def test_one_hot(self):
y = np.array([0, 0, 1, 0, 1, 1, 0])
y_hot = metrics.to_one_hot(y)
expected = np.array([[1, 0], [1, 0], [0, 1], [1, 0], [0, 1], [0, 1], [1,
0]])
yp = metrics.from_one_hot(y_hot)
assert np.array_equal(expected, y_hot)
assert np.array_equal(y, yp)
def test_one_hot(self):
y = np.array([0, 0, 1, 0, 1, 1, 0])
y_hot = metrics.to_one_hot(y)
expected = np.array([[1, 0], [1, 0], [0, 1], [1, 0], [0, 1], [0, 1],
[1, 0]])
yp = metrics.from_one_hot(y_hot)
assert np.array_equal(expected, y_hot)
assert np.array_equal(y, yp)
def test_one_hot(): """Test the one hot encoding.""" y = np.array([0, 0, 1, 0, 1, 1, 0]) y_hot = to_one_hot(y) expected = np.array([[1, 0], [1, 0], [0, 1], [1, 0], [0, 1], [0, 1], [1, 0]]) yp = from_one_hot(y_hot) assert np.array_equal(expected, y_hot) assert np.array_equal(y, yp)
def predict_on_batch(self, X, pad_batch=False):
"""Return model output for the provided input.
Restore(checkpoint) must have previously been called on this object.
Args:
dataset: dc.data.dataset object.
Returns:
Tuple of three numpy arrays with shape n_examples x n_tasks (x ...):
output: Model outputs.
labels: True labels.
weights: Example weights.
Note that the output and labels arrays may be more than 2D, e.g. for
classifier models that return class probabilities.
Raises:
AssertionError: If model is not in evaluation mode.
ValueError: If output and labels are not both 3D or both 2D.
"""
len_unpadded = len(X)
if pad_batch:
X = pad_features(self.batch_size, X)
if not self._restored_model:
self.restore()
with self.eval_graph.graph.as_default():
# run eval data through the model
n_tasks = self.n_tasks
output = []
start = time.time()
with self._get_shared_session(train=False).as_default():
feed_dict = self.construct_feed_dict(X)
data = self._get_shared_session(train=False).run(
self.eval_graph.output, feed_dict=feed_dict)
batch_output = np.asarray(data[:n_tasks], dtype=float)
# reshape to batch_size x n_tasks x ...
if batch_output.ndim == 3:
batch_output = batch_output.transpose((1, 0, 2))
elif batch_output.ndim == 2:
batch_output = batch_output.transpose((1, 0))
else:
raise ValueError(
'Unrecognized rank combination for output: %s' %
(batch_output.shape,))
output.append(batch_output)
outputs = np.array(from_one_hot(
np.squeeze(np.concatenate(output)), axis=-1))
outputs = np.copy(outputs)
outputs = np.reshape(outputs, (len(X), n_tasks))
outputs = outputs[:len_unpadded]
return outputs
def predict_on_batch(self, X, pad_batch=False):
"""Return model output for the provided input.
Restore(checkpoint) must have previously been called on this object.
Args:
dataset: dc.data.dataset object.
Returns:
Tuple of three numpy arrays with shape n_examples x n_tasks (x ...):
output: Model outputs.
labels: True labels.
weights: Example weights.
Note that the output and labels arrays may be more than 2D, e.g. for
classifier models that return class probabilities.
Raises:
AssertionError: If model is not in evaluation mode.
ValueError: If output and labels are not both 3D or both 2D.
"""
len_unpadded = len(X)
if pad_batch:
X = pad_features(self.batch_size, X)
if not self._restored_model:
self.restore()
with self.eval_graph.graph.as_default():
# run eval data through the model
n_tasks = self.n_tasks
output = []
with self._get_shared_session(train=False).as_default():
feed_dict = self.construct_feed_dict(X)
data = self._get_shared_session(train=False).run(
self.eval_graph.output, feed_dict=feed_dict)
batch_output = np.asarray(data[:n_tasks], dtype=float)
# reshape to batch_size x n_tasks x ...
if batch_output.ndim == 3:
batch_output = batch_output.transpose((1, 0, 2))
elif batch_output.ndim == 2:
batch_output = batch_output.transpose((1, 0))
else:
raise ValueError(
'Unrecognized rank combination for output: %s' %
(batch_output.shape,))
output.append(batch_output)
outputs = np.array(from_one_hot(
np.squeeze(np.concatenate(output)), axis=-1))
outputs = np.copy(outputs)
outputs = np.reshape(outputs, (len(X), n_tasks))
outputs = outputs[:len_unpadded]
return outputs
def predict_on_batch(self, X):
"""Return model output for the provided input.
Restore(checkpoint) must have previously been called on this object.
Args:
dataset: deepchem.datasets.dataset object.
Returns:
Tuple of three numpy arrays with shape num_examples x num_tasks (x ...):
output: Model outputs.
labels: True labels.
weights: Example weights.
Note that the output and labels arrays may be more than 2D, e.g. for
classifier models that return class probabilities.
Raises:
AssertionError: If model is not in evaluation mode.
ValueError: If output and labels are not both 3D or both 2D.
"""
if not self._restored_model:
self.restore()
with self.graph.as_default():
assert not model_ops.is_training()
self.require_attributes(['output'])
# run eval data through the model
num_tasks = self.num_tasks
output = []
start = time.time()
with self._get_shared_session().as_default():
feed_dict = self.construct_feed_dict(X)
data = self._get_shared_session().run(
self.output, feed_dict=feed_dict)
batch_output = np.asarray(data[:num_tasks], dtype=float)
# reshape to batch_size x num_tasks x ...
if batch_output.ndim == 3:
batch_output = batch_output.transpose((1, 0, 2))
elif batch_output.ndim == 2:
batch_output = batch_output.transpose((1, 0))
else:
raise ValueError(
'Unrecognized rank combination for output: %s' %
(batch_output.shape,))
output.append(batch_output)
outputs = np.array(from_one_hot(
np.squeeze(np.concatenate(output)), axis=-1))
return np.copy(outputs)
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_on_batch(self, X, sess=None):
"""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_batch(X, sess)
if self.mode == 'classification':
return from_one_hot(retval, axis=2)
return retval
def predict_on_batch(self, X, sess=None):
"""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_batch(X, sess)
if self.mode == 'classification':
return from_one_hot(retval, axis=2)
return retval
def predict_on_batch(self, X, pad_batch=False):
if pad_batch:
X = pad_features(self.batch_size, X)
if not self._restored_model:
self.restore()
with self.eval_graph.graph.as_default():
# run eval data through the model
n_tasks = self.n_tasks
output = []
start = time.time()
with self._get_shared_session(train=False).as_default():
feed_dict = self.construct_feed_dict(X)
data = self._get_shared_session(train=False).run(
self.eval_graph.output, feed_dict=feed_dict)
batch_output = np.asarray(data[:n_tasks], dtype=float)
# transfer 2D prediction tensor to 2D x n_classes(=2)
complimentary = np.ones(np.shape(batch_output))
complimentary = complimentary - batch_output
batch_output = np.squeeze(np.stack(arrays = [complimentary,
batch_output],
axis = 2))
# reshape to batch_size x n_tasks x ...
if batch_output.ndim == 3:
batch_output = batch_output.transpose((1, 0, 2))
elif batch_output.ndim == 2:
batch_output = batch_output.transpose((1, 0))
else:
raise ValueError(
'Unrecognized rank combination for output: %s' %
(batch_output.shape,))
output.append(batch_output)
outputs = np.array(from_one_hot(
np.squeeze(np.concatenate(output)), axis=-1))
return np.copy(outputs)
def predict_on_batch(self, X):
if self.pad_batches:
X = pad_features(self.batch_size, X)
if not self._restored_model:
self.restore()
with self.eval_graph.graph.as_default():
# run eval data through the model
n_tasks = self.n_tasks
output = []
start = time.time()
with self._get_shared_session(train=False).as_default():
feed_dict = self.construct_feed_dict(X)
data = self._get_shared_session(train=False).run(
self.eval_graph.output, feed_dict=feed_dict)
batch_output = np.asarray(data[:n_tasks], dtype=float)
# transfer 2D prediction tensor to 2D x n_classes(=2)
complimentary = np.ones(np.shape(batch_output))
complimentary = complimentary - batch_output
batch_output = np.squeeze(np.stack(arrays = [complimentary,
batch_output],
axis = 2))
# reshape to batch_size x n_tasks x ...
if batch_output.ndim == 3:
batch_output = batch_output.transpose((1, 0, 2))
elif batch_output.ndim == 2:
batch_output = batch_output.transpose((1, 0))
else:
raise ValueError(
'Unrecognized rank combination for output: %s' %
(batch_output.shape,))
output.append(batch_output)
outputs = np.array(from_one_hot(
np.squeeze(np.concatenate(output)), axis=-1))
return np.copy(outputs)
def predict_on_generator(self, generator, transformers=[]):
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_on_batch(self, X_batch):
X_batch = torch.autograd.Variable(torch.cuda.FloatTensor(X_batch))
outputs = self.forward(X_batch, training=False)
y_pred_batch = torch.stack(outputs, 1).data.cpu().numpy()[:]
y_pred_batch = from_one_hot(y_pred_batch, 2)
return y_pred_batch
def compute_model_performance(self,
metrics,
csv_out=None,
stats_out=None,
per_task_metrics=False,
no_r2=False,
no_concordance_index=False,
plot=False):
"""
Computes statistics of model on test data and saves results to csv.
Parameters
----------
metrics: list
List of dc.metrics.Metric objects
per_task_metrics: bool, optional
If true, return computed metric for each task on multitask dataset.
"""
self.model.build()
y = []
w = []
def generator_closure():
for feed_dict in self.generator:
y.append(feed_dict[self.label_keys[0]])
if len(self.weights) > 0:
w.append(feed_dict[self.weights[0]])
yield feed_dict
if not len(metrics):
return {}
else:
mode = metrics[0].mode
if mode == "classification":
y_pred = self.model.predict_proba_on_generator(generator_closure())
y = np.transpose(np.array(y), axes=[0, 2, 1, 3])
y = np.reshape(y, newshape=(-1, self.n_tasks, self.n_classes))
y = from_one_hot(y, axis=-1)
else:
y_pred = self.model.predict_proba_on_generator(generator_closure())
y = np.transpose(np.array(y), axes=[0, 2, 1, 3])
y = np.reshape(y, newshape=(-1, self.n_tasks))
y_pred = np.reshape(y_pred, newshape=(-1, self.n_tasks))
y_pred = self.model.predict_on_generator(generator_closure())
y = np.concatenate(y, axis=0)
multitask_scores = {}
all_task_scores = {}
y = undo_transforms(y, self.output_transformers)
y_pred = undo_transforms(y_pred, self.output_transformers)
if len(w) != 0:
w = np.array(w)
w = np.reshape(w, newshape=y.shape)
if csv_out is not None:
log("Saving predictions to %s" % csv_out, self.verbose)
self.output_predictions(y_pred, csv_out)
plot_finished = False
# Compute multitask metrics
for i, metric in enumerate(metrics):
mtc_name = metric.metric.__name__
if no_r2 and (mtc_name == 'r2_score'
or mtc_name == 'pearson_r2_score'):
continue
if per_task_metrics:
if self.is_training_set:
if no_concordance_index and metric.metric.__name__ == "concordance_index":
multitask_scores[metric.name] = None
all_task_scores[metric.name] = None
continue
if plot and not plot_finished:
multitask_scores[
metric.
name], computed_metrics = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=True,
n_classes=self.n_classes,
plot=True,
all_metrics=metrics,
is_training_set=self.is_training_set,
no_concordance_index=no_concordance_index,
tasks=self.tasks,
model_name=self.model_name)
all_task_scores[metric.name] = computed_metrics
plot_finished = True
else:
multitask_scores[
metric.
name], computed_metrics = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=True,
n_classes=self.n_classes,
plot=False,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
all_task_scores[metric.name] = computed_metrics
elif plot and (i == len(metrics) - 1 or metric.metric.__name__
== "concordance_index") and (not plot_finished):
multitask_scores[
metric.name], computed_metrics = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=True,
n_classes=self.n_classes,
plot=True,
all_metrics=metrics,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
all_task_scores[metric.name] = computed_metrics
plot_finished = True
else: #Otherwise don't need to plot.
multitask_scores[
metric.name], computed_metrics = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=True,
n_classes=self.n_classes,
plot=False,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
all_task_scores[metric.name] = computed_metrics
else:
if self.is_training_set:
if no_concordance_index and metric.metric.__name__ == "concordance_index":
multitask_scores[metric.name] = None
continue
if plot and not plot_finished:
multitask_scores[metric.name] = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=False,
n_classes=self.n_classes,
plot=True,
all_metrics=metrics,
is_training_set=self.is_training_set,
no_concordance_index=no_concordance_index,
tasks=self.tasks,
model_name=self.model_name)
plot_finished = True
else:
multitask_scores[metric.name] = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=False,
n_classes=self.n_classes,
plot=False,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
elif plot and (i == len(metrics) - 1 or metric.metric.__name__
== "concordance_index") and (not plot_finished):
multitask_scores[metric.name] = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=False,
n_classes=self.n_classes,
plot=True,
all_metrics=metrics,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
plot_finished = True
else: #Otherwise don't need to plot.
multitask_scores[metric.name] = metric.compute_metric(
y,
y_pred,
w,
per_task_metrics=False,
n_classes=self.n_classes,
plot=False,
is_training_set=self.is_training_set,
tasks=self.tasks,
model_name=self.model_name)
if not per_task_metrics:
return multitask_scores
else:
return multitask_scores, all_task_scores
def compute_model_performance(self, metrics, per_task_metrics=False):
"""
Computes statistics of model on test data and saves results to csv.
Parameters
----------
metrics: list
List of dc.metrics.Metric objects
per_task_metrics: bool, optional
If true, return computed metric for each task on multitask dataset.
"""
self.model.build()
y = []
w = []
def generator_closure():
for feed_dict in self.generator:
labels = []
for layer in self.label_keys:
labels.append(feed_dict[layer])
del feed_dict[layer]
for weight in self.weights:
w.append(feed_dict[weight])
del feed_dict[weight]
y.append(np.array(labels))
yield feed_dict
if not len(metrics):
return {}
else:
mode = metrics[0].mode
if mode == "classification":
y_pred = self.model.predict_proba_on_generator(generator_closure())
y = np.transpose(np.array(y), axes=[0, 2, 1, 3])
y = np.reshape(y, newshape=(-1, self.n_tasks, self.n_classes))
y = from_one_hot(y, axis=-1)
else:
y_pred = self.model.predict_proba_on_generator(generator_closure())
y = np.transpose(np.array(y), axes=[0, 2, 1, 3])
y = np.reshape(y, newshape=(-1, self.n_tasks))
y_pred = np.reshape(y_pred, newshape=(-1, self.n_tasks))
multitask_scores = {}
all_task_scores = {}
y = undo_transforms(y, self.output_transformers)
y_pred = undo_transforms(y_pred, self.output_transformers)
if len(w) != 0:
w = np.array(w)
w = np.reshape(w, newshape=y.shape)
# Compute multitask metrics
for metric in metrics:
if per_task_metrics:
multitask_scores[metric.name], computed_metrics = metric.compute_metric(
y, y_pred, w, per_task_metrics=True, n_classes=self.n_classes)
all_task_scores[metric.name] = computed_metrics
else:
multitask_scores[metric.name] = metric.compute_metric(
y, y_pred, w, per_task_metrics=False, n_classes=self.n_classes)
if not per_task_metrics:
return multitask_scores
else:
return multitask_scores, all_task_scores