def test_sequence_config():
"""Train, predict and evaluate on dummy data.
create: YES
Input args: Dataset
validation_set: YES
batch_size: None
"""
inputs = Array("x", np.random.random((100, 10)))
outputs = Array('y',
np.random.randint(2, size=(100, 1)),
conditions=['random'])
jseq = JangguSequence(inputs.data,
outputs.data,
batch_size=10,
as_dict=False)
assert len(jseq) == 10
for x, y, _ in jseq:
assert x[0].shape == (10, 10)
assert y[0].shape == (10, 1)
break
jseq = JangguSequence(inputs, outputs, batch_size=10, as_dict=False)
assert len(jseq) == 10
for x, y, _ in jseq:
assert x[0].shape == (10, 10)
assert y[0].shape == (10, 1)
break
jseq = JangguSequence(inputs, outputs, batch_size=10, as_dict=True)
assert len(jseq) == 10
for x, y, _ in jseq:
assert x['x'].shape == (10, 10)
assert y['y'].shape == (10, 1)
break
def test_janggu_train_predict_sequence(tmpdir):
"""Train, predict and evaluate on dummy data.
create: YES
Input args: Dataset
validation_set: YES
batch_size: None
"""
os.environ['JANGGU_OUTPUT'] = tmpdir.strpath
inputs = {'x': Array("x", np.random.random((100, 10)))}
outputs = {
'y': Array('y',
np.random.randint(2, size=(100, 1)),
conditions=['random'])
}
jseq = JangguSequence(10, inputs, outputs)
@inputlayer
@outputdense('sigmoid')
def _model(inputs, inp, oup, params):
return inputs, inputs[0]
bwm = Janggu.create(_model,
inputs=jseq.inputs['x'],
outputs=jseq.outputs['y'],
name='nptest')
bwm.compile(optimizer='adadelta', loss='binary_crossentropy')
storage = bwm._storage_path(bwm.name, outputdir=tmpdir.strpath)
print('storage', storage)
print('env', os.environ['JANGGU_OUTPUT'])
print('name', bwm.name)
print('outputdir', bwm.outputdir)
assert not os.path.exists(storage)
bwm.fit(jseq, epochs=2, validation_data=jseq, use_multiprocessing=False)
assert os.path.exists(storage)
pred = bwm.predict(jseq, use_multiprocessing=False)
np.testing.assert_equal(len(pred[:, np.newaxis]), len(inputs['x']))
np.testing.assert_equal(pred.shape, outputs['y'].shape)
bwm.evaluate(jseq, use_multiprocessing=False)
def evaluate(self, inputs=None, outputs=None, # pylint: disable=too-many-locals
batch_size=None,
sample_weight=None,
steps=None,
datatags=None,
callbacks=None,
use_multiprocessing=False,
workers=1):
"""Evaluates the performance.
This method is used to evaluate a given model.
All of the parameters are directly delegated the
evalute_generator of the keras model.
See https://keras.io/models/model/#methods.
Parameters
----------
inputs : :code:`Dataset`, list(Dataset) or Sequence (keras.utils.Sequence)
Input Dataset or Sequence to use for evaluating the model.
outputs : :code:`Dataset`, list(Dataset) or None
Output Dataset containing the training targets. If a Sequence
is used for inputs, outputs will have no effect.
batch_size : int or None
Batch size. If set to None a batch size of 32 is used.
sample_weight : np.array or None
Sample weights. See https://keras.io.
steps : int, None.
Number of predict steps. If None, this value is determined from
the dataset size and the batch_size.
datatags : list(str) or None
Tags to annotate the evaluation results. Default: None.
callbacks : List(:code:`Scorer` or str)
Scorer instances to be applied on the predictions. Furthermore,
commonly used scoring metrics can be added by name, including
'roc', 'auroc', 'prc', 'auprc' for evaluating binary classification
applications and 'cor' (for Pearson's correlation), 'mae', 'mse'
and 'var_explained' for regression applications.
use_multiprocessing : boolean
Whether to use multiprocessing for the prediction. Default: False.
workers : int
Number of workers to use. Default: 1.
Examples
--------
.. code-block:: python
model.evaluate(DATA, LABELS)
# binary classification evaluation with callbacks
model.evaluate(DATA, LABELS, callcacks=['auprc', 'auroc'])
"""
self.logger.info('Evaluate: %s', self.name)
if isinstance(inputs, Sequence):
inputs_ = _convert_data(self.kerasmodel, inputs.inputs, 'input_layers')
outputs_ = _convert_data(self.kerasmodel, inputs.outputs, 'output_layers')
self.logger.info('Using custom Sequence.')
self.logger.info("Input:")
self.__dim_logging(inputs_)
self.logger.info("Output:")
self.__dim_logging(outputs_)
else:
inputs_ = _convert_data(self.kerasmodel, inputs, 'input_layers')
outputs_ = _convert_data(self.kerasmodel, outputs, 'output_layers')
self.logger.info("Input:")
self.__dim_logging(inputs_)
self.logger.info("Output:")
self.__dim_logging(outputs_)
self.timer = time.time()
if not batch_size:
batch_size = 32
if isinstance(inputs, Sequence):
jseq = inputs
else:
jseq = JangguSequence(batch_size, inputs_, outputs_, sample_weight)
try:
values = self.kerasmodel.evaluate_generator(
jseq,
steps=steps,
use_multiprocessing=use_multiprocessing,
workers=workers)
except Exception: # pragma: no cover
self.logger.exception('evaluate_generator failed:')
raise
self.logger.info('#' * 40)
values = _to_list(values)
for i, value in enumerate(values):
self.logger.info('%s: %f', self.kerasmodel.metrics_names[i], value)
self.logger.info('#' * 40)
self.logger.info("Evaluation finished in %1.3f s",
time.time() - self.timer)
preds = self.kerasmodel.predict_generator(jseq, steps=steps,
use_multiprocessing=use_multiprocessing,
workers=workers)
preds = _convert_data(self.kerasmodel, preds, 'output_layers')
for callback in callbacks or []:
callback = get_scorer(callback)
callback.score(self, preds, outputs=outputs_, datatags=datatags)
return values
def predict(self, inputs, # pylint: disable=too-many-locals
batch_size=None,
verbose=0,
steps=None,
layername=None,
datatags=None,
callbacks=None,
use_multiprocessing=False,
workers=1):
"""Performs a prediction.
This method predicts the targets.
All of the parameters are directly delegated the
predict_generator of the keras model.
See https://keras.io/models/model/#methods.
Parameters
----------
inputs : :code:`Dataset`, list(Dataset) or Sequence (keras.utils.Sequence)
Input Dataset or Sequence to use for fitting the model.
batch_size : int or None
Batch size. If set to None a batch size of 32 is used.
verbose : int
Verbosity level. See https://keras.io.
steps : int, None.
Number of predict steps. If None, this value is determined from
the dataset size and the batch_size.
layername : str or None
Layername for which the prediction should be performed. If None,
the output layer will be used automatically.
datatags : list(str) or None
Tags to annotate the evaluation results. Default: None.
callbacks : List(:code:`Scorer`)
Scorer instances to be applied on the predictions.
use_multiprocessing : boolean
Whether to use multiprocessing for the prediction. Default: False.
workers : int
Number of workers to use. Default: 1.
Examples
--------
.. code-block:: python
model.predict(DATA)
"""
if not isinstance(inputs, Sequence):
inputs = _convert_data(self.kerasmodel, inputs, 'input_layers')
self.logger.info('Predict: %s', self.name)
if isinstance(inputs, Sequence):
self.logger.info('using custom Sequence')
else:
self.logger.info("Input:")
self.__dim_logging(inputs)
self.timer = time.time()
# if a desired layername is specified, the features
# will be predicted.
if layername:
model = Janggu(self.kerasmodel.input,
self.kerasmodel.get_layer(layername).output,
name=self.name)
else:
model = self
if not batch_size:
batch_size = 32
if isinstance(inputs, Sequence):
jseq = inputs
else:
jseq = JangguSequence(batch_size, inputs, None, None)
try:
preds = model.kerasmodel.predict_generator(
jseq,
steps=steps,
use_multiprocessing=use_multiprocessing,
workers=workers,
verbose=verbose)
except Exception: # pragma: no cover
self.logger.exception('predict_generator failed:')
raise
prd = _convert_data(model.kerasmodel, preds, 'output_layers')
if layername is not None:
# no need to set an extra datatag.
# if layername is present, it will be added to the tags
if datatags is None:
datatags = [layername]
else:
datatags.append(layername)
for callback in callbacks or []:
callback.score(model, prd, datatags=datatags)
return preds
def fit(self, # pylint: disable=too-many-locals
inputs=None,
outputs=None,
batch_size=None,
epochs=1,
verbose=1,
callbacks=None,
validation_data=None,
shuffle=True,
class_weight=None,
sample_weight=None,
initial_epoch=0,
steps_per_epoch=None,
use_multiprocessing=False,
workers=1):
"""Model fitting.
This method is used to fit a given model.
Most of parameters are directly delegated the
fit_generator of the keras model.
Parameters
----------
inputs : :code:`Dataset`, list(Dataset) or Sequence (keras.utils.Sequence)
Input Dataset or Sequence to use for fitting the model.
outputs : :code:`Dataset`, list(Dataset) or None
Output Dataset containing the training targets. If a Sequence
is used for inputs, outputs will have no effect.
batch_size : int or None
Batch size. If set to None a batch size of 32 is used.
epochs : int
Number of epochs. Default: 1.
verbose : int
Verbosity level. See https://keras.io.
callbacks : List(keras.callbacks.Callback)
Callbacks to be applied during training. See https://keras.io/callbacks
validation_data : tuple, Sequence or None
Validation data can be a tuple (input_dataset, output_dataset),
or (input_dataset, output_dataset, sample_weights) or
a keras.utils.Sequence instance or a list of validation chromsomoes.
The latter choice only works with when using Cover and Bioseq dataset.
This allows you to train on a dedicated set of chromosomes
and to validate the performance on respective heldout chromosomes.
If None, validation is not applied.
shuffle : boolean
shuffle batches. Default: True.
class_weight : dict
Class weights. See https://keras.io.
sample_weight : np.array or None
Sample weights. See https://keras.io.
initial_epoch : int
Initial epoch at which to start training.
steps_per_epoch : int, None.
Number of steps per epoch. If None, this value is determined from
the dataset size and the batch_size.
use_multiprocessing : boolean
Whether to use multiprocessing. See https://keras.io. Default: False.
workers : int
Number of workers to use in multiprocessing mode. Default: 1.
Examples
--------
.. code-block:: python
model.fit(DATA, LABELS)
"""
if not isinstance(inputs, Sequence):
inputs = _convert_data(self.kerasmodel, inputs, 'input_layers')
outputs = _convert_data(self.kerasmodel, outputs, 'output_layers')
hyper_params = {
'epochs': epochs,
'batch_size': batch_size,
'shuffle': shuffle,
'class_weight': class_weight,
'initial_epoch': initial_epoch,
'steps_per_epoch': steps_per_epoch,
'use_multiprocessing': use_multiprocessing,
'workers': workers
}
self.logger.info('Fit: %s', self.name)
if isinstance(inputs, Sequence):
self.logger.info('using custom Sequence')
else:
self.logger.info("Input:")
self.__dim_logging(inputs)
self.logger.info("Output:")
self.__dim_logging(outputs)
self.timer = time.time()
history = None
self.logger.info("Hyper-parameters:")
for par_ in hyper_params:
self.logger.info('%s: %s', par_, str(hyper_params[par_]))
callbacks = [] if callbacks is None else callbacks
callbacks.append(LambdaCallback(on_epoch_end=lambda epoch, logs: self.logger.info(
"epoch %s: %s",
epoch + 1,
' '.join(["{}=".format(k) +
('{:.4f}' if
abs(logs[k]) > 1e-3
else '{:.4e}').format(logs[k]) for k in logs]))))
if not os.path.exists(os.path.join(self.outputdir, 'evaluation')):
os.mkdir(os.path.join(self.outputdir, 'evaluation'))
if not os.path.exists(os.path.join(self.outputdir, 'evaluation', self.name)):
os.mkdir(os.path.join(self.outputdir, 'evaluation', self.name))
callbacks.append(CSVLogger(os.path.join(self.outputdir,
'evaluation',
self.name,
'training.log')))
if not batch_size:
batch_size = 32
if isinstance(inputs, Sequence):
# input could be a sequence
jseq = inputs
else:
jseq = JangguSequence(batch_size, inputs, outputs, sample_weight, shuffle=shuffle)
if isinstance(validation_data, tuple):
valinputs = _convert_data(self.kerasmodel, validation_data[0],
'input_layers')
valoutputs = _convert_data(self.kerasmodel, validation_data[1],
'output_layers')
sweights = validation_data[2] if len(validation_data) == 3 else None
valjseq = JangguSequence(batch_size, valinputs, valoutputs, sweights, shuffle=False)
elif isinstance(validation_data, Sequence):
valjseq = validation_data
elif isinstance(validation_data, list) and isinstance(validation_data[0], str):
# if the validation data is a list of chromosomes that should
# be used as validation dataset we end up here.
# This is only possible, however, if all input and output datasets
# are Cover or Bioseq dataset.
if not all(hasattr(datum, 'gindexer') \
for datum in [jseq.inputs[k] for k in jseq.inputs] +
[jseq.outputs[k] for k in jseq.outputs]):
raise ValueError("Not all dataset are Cover or Bioseq dataset"
" which is required for this options.")
# then split the original dataset into training and validation set.
train, val = split_train_test((jseq.inputs, jseq.outputs), validation_data)
traininp, trainoup = train
valinp, valoup = val
self.logger.info("Split in training and validation set:")
self.logger.info("Training-Input:")
self.__dim_logging(traininp)
self.logger.info("Training-Output:")
self.__dim_logging(trainoup)
self.logger.info("Validation-Input:")
self.__dim_logging(valinp)
self.logger.info("Validation-Output:")
self.__dim_logging(valoup)
jseq = JangguSequence(jseq.batch_size,
_convert_data(self.kerasmodel, traininp,
'input_layers'),
_convert_data(self.kerasmodel, trainoup,
'output_layers'),
sample_weights=None, shuffle=jseq.shuffle)
valjseq = JangguSequence(jseq.batch_size,
_convert_data(self.kerasmodel, valinp,
'input_layers'),
_convert_data(self.kerasmodel, valoup,
'output_layers'),
sample_weights=None, shuffle=False)
else:
valjseq = None
try:
history = self.kerasmodel.fit_generator(
jseq,
epochs=epochs,
validation_data=valjseq,
class_weight=class_weight,
initial_epoch=initial_epoch,
shuffle=shuffle,
use_multiprocessing=use_multiprocessing,
max_queue_size=50,
workers=workers,
verbose=verbose,
callbacks=callbacks)
except Exception: # pragma: no cover
# ignore the linter warning, the exception
# is reraised anyways.
self.logger.exception('fit_generator failed:')
raise
self.logger.info('#' * 40)
for k in history.history:
self.logger.info('%s: %f', k, history.history[k][-1])
self.logger.info('#' * 40)
self.save()
self._save_hyper(hyper_params)
self.logger.info("Training finished after %1.3f s",
time.time() - self.timer)
return history
layer = Dense(1, activation='sigmoid')(layer)
# the last one is used to make the dimensionality compatible with
# the coverage dataset dimensions.
# Alternatively, the ReduceDim dataset wrapper may be used to transform
# the output to a 2D dataset object.
output = Reshape((1, 1, 1), name="peaks")(layer)
model = Model(xin, output)
model.compile(optimizer='adadelta',
loss='binary_crossentropy',
metrics=['acc'])
model.summary()
trainseq = JangguSequence(DNA, LABELS, batch_size=32)
valseq = JangguSequence(DNA_TEST, LABELS_TEST)
hist = model.fit(trainseq, epochs=500, validation_data=valseq)
print('#' * 40)
print('loss: {}, acc: {}'.format(hist.history['loss'][-1],
hist.history['acc'][-1]))
print('#' * 40)
# convert the prediction to a cover object
pred = model.predict(valseq)
cov_pred = Cover.create_from_array('BindingProba', pred, LABELS_TEST.gindexer)
print('Prediction score examples for Oct4')
for i in range(4):