def transform(self, dataset):
"""Performs power transform on data."""
X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
w_t = w
ids_t = ids
n_powers = len(self.powers)
if self.transform_X:
X_t = np.power(X, self.powers[0])
for i in range(1, n_powers):
X_t = np.hstack((X_t, np.power(X, self.powers[i])))
y_t = y
if self.transform_y:
print("y will not be transformed by PowerTransformer, for now.")
"""
y_t = np.power(y, self.powers[0])
for i in range(1, n_powers):
y_t = np.hstack((y_t,np.power(y, self.powers[i])))
X_t = X
"""
# TODO (rbharath): Find a more elegant solution to saving the data?
shutil.rmtree(dataset.data_dir)
os.makedirs(dataset.data_dir)
DiskDataset.from_numpy(X_t, y_t, w_t, ids_t, data_dir=dataset.data_dir)
return dataset
def transform(self, dataset):
"""Performs power transform on data."""
X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
w_t = w
ids_t = ids
n_powers = len(self.powers)
if self.transform_X:
X_t = np.power(X, self.powers[0])
for i in range(1, n_powers):
X_t = np.hstack((X_t,np.power(X, self.powers[i])))
y_t = y
if self.transform_y:
print("y will not be transformed by PowerTransformer, for now.")
"""
y_t = np.power(y, self.powers[0])
for i in range(1, n_powers):
y_t = np.hstack((y_t,np.power(y, self.powers[i])))
X_t = X
"""
# TODO (rbharath): Find a more elegant solution to saving the data?
shutil.rmtree(dataset.data_dir)
os.makedirs(dataset.data_dir)
DiskDataset.from_numpy(X_t, y_t, w_t, ids_t, data_dir=dataset.data_dir)
return dataset
def test_fit(self):
tf_enc = TensorflowMoleculeEncoder.zinc_encoder()
smiles = [
"Cn1cnc2c1c(=O)n(C)c(=O)n2C",
"O=C(O)[C@@H]1/C(=C/CO)O[C@@H]2CC(=O)N21",
"Cn1c2nncnc2c(=O)n(C)c1=O", "Cn1cnc2c1c(=O)[nH]c(=O)n2C",
"NC(=O)c1ncc[nH]c1=O", "O=C1OCc2c1[nH]c(=O)[nH]c2=O",
"Cn1c(N)c(N)c(=O)n(C)c1=O", "CNc1nc2c([nH]1)c(=O)[nH]c(=O)n2C",
"CC(=O)N1CN(C(C)=O)[C@@H](O)[C@@H]1O",
"CC(=O)N1CN(C(C)=O)[C@H](O)[C@H]1O", "Cc1[nH]c(=O)[nH]c(=O)c1CO",
"O=C1NCCCc2c1no[n+]2[O-]", "Cc1nc(C(N)=O)c(N)n1CCO",
"O=c1[nH]cc(N2CCOCC2)c(=O)[nH]1"
]
featurizer = dc.feat.one_hot.OneHotFeaturizer(zinc_charset, 120)
mols = [Chem.MolFromSmiles(x) for x in smiles]
features = featurizer.featurize(mols)
dataset = DiskDataset.from_numpy(features, features)
prediction = tf_enc.predict_on_batch(dataset.X)
tf_de = TensorflowMoleculeDecoder.zinc_decoder()
one_hot_decoded = tf_de.predict_on_batch(prediction)
decoded_smiles = featurizer.untransform(one_hot_decoded)
assert_equals(len(decoded_smiles), len(smiles))
def featurize_complexes(self, mol_files, protein_files):
pool = multiprocessing.Pool()
results = []
for i, (mol_file,
protein_pdb) in enumerate(zip(mol_files, protein_files)):
log_message = "Featurizing %d / %d" % (i, len(mol_files))
results.append(
pool.apply_async(_featurize_complex,
(self, mol_file, protein_pdb, log_message)))
pool.close()
features = []
failures = []
for ind, result in enumerate(results):
new_features = result.get()
# Handle loading failures which return None
if new_features is not None:
features.append(new_features)
else:
failures.append(ind)
features = np.asarray(features)
labels = np.delete(self.labels, failures)
dataset = DiskDataset.from_numpy(features, labels)
# Fit atomic conv model
self.atomic_conv_model.fit(dataset, nb_epoch=self.epochs)
# Add the Atomic Convolution layers to fetches
layers_to_fetch = list()
for layer in self.atomic_conv_model.layers.values():
if isinstance(layer, dc.models.atomic_conv.AtomicConvolution):
layers_to_fetch.append(layer)
# Extract the atomic convolution features
atomic_conv_features = list()
feed_dict_generator = self.atomic_conv_model.default_generator(
dataset=dataset, epochs=1)
for feed_dict in self.atomic_conv_model._create_feed_dicts(
feed_dict_generator, training=False):
frag1_conv, frag2_conv, complex_conv = self.atomic_conv_model._run_graph(
outputs=layers_to_fetch, feed_dict=feed_dict, training=False)
concatenated = np.concatenate(
[frag1_conv, frag2_conv, complex_conv], axis=1)
atomic_conv_features.append(concatenated)
batch_size = self.atomic_conv_model.batch_size
if len(features) % batch_size != 0:
num_batches = (len(features) // batch_size) + 1
num_to_skip = num_batches * batch_size - len(features)
else:
num_to_skip = 0
atomic_conv_features = np.asarray(atomic_conv_features)
atomic_conv_features = atomic_conv_features[-num_to_skip:]
atomic_conv_features = np.squeeze(atomic_conv_features)
return atomic_conv_features, failures
def featurize_complexes(self, mol_files, protein_files):
pool = multiprocessing.Pool()
results = []
for i, (mol_file, protein_pdb) in enumerate(zip(mol_files, protein_files)):
log_message = "Featurizing %d / %d" % (i, len(mol_files))
results.append(
pool.apply_async(_featurize_complex,
(self, mol_file, protein_pdb, log_message)))
pool.close()
features = []
failures = []
for ind, result in enumerate(results):
new_features = result.get()
# Handle loading failures which return None
if new_features is not None:
features.append(new_features)
else:
failures.append(ind)
features = np.asarray(features)
labels = np.delete(self.labels, failures)
dataset = DiskDataset.from_numpy(features, labels)
# Fit atomic conv model
self.atomic_conv_model.fit(dataset, nb_epoch=self.epochs)
# Add the Atomic Convolution layers to fetches
layers_to_fetch = list()
for layer in self.atomic_conv_model.layers.values():
if isinstance(layer,
dc.models.tensorgraph.models.atomic_conv.AtomicConvolution):
layers_to_fetch.append(layer)
# Extract the atomic convolution features
atomic_conv_features = list()
feed_dict_generator = self.atomic_conv_model.default_generator(
dataset=dataset, epochs=1)
for feed_dict in self.atomic_conv_model._create_feed_dicts(
feed_dict_generator, training=False):
frag1_conv, frag2_conv, complex_conv = self.atomic_conv_model._run_graph(
outputs=layers_to_fetch, feed_dict=feed_dict, training=False)
concatenated = np.concatenate(
[frag1_conv, frag2_conv, complex_conv], axis=1)
atomic_conv_features.append(concatenated)
batch_size = self.atomic_conv_model.batch_size
if len(features) % batch_size != 0:
num_batches = (len(features) // batch_size) + 1
num_to_skip = num_batches * batch_size - len(features)
else:
num_to_skip = 0
atomic_conv_features = np.asarray(atomic_conv_features)
atomic_conv_features = atomic_conv_features[-num_to_skip:]
atomic_conv_features = np.squeeze(atomic_conv_features)
return atomic_conv_features, failures
def k_fold_split(self, dataset, k, directories=None, **kwargs):
"""
Parameters
----------
dataset: `dc.data.Dataset`
Dataset to do a k-fold split
k: int
Number of folds to split `dataset` into.
directories: list[str]
list of length 2*k filepaths to save the result disk-datasets
Returns
-------
list of length k tuples of (train, cv) where `train` and `cv` are both
lists of `Dataset`s.
"""
logger.info("Computing K-fold split")
if directories is None:
directories = [tempfile.mkdtemp() for _ in range(2 * k)]
else:
assert len(directories) == 2 * k
cv_datasets = []
train_ds_base = None
train_datasets = []
# rem_dataset is remaining portion of dataset
if isinstance(dataset, DiskDataset):
rem_dataset = dataset
else:
rem_dataset = DiskDataset.from_numpy(dataset.X, dataset.y,
dataset.w, dataset.ids)
for fold in range(k):
# Note starts as 1/k since fold starts at 0. Ends at 1 since fold goes up
# to k-1.
frac_fold = 1. / (k - fold)
train_dir, cv_dir = directories[2 * fold], directories[2 * fold +
1]
fold_inds, rem_inds, _ = self.split(rem_dataset,
frac_train=frac_fold,
frac_valid=1 - frac_fold,
frac_test=0,
**kwargs)
cv_dataset = rem_dataset.select(fold_inds, select_dir=cv_dir)
cv_datasets.append(cv_dataset)
rem_dataset = rem_dataset.select(rem_inds)
train_ds_to_merge = filter(lambda x: x is not None,
[train_ds_base, rem_dataset])
train_ds_to_merge = filter(lambda x: len(x) > 0, train_ds_to_merge)
train_dataset = DiskDataset.merge(train_ds_to_merge,
merge_dir=train_dir)
train_datasets.append(train_dataset)
update_train_base_merge = filter(lambda x: x is not None,
[train_ds_base, cv_dataset])
train_ds_base = DiskDataset.merge(update_train_base_merge)
return list(zip(train_datasets, cv_datasets))
def test_select_attrs_by_dset_smiles():
#testing that the method can split a attr according to a disk dataset. In this case, the attr_ids need to be converted back to smiles to match the input dataset.
dataset = DiskDataset.from_numpy(
test_scaffold.X,
test_scaffold.y,
ids=test_scaffold_attr[data_obj_scaffold.params.smiles_col].values)
newDD = split.select_attrs_by_dset_smiles(
dataset, data_obj_scaffold.attr, data_obj_scaffold.params.smiles_col)
assert newDD.equals(test_scaffold_attr)
def test_select_dset_by_attr_ids_using_smiles():
#testing that the method can split a dataset according to its attr ids into the correct deepchem diskdataframe. In this case, the attr_ids are converted back to smiles to match the input dataset.
dataset = DiskDataset.from_numpy(
data_obj_scaffold.dataset.X,
data_obj_scaffold.dataset.y,
ids=data_obj_scaffold.attr[data_obj_scaffold.params.smiles_col].values)
newdf = pd.DataFrame({'compound_ids': test_scaffold_attr.index.tolist()},
index=test_scaffold_attr.smiles)
newDD = split.select_dset_by_attr_ids(dataset, newdf)
assert (newDD.y == test_scaffold.y).all()
def split(self, dataset, frac_split, split_dirs=None):
"""
Method that does bulk of splitting dataset.
"""
if split_dirs is not None:
assert len(split_dirs) == 2
else:
split_dirs = [tempfile.mkdtemp(), tempfile.mkdtemp()]
# Handle edge case where frac_split is 1
if frac_split == 1:
dataset_1 = DiskDataset.from_numpy(dataset.X, dataset.y, dataset.w,
dataset.ids)
dataset_2 = None
return dataset_1, dataset_2
X, y, w, ids = randomize_arrays((dataset.X, dataset.y, dataset.w,
dataset.ids))
if len(y.shape) == 1:
y = np.expand_dims(y, 1)
if len(w.shape) == 1:
w = np.expand_dims(w, 1)
split_indices = self.get_task_split_indices(y, w, frac_split)
# Create weight matrices fpor two haves.
w_1, w_2 = np.zeros_like(w), np.zeros_like(w)
for task, split_index in enumerate(split_indices):
# copy over up to required index for weight first_split
w_1[:split_index, task] = w[:split_index, task]
w_2[split_index:, task] = w[split_index:, task]
# check out if any rows in either w_1 or w_2 are just zeros
rows_1 = w_1.any(axis=1)
X_1, y_1, w_1, ids_1 = X[rows_1], y[rows_1], w_1[rows_1], ids[rows_1]
dataset_1 = DiskDataset.from_numpy(X_1, y_1, w_1, ids_1)
rows_2 = w_2.any(axis=1)
X_2, y_2, w_2, ids_2 = X[rows_2], y[rows_2], w_2[rows_2], ids[rows_2]
dataset_2 = DiskDataset.from_numpy(X_2, y_2, w_2, ids_2)
return dataset_1, dataset_2
def split(self, dataset, frac_split, split_dirs=None):
"""
Method that does bulk of splitting dataset.
"""
if split_dirs is not None:
assert len(split_dirs) == 2
else:
split_dirs = [tempfile.mkdtemp(), tempfile.mkdtemp()]
# Handle edge case where frac_split is 1
if frac_split == 1:
dataset_1 = DiskDataset.from_numpy(dataset.X, dataset.y, dataset.w,
dataset.ids)
dataset_2 = None
return dataset_1, dataset_2
X, y, w, ids = randomize_arrays(
(dataset.X, dataset.y, dataset.w, dataset.ids))
if len(y.shape) == 1:
y = np.expand_dims(y, 1)
if len(w.shape) == 1:
w = np.expand_dims(w, 1)
split_indices = self.get_task_split_indices(y, w, frac_split)
# Create weight matrices fpor two haves.
w_1, w_2 = np.zeros_like(w), np.zeros_like(w)
for task, split_index in enumerate(split_indices):
# copy over up to required index for weight first_split
w_1[:split_index, task] = w[:split_index, task]
w_2[split_index:, task] = w[split_index:, task]
# check out if any rows in either w_1 or w_2 are just zeros
rows_1 = w_1.any(axis=1)
X_1, y_1, w_1, ids_1 = X[rows_1], y[rows_1], w_1[rows_1], ids[rows_1]
dataset_1 = DiskDataset.from_numpy(X_1, y_1, w_1, ids_1)
rows_2 = w_2.any(axis=1)
X_2, y_2, w_2, ids_2 = X[rows_2], y[rows_2], w_2[rows_2], ids[rows_2]
dataset_2 = DiskDataset.from_numpy(X_2, y_2, w_2, ids_2)
return dataset_1, dataset_2
def featurize_complexes(self, mol_files, protein_files):
features = []
failures = []
for i, (mol_file,
protein_pdb) in enumerate(zip(mol_files, protein_files)):
logging.info("Featurizing %d / %d" % (i, len(mol_files)))
new_features = self._featurize_complex(mol_file, protein_pdb)
# Handle loading failures which return None
if new_features is not None:
features.append(new_features)
else:
failures.append(ind)
features = np.asarray(features)
labels = np.delete(self.labels, failures)
dataset = DiskDataset.from_numpy(features, labels)
# Fit atomic conv model
self.atomic_conv_model.fit(dataset, nb_epoch=self.epochs)
# Add the Atomic Convolution layers to fetches
layers_to_fetch = [
self.atomic_conv_model._frag1_conv,
self.atomic_conv_model._frag2_conv,
self.atomic_conv_model._complex_conv
]
# Extract the atomic convolution features
atomic_conv_features = list()
batch_generator = self.atomic_conv_model.default_generator(
dataset=dataset, epochs=1)
for X, y, w in batch_generator:
frag1_conv, frag2_conv, complex_conv = self.atomic_conv_model.predict_on_generator(
[(X, y, w)], outputs=layers_to_fetch)
concatenated = np.concatenate(
[frag1_conv, frag2_conv, complex_conv], axis=1)
atomic_conv_features.append(concatenated)
batch_size = self.atomic_conv_model.batch_size
if len(features) % batch_size != 0:
num_batches = (len(features) // batch_size) + 1
num_to_skip = num_batches * batch_size - len(features)
else:
num_to_skip = 0
atomic_conv_features = np.asarray(atomic_conv_features)
atomic_conv_features = atomic_conv_features[-num_to_skip:]
atomic_conv_features = np.squeeze(atomic_conv_features)
return atomic_conv_features, failures
def load_core_pdbbind_coordinates(pdbbind_dir, base_dir, reload=True):
"""Load PDBBind datasets. Does not do train/test split"""
# Set some global variables up top
reload = True
verbosity = "high"
model = "logistic"
regen = False
neighbor_cutoff = 4
max_num_neighbors = 10
# Create some directories for analysis
# The base_dir holds the results of all analysis
if not reload:
if os.path.exists(base_dir):
shutil.rmtree(base_dir)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
current_dir = os.path.dirname(os.path.realpath(__file__))
#Make directories to store the raw and featurized datasets.
data_dir = os.path.join(base_dir, "dataset")
# Load PDBBind dataset
labels_file = os.path.join(pdbbind_dir, "INDEX_core_data.2013")
pdb_subdirs = os.path.join(pdbbind_dir, "website-core-set")
tasks = ["-logKd/Ki"]
print("About to load contents.")
contents_df = load_pdbbind_labels(labels_file)
ids = contents_df["PDB code"].values
y = np.array([float(val) for val in contents_df["-logKd/Ki"].values])
# Define featurizers
featurizer = NeighborListComplexAtomicCoordinates(max_num_neighbors,
neighbor_cutoff)
# Featurize Dataset
features = []
for ind, pdb_code in enumerate(ids):
print("Processing %s" % str(pdb_code))
pdb_subdir = os.path.join(pdb_subdirs, pdb_code)
computed_feature = compute_pdbbind_coordinate_features(
featurizer, pdb_subdir, pdb_code)
features.append(computed_feature)
X = np.array(features, dtype - object)
w = np.ones_like(y)
dataset = DiskDataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
def load_core_pdbbind_coordinates(pdbbind_dir, base_dir, reload=True):
"""Load PDBBind datasets. Does not do train/test split"""
# Set some global variables up top
reload = True
verbosity = "high"
model = "logistic"
regen = False
neighbor_cutoff = 4
max_num_neighbors = 10
# Create some directories for analysis
# The base_dir holds the results of all analysis
if not reload:
if os.path.exists(base_dir):
shutil.rmtree(base_dir)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
current_dir = os.path.dirname(os.path.realpath(__file__))
#Make directories to store the raw and featurized datasets.
data_dir = os.path.join(base_dir, "dataset")
# Load PDBBind dataset
labels_file = os.path.join(pdbbind_dir, "INDEX_core_data.2013")
pdb_subdirs = os.path.join(pdbbind_dir, "website-core-set")
tasks = ["-logKd/Ki"]
print("About to load contents.")
contents_df = load_pdbbind_labels(labels_file)
ids = contents_df["PDB code"].values
y = np.array([float(val) for val in contents_df["-logKd/Ki"].values])
# Define featurizers
featurizer = NeighborListComplexAtomicCoordinates(
max_num_neighbors, neighbor_cutoff)
# Featurize Dataset
features = []
for ind, pdb_code in enumerate(ids):
print("Processing %s" % str(pdb_code))
pdb_subdir = os.path.join(pdb_subdirs, pdb_code)
computed_feature = compute_pdbbind_coordinate_features(
featurizer, pdb_subdir, pdb_code)
features.append(computed_feature)
X = np.array(features, dtype-object)
w = np.ones_like(y)
dataset = DiskDataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
def test_fit(self):
tf_enc = TensorflowMoleculeEncoder.zinc_encoder()
smiles = [
"Cn1cnc2c1c(=O)n(C)c(=O)n2C", "O=C(O)[C@@H]1/C(=C/CO)O[C@@H]2CC(=O)N21",
"Cn1c2nncnc2c(=O)n(C)c1=O", "Cn1cnc2c1c(=O)[nH]c(=O)n2C",
"NC(=O)c1ncc[nH]c1=O", "O=C1OCc2c1[nH]c(=O)[nH]c2=O",
"Cn1c(N)c(N)c(=O)n(C)c1=O", "CNc1nc2c([nH]1)c(=O)[nH]c(=O)n2C",
"CC(=O)N1CN(C(C)=O)[C@@H](O)[C@@H]1O",
"CC(=O)N1CN(C(C)=O)[C@H](O)[C@H]1O", "Cc1[nH]c(=O)[nH]c(=O)c1CO",
"O=C1NCCCc2c1no[n+]2[O-]", "Cc1nc(C(N)=O)c(N)n1CCO",
"O=c1[nH]cc(N2CCOCC2)c(=O)[nH]1"
]
featurizer = dc.feat.one_hot.OneHotFeaturizer(zinc_charset, 120)
mols = [Chem.MolFromSmiles(x) for x in smiles]
features = featurizer.featurize(mols)
dataset = DiskDataset.from_numpy(features, features)
prediction = tf_enc.predict_on_batch(dataset.X)
tf_de = TensorflowMoleculeDecoder.zinc_decoder()
one_hot_decoded = tf_de.predict_on_batch(prediction)
decoded_smiles = featurizer.untransform(one_hot_decoded)
assert_equals(len(decoded_smiles), len(smiles))
def split_dataset(self, dataset, attr_df, smiles_col):
#smiles_col is a hack for now until deepchem fixes their scaffold and butina splitters
"""Splits dataset into training, testing and validation sets.
Args:
dataset (deepchem Dataset): full featurized dataset
attr_df (Pandas DataFrame): dataframe containing SMILES strings indexed by compound IDs,
smiles_col (string): name of SMILES column (hack for now until deepchem fixes scaffold and butina splitters)
Returns:
[(train, valid)], test, [(train_attr, valid_attr)], test_attr:
train (deepchem Dataset): training dataset.
valid (deepchem Dataset): validation dataset.
test (deepchem Dataset): testing dataset.
train_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for training set.
valid_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for validation set.
test_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for test set.
Raises:
Exception if there are duplicate ids or smiles strings in the dataset or the attr_df
"""
if check_if_dupe_smiles_dataset(dataset, attr_df, smiles_col):
raise Exception("Duplicate ids or smiles in the dataset")
if self.needs_smiles():
# Some DeepChem splitters require compound IDs in dataset to be SMILES strings. Swap in the
# SMILES strings now; we'll reverse this later.
dataset = DiskDataset.from_numpy(dataset.X,
dataset.y,
ids=attr_df[smiles_col].values,
verbose=False)
# Under k-fold CV, the training/validation splits are determined by num_folds; only the test set fraction
# is directly specified through command line parameters. If we use Butina splitting, we can't control
# the test set size either.
train_frac = 1.0 - self.params.split_test_frac
# Use DeepChem train_test_split() to select held-out test set; then use k_fold_split on the
# training set to split it into training/validation folds.
if self.split == 'butina':
# TODO: Splitter.train_test_split() doesn't provide a way to pass the cutoff parameter
# through to the ButinaSplitter.split() function. Simple fix would be to reimplement
# train_test_split() here (it's not a complicated function). For now, allow cutoff to default.
#train_cv, test = self.splitter.train_test_split(dataset, cutoff=self.params.butina_cutoff)
train_cv, test, _ = self.splitter.train_valid_test_split(dataset)
self.splitter = dc.splits.ScaffoldSplitter()
train_cv_pairs = self.splitter.k_fold_split(
train_cv, self.num_folds)
else:
# TODO: Add special handling for AVE splitter
train_cv, test = self.splitter.train_test_split(
dataset, seed=np.random.seed(123), frac_train=train_frac)
train_cv_pairs = self.splitter.k_fold_split(
train_cv, self.num_folds)
train_valid_dsets = []
train_valid_attr = []
if self.needs_smiles():
# Now that DeepChem splitters have done their work, replace the SMILES strings in the split
# dataset objects with actual compound IDs.
for train, valid in train_cv_pairs:
train_attr = select_attrs_by_dset_smiles(
train, attr_df, smiles_col)
train = DiskDataset.from_numpy(train.X,
train.y,
ids=train_attr.index.values,
verbose=False)
valid_attr = select_attrs_by_dset_smiles(
valid, attr_df, smiles_col)
valid = DiskDataset.from_numpy(valid.X,
valid.y,
ids=valid_attr.index.values,
verbose=False)
train_valid_dsets.append((train, valid))
train_valid_attr.append((train_attr, valid_attr))
test_attr = select_attrs_by_dset_smiles(test, attr_df, smiles_col)
test = DiskDataset.from_numpy(test.X,
test.y,
ids=test_attr.index.values,
verbose=False)
else:
# Otherwise just subset the ID-to-SMILES maps.
for train, valid in train_cv_pairs:
train_attr = select_attrs_by_dset_ids(train, attr_df)
valid_attr = select_attrs_by_dset_ids(valid, attr_df)
train_valid_attr.append((train_attr, valid_attr))
train_valid_dsets = train_cv_pairs
test_attr = select_attrs_by_dset_ids(test, attr_df)
return train_valid_dsets, test, train_valid_attr, test_attr
# REPLACE WITH DOWNLOADED PDBBIND EXAMPLE
pdbbind_dir = "/tmp/deep-docking/datasets/pdbbind"
pdbbind_tasks, dataset, transformers = load_core_pdbbind_grid(
pdbbind_dir, base_dir)
print("About to perform train/valid/test split.")
num_train = .8 * len(dataset)
X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
X_train, X_valid = X[:num_train], X[num_train:]
y_train, y_valid = y[:num_train], y[num_train:]
w_train, w_valid = w[:num_train], w[num_train:]
ids_train, ids_valid = ids[:num_train], ids[num_train:]
train_dataset = DiskDataset.from_numpy(train_dir, X_train, y_train,
w_train, ids_train, pdbbind_tasks)
valid_dataset = DiskDataset.from_numpy(valid_dir, X_valid, y_valid,
w_valid, ids_valid, pdbbind_tasks)
classification_metric = Metric(metrics.pearson_r2_score, verbosity=verbosity,
mode="regression")
n_features = dataset.get_data_shape()[0]
tensorflow_model = TensorflowMultiTaskRegressor(
len(pdbbind_tasks), n_features, model_dir, dropouts=[.25],
learning_rate=0.0003, weight_init_stddevs=[.1],
batch_size=64, verbosity=verbosity)
model = TensorflowModel(tensorflow_model, model_dir)
# Fit trained model
model.fit(train_dataset, nb_epoch=20)
def split_dataset(self, dataset, attr_df, smiles_col):
#smiles_col is a hack for now until deepchem fixes their scaffold and butina splitters
"""Splits dataset into training, testing and validation sets.
Args:
dataset (deepchem Dataset): full featurized dataset
attr_df (Pandas DataFrame): dataframe containing SMILES strings indexed by compound IDs,
smiles_col (string): name of SMILES column (hack for now until deepchem fixes scaffold and butina splitters)
Returns:
[(train, valid)], test, [(train_attr, valid_attr)], test_attr:
train (deepchem Dataset): training dataset.
valid (deepchem Dataset): validation dataset.
test (deepchem Dataset): testing dataset.
train_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for training set.
valid_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for validation set.
test_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for test set.
Raises:
Exception if there are duplicate ids or smiles strings in the dataset or the attr_df
"""
dataset_dup = False
if check_if_dupe_smiles_dataset(dataset, attr_df, smiles_col):
log.info("Duplicate ids or smiles in the dataset, will deduplicate first and assign all records per compound ID to same partition")
dataset_dup = True
dataset_ori = copy.deepcopy(dataset)
id_df = pd.DataFrame({'indices' : np.arange(len(dataset.ids), dtype=np.int32), "compound_id": [str(e) for e in dataset.ids]})
sel_df = id_df.drop_duplicates(subset="compound_id")
dataset = dataset.select(sel_df.indices.values)
if self.needs_smiles():
# Some DeepChem splitters require compound IDs in dataset to be SMILES strings. Swap in the
# SMILES strings now; we'll reverse this later.
dataset = DiskDataset.from_numpy(dataset.X, dataset.y, w=dataset.w, ids=attr_df.drop_duplicates(subset=smiles_col)[smiles_col].values)
if dataset_dup:
dataset_ori = DiskDataset.from_numpy(dataset_ori.X, dataset_ori.y, w=dataset_ori.w, ids=attr_df[smiles_col].values)
# Under k-fold CV, the training/validation splits are determined by num_folds; only the test set fraction
# is directly specified through command line parameters. If we use Butina splitting, we can't control
# the test set size either.
train_frac = 1.0 - self.params.split_test_frac
# Use DeepChem train_test_split() to select held-out test set; then use k_fold_split on the
# training set to split it into training/validation folds.
if self.split == 'butina':
train_cv, test, _ = self.splitter.train_valid_test_split(dataset)
self.splitter = dc.splits.ScaffoldSplitter()
train_cv_pairs = self.splitter.k_fold_split(train_cv, self.num_folds)
else:
# TODO: Add special handling for AVE splitter
train_cv, test = self.splitter.train_test_split(dataset, seed=np.random.seed(123), frac_train=train_frac)
train_cv_pairs = self.splitter.k_fold_split(train_cv, self.num_folds)
train_valid_dsets = []
train_valid_attr = []
if self.needs_smiles():
# Now that DeepChem splitters have done their work, replace the SMILES strings in the split
# dataset objects with actual compound IDs.
for train, valid in train_cv_pairs:
# assign the subsets to the original dataset if duplicated compounds exist
if dataset_dup:
train = select_dset_by_id_list(dataset_ori, train.ids)
valid = select_dset_by_id_list(dataset_ori, valid.ids)
train_attr = select_attrs_by_dset_smiles(train, attr_df, smiles_col)
train = DiskDataset.from_numpy(train.X, train.y, w=train.w, ids=train_attr.index.values)
valid_attr = select_attrs_by_dset_smiles(valid, attr_df, smiles_col)
valid = DiskDataset.from_numpy(valid.X, valid.y, w=valid.w, ids=valid_attr.index.values)
train_valid_dsets.append((train, valid))
train_valid_attr.append((train_attr, valid_attr))
if dataset_dup:
test = select_dset_by_id_list(dataset_ori, test.ids)
test_attr = select_attrs_by_dset_smiles(test, attr_df, smiles_col)
test = DiskDataset.from_numpy(test.X, test.y, w=test.w, ids=test_attr.index.values)
else:
# Otherwise just subset the ID-to-SMILES maps.
for train, valid in train_cv_pairs:
if dataset_dup:
train = select_dset_by_id_list(dataset_ori, train.ids)
valid = select_dset_by_id_list(dataset_ori, valid.ids)
train_attr = select_attrs_by_dset_ids(train, attr_df)
valid_attr = select_attrs_by_dset_ids(valid, attr_df)
train_valid_attr.append((train_attr, valid_attr))
train_valid_dsets = train_cv_pairs
if dataset_dup:
test = select_dset_by_id_list(dataset_ori, test.ids)
test_attr = select_attrs_by_dset_ids(test, attr_df)
return train_valid_dsets, test, train_valid_attr, test_attr
def k_fold_split(self, dataset, k, directories=None, **kwargs):
"""
Parameters
----------
dataset: Dataset
Dataset to do a k-fold split
k: int
number of folds
directories: list of str
list of length 2*k filepaths to save the result disk-datasets
kwargs
Returns
-------
list of length k tuples of (train, cv)
"""
"""
:param dataset:
:param k:
:param directories:
:param kwargs:
:return: list of length k tuples of (train, cv)
"""
log("Computing K-fold split", self.verbose)
if directories is None:
directories = [tempfile.mkdtemp() for _ in range(2 * k)]
else:
assert len(directories) == 2 * k
cv_datasets = []
train_ds_base = None
train_datasets = []
# rem_dataset is remaining portion of dataset
if isinstance(dataset, DiskDataset):
rem_dataset = dataset
else:
rem_dataset = DiskDataset.from_numpy(dataset.X, dataset.y, dataset.w,
dataset.ids)
for fold in range(k):
# Note starts as 1/k since fold starts at 0. Ends at 1 since fold goes up
# to k-1.
frac_fold = 1. / (k - fold)
train_dir, cv_dir = directories[2 * fold], directories[2 * fold + 1]
fold_inds, rem_inds, _ = self.split(
rem_dataset,
frac_train=frac_fold,
frac_valid=1 - frac_fold,
frac_test=0,
**kwargs)
cv_dataset = rem_dataset.select(fold_inds, select_dir=cv_dir)
cv_datasets.append(cv_dataset)
rem_dataset = rem_dataset.select(rem_inds)
train_ds_to_merge = filter(lambda x: x is not None,
[train_ds_base, rem_dataset])
train_ds_to_merge = filter(lambda x: len(x) > 0, train_ds_to_merge)
train_dataset = DiskDataset.merge(train_ds_to_merge, merge_dir=train_dir)
train_datasets.append(train_dataset)
update_train_base_merge = filter(lambda x: x is not None,
[train_ds_base, cv_dataset])
train_ds_base = DiskDataset.merge(update_train_base_merge)
return list(zip(train_datasets, cv_datasets))
def load_uspto(featurizer="plain",
split=None,
num_to_load=10000,
reload=True,
verbose=False):
"""Load USPTO dataset.
For now, only loads the subset of data for 2008-2011 reactions. See https://figshare.com/articles/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873 for more details.
The full dataset contains some 400K reactions. This causes an out-of-memory error on development laptop if full dataset is featurized. For now, return a truncated subset of dataset.
Reloading is not entirely supported for this dataset.
"""
# Most reaction dataset ML tasks train the prediction of products from
# ractants. Both of these are contained in the rxn object that is output,
# so there is no "tasks" field.
uspto_tasks = []
if split is not None:
raise ValueError("Train/valid/test not yet supported.")
# Download USPTO dataset
data_dir = deepchem.utils.get_data_dir()
if reload:
save_dir = os.path.join(data_dir, "uspto/" + featurizer + "/")
loaded, all_dataset, transformers = deepchem.utils.save.load_dataset_from_disk(
save_dir)
if loaded:
return uspto_tasks, all_dataset, transformers
dataset_file = os.path.join(data_dir,
"2008-2011_USPTO_reactionSmiles_filtered.zip")
if not os.path.exists(dataset_file):
deepchem.utils.download_url(
"https://bitbucket.org/dan2097/patent-reaction-extraction/downloads/2008-2011_USPTO_reactionSmiles_filtered.zip"
)
# Unzip
unzip_dir = os.path.join(data_dir,
"2008-2011_USPTO_reactionSmiles_filtered")
if not os.path.exists(unzip_dir):
deepchem.utils.unzip_file(dataset_file, dest_dir=unzip_dir)
# Unzipped file is a tap seperated values file (despite the .txt)
filename = os.path.join(unzip_dir,
"2008-2011_USPTO_reactionSmiles_filtered.txt")
rxns = []
from rdkit.Chem import rdChemReactions
with open(filename) as tsvfile:
reader = csv.reader(tsvfile, delimiter="\t")
for ind, row in enumerate(reader):
if ind > num_to_load:
break
if verbose:
print("Loading reaction %d" % ind)
# The first element in the row is the reaction smarts
smarts = row[0]
# Sometimes smarts have extraneous information at end of form "
# |f:0" that causes parsing to fail. Not sure what this information
# is, but just ignoring for now.
smarts = smarts.split(" ")[0]
rxn = rdChemReactions.ReactionFromSmarts(smarts)
rxns.append(rxn)
rxn_array = np.array(rxns)
# Make up dummy labels since DiskDataset.from_numpy doesn't allow
# creation from just features for now.
y = np.ones(len(rxn_array))
# TODO: This dataset isn't saved to disk so reload doesn't happen.
rxn_dataset = DiskDataset.from_numpy(rxn_array, y)
transformers = []
return uspto_tasks, (rxn_dataset, None, None), transformers
def featurize(self, input_files, in_memory=True):
"""Featurizes image files.
Parameters
----------
input_files: list
Each file in this list should either be of a supported image format
(.png, .tif only for now) or of a compressed folder of image files
(only .zip for now).
in_memory: bool
If true, return in-memory NumpyDataset. Else return DiskDataset.
"""
if not isinstance(input_files, list):
input_files = [input_files]
image_files = []
# Sometimes zip files contain directories within. Traverse directories
while len(input_files) > 0:
remainder = []
for input_file in input_files:
filename, extension = os.path.splitext(input_file)
# TODO(rbharath): Add support for more extensions
if os.path.isdir(input_file):
dirfiles = [
os.path.join(input_file, subfile)
for subfile in os.listdir(input_file)
]
remainder += dirfiles
elif extension == ".zip":
zip_dir = tempfile.mkdtemp()
zip_ref = zipfile.ZipFile(input_file, 'r')
zip_ref.extractall(path=zip_dir)
zip_ref.close()
zip_files = [
os.path.join(zip_dir, name)
for name in zip_ref.namelist()
]
for zip_file in zip_files:
_, extension = os.path.splitext(zip_file)
if extension in [".png", ".tif"]:
image_files.append(zip_file)
elif extension in [".png", ".tif"]:
image_files.append(input_file)
else:
raise ValueError("Unsupported file format")
input_files = remainder
images = []
for image_file in image_files:
_, extension = os.path.splitext(image_file)
if extension == ".png":
image = misc.imread(image_file)
images.append(image)
elif extension == ".tif":
im = Image.open(image_file)
imarray = np.array(im)
images.append(imarray)
else:
raise ValueError("Unsupported image filetype for %s" %
image_file)
images = np.array(images)
if in_memory:
return NumpyDataset(images)
else:
# from_numpy currently requires labels. Make dummy labels
labels = np.zeros(len(images))
return DiskDataset.from_numpy(images, labels)
def load_gpcr(dataset_file,
featurizer='ECFP',
transformers=True,
reload=True,
sep='OnePositiveSplit',
K=5):
# data_dir=os.path.dirname(dataset_file)
save_dir = os.path.join(
os.path.dirname(dataset_file),
'.'.join(os.path.basename(dataset_file).split('.')[:-1]), "ecfp",
"split")
train, valid, test = os.path.join(save_dir, 'train'), os.path.join(
save_dir, 'valid'), os.path.join(save_dir, 'test')
fopen = open(dataset_file, "r")
ss = fopen.readlines()
m = ss[0].strip('\n').split(',')
m.remove('SMILES')
if os.path.isdir(save_dir):
if reload:
dataset, train_dataset, valid_dataset, test_dataset = DiskDataset(
data_dir=save_dir), DiskDataset(data_dir=train), DiskDataset(
data_dir=valid), DiskDataset(data_dir=test)
transformers = [
deepchem.trans.NormalizationTransformer(transform_w=True,
dataset=train_dataset)
]
all_dataset = (dataset, train_dataset, valid_dataset, test_dataset)
return m, all_dataset, transformers
if featurizer == 'ECFP':
featurizer = deepchem.feat.CircularFingerprint(size=1024)
elif featurizer == 'GraphConv':
featurizer = deepchem.feat.ConvMolFeaturizer()
elif featurizer == 'Weave':
featurizer = deepchem.feat.WeaveFeaturizer()
elif featurizer == 'Raw':
featurizer = deepchem.feat.RawFeaturizer()
elif featurizer == 'AdjacencyConv':
featurizer = deepchem.feat.AdjacencyFingerprint(max_n_atoms=150,
max_valence=6)
elif featurizer == 'SelfDefine':
featurizer = deepchem.feat.UserDefinedFeaturizer(feature_field)
loader = deepchem.data.CSVLoader(tasks=m,
smiles_field="SMILES",
featurizer=featurizer)
dataset = loader.featurize(dataset_file,
data_dir=save_dir,
shard_size=8192)
# dataset = loader.featurize(dataset_file, shard_size=8192)
# Initialize transformers
if transformers:
transformers = [
deepchem.trans.NormalizationTransformer(transform_w=True,
dataset=dataset)
]
for transformer in transformers:
dataset = transformer.transform(dataset)
splitters = {
'index': deepchem.splits.IndexSplitter(),
'random': deepchem.splits.RandomSplitter(),
'random_stratified': deepchem.splits.RandomStratifiedSplitter(),
'scaffold': deepchem.splits.ScaffoldSplitter(),
'butina': deepchem.splits.ButinaSplitter(),
'task': deepchem.splits.TaskSplitter(),
'Harmonious_positive': Harmonious_positive(),
'OnePositiveSplit': OnePositiveSplit()
}
splitter = splitters[sep]
if sep == 'task':
fold_datasets = splitter.k_fold_split(dataset, K)
all_dataset = fold_datasets
elif sep == 'Harmonious_positive':
train_dataset, valid_dataset, test_dataset = splitter.train_valid_test_split(
dataset)
train_dataset = DiskDataset.from_numpy(train_dataset.X,
train_dataset.y,
train_dataset.w,
train_dataset.ids,
dataset.tasks,
data_dir=train)
valid_dataset = DiskDataset.from_numpy(valid_dataset.X,
valid_dataset.y,
valid_dataset.w,
valid_dataset.ids,
dataset.tasks,
data_dir=valid)
test_dataset = DiskDataset.from_numpy(test_dataset.X,
test_dataset.y,
test_dataset.w,
test_dataset.ids,
dataset.tasks,
data_dir=test)
all_dataset = (dataset, train_dataset, valid_dataset, test_dataset)
elif sep == 'Harmonious_positive' and K:
# train_dataset, valid_dataset, test_dataset = splitter.train_valid_test_split(
# dataset,
# frac_train=frac_train,
# frac_valid=0,
# frac_test=1- frac_train,
# )
# train_dataset = DiskDataset.from_numpy(train_dataset.X,train_dataset.y,train_dataset.w,train_dataset.ids,
# dataset.tasks,data_dir=train)
# train_dataset.reshard(8192)
# test_dataset = DiskDataset.from_numpy(test_dataset.X,test_dataset.y,test_dataset.w,test_dataset.ids,
# dataset.tasks,data_dir=test)
# test_dataset.reshard(8192)
# fold_dataset = splitter.k_fold_split(
# train_dataset, K, directories=[os.path.join(valid,str(i)) for i in range(K)],verbose=True)
fold_dataset = splitter.k_fold_split(
dataset,
K,
directories=[os.path.join(valid, str(i)) for i in range(K)],
verbose=True)
folds = []
for i in range(K):
print('merge fold dataset {}...'.format(i))
train_fold = DiskDataset.merge(
[fold_dataset[j] for j in range(K) if j != i],
merge_dir=os.path.join(valid, str(i), 'train_fold'))
test_fold = DiskDataset.merge([fold_dataset[i]],
merge_dir=os.path.join(
valid, str(i), 'valid_fold'))
folds.append([train_fold, test_fold])
all_dataset = (dataset, [], folds, [])
else:
train_dataset, valid_dataset, test_dataset = splitter.train_valid_test_split(
dataset,
train_dir=train,
valid_dir=valid,
test_dir=test,
frac_train=frac_train,
frac_valid=frac_valid,
frac_test=frac_test)
all_dataset = (dataset, train_dataset, valid_dataset, test_dataset)
# else:
# train_dataset, valid_dataset, test_dataset = splitter.train_valid_test_split(dataset,train_dir=train, valid_dir=valid, test_dir=test)
# all_dataset = (dataset,train_dataset, valid_dataset, test_dataset)
# if reload:
# deepchem.utils.save.save_dataset_to_disk(save_dir, train, valid, test,transformers)
return m, all_dataset, transformers
def load_core_pdbbind_grid(pdbbind_dir, base_dir, reload=True):
"""Load PDBBind datasets. Does not do train/test split"""
# Set some global variables up top
reload = True
verbosity = "high"
model = "logistic"
regen = False
# Create some directories for analysis
# The base_dir holds the results of all analysis
if not reload:
if os.path.exists(base_dir):
shutil.rmtree(base_dir)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
current_dir = os.path.dirname(os.path.realpath(__file__))
#Make directories to store the raw and featurized datasets.
data_dir = os.path.join(base_dir, "dataset")
# Load PDBBind dataset
labels_file = os.path.join(pdbbind_dir, "INDEX_core_data.2013")
pdb_subdirs = os.path.join(pdbbind_dir, "website-core-set")
tasks = ["-logKd/Ki"]
print("About to load contents.")
contents_df = load_pdbbind_labels(labels_file)
ids = contents_df["PDB code"].values
y = np.array([float(val) for val in contents_df["-logKd/Ki"].values])
# Define featurizers
grid_featurizer = GridFeaturizer(
voxel_width=16.0,
feature_types="voxel_combined",
# TODO(rbharath, enf): Figure out why pi_stack is slow and cation_pi
# causes segfaults.
#voxel_feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
#"salt_bridge"], ecfp_power=9, splif_power=9,
voxel_feature_types=["ecfp", "splif", "hbond", "salt_bridge"],
ecfp_power=9,
splif_power=9,
parallel=True,
flatten=True,
verbosity=verbosity)
compound_featurizers = [CircularFingerprint(size=1024)]
complex_featurizers = [grid_featurizer]
# Featurize Dataset
features = []
feature_len = None
y_inds = []
for ind, pdb_code in enumerate(ids):
print("Processing %s" % str(pdb_code))
pdb_subdir = os.path.join(pdb_subdirs, pdb_code)
computed_feature = compute_pdbbind_grid_feature(
compound_featurizers, complex_featurizers, pdb_subdir, pdb_code)
if feature_len is None:
feature_len = len(computed_feature)
if len(computed_feature) != feature_len:
print("Featurization failed for %s!" % pdb_code)
continue
y_inds.append(ind)
features.append(computed_feature)
y = y[y_inds]
X = np.vstack(features)
w = np.ones_like(y)
dataset = DiskDataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
def split_dataset(self, dataset, attr_df, smiles_col):
#smiles_col is a hack for now until deepchem fixes their scaffold and butina splitters
"""Splits dataset into training, testing and validation sets.
For ave_min, random, scaffold, index splits
self.params.split_valid_frac & self.params.split_test_frac should be defined and
train_frac = 1.0 - self.params.split_valid_frac - self.params.split_test_frac
For butina split, test size is not user defined, and depends on available clusters that qualify for placement in the test set
train_frac = 1.0 - self.params.split_valid_frac
For temporal split, test size is also not user defined, and depends on number of compounds with dates after cutoff date.
train_frac = 1.0 - self.params.split_valid_frac
Args:
dataset (deepchem Dataset): full featurized dataset
attr_df (Pandas DataFrame): dataframe containing SMILES strings indexed by compound IDs,
smiles_col (string): name of SMILES column (hack for now until deepchem fixes scaffold and butina splitters)
Returns:
[(train, valid)], test, [(train_attr, valid_attr)], test_attr:
train (deepchem Dataset): training dataset.
valid (deepchem Dataset): validation dataset.
test (deepchem Dataset): testing dataset.
train_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for training set.
valid_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for validation set.
test_attr (Pandas DataFrame): dataframe of SMILES strings indexed by compound IDs for test set.
Raises:
Exception if there are duplicate ids or smiles strings in the dataset or the attr_df
"""
if check_if_dupe_smiles_dataset(dataset, attr_df, smiles_col):
raise Exception("Duplicate ids or smiles in the dataset")
log.warning("Splitting data by %s" % self.params.splitter)
if self.needs_smiles():
# Some DeepChem splitters require compound IDs in dataset to be SMILES strings. Swap in the
# SMILES strings now; we'll reverse this later.
dataset = DiskDataset.from_numpy(dataset.X,
dataset.y,
ids=attr_df[smiles_col].values,
verbose=False)
if self.split == 'butina':
#train_valid, test = self.splitter.train_test_split(dataset, cutoff=self.params.butina_cutoff)
# Can't use train_test_split with Butina because Butina splits into train and valid sets only.
train_valid, test, _ = self.splitter.train_valid_test_split(
dataset)
self.splitter = dc.splits.ScaffoldSplitter()
# With Butina splitting, we don't have control over the size of the test set
train_frac = 1.0 - self.params.split_valid_frac
train, valid = self.splitter.train_test_split(
train_valid, seed=np.random.seed(123), frac_train=train_frac)
elif self.split == 'ave_min':
# AVEMinSplitter also only does train-valid splits, but at least nested splits seem to work.
# TODO: Change this if we modify AVE splitter to do 3-way splits internally.
train_valid_frac = 1.0 - self.params.split_test_frac
train_frac = train_valid_frac - self.params.split_valid_frac
log.info("Performing split for test set")
train_valid, test, _ = self.splitter.train_valid_test_split(
dataset,
frac_train=train_valid_frac,
frac_valid=self.params.split_test_frac,
frac_test=0.0)
log.info("Performing split of training and validation sets")
train, valid, _ = self.splitter.train_valid_test_split(
train_valid,
frac_train=train_frac / train_valid_frac,
frac_valid=self.params.split_valid_frac / train_valid_frac,
frac_test=0.0)
log.info(
"Results of 3-way split: %d training, %d validation, %d test compounds"
% (train.X.shape[0], valid.X.shape[0], test.X.shape[0]))
elif self.split == 'temporal':
# TemporalSplitter requires that we pass attr_df so it can get the dates for each compound
train_frac = 1.0 - self.params.split_valid_frac
train, valid, test = self.splitter.train_valid_test_split(
dataset,
attr_df,
frac_train=train_frac,
frac_valid=self.params.split_valid_frac)
else:
train_frac = 1.0 - self.params.split_valid_frac - self.params.split_test_frac
train, valid, test = self.splitter.train_valid_test_split(
dataset,
frac_train=train_frac,
frac_valid=self.params.split_valid_frac,
frac_test=self.params.split_test_frac,
seed=np.random.seed(123))
# Extract the ID-to_SMILES maps from attr_df for each subset.
if self.needs_smiles():
# Now that DeepChem splitters have done their work, replace the SMILES strings in the split
# dataset objects with actual compound IDs.
train_attr = select_attrs_by_dset_smiles(train, attr_df,
smiles_col)
train = DiskDataset.from_numpy(train.X,
train.y,
ids=train_attr.index.values,
verbose=False)
valid_attr = select_attrs_by_dset_smiles(valid, attr_df,
smiles_col)
valid = DiskDataset.from_numpy(valid.X,
valid.y,
ids=valid_attr.index.values,
verbose=False)
test_attr = select_attrs_by_dset_smiles(test, attr_df, smiles_col)
test = DiskDataset.from_numpy(test.X,
test.y,
ids=test_attr.index.values,
verbose=False)
else:
# Otherwise just subset the ID-to-SMILES maps.
train_attr = select_attrs_by_dset_ids(train, attr_df)
valid_attr = select_attrs_by_dset_ids(valid, attr_df)
test_attr = select_attrs_by_dset_ids(test, attr_df)
# Note grouping of train/valid return values as tuple lists, to match format of
# KFoldSplitting.split_dataset().
return [(train, valid)], test, [(train_attr, valid_attr)], test_attr
def load_core_pdbbind_grid(pdbbind_dir, base_dir, reload=True):
"""Load PDBBind datasets. Does not do train/test split"""
# Set some global variables up top
regen = False
# Create some directories for analysis
# The base_dir holds the results of all analysis
if not reload:
if os.path.exists(base_dir):
shutil.rmtree(base_dir)
if not os.path.exists(base_dir):
os.makedirs(base_dir)
current_dir = os.path.dirname(os.path.realpath(__file__))
#Make directories to store the raw and featurized datasets.
data_dir = os.path.join(base_dir, "dataset")
# Load PDBBind dataset
labels_file = os.path.join(pdbbind_dir, "INDEX_core_data.2013")
pdb_subdirs = os.path.join(pdbbind_dir, "website-core-set")
tasks = ["-logKd/Ki"]
print("About to load contents.")
contents_df = load_pdbbind_labels(labels_file)
ids = contents_df["PDB code"].values
y = np.array([float(val) for val in contents_df["-logKd/Ki"].values])
# Define featurizers
grid_featurizer = GridFeaturizer(
voxel_width=16.0, feature_types="voxel_combined",
# TODO(rbharath, enf): Figure out why pi_stack is slow and cation_pi
# causes segfaults.
#voxel_feature_types=["ecfp", "splif", "hbond", "pi_stack", "cation_pi",
#"salt_bridge"], ecfp_power=9, splif_power=9,
voxel_feature_types=["ecfp", "splif", "hbond",
"salt_bridge"], ecfp_power=9, splif_power=9,
parallel=True, flatten=True)
compound_featurizers = [CircularFingerprint(size=1024)]
complex_featurizers = [grid_featurizer]
# Featurize Dataset
features = []
feature_len = None
y_inds = []
for ind, pdb_code in enumerate(ids):
print("Processing %s" % str(pdb_code))
pdb_subdir = os.path.join(pdb_subdirs, pdb_code)
computed_feature = compute_pdbbind_grid_feature(
compound_featurizers, complex_featurizers, pdb_subdir, pdb_code)
if feature_len is None:
feature_len = len(computed_feature)
if len(computed_feature) != feature_len:
print("Featurization failed for %s!" % pdb_code)
continue
y_inds.append(ind)
features.append(computed_feature)
y = y[y_inds]
X = np.vstack(features)
w = np.ones_like(y)
dataset = DiskDataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
train_attr.smiles.tolist(),
valid_attr.smiles.tolist(),
test_attr.smiles.tolist()
], [])
test.append(len(full_dataset_smiles) == len(set(full_dataset_smiles)))
assert all(test)
#***********************************************************************************
([(train, valid)], test_scaffold, [(train_attr, valid_attr)],
test_scaffold_attr) = splitter_scaffold.split_dataset(
data_obj_scaffold.dataset, data_obj_scaffold.attr,
data_obj_scaffold.params.smiles_col)
dataset_scaffold = DiskDataset.from_numpy(data_obj_scaffold.dataset.X,
data_obj_scaffold.dataset.y,
ids=data_obj_scaffold.attr.index)
def test_select_dset_by_attr_ids_using_smiles():
#testing that the method can split a dataset according to its attr ids into the correct deepchem diskdataframe. In this case, the attr_ids are converted back to smiles to match the input dataset.
dataset = DiskDataset.from_numpy(
data_obj_scaffold.dataset.X,
data_obj_scaffold.dataset.y,
ids=data_obj_scaffold.attr[data_obj_scaffold.params.smiles_col].values)
newdf = pd.DataFrame({'compound_ids': test_scaffold_attr.index.tolist()},
index=test_scaffold_attr.smiles)
newDD = split.select_dset_by_attr_ids(dataset, newdf)
assert (newDD.y == test_scaffold.y).all()
def create_dataset(self,
inputs: Union[OneOrMany[str], Tuple[Any]],
data_dir: Optional[str] = None,
shard_size: Optional[int] = 8192,
in_memory: bool = False) -> Dataset:
"""Creates and returns a `Dataset` object by featurizing provided image files and labels/weights.
Parameters
----------
inputs: `Union[OneOrMany[str], Tuple[Any]]`
The inputs provided should be one of the following
- filename
- list of filenames
- Tuple (list of filenames, labels)
- Tuple (list of filenames, labels, weights)
Each file in a given list of filenames should either be of a supported
image format (.png, .tif only for now) or of a compressed folder of
image files (only .zip for now). If `labels` or `weights` are provided,
they must correspond to the sorted order of all filenames provided, with
one label/weight per file.
data_dir: str, optional
Directory to store featurized dataset.
in_memory: bool
If true, return in-memory NumpyDataset. Else return ImageDataset.
Returns
-------
A `Dataset` object containing a featurized representation of data
from `input_files`, `labels`, and `weights`.
"""
labels, weights = None, None
if isinstance(inputs, tuple):
if len(inputs) == 1:
input_files = inputs[0]
if isinstance(inputs, str):
input_files = [inputs]
elif len(inputs) == 2:
input_files, labels = inputs
elif len(inputs) == 3:
input_files, labels, weights = inputs
else:
raise ValueError("Input must be a tuple of length 1, 2, or 3")
else:
input_files = inputs
if isinstance(input_files, str):
input_files = [input_files]
image_files = []
# Sometimes zip files contain directories within. Traverse directories
while len(input_files) > 0:
remainder = []
for input_file in input_files:
filename, extension = os.path.splitext(input_file)
extension = extension.lower()
# TODO(rbharath): Add support for more extensions
if os.path.isdir(input_file):
dirfiles = [
os.path.join(input_file, subfile)
for subfile in os.listdir(input_file)
]
remainder += dirfiles
elif extension == ".zip":
zip_dir = tempfile.mkdtemp()
zip_ref = zipfile.ZipFile(input_file, 'r')
zip_ref.extractall(path=zip_dir)
zip_ref.close()
zip_files = [
os.path.join(zip_dir, name)
for name in zip_ref.namelist()
]
for zip_file in zip_files:
_, extension = os.path.splitext(zip_file)
extension = extension.lower()
if extension in [".png", ".tif"]:
image_files.append(zip_file)
elif extension in [".png", ".tif"]:
image_files.append(input_file)
else:
raise ValueError("Unsupported file format")
input_files = remainder
# Sort image files
image_files = sorted(image_files)
if in_memory:
if data_dir is None:
return NumpyDataset(self.load_img(image_files),
y=labels,
w=weights,
ids=image_files)
else:
dataset = DiskDataset.from_numpy(self.load_img(image_files),
y=labels,
w=weights,
ids=image_files,
tasks=self.tasks,
data_dir=data_dir)
if shard_size is not None:
dataset.reshard(shard_size)
return dataset
else:
return ImageDataset(image_files,
y=labels,
w=weights,
ids=image_files)
# REPLACE WITH DOWNLOADED PDBBIND EXAMPLE
pdbbind_dir = "/tmp/deep-docking/datasets/pdbbind"
pdbbind_tasks, dataset, transformers = load_core_pdbbind_grid(
pdbbind_dir, base_dir)
print("About to perform train/valid/test split.")
num_train = .8 * len(dataset)
X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)
X_train, X_valid = X[:num_train], X[num_train:]
y_train, y_valid = y[:num_train], y[num_train:]
w_train, w_valid = w[:num_train], w[num_train:]
ids_train, ids_valid = ids[:num_train], ids[num_train:]
train_dataset = DiskDataset.from_numpy(train_dir, X_train, y_train, w_train,
ids_train, pdbbind_tasks)
valid_dataset = DiskDataset.from_numpy(valid_dir, X_valid, y_valid, w_valid,
ids_valid, pdbbind_tasks)
classification_metric = Metric(metrics.pearson_r2_score,
verbosity=verbosity,
mode="regression")
n_features = dataset.get_data_shape()[0]
tensorflow_model = TensorflowMultiTaskRegressor(len(pdbbind_tasks),
n_features,
model_dir,
dropouts=[.25],
learning_rate=0.0003,
weight_init_stddevs=[.1],
batch_size=64,