStep" returns the global step.
Returns
-------
TensorFlow Object
"""
if obj in self.tensor_objects and self.tensor_objects[obj] is not None:
return self.tensor_objects[obj]
if obj == "Graph":
self.tensor_objects['Graph'] = tf.Graph()
elif obj == "FileWriter":
self.tensor_objects['FileWriter'] = tf.summary.FileWriter(self.model_dir)
elif obj == 'Optimizer':
self.tensor_objects['Optimizer'] = self.optimizer._create_optimizer(
self._get_tf('GlobalStep'))
elif obj == 'train_op':
opt = self._get_tf('Optimizer')
global_step = self._get_tf('GlobalStep')
try:
self.tensor_objects['train_op'] = opt.minimize(
self.loss.out_tensor, global_step=global_step)
except ValueError:
# The loss doesn't depend on any variables.
self.tensor_objects['train_op'] = 0
elif obj == 'summary_op':
self.tensor_objects['summary_op'] = tf.summary.merge_all(
key=tf.GraphKeys.SUMMARIES)
elif obj == 'GlobalStep':
with self._get_tf("Graph").as_default():
self.tensor_objects['GlobalStep'] = create_variable(0, trainable=False)
return self._get_tf(obj)
def save_checkpoint(self, max_checkpoints_to_keep=5):
"""Save a checkpoint to disk.
Usually you do not need to call this method, since fit() saves checkpoints
automatically. If you have disabled automatic checkpointing during fitting,
this can be called to manually write checkpoints.
Parameters
----------
max_checkpoints_to_keep: int
the maximum number of checkpoints to keep. Older checkpoints are discarded.
"""
saver = tf.train.Saver(
self.get_variables(), max_to_keep=max_checkpoints_to_keep)
saver.save(self.session, self.save_file, global_step=self.global_step)
def get_checkpoints(self):
"""Get a list of all available checkpoint files."""
return tf.train.get_checkpoint_state(
self.model_dir).all_model_checkpoint_paths
def restore(self, checkpoint=None):
"""Reload the values of all variables from a checkpoint file.
Parameters
----------
checkpoint: str
the path to the checkpoint file to load. If this is None, the most recent
checkpoint will be chosen automatically. Call get_checkpoints() to get a
list of all available checkpoints.
"""
if not self.built:
self.build()
if checkpoint is None:
checkpoint = tf.train.latest_checkpoint(self.model_dir)
if checkpoint is None:
raise ValueError('No checkpoint found')
with self._get_tf("Graph").as_default():
reader = NewCheckpointReader(checkpoint)
var_names = set([x for x in reader.get_variable_to_shape_map()])
var_list = []
for var in self.get_variables():
name = var.name
if ':' in name:
name = name[:name.rfind(':')]
if name in var_names:
var_list.append(var)
saver = tf.train.Saver(var_list=var_list)
saver.restore(self.session, checkpoint)
def get_num_tasks(self):
return len(self.outputs)
def get_pre_q_input(self, input_layer):
layer_name = input_layer.name
pre_q_name = "%s_pre_q" % layer_name
return self.layers[pre_q_name]
@staticmethod
def load_from_dir(model_dir, restore=True):
pickle_name = os.path.join(model_dir, "model.pickle")
with open(pickle_name, 'rb') as fout:
tensorgraph = pickle.load(fout)
tensorgraph.built = False
tensorgraph.model_dir = model_dir
if restore:
try:
tensorgraph.restore()
except ValueError:
pass # No checkpoint to load
return tensorgraph
def __del__(self):
pass
def _create_feed_dicts(self, generator, training):
"""Create feed dicts for use in fitting or prediction.
Parameters
----------
generator: Generator
the feed dict generator that was passed to fit_generator() or predict_on_generator()
training: bool
True during training, False during prediction
"""
train_value = 1.0 if training else 0.0
if self.queue_installed:
while True:
yield {self._training_placeholder: train_value}
else:
for d in generator:
feed_dict = {}
for key, value in d.items():
if isinstance(key, Input):
value = _ensure_value_shape(value, key)
if tfe.in_eager_mode():
value = tf.cast(value, key.dtype)
feed_dict[key] = value
else:
feed_dict[key] = value
if not tfe.in_eager_mode():
feed_dict[self._training_placeholder] = train_value
yield feed_dict
def _run_graph(self, outputs, feed_dict, training):
"""Run the calculations in the graph to compute some outputs.
In graph mode, this just calls session.run(). In eager mode, it executes
all required layers to compute the output.
Parameters
----------
outputs: list of Layers
the output layers to compute
feed_dict: dict
maps input layers to values
training: bool
whether this is being executed in training mode
"""
if not tfe.in_eager_mode():
return self.session.run(outputs, feed_dict)
def run_layers(layer, tensors):
if layer in tensors:
return tensors[layer]
inputs = [run_layers(input, tensors) for input in layer.in_layers]
tensor = layer.create_tensor(
in_layers=inputs, set_tensors=False, training=training)
tensors[layer] = tensor
return tensor
tensors = feed_dict.copy()
return [run_layers(o, tensors) for o in outputs]
def make_estimator(self,
feature_columns,
weight_column=None,
metrics={},
model_dir=None,
config=None):
"""Construct a Tensorflow Estimator from this model.
tf.estimator.Estimator is the standard Tensorflow API for representing models.
This method provides interoperability between DeepChem and other Tensorflow
based tools by allowing any model to be used an Estimator.
Once this method returns, the Estimator it created is independent of the model
it was created from. They do not share tensors, variables, save files, or any
other resources. The Estimator is a self contained object with its own methods
for training, evaluation, prediction, checkpointing, etc.
Parameters
----------
feature_columns: list of tf.feature_column objects
this describes the input features to the models. There must be one entry
for each Feature layer in this model's features field.
weight_column: tf.feature_column or None
if this model includes a Weights layer, this describes the input weights.
Otherwise, this should be None.
metrics: map
metrics that should be computed in calls to evaluate(). For each entry,
the key is the name to report for the metric, and the value is a function
of the form f(labels, predictions, weights) that returns the tensors for
computing the metric. Any of the functions in tf.metrics can be used, as
can other functions that satisfy the same interface.
model_dir: str
the directory in which the Estimator should save files. If None, this
defaults to the model's model_dir.
config: RunConfig
configuration options for the Estimator
"""
# Check the inputs.
if tfe.in_eager_mode():
raise ValueError('make_estimator() is not supported in eager mode')
if len(feature_columns) != len(self.features):
raise ValueError(
'This model requires %d feature column(s)' % len(self.features))
if len(self.labels) != 1:
raise ValueError(
'Can only create an Estimator from a model with exactly one Label input'
)
if len(self.task_weights) > 1:
raise ValueError(
'Cannot create an Estimator from a model with multiple Weight inputs')
if weight_column is None:
if len(self.task_weights) > 0:
raise ValueError('This model requires a weight column')
else:
if len(self.task_weights) == 0:
raise ValueError(
'Cannot specify weight_column for a model with no Weight inputs')
if model_dir is None:
model_dir = self.model_dir
# Define a function that recursively creates tensors from layers.
def create_tensors(layer, tensors, training):
if layer in tensors:
return tensors[layer]
inputs = [
create_tensors(in_layer, tensors, training)
for in_layer in layer.in_layers
]
tensor = layer.create_tensor(
in_layers=inputs, set_tensors=False, training=training)
tensors[layer] = tensor
vars = tf.get_collection(
tf.GraphKeys.TRAINABLE_VARIABLES, scope=layer.name)
layer.add_summary_to_tg(tensor, vars)
return tensor
# Define the model function.
def model_fn(features, labels, mode):
# Define the inputs.
tensors = self.create_estimator_inputs(feature_columns, weight_column,
features, labels, mode)
for layer, tensor in tensors.items():
layer.add_summary_to_tg(tensor, [])
# Create the correct outputs, based on the mode.
if mode == tf.estimator.ModeKeys.PREDICT:
predictions = {}
for i, output in enumerate(self.outputs):
predictions[i] = create_tensors(output, tensors, 0)
return tf.estimator.EstimatorSpec(mode, predictions=predictions)
if mode == tf.estimator.ModeKeys.EVAL:
loss = create_tensors(self.loss, tensors, 0)
predictions = create_tensors(self.outputs[0], tensors, 0)
if len(self.task_weights) == 0:
weights = None
else:
weights = tensors[self.task_weights[0]]
eval_metric_ops = {}
for name, function in metrics.items():
eval_metric_ops[name] = function(tensors[self.labels[0]], predictions,
weights)
return tf.estimator.EstimatorSpec(
mode, loss=loss, eval_metric_ops=eval_metric_ops)
if mode == tf.estimator.ModeKeys.TRAIN:
loss = create_tensors(self.loss, tensors, 1)
global_step = tf.train.get_global_step()
optimizer = self.optimizer._create_optimizer(global_step)
train_op = optimizer.minimize(loss, global_step=global_step)
return tf.estimator.EstimatorSpec(mode, loss=loss, train_op=train_op)
raise ValueError('Unknown mode')
# Create the Estimator.
return tf.estimator.Estimator(
model_fn=model_fn, model_dir=model_dir, config=config)
def create_estimator_inputs(self, feature_columns, weight_column, features,
labels, mode):
"""This is called by make_estimator() to create tensors for the inputs.
feature_columns and weight_column are the arguments passed to
make_estimator(). features, labels, and mode are the arguments passed to
the estimator's model function. This method creates and returns a dict with
one entry for every Feature, Label, or Weights layer in the graph. The keys
are the layers, and the values are the tensors that correspond to them.
Any subclass that overrides default_generator() must also override this
method.
"""
if self.__class__.default_generator != TensorGraph.default_generator:
raise ValueError(
"Class overrides default_generator() but not create_estimator_inputs()"
)
tensors = {}
for layer, column in zip(self.features, feature_columns):
tensors[layer] = tf.feature_column.input_layer(features, [column])
if weight_column is not None:
tensors[self.task_weights[0]] = tf.feature_column.input_layer(
features, [weight_column])
if labels is not None:
tensors[self.labels[0]] = tf.cast(labels, self.labels[0].dtype)
return tensors