def predict(self,
dataset: Dataset,
transformers: List[Transformer] = []) -> np.ndarray:
"""
Uses self to make predictions on provided Dataset object.
Parameters
----------
dataset: Dataset
Dataset to make prediction on
transformers: List[Transformer]
Transformers that the input data has been transformed by. The output
is passed through these transformers to undo the transformations.
Returns
-------
np.ndarray
A numpy array of predictions the model produces.
"""
y_preds = []
for (X_batch, _, _,
ids_batch) in dataset.iterbatches(deterministic=True):
n_samples = len(X_batch)
y_pred_batch = self.predict_on_batch(X_batch)
# Discard any padded predictions
y_pred_batch = y_pred_batch[:n_samples]
y_pred_batch = undo_transforms(y_pred_batch, transformers)
y_preds.append(y_pred_batch)
y_pred = np.concatenate(y_preds)
return y_pred
def fit(self, dataset: Dataset, nb_epoch: int = 10) -> float:
"""
Fits a model on data in a Dataset object.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
Returns
-------
float
The average loss over the most recent checkpoint interval.
"""
for epoch in range(nb_epoch):
logger.info("Starting epoch %s" % str(epoch + 1))
losses = []
for (X_batch, y_batch, w_batch,
ids_batch) in dataset.iterbatches():
losses.append(self.fit_on_batch(X_batch, y_batch, w_batch))
logger.info("Avg loss for epoch %d: %f" %
(epoch + 1, np.array(losses).mean()))
return np.array(losses).mean()
def predict(self,
dataset: Dataset,
transformers: List[Transformer] = []) -> OneOrMany[np.ndarray]:
"""
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
"""
y_preds = []
n_tasks = self.get_num_tasks()
ind = 0
for (X_batch, _, _,
ids_batch) in dataset.iterbatches(deterministic=True):
n_samples = len(X_batch)
y_pred_batch = self.predict_on_batch(X_batch)
# Discard any padded predictions
y_pred_batch = y_pred_batch[:n_samples]
y_pred_batch = undo_transforms(y_pred_batch, transformers)
y_preds.append(y_pred_batch)
y_pred = np.concatenate(y_preds)
return y_pred
def fit(self, dataset: Dataset, nb_epoch: int = 10) -> float:
"""
Fits a model on data in a Dataset object.
Parameters
----------
dataset: Dataset
the Dataset to train on
nb_epoch: int
the number of epochs to train for
Returns
-------
the average loss over the most recent epoch
"""
# TODO(rbharath/enf): We need a structured way to deal with potential GPU
# memory overflows.
for epoch in range(nb_epoch):
logger.info("Starting epoch %s" % str(epoch + 1))
losses = []
for (X_batch, y_batch, w_batch,
ids_batch) in dataset.iterbatches():
losses.append(self.fit_on_batch(X_batch, y_batch, w_batch))
logger.info("Avg loss for epoch %d: %f" %
(epoch + 1, np.array(losses).mean()))
return np.array(losses).mean()
def default_generator(
self,
dataset: Dataset,
epochs: int = 1,
mode: str = 'fit',
deterministic: bool = True,
pad_batches: bool = True) -> Iterable[Tuple[List, List, List]]:
"""Create a generator that iterates batches for a dataset.
Subclasses may override this method to customize how model inputs are
generated from the data.
Parameters
----------
dataset: Dataset
the data to iterate
epochs: int
the number of times to iterate over the full dataset
mode: str
allowed values are 'fit' (called during training), 'predict' (called
during prediction), and 'uncertainty' (called during uncertainty
prediction)
deterministic: bool
whether to iterate over the dataset in order, or randomly shuffle the
data for each epoch
pad_batches: bool
whether to pad each batch up to this model's preferred batch size
Returns
-------
a generator that iterates batches, each represented as a tuple of lists:
([inputs], [outputs], [weights])
"""
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 default_generator(
self,
dataset: Dataset,
epochs: int = 1,
mode: str = 'fit',
deterministic: bool = True,
pad_batches: bool = True) -> Iterable[Tuple[List, List, List]]:
"""Convert a dataset into the tensors needed for learning.
Parameters
----------
dataset: `dc.data.Dataset`
Dataset to convert
epochs: int, optional (Default 1)
Number of times to walk over `dataset`
mode: str, optional (Default 'fit')
Ignored in this implementation.
deterministic: bool, optional (Default True)
Whether the dataset should be walked in a deterministic fashion
pad_batches: bool, optional (Default True)
If true, each returned batch will have size `self.batch_size`.
Returns
-------
Iterator which walks over the batches
"""
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):
if y_b is not None:
if self.mode == 'classification':
y_b = to_one_hot(y_b.flatten(), self.n_classes).reshape(
-1, self.n_tasks, self.n_classes)
inputs = self.compute_features_on_batch(X_b)
yield (inputs, [y_b], [w_b])
def default_generator(
self,
dataset: Dataset,
epochs: int = 1,
mode: str = 'fit',
deterministic: bool = True,
pad_batches: bool = True) -> Iterable[Tuple[List, List, List]]:
"""Convert a dataset into the tensors needed for learning.
Parameters
----------
dataset: `dc.data.Dataset`
Dataset to convert
epochs: int, optional (Default 1)
Number of times to walk over `dataset`
mode: str, optional (Default 'fit')
Ignored in this implementation.
deterministic: bool, optional (Default True)
Whether the dataset should be walked in a deterministic fashion
pad_batches: bool, optional (Default True)
If true, each returned batch will have size `self.batch_size`.
Returns
-------
Iterator which walks over the batches
"""
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):
if y_b is not None:
if self.mode == 'classification':
y_b = to_one_hot(y_b.flatten(), self.n_classes).reshape(
-1, self.n_tasks, self.n_classes)
atom_feat = []
pair_feat = []
atom_split = []
atom_to_pair = []
pair_split = []
start = 0
for im, mol in enumerate(X_b):
n_atoms = mol.get_num_atoms()
# number of atoms in each molecule
atom_split.extend([im] * n_atoms)
# index of pair features
C0, C1 = np.meshgrid(np.arange(n_atoms), np.arange(n_atoms))
atom_to_pair.append(
np.transpose(
np.array([C1.flatten() + start,
C0.flatten() + start])))
# number of pairs for each atom
pair_split.extend(C1.flatten() + start)
start = start + n_atoms
# atom features
atom_feat.append(mol.get_atom_features())
# pair features
pair_feat.append(
np.reshape(mol.get_pair_features(),
(n_atoms * n_atoms, self.n_pair_feat[0])))
inputs = [
np.concatenate(atom_feat, axis=0),
np.concatenate(pair_feat, axis=0),
np.array(pair_split),
np.array(atom_split),
np.concatenate(atom_to_pair, axis=0)
]
yield (inputs, [y_b], [w_b])