def train_valid_test_split(self,
dataset,
train_dir,
valid_dir,
test_dir,
frac_train=.8,
frac_valid=.1,
frac_test=.1,
seed=None,
log_every_n=1000):
# Obtain original x, y, and w arrays and shuffle
X, y, w, ids = self.__randomize_arrays(dataset.to_numpy())
X_train, y_train, w_train, ids_train, X_test, y_test, w_test, ids_test = self.__split(
X, y, w, ids, frac_train)
# calculate percent split for valid (out of test and valid)
valid_percentage = frac_valid / (frac_valid + frac_test)
# split test data into valid and test, treating sub test set also as sparse
X_valid, y_valid, w_valid, ids_valid, X_test, y_test, w_test, ids_test = self.__split(
X_test, y_test, w_test, ids_test, valid_percentage)
# turn back into dataset objects
train_data = Dataset.from_numpy(train_dir, X_train, y_train, w_train,
ids_train)
valid_data = Dataset.from_numpy(valid_dir, X_valid, y_valid, w_valid,
ids_valid)
test_data = Dataset.from_numpy(test_dir, X_test, y_test, w_test,
ids_test)
return train_data, valid_data, test_data
def test_move_load(self):
"""Test that datasets can be moved and loaded."""
verbosity = "high"
current_dir = os.path.dirname(os.path.realpath(__file__))
data_dir = os.path.join(self.base_dir, "data")
moved_data_dir = os.path.join(self.base_dir, "moved_data")
dataset_file = os.path.join(current_dir,
"../../models/tests/example.csv")
featurizer = CircularFingerprint(size=1024)
tasks = ["log-solubility"]
loader = DataLoader(tasks=tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
dataset = loader.featurize(dataset_file, data_dir)
X, y, w, ids = dataset.to_numpy()
shutil.move(data_dir, moved_data_dir)
moved_dataset = Dataset(moved_data_dir, reload=reload)
X_moved, y_moved, w_moved, ids_moved = moved_dataset.to_numpy()
np.testing.assert_allclose(X, X_moved)
np.testing.assert_allclose(y, y_moved)
np.testing.assert_allclose(w, w_moved)
np.testing.assert_array_equal(ids, ids_moved)
def test_move_load(self):
"""Test that datasets can be moved and loaded."""
verbosity = "high"
current_dir = os.path.dirname(os.path.realpath(__file__))
data_dir = os.path.join(self.base_dir, "data")
moved_data_dir = os.path.join(self.base_dir, "moved_data")
dataset_file = os.path.join(
current_dir, "../../models/tests/example.csv")
featurizer = CircularFingerprint(size=1024)
tasks = ["log-solubility"]
loader = DataLoader(tasks=tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
dataset = loader.featurize(dataset_file, data_dir)
X, y, w, ids = dataset.to_numpy()
shutil.move(data_dir, moved_data_dir)
moved_dataset = Dataset(
moved_data_dir, reload=reload)
X_moved, y_moved, w_moved, ids_moved = moved_dataset.to_numpy()
np.testing.assert_allclose(X, X_moved)
np.testing.assert_allclose(y, y_moved)
np.testing.assert_allclose(w, w_moved)
np.testing.assert_array_equal(ids, ids_moved)
def test_sklearn_regression(self):
"""Test that sklearn models can learn on simple regression datasets."""
np.random.seed(123)
dataset = sklearn.datasets.load_diabetes()
X, y = dataset.data, dataset.target
frac_train = .7
n_samples = len(X)
X_train, y_train = X[:frac_train * n_samples], y[:frac_train *
n_samples]
X_test, y_test = X[frac_train * n_samples:], y[frac_train * n_samples:]
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train)
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test)
tasks = train_dataset.get_task_names()
task_types = {task: "regression" for task in tasks}
model_params = {
"batch_size": None,
"data_shape": train_dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = SklearnModel(tasks,
task_types,
model_params,
self.model_dir,
mode="regression",
model_instance=LinearRegression())
# Fit trained model
model.fit(train_dataset)
model.save()
# Eval model on train
transformers = []
train_evaluator = Evaluator(model,
train_dataset,
transformers,
verbosity=verbosity)
train_scores = train_evaluator.compute_model_performance(
[regression_metric])
print("train_scores")
print(train_scores)
# Eval model on test
transformers = []
evaluator = Evaluator(model,
test_dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
print("scores")
print(scores)
assert scores[regression_metric.name] > .5
def test_singletask_to_multitask_classification(self):
splittype = "scaffold"
compound_featurizers = [CircularFingerprint(size=1024)]
complex_featurizers = []
output_transformers = []
tasks = ["task0", "task1", "task2", "task3", "task4", "task5", "task6",
"task7", "task8", "task9", "task10", "task11", "task12",
"task13", "task14", "task15", "task16"]
task_types = {task: "classification" for task in tasks}
input_file = "multitask_example.csv"
n_features = 10
n_tasks = len(tasks)
# Define train dataset
n_train = 100
X_train = np.random.rand(n_train, n_features)
y_train = np.random.randint(2, size=(n_train, n_tasks))
w_train = np.ones_like(y_train)
ids_train = ["C"] * n_train
train_dataset = Dataset.from_numpy(self.train_dir,
X_train, y_train, w_train, ids_train,
tasks)
# Define test dataset
n_test = 10
X_test = np.random.rand(n_test, n_features)
y_test = np.random.randint(2, size=(n_test, n_tasks))
w_test = np.ones_like(y_test)
ids_test = ["C"] * n_test
test_dataset = Dataset.from_numpy(self.test_dir,
X_test, y_test, w_test, ids_test,
tasks)
params_dict = {
"batch_size": 32,
"data_shape": train_dataset.get_data_shape()
}
classification_metrics = [Metric(metrics.roc_auc_score)]
def model_builder(tasks, task_types, model_params, model_builder, verbosity=None):
return SklearnModel(tasks, task_types, model_params, model_builder,
model_instance=LogisticRegression())
multitask_model = SingletaskToMultitask(tasks, task_types, params_dict,
self.model_dir, model_builder)
# Fit trained model
multitask_model.fit(train_dataset)
multitask_model.save()
# Eval multitask_model on train
evaluator = Evaluator(multitask_model, train_dataset, output_transformers,
verbosity=True)
_ = evaluator.compute_model_performance(classification_metrics)
# Eval multitask_model on test
evaluator = Evaluator(multitask_model, test_dataset, output_transformers,
verbosity=True)
_ = evaluator.compute_model_performance(classification_metrics)
def test_sklearn_multitask_classification(self):
"""Test that sklearn models can learn on simple multitask classification."""
np.random.seed(123)
n_tasks = 4
dataset = sklearn.datasets.load_digits(n_class=2)
X, y = dataset.data, dataset.target
y = np.reshape(y, (len(y), 1))
y = np.hstack([y] * n_tasks)
frac_train = .7
n_samples = len(X)
X_train, y_train = X[:frac_train*n_samples], y[:frac_train*n_samples]
X_test, y_test = X[frac_train*n_samples:], y[frac_train*n_samples:]
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train)
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test)
tasks = train_dataset.get_task_names()
task_types = {task: "classification" for task in tasks}
model_params = {
"batch_size": None,
"data_shape": train_dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
def model_builder(tasks, task_types, model_params, model_dir, verbosity=None):
return SklearnModel(tasks, task_types, model_params, model_dir,
mode="classification",
model_instance=LogisticRegression(),
verbosity=verbosity)
model = SingletaskToMultitask(tasks, task_types, model_params, self.model_dir,
model_builder, verbosity=verbosity)
# Fit trained model
model.fit(train_dataset)
model.save()
# Eval model on train
transformers = []
train_evaluator = Evaluator(model, train_dataset, transformers, verbosity=verbosity)
train_scores = train_evaluator.compute_model_performance([classification_metric])
print("train_scores")
print(train_scores)
# Eval model on test
transformers = []
evaluator = Evaluator(model, test_dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
print("scores")
print(scores)
for score in scores[classification_metric.name]:
assert score > .5
def test_singletask_to_multitask_sklearn_hyperparam_opt(self):
"""Test of hyperparam_opt with singletask_to_multitask."""
splittype = "scaffold"
output_transformers = []
tasks = ["task0", "task1", "task2", "task3", "task4", "task5", "task6",
"task7", "task8", "task9", "task10", "task11", "task12",
"task13", "task14", "task15", "task16"]
task_types = {task: "classification" for task in tasks}
input_file = "multitask_example.csv"
n_features = 10
n_tasks = len(tasks)
# Define train dataset
n_train = 100
X_train = np.random.rand(n_train, n_features)
y_train = np.random.randint(2, size=(n_train, n_tasks))
w_train = np.ones_like(y_train)
ids_train = ["C"] * n_train
train_dataset = Dataset.from_numpy(self.train_dir,
X_train, y_train, w_train, ids_train,
tasks)
# Define validation dataset
n_valid = 10
X_valid = np.random.rand(n_valid, n_features)
y_valid = np.random.randint(2, size=(n_valid, n_tasks))
w_valid = np.ones_like(y_valid)
ids_valid = ["C"] * n_valid
valid_dataset = Dataset.from_numpy(self.valid_dir,
X_valid, y_valid, w_valid, ids_valid,
tasks)
params_dict = {
"batch_size": [32],
"data_shape": [train_dataset.get_data_shape()],
}
classification_metric = Metric(metrics.matthews_corrcoef, np.mean,
mode="classification")
def model_builder(tasks, task_types, model_params, task_model_dir,
verbosity=None):
return SklearnModel(tasks, task_types, model_params, task_model_dir,
model_instance=LogisticRegression())
def multitask_model_builder(tasks, task_types, params_dict, logdir=None,
verbosity=None):
return SingletaskToMultitask(tasks, task_types, params_dict,
self.model_dir, model_builder)
optimizer = HyperparamOpt(multitask_model_builder, tasks, task_types,
verbosity="low")
best_model, best_hyperparams, all_results = optimizer.hyperparam_search(
params_dict, train_dataset, valid_dataset, output_transformers,
classification_metric, logdir=None)
def test_sklearn_classification(self):
"""Test that sklearn models can learn on simple classification datasets."""
np.random.seed(123)
dataset = sklearn.datasets.load_digits(n_class=2)
X, y = dataset.data, dataset.target
frac_train = .7
n_samples = len(X)
X_train, y_train = X[:frac_train*n_samples], y[:frac_train*n_samples]
X_test, y_test = X[frac_train*n_samples:], y[frac_train*n_samples:]
print("X_train.shape, y_train.shape, X_test.shape, y_test.shape")
print(X_train.shape, y_train.shape, X_test.shape, y_test.shape)
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train)
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test)
tasks = train_dataset.get_task_names()
task_types = {task: "classification" for task in tasks}
model_params = {
"batch_size": None,
"data_shape": train_dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = SklearnModel(tasks, task_types, model_params, self.model_dir,
mode="classification",
model_instance=LogisticRegression())
# Fit trained model
model.fit(train_dataset)
model.save()
# Eval model on train
transformers = []
train_evaluator = Evaluator(model, train_dataset, transformers, verbosity=verbosity)
train_scores = train_evaluator.compute_model_performance([classification_metric])
print("train_scores")
print(train_scores)
# Eval model on test
transformers = []
evaluator = Evaluator(model, test_dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
print("scores")
print(scores)
assert scores[classification_metric.name] > .5
def test_samples_move(self):
"""Test that featurized samples can be moved and reloaded."""
verbosity = "high"
data_dir = os.path.join(self.base_dir, "data")
moved_data_dir = os.path.join(self.base_dir, "moved_data")
dataset_file = os.path.join(
self.current_dir, "example.csv")
featurizer = CircularFingerprint(size=1024)
tasks = ["log-solubility"]
loader = DataLoader(tasks=tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
featurized_dataset = loader.featurize(
dataset_file, data_dir)
n_dataset = len(featurized_dataset)
# Now perform move
shutil.move(data_dir, moved_data_dir)
moved_featurized_dataset = Dataset(
data_dir=moved_data_dir, reload=True)
assert len(moved_featurized_dataset) == n_dataset
def test_to_singletask(self):
"""Test that to_singletask works."""
num_datapoints = 100
num_features = 10
num_tasks = 10
# Generate data
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.random.randint(2, size=(num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids, verbosity="high")
task_dirs = []
try:
for task in range(num_tasks):
task_dirs.append(tempfile.mkdtemp())
singletask_datasets = dataset.to_singletask(task_dirs)
for task in range(num_tasks):
singletask_dataset = singletask_datasets[task]
X_task, y_task, w_task, ids_task = singletask_dataset.to_numpy()
w_nonzero = w[:, task] != 0
np.testing.assert_array_equal(X_task, X[w_nonzero != 0])
np.testing.assert_array_equal(y_task.flatten(), y[:, task][w_nonzero != 0])
np.testing.assert_array_equal(w_task.flatten(), w[:, task][w_nonzero != 0])
np.testing.assert_array_equal(ids_task, ids[w_nonzero != 0])
finally:
# Cleanup
for task_dir in task_dirs:
shutil.rmtree(task_dir)
def test_shuffle_each_shard(self):
"""Test that shuffle_each_shard works."""
n_samples = 100
n_tasks = 10
n_features = 10
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.random.randint(2, size=(n_samples, n_tasks))
ids = np.arange(n_samples)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids)
dataset.reshard(shard_size=10)
dataset.shuffle_each_shard()
X_s, y_s, w_s, ids_s = dataset.to_numpy()
assert X_s.shape == X.shape
assert y_s.shape == y.shape
assert ids_s.shape == ids.shape
assert w_s.shape == w.shape
# The ids should now store the performed permutation. Check that the
# original dataset is recoverable.
for i in range(n_samples):
np.testing.assert_array_equal(X_s[i], X[ids_s[i]])
np.testing.assert_array_equal(y_s[i], y[ids_s[i]])
np.testing.assert_array_equal(w_s[i], w[ids_s[i]])
np.testing.assert_array_equal(ids_s[i], ids[ids_s[i]])
def test_get_shape(self):
"""Test that get_shape works."""
num_datapoints = 100
num_features = 10
num_tasks = 10
# Generate data
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.random.randint(2, size=(num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids, verbosity="high")
X_shape, y_shape, w_shape, ids_shape = dataset.get_shape()
print("type(X_shape), type(y_shape), type(w_shape), type(ids_shape)")
print(type(X_shape), type(y_shape), type(w_shape), type(ids_shape))
print("type(X.shape), type(y.shape), type(w.shape), type(ids.shape)")
print(type(X.shape), type(y.shape), type(w.shape), type(ids.shape))
print("X_shape, y_shape, w_shape, ids_shape")
print(X_shape, y_shape, w_shape, ids_shape)
print("X.shape, y.shape, w.shape, ids.shape")
print(X.shape, y.shape, w.shape, ids.shape)
assert X_shape == X.shape
assert y_shape == y.shape
assert w_shape == w.shape
assert ids_shape == ids.shape
def test_shuffle_shards(self):
"""Test that shuffle_shards works."""
n_samples = 100
n_tasks = 10
n_features = 10
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.random.randint(2, size=(n_samples, n_tasks))
ids = np.arange(n_samples)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids)
dataset.reshard(shard_size=10)
dataset.shuffle_shards()
X_s, y_s, w_s, ids_s = dataset.to_numpy()
assert X_s.shape == X.shape
assert y_s.shape == y.shape
assert ids_s.shape == ids.shape
assert w_s.shape == w.shape
# The ids should now store the performed permutation. Check that the
# original dataset is recoverable.
for i in range(n_samples):
np.testing.assert_array_equal(X_s[i], X[ids_s[i]])
np.testing.assert_array_equal(y_s[i], y[ids_s[i]])
np.testing.assert_array_equal(w_s[i], w[ids_s[i]])
np.testing.assert_array_equal(ids_s[i], ids[ids_s[i]])
def test_to_singletask(self):
"""Test that to_singletask works."""
num_datapoints = 100
num_features = 10
num_tasks = 10
# Generate data
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.random.randint(2, size=(num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids, verbosity="high")
task_dirs = []
try:
for task in range(num_tasks):
task_dirs.append(tempfile.mkdtemp())
singletask_datasets = dataset.to_singletask(task_dirs)
for task in range(num_tasks):
singletask_dataset = singletask_datasets[task]
X_task, y_task, w_task, ids_task = singletask_dataset.to_numpy()
w_nonzero = w[:, task] != 0
np.testing.assert_array_equal(X_task, X[w_nonzero != 0])
np.testing.assert_array_equal(y_task.flatten(), y[:, task][w_nonzero != 0])
np.testing.assert_array_equal(w_task.flatten(), w[:, task][w_nonzero != 0])
np.testing.assert_array_equal(ids_task, ids[w_nonzero != 0])
finally:
# Cleanup
for task_dir in task_dirs:
shutil.rmtree(task_dir)
def test_tf_skewed_classification_overfit(self):
"""Test tensorflow models can overfit 0/1 datasets with few actives."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
#n_samples = 100
n_samples = 100
n_features = 3
n_tasks = len(tasks)
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
p = .05
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.binomial(1, p, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1500],
"dropouts": [.0],
"learning_rate": 0.003,
"momentum": .9,
"batch_size": n_samples,
"num_classification_tasks": 1,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [1.],
"bias_init_consts": [1.],
"nb_epoch": 200,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score,
verbosity=verbosity)
model = TensorflowModel(tasks,
task_types,
model_params,
self.model_dir,
tf_class=TensorflowMultiTaskClassifier,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .8
def test_sklearn_multitask_classification_overfit(self):
"""Test SKLearn singletask-to-multitask overfits tiny data."""
n_tasks = 10
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score,
verbosity=verbosity)
def model_builder(tasks,
task_types,
model_params,
model_dir,
verbosity=None):
return SklearnModel(tasks,
task_types,
model_params,
model_dir,
mode="classification",
model_instance=RandomForestClassifier(),
verbosity=verbosity)
model = SingletaskToMultitask(tasks,
task_types,
model_params,
self.model_dir,
model_builder,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .9
def load_pdbbind(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",
voxel_feature_types=[
"ecfp", "splif", "hbond", "pi_stack",
"cation_pi", "salt_bridge"
],
ecfp_power=9,
splif_power=9,
parallel=True,
flatten=True)
compound_featurizers = [CircularFingerprint(size=1024)]
complex_featurizers = [grid_featurizer]
# Featurize Dataset
features = []
for pdb_code in ids:
pdb_subdir = os.path.join(pdb_subdirs, pdb_code)
computed_feature = compute_pdbbind_feature(compound_featurizers,
complex_featurizers,
pdb_subdir, pdb_code)
if len(computed_feature) == 0:
computed_feature = np.zeros(1024)
features.append(computed_feature)
X = np.vstack(features)
w = np.ones_like(y)
dataset = Dataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
def test_tf_multitask_classification_overfit(self):
"""Test tf multitask overfits tiny data."""
n_tasks = 10
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
#y = np.random.randint(n_classes, size=(n_samples, n_tasks))
y = np.zeros((n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1000],
"dropouts": [.0],
"learning_rate": 0.0003,
"momentum": .9,
"batch_size": n_samples,
"num_classification_tasks": n_tasks,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [.1],
"bias_init_consts": [1.],
"nb_epoch": 100,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.accuracy_score,
verbosity=verbosity)
model = TensorflowModel(tasks,
task_types,
model_params,
self.model_dir,
tf_class=TensorflowMultiTaskClassifier,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .9
def test_tf_reload(self):
"""Test that tensorflow models can overfit simple classification datasets."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(n_classes, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1000],
"dropouts": [0.0],
"learning_rate": 0.003,
"momentum": 0.9,
"batch_size": n_samples,
"num_classification_tasks": 1,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [1.0],
"bias_init_consts": [1.0],
"nb_epoch": 100,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape(),
}
verbosity = "high"
classification_metric = Metric(metrics.accuracy_score, verbosity=verbosity)
model = TensorflowModel(
tasks, task_types, model_params, self.model_dir, tf_class=TensorflowMultiTaskClassifier, verbosity=verbosity
)
# Fit trained model
model.fit(dataset)
model.save()
# Load trained model
reloaded_model = TensorflowModel(
tasks, task_types, model_params, self.model_dir, tf_class=TensorflowMultiTaskClassifier, verbosity=verbosity
)
reloaded_model.reload()
assert reloaded_model.eval_model._restored_model
# Eval model on train
transformers = []
evaluator = Evaluator(reloaded_model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > 0.9
def test_tf_regression_overfit(self):
"""Test that TensorFlow models can overfit simple regression datasets."""
tasks = ["task0"]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.zeros((n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1000],
"dropouts": [.0],
"learning_rate": 0.003,
"momentum": .9,
"batch_size": n_samples,
"num_regression_tasks": 1,
"num_features": n_features,
"weight_init_stddevs": [np.sqrt(6) / np.sqrt(1000)],
"bias_init_consts": [1.],
"nb_epoch": 100,
"penalty": 0.0,
"optimizer": "momentum",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.mean_squared_error,
verbosity=verbosity)
model = TensorflowModel(tasks,
task_types,
model_params,
self.model_dir,
tf_class=TensorflowMultiTaskRegressor,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] < .1
def test_keras_skewed_classification_overfit(self):
"""Test keras models can overfit 0/1 datasets with few actives."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 100
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
p = .05
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.binomial(1, p, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"nb_hidden": 1000,
"activation": "relu",
"dropout": .0,
"learning_rate": .15,
"momentum": .9,
"nesterov": False,
"decay": 1e-4,
"batch_size": n_samples,
"nb_epoch": 200,
"init": "glorot_uniform",
"nb_layers": 1,
"batchnorm": False,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score,
verbosity=verbosity)
model = MultiTaskDNN(tasks,
task_types,
model_params,
self.model_dir,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .9
def test_keras_reload(self):
"""Test that trained keras models can be reloaded correctly."""
g = tf.Graph()
sess = tf.Session(graph=g)
K.set_session(sess)
with g.as_default():
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"nb_hidden": 1000,
"activation": "relu",
"dropout": 0.0,
"learning_rate": 0.15,
"momentum": 0.9,
"nesterov": False,
"decay": 1e-4,
"batch_size": n_samples,
"nb_epoch": 200,
"init": "glorot_uniform",
"nb_layers": 1,
"batchnorm": False,
"data_shape": dataset.get_data_shape(),
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = MultiTaskDNN(tasks, task_types, model_params, self.model_dir, verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Load trained model
reloaded_model = MultiTaskDNN(tasks, task_types, model_params, self.model_dir, verbosity=verbosity)
reloaded_model.reload()
# Eval model on train
transformers = []
evaluator = Evaluator(reloaded_model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > 0.9
def test_tf_skewed_classification_overfit(self):
"""Test tensorflow models can overfit 0/1 datasets with few actives."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
#n_samples = 100
n_samples = 100
n_features = 3
n_tasks = len(tasks)
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
p = .05
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.binomial(1, p, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1500],
"dropouts": [.0],
"learning_rate": 0.003,
"momentum": .9,
"batch_size": n_samples,
"num_classification_tasks": 1,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [1.],
"bias_init_consts": [1.],
"nb_epoch": 200,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = TensorflowModel(
tasks, task_types, model_params, self.model_dir,
tf_class=TensorflowMultiTaskClassifier,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .8
def train_valid_test_split(self, dataset, train_dir,
valid_dir, test_dir, frac_train=.8,
frac_valid=.1, frac_test=.1, seed=None,
log_every_n=1000):
# Obtain original x, y, and w arrays and shuffle
X, y, w, ids = self.__randomize_arrays(dataset.to_numpy())
X_train, y_train, w_train, ids_train, X_test, y_test, w_test, ids_test = self.__split(X, y, w, ids, frac_train)
# calculate percent split for valid (out of test and valid)
valid_percentage = frac_valid / (frac_valid + frac_test)
# split test data into valid and test, treating sub test set also as sparse
X_valid, y_valid, w_valid, ids_valid, X_test, y_test, w_test, ids_test = self.__split(X_test, y_test, w_test,
ids_test, valid_percentage)
# turn back into dataset objects
train_data = Dataset.from_numpy(train_dir, X_train, y_train, w_train, ids_train)
valid_data = Dataset.from_numpy(valid_dir, X_valid, y_valid, w_valid, ids_valid)
test_data = Dataset.from_numpy(test_dir, X_test, y_test, w_test, ids_test)
return train_data, valid_data, test_data
def load_muv(base_dir, reload=True):
"""Load MUV 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 MUV dataset
print("About to load MUV dataset.")
dataset_file = os.path.join(
current_dir, "../../datasets/muv.csv.gz")
dataset = load_from_disk(dataset_file)
print("Columns of dataset: %s" % str(dataset.columns.values))
print("Number of examples in dataset: %s" % str(dataset.shape[0]))
# Featurize MUV dataset
print("About to featurize MUV dataset.")
featurizer = CircularFingerprint(size=1024)
all_MUV_tasks = sorted(['MUV-692', 'MUV-689', 'MUV-846', 'MUV-859', 'MUV-644',
'MUV-548', 'MUV-852', 'MUV-600', 'MUV-810', 'MUV-712',
'MUV-737', 'MUV-858', 'MUV-713', 'MUV-733', 'MUV-652',
'MUV-466', 'MUV-832'])
loader = DataLoader(tasks=all_MUV_tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
if not reload or not os.path.exists(data_dir):
dataset = loader.featurize(dataset_file, data_dir)
regen = True
else:
dataset = Dataset(data_dir, reload=True)
# Initialize transformers
transformers = [
BalancingTransformer(transform_w=True, dataset=dataset)]
if regen:
print("About to transform data")
for transformer in transformers:
transformer.transform(dataset)
return all_MUV_tasks, dataset, transformers
def test_keras_multitask_regression_overfit(self):
"""Test keras multitask overfits tiny data."""
n_tasks = 10
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"nb_hidden": 1000,
"activation": "relu",
"dropout": .0,
"learning_rate": .15,
"momentum": .9,
"nesterov": False,
"decay": 1e-4,
"batch_size": n_samples,
"nb_epoch": 200,
"init": "glorot_uniform",
"nb_layers": 1,
"batchnorm": False,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = MultiTaskDNN(tasks,
task_types,
model_params,
self.model_dir,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .9
def test_sklearn_reload(self):
"""Test that trained model can be reloaded correctly."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score,
verbosity=verbosity)
model = SklearnModel(tasks,
task_types,
model_params,
self.model_dir,
mode="classification",
model_instance=RandomForestClassifier())
# Fit trained model
model.fit(dataset)
model.save()
# Load trained model
reloaded_model = SklearnModel(tasks,
task_types,
model_params,
self.model_dir,
mode="classification")
reloaded_model.reload()
# Eval model on train
transformers = []
evaluator = Evaluator(reloaded_model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .9
def test_tf_multitask_regression_overfit(self):
"""Test tf multitask overfits tiny data."""
n_tasks = 10
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
#y = np.random.randint(n_classes, size=(n_samples, n_tasks))
y = np.zeros((n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1000],
"dropouts": [.0],
"learning_rate": 0.0003,
"momentum": .9,
"batch_size": n_samples,
"num_regression_tasks": n_tasks,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [.1],
"bias_init_consts": [1.],
"nb_epoch": 100,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = TensorflowModel(
tasks, task_types, model_params, self.model_dir,
tf_class=TensorflowMultiTaskRegressor,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .9
def load_tox21(base_dir, reload=True):
"""Load Tox21 datasets. Does not do train/test split"""
# Set some global variables up top
reload = True
verbosity = "high"
model = "logistic"
# 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.
samples_dir = os.path.join(base_dir, "samples")
data_dir = os.path.join(base_dir, "dataset")
# Load Tox21 dataset
print("About to load Tox21 dataset.")
dataset_file = os.path.join(
current_dir, "../../datasets/tox21.csv.gz")
dataset = load_from_disk(dataset_file)
print("Columns of dataset: %s" % str(dataset.columns.values))
print("Number of examples in dataset: %s" % str(dataset.shape[0]))
# Featurize Tox21 dataset
print("About to featurize Tox21 dataset.")
featurizer = CircularFingerprint(size=1024)
all_tox21_tasks = ['NR-AR', 'NR-AR-LBD', 'NR-AhR', 'NR-Aromatase', 'NR-ER',
'NR-ER-LBD', 'NR-PPAR-gamma', 'SR-ARE', 'SR-ATAD5',
'SR-HSE', 'SR-MMP', 'SR-p53']
if not reload or not os.path.exists(data_dir):
loader = DataLoader(tasks=all_tox21_tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
dataset = loader.featurize(
dataset_file, data_dir, shard_size=8192)
else:
dataset = Dataset(data_dir, all_tox21_tasks, reload=True)
# Initialize transformers
transformers = [
BalancingTransformer(transform_w=True, dataset=dataset)]
if not reload:
print("About to transform data")
for transformer in transformers:
transformer.transform(dataset)
return all_tox21_tasks, dataset, transformers
def test_keras_multitask_regression_overfit(self):
"""Test keras multitask overfits tiny data."""
g = tf.Graph()
sess = tf.Session(graph=g)
K.set_session(sess)
with g.as_default():
n_tasks = 10
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"nb_hidden": 1000,
"activation": "relu",
"dropout": .0,
"learning_rate": .15,
"momentum": .9,
"nesterov": False,
"decay": 1e-4,
"batch_size": n_samples,
"nb_epoch": 200,
"init": "glorot_uniform",
"nb_layers": 1,
"batchnorm": False,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = MultiTaskDNN(tasks, task_types, model_params, self.model_dir,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .9
def test_get_shape(self):
"""Test that get_shape works."""
num_datapoints = 100
num_features = 10
num_tasks = 10
# Generate data
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.random.randint(2, size=(num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids, verbosity="high")
X_shape, y_shape, w_shape, ids_shape = dataset.get_shape()
assert X_shape == X.shape
assert y_shape == y.shape
assert w_shape == w.shape
assert ids_shape == ids.shape
def test_multitask_data(self):
"""Test that data associated with a tasks stays associated with it."""
tasks = ["task0", "task1"]
n_samples = 100
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
ids = np.array(["C"] * n_samples, dtype=object)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
X_out, y_out, w_out, _ = dataset.to_numpy()
np.testing.assert_allclose(X, X_out)
np.testing.assert_allclose(y, y_out)
np.testing.assert_allclose(w, w_out)
def test_multitask_data(self): """Test that data associated with a tasks stays associated with it.""" tasks = ["task0", "task1"] n_samples = 100 n_features = 3 n_tasks = len(tasks) # Generate dummy dataset ids = np.array(["C"] * n_samples, dtype=object) X = np.random.rand(n_samples, n_features) y = np.random.randint(2, size=(n_samples, n_tasks)) w = np.ones((n_samples, n_tasks)) dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks) X_out, y_out, w_out, _ = dataset.to_numpy() np.testing.assert_allclose(X, X_out) np.testing.assert_allclose(y, y_out) np.testing.assert_allclose(w, w_out)
def test_sklearn_reload(self):
"""Test that trained model can be reloaded correctly."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.randint(2, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {"batch_size": None, "data_shape": dataset.get_data_shape()}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = SklearnModel(
tasks,
task_types,
model_params,
self.model_dir,
mode="classification",
model_instance=RandomForestClassifier(),
)
# Fit trained model
model.fit(dataset)
model.save()
# Load trained model
reloaded_model = SklearnModel(tasks, task_types, model_params, self.model_dir, mode="classification")
reloaded_model.reload()
# Eval model on train
transformers = []
evaluator = Evaluator(reloaded_model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > 0.9
def test_sklearn_regression_overfit(self):
"""Test that sklearn models can overfit simple regression datasets."""
tasks = ["task0"]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.rand(n_samples, n_tasks)
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = SklearnModel(tasks,
task_types,
model_params,
self.model_dir,
mode="regression",
model_instance=RandomForestRegressor())
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model,
dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .7
def test_merge(self):
"""Test that datasets can be merged."""
verbosity = "high"
current_dir = os.path.dirname(os.path.realpath(__file__))
first_data_dir = os.path.join(self.base_dir, "first_dataset")
second_data_dir = os.path.join(self.base_dir, "second_dataset")
merged_data_dir = os.path.join(self.base_dir, "merged_data")
dataset_file = os.path.join(current_dir, "../../models/tests/example.csv")
featurizer = CircularFingerprint(size=1024)
tasks = ["log-solubility"]
loader = DataLoader(tasks=tasks, smiles_field="smiles", featurizer=featurizer, verbosity=verbosity)
first_dataset = loader.featurize(dataset_file, first_data_dir)
second_dataset = loader.featurize(dataset_file, second_data_dir)
merged_dataset = Dataset.merge(merged_data_dir, [first_dataset, second_dataset])
assert len(merged_dataset) == len(first_dataset) + len(second_dataset)
def test_sklearn_multitask_regression_overfit(self):
"""Test SKLearn singletask-to-multitask overfits tiny regression data."""
n_tasks = 2
tasks = ["task%d" % task for task in range(n_tasks)]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.rand(n_samples, n_tasks)
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
def model_builder(tasks, task_types, model_params, model_dir, verbosity=None):
return SklearnModel(tasks, task_types, model_params, model_dir,
mode="regression",
model_instance=RandomForestRegressor(),
verbosity=verbosity)
model = SingletaskToMultitask(tasks, task_types, model_params, self.model_dir,
model_builder, verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .7
def test_select(self):
"""Test that dataset select works."""
num_datapoints = 10
num_features = 10
num_tasks = 1
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.ones((num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids)
select_dir = tempfile.mkdtemp()
indices = [0, 4, 5, 8]
select_dataset = dataset.select(select_dir, indices)
X_sel, y_sel, w_sel, ids_sel = select_dataset.to_numpy()
np.testing.assert_array_equal(X[indices], X_sel)
np.testing.assert_array_equal(y[indices], y_sel)
np.testing.assert_array_equal(w[indices], w_sel)
np.testing.assert_array_equal(ids[indices], ids_sel)
shutil.rmtree(select_dir)
def test_select(self):
"""Test that dataset select works."""
num_datapoints = 10
num_features = 10
num_tasks = 1
X = np.random.rand(num_datapoints, num_features)
y = np.random.randint(2, size=(num_datapoints, num_tasks))
w = np.ones((num_datapoints, num_tasks))
ids = np.array(["id"] * num_datapoints)
dataset = Dataset.from_numpy(self.data_dir, X, y, w, ids)
select_dir = tempfile.mkdtemp()
indices = [0, 4, 5, 8]
select_dataset = dataset.select(select_dir, indices)
X_sel, y_sel, w_sel, ids_sel = select_dataset.to_numpy()
np.testing.assert_array_equal(X[indices], X_sel)
np.testing.assert_array_equal(y[indices], y_sel)
np.testing.assert_array_equal(w[indices], w_sel)
np.testing.assert_array_equal(ids[indices], ids_sel)
shutil.rmtree(select_dir)
def classify(document):
doc = document.strip().split('\r\n')
mol = [Chem.MolFromSmiles(x) for x in doc if x is not None]
fp = [
AllChem.GetMorganFingerprintAsBitVect(x, 2, nBits=1024) for x in mol
if x is not None
]
fp = np.array(fp)
if len(fp.shape) == 1:
fp = np.reshape(fp, (1, -1))
o = np.ones((fp.shape[0], len(kinase_tasks)))
d = Dataset.from_numpy(data_dir, fp, o, tasks=kinase_tasks)
y = np.squeeze(np.delete(model.predict_proba(d), 0, 2))
if len(y.shape) == 1:
y = np.reshape(y, (1, -1))
yy = pd.DataFrame(y)
yy.columns = kinase_tasks
yy = yy.T
yy.columns = doc
yy.index.name = 'kinase'
yy.to_csv(os.path.join(data_dir, 'pred.csv'))
return doc, yy
def test_sklearn_skewed_classification_overfit(self):
"""Test sklearn models can overfit 0/1 datasets with few actives."""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 100
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
p = .05
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.binomial(1, p, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = SklearnModel(tasks, task_types, model_params, self.model_dir,
mode="classification",
model_instance=RandomForestClassifier())
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .9
def test_sklearn_regression_overfit(self):
"""Test that sklearn models can overfit simple regression datasets."""
tasks = ["task0"]
task_types = {task: "regression" for task in tasks}
n_samples = 10
n_features = 3
n_tasks = len(tasks)
# Generate dummy dataset
np.random.seed(123)
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.rand(n_samples, n_tasks)
w = np.ones((n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"batch_size": None,
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = SklearnModel(tasks, task_types, model_params, self.model_dir,
mode="regression",
model_instance=RandomForestRegressor())
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
assert scores[regression_metric.name] > .7
def test_merge(self):
"""Test that datasets can be merged."""
verbosity = "high"
current_dir = os.path.dirname(os.path.realpath(__file__))
first_data_dir = os.path.join(self.base_dir, "first_dataset")
second_data_dir = os.path.join(self.base_dir, "second_dataset")
merged_data_dir = os.path.join(self.base_dir, "merged_data")
dataset_file = os.path.join(current_dir,
"../../models/tests/example.csv")
featurizer = CircularFingerprint(size=1024)
tasks = ["log-solubility"]
loader = DataLoader(tasks=tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
first_dataset = loader.featurize(dataset_file, first_data_dir)
second_dataset = loader.featurize(dataset_file, second_data_dir)
merged_dataset = Dataset.merge(merged_data_dir,
[first_dataset, second_dataset])
assert len(merged_dataset) == len(first_dataset) + len(second_dataset)
def test_singletask_to_multitask_classification(self):
splittype = "scaffold"
compound_featurizers = [CircularFingerprint(size=1024)]
complex_featurizers = []
output_transformers = []
tasks = [
"task0", "task1", "task2", "task3", "task4", "task5", "task6",
"task7", "task8", "task9", "task10", "task11", "task12", "task13",
"task14", "task15", "task16"
]
task_types = {task: "classification" for task in tasks}
input_file = "multitask_example.csv"
n_features = 10
n_tasks = len(tasks)
# Define train dataset
n_train = 100
X_train = np.random.rand(n_train, n_features)
y_train = np.random.randint(2, size=(n_train, n_tasks))
w_train = np.ones_like(y_train)
ids_train = ["C"] * n_train
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train,
w_train, ids_train, tasks)
# Define test dataset
n_test = 10
X_test = np.random.rand(n_test, n_features)
y_test = np.random.randint(2, size=(n_test, n_tasks))
w_test = np.ones_like(y_test)
ids_test = ["C"] * n_test
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test,
w_test, ids_test, tasks)
params_dict = {
"batch_size": 32,
"data_shape": train_dataset.get_data_shape()
}
classification_metrics = [Metric(metrics.roc_auc_score)]
def model_builder(tasks,
task_types,
model_params,
model_builder,
verbosity=None):
return SklearnModel(tasks,
task_types,
model_params,
model_builder,
model_instance=LogisticRegression())
multitask_model = SingletaskToMultitask(tasks, task_types, params_dict,
self.model_dir, model_builder)
# Fit trained model
multitask_model.fit(train_dataset)
multitask_model.save()
# Eval multitask_model on train
evaluator = Evaluator(multitask_model,
train_dataset,
output_transformers,
verbosity=True)
_ = evaluator.compute_model_performance(classification_metrics)
# Eval multitask_model on test
evaluator = Evaluator(multitask_model,
test_dataset,
output_transformers,
verbosity=True)
_ = evaluator.compute_model_performance(classification_metrics)
tox21_tasks, tox21_dataset, transformers = load_tox21(data_dir, reload=reload)
num_train = 7200
X, y, w, ids = tox21_dataset.to_numpy()
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:]
# Not sure if we need to constantly delete these directories...
if os.path.exists(train_dir):
shutil.rmtree(train_dir)
train_dataset = Dataset.from_numpy(train_dir,
X_train,
y_train,
w_train,
ids_train,
tox21_tasks,
verbosity=verbosity)
if os.path.exists(valid_dir):
shutil.rmtree(valid_dir)
valid_dataset = Dataset.from_numpy(valid_dir, X_valid, y_valid, w_valid,
ids_valid, tox21_tasks, verbosity)
# Fit models
tox21_task_types = {task: "classification" for task in tox21_tasks}
classification_metric = Metric(metrics.roc_auc_score,
np.mean,
verbosity=verbosity,
print("About to perform train/valid/test split.")
num_train = .8 * len(dataset)
X, y, w, ids = dataset.to_numpy()
num_tasks = 120
pcba_tasks = pcba_tasks[:num_tasks]
print("Using following tasks")
print(pcba_tasks)
X_train, X_valid = X[:num_train], X[num_train:]
y_train, y_valid = y[:num_train, :num_tasks], y[num_train:, :num_tasks]
w_train, w_valid = w[:num_train, :num_tasks], w[num_train:, :num_tasks]
ids_train, ids_valid = ids[:num_train], ids[num_train:]
if os.path.exists(train_dir):
shutil.rmtree(train_dir)
train_dataset = Dataset.from_numpy(train_dir, X_train, y_train,
w_train, ids_train, pcba_tasks)
if os.path.exists(valid_dir):
shutil.rmtree(valid_dir)
valid_dataset = Dataset.from_numpy(valid_dir, X_valid, y_valid,
w_valid, ids_valid, pcba_tasks)
# Fit Logistic Regression models
pcba_task_types = {task: "classification" for task in pcba_tasks}
classification_metric = Metric(metrics.roc_auc_score, np.mean,
verbosity=verbosity,
mode="classification")
params_dict = {
"batch_size": 64,
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)
############################################################# DEBUG
y = y[y_inds]
############################################################# DEBUG
X = np.vstack(features)
w = np.ones_like(y)
dataset = Dataset.from_numpy(data_dir, X, y, w, ids)
transformers = []
return tasks, dataset, transformers
def test_sklearn_multitask_classification(self):
"""Test that sklearn models can learn on simple multitask classification."""
np.random.seed(123)
n_tasks = 4
dataset = sklearn.datasets.load_digits(n_class=2)
X, y = dataset.data, dataset.target
y = np.reshape(y, (len(y), 1))
y = np.hstack([y] * n_tasks)
frac_train = .7
n_samples = len(X)
X_train, y_train = X[:frac_train * n_samples], y[:frac_train *
n_samples]
X_test, y_test = X[frac_train * n_samples:], y[frac_train * n_samples:]
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train)
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test)
tasks = train_dataset.get_task_names()
task_types = {task: "classification" for task in tasks}
model_params = {
"batch_size": None,
"data_shape": train_dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score,
verbosity=verbosity)
def model_builder(tasks,
task_types,
model_params,
model_dir,
verbosity=None):
return SklearnModel(tasks,
task_types,
model_params,
model_dir,
mode="classification",
model_instance=LogisticRegression(),
verbosity=verbosity)
model = SingletaskToMultitask(tasks,
task_types,
model_params,
self.model_dir,
model_builder,
verbosity=verbosity)
# Fit trained model
model.fit(train_dataset)
model.save()
# Eval model on train
transformers = []
train_evaluator = Evaluator(model,
train_dataset,
transformers,
verbosity=verbosity)
train_scores = train_evaluator.compute_model_performance(
[classification_metric])
print("train_scores")
print(train_scores)
# Eval model on test
transformers = []
evaluator = Evaluator(model,
test_dataset,
transformers,
verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
print("scores")
print(scores)
for score in scores[classification_metric.name]:
assert score > .5
def test_tf_skewed_missing_classification_overfit(self):
"""TF, skewed data, few actives
Test tensorflow models overfit 0/1 datasets with missing data and few
actives. This is intended to be as close to singletask MUV datasets as
possible.
"""
tasks = ["task0"]
task_types = {task: "classification" for task in tasks}
n_samples = 5120
n_features = 6
n_tasks = len(tasks)
n_classes = 2
# Generate dummy dataset
np.random.seed(123)
p = .002
ids = np.arange(n_samples)
X = np.random.rand(n_samples, n_features)
y = np.random.binomial(1, p, size=(n_samples, n_tasks))
w = np.ones((n_samples, n_tasks))
y_flat, w_flat = np.squeeze(y), np.squeeze(w)
y_nonzero = y_flat[w_flat != 0]
num_nonzero = np.count_nonzero(y_nonzero)
weight_nonzero = len(y_nonzero)/num_nonzero
w_flat[y_flat != 0] = weight_nonzero
w = np.reshape(w_flat, (n_samples, n_tasks))
dataset = Dataset.from_numpy(self.train_dir, X, y, w, ids, tasks)
model_params = {
"layer_sizes": [1200],
"dropouts": [.0],
"learning_rate": 0.003,
"momentum": .9,
"batch_size": 75,
"num_classification_tasks": 1,
"num_classes": n_classes,
"num_features": n_features,
"weight_init_stddevs": [1.],
"bias_init_consts": [1.],
"nb_epoch": 250,
"penalty": 0.0,
"optimizer": "adam",
"data_shape": dataset.get_data_shape()
}
verbosity = "high"
classification_metric = Metric(metrics.roc_auc_score, verbosity=verbosity)
model = TensorflowModel(
tasks, task_types, model_params, self.model_dir,
tf_class=TensorflowMultiTaskClassifier,
verbosity=verbosity)
# Fit trained model
model.fit(dataset)
model.save()
# Eval model on train
transformers = []
evaluator = Evaluator(model, dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([classification_metric])
assert scores[classification_metric.name] > .8
print("About to perform train/valid/test split.")
num_train = .8 * len(dataset)
X, y, w, ids = dataset.to_numpy()
num_tasks = 120
pcba_tasks = pcba_tasks[:num_tasks]
print("Using following tasks")
print(pcba_tasks)
X_train, X_valid = X[:num_train], X[num_train:]
y_train, y_valid = y[:num_train, :num_tasks], y[num_train:, :num_tasks]
w_train, w_valid = w[:num_train, :num_tasks], w[num_train:, :num_tasks]
ids_train, ids_valid = ids[:num_train], ids[num_train:]
if os.path.exists(train_dir):
shutil.rmtree(train_dir)
train_dataset = Dataset.from_numpy(train_dir, X_train, y_train,
w_train, ids_train, pcba_tasks)
if os.path.exists(valid_dir):
shutil.rmtree(valid_dir)
valid_dataset = Dataset.from_numpy(valid_dir, X_valid, y_valid,
w_valid, ids_valid, pcba_tasks)
# Fit Logistic Regression models
pcba_task_types = {task: "classification" for task in pcba_tasks}
classification_metric = Metric(metrics.roc_auc_score, np.mean,
verbosity=verbosity,
mode="classification")
params_dict = {
"batch_size": None,
def featurize(self,
input_files,
data_dir,
shard_size=8192,
num_shards_per_batch=24,
worker_pool=None,
logging=True,
debug=False):
"""Featurize provided files and write to specified location."""
############################################################## TIMING
time1 = time.time()
############################################################## TIMING
log("Loading raw samples now.", self.verbosity)
log("shard_size: %d" % shard_size, self.verbosity)
log("num_shards_per_batch: %d" % num_shards_per_batch, self.verbosity)
# Allow users to specify a single file for featurization
if not isinstance(input_files, list):
input_files = [input_files]
if not os.path.exists(data_dir):
os.makedirs(data_dir)
# Construct partial function to write datasets.
if not len(input_files):
return None
input_type = get_input_type(input_files[0])
if logging:
mp.log_to_stderr()
if worker_pool is None:
if logging:
worker_pool = LoggingPool(processes=1)
else:
worker_pool = mp.Pool(processes=1)
log("Spawning workers now.", self.verbosity)
metadata_rows = []
data_iterator = it.izip(
it.repeat((self, shard_size, input_type, data_dir)),
enumerate(load_data(input_files, shard_size, self.verbosity)))
# Turns out python map is terrible and exhausts the generator as given.
# Solution seems to be to to manually pull out N elements from iterator,
# then to map on only those N elements. BLECH. Python should do a better
# job here.
num_batches = 0
############################################################## TIMING
time2 = time.time()
log("TIMING: pre-map featurization took %0.3f s" % (time2 - time1))
############################################################## TIMING
while True:
log("About to start processing next batch of shards",
self.verbosity)
############################################################## TIMING
time1 = time.time()
############################################################## TIMING
iterator = itertools.islice(data_iterator, num_shards_per_batch)
if not debug:
batch_metadata = worker_pool.map(featurize_map_function,
iterator)
else:
batch_metadata = []
for elt in iterator:
batch_metadata.append(featurize_map_function(elt))
############################################################## TIMING
time2 = time.time()
log("TIMING: map call on batch took %0.3f s" % (time2 - time1),
self.verbosity)
############################################################## TIMING
if batch_metadata:
metadata_rows.extend(
[elt for elt in batch_metadata if elt is not None])
num_batches += 1
log(
"Featurized %d datapoints\n" %
(shard_size * num_shards_per_batch * num_batches),
self.verbosity)
else:
break
############################################################## TIMING
time1 = time.time()
############################################################## TIMING
# TODO(rbharath): This whole bit with metadata_rows is an awkward way of
# creating a Dataset. Is there a more elegant solutions?
dataset = Dataset(data_dir=data_dir,
metadata_rows=metadata_rows,
reload=reload,
verbosity=self.verbosity)
############################################################## TIMING
time2 = time.time()
print("TIMING: dataset construction took %0.3f s" % (time2 - time1),
self.verbosity)
############################################################## TIMING
return dataset
def test_multiload(self):
"""Check can re-use featurization for multiple task selections.
TODO(rbharath): This test seems silly after the recent round of
refactoring. Can it be removed?
"""
# Only for debug!
np.random.seed(123)
# Set some global variables up top
reload = True
verbosity = "high"
current_dir = os.path.dirname(os.path.realpath(__file__))
#Make directories to store the raw and featurized datasets.
data_dir = os.path.join(self.base_dir, "dataset")
train_dir = os.path.join(self.base_dir, "train_dataset")
valid_dir = os.path.join(self.base_dir, "valid_dataset")
test_dir = os.path.join(self.base_dir, "test_dataset")
model_dir = os.path.join(self.base_dir, "model")
# Load dataset
print("About to load dataset.")
dataset_file = os.path.join(
current_dir, "../../models/tests/multitask_example.csv")
dataset = load_from_disk(dataset_file)
print("Columns of dataset: %s" % str(dataset.columns.values))
print("Number of examples in dataset: %s" % str(dataset.shape[0]))
# Featurize tox21 dataset
print("About to featurize dataset.")
featurizer = CircularFingerprint(size=1024)
all_tasks = ["task%d"%i for i in range(17)]
####### Do featurization
loader = DataLoader(tasks=all_tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
dataset = loader.featurize(
dataset_file, data_dir)
# Do train/valid split.
X_multi, y_multi, w_multi, ids_multi = dataset.to_numpy()
####### Do singletask load
y_tasks, w_tasks, = [], []
for ind, task in enumerate(all_tasks):
print("Processing task %s" % task)
dataset = Dataset(data_dir, verbosity=verbosity, reload=reload)
X_task, y_task, w_task, ids_task = dataset.to_numpy()
y_tasks.append(y_task[:, ind])
w_tasks.append(w_task[:, ind])
################## Do comparison
for ind, task in enumerate(all_tasks):
y_multi_task = y_multi[:, ind]
w_multi_task = w_multi[:, ind]
y_task = y_tasks[ind]
w_task = w_tasks[ind]
np.testing.assert_allclose(y_multi_task.flatten(), y_task.flatten())
np.testing.assert_allclose(w_multi_task.flatten(), w_task.flatten())
from deepchem.datasets import Dataset
from deepchem.models.tensorflow_models import TensorflowModel
from deepchem.models.tensorflow_models.fcnet import TensorflowMultiTaskClassifier
from bokeh.plotting import figure
from bokeh.models import HoverTool, ColumnDataSource
from bokeh.embed import components
from bokeh.palettes import Plasma256
import pandas as pd
app = Flask(__name__)
Plasma256.extend(Plasma256[::-1])
cur_dir = os.path.dirname(__file__)
data_dir = os.path.join(cur_dir, 'data')
base_dir = '/data/ballen/ML/kinaseDeepLearningAllKinase_081516'
test_dir = os.path.join(base_dir, 'test_dataset_random')
kinase_tasks = Dataset(test_dir, reload=True).get_task_names()
kinase_task_types = {task: 'classification' for task in kinase_tasks}
params_dict = {
"activation": "relu",
"momentum": .9,
"batch_size": 128,
"init": "glorot_uniform",
"data_shape": (1024, ),
"learning_rate": 1e-3,
"decay": 1e-6,
"nb_hidden": (2000, 500),
"nb_epoch": 100,
"nesterov": False,
"dropouts": (.5, .5),
"nb_layers": 2,
"batchnorm": False,
model_dir = os.path.join(base_dir, "model")
print("About to perform train/valid/test split.")
num_train = .8 * len(dataset)
X, y, w, ids = dataset.to_numpy()
num_tasks = 17
muv_tasks = muv_tasks[:num_tasks]
X_train, X_valid = X[:num_train], X[num_train:]
y_train, y_valid = y[:num_train, :num_tasks], y[num_train:, :num_tasks]
w_train, w_valid = w[:num_train, :num_tasks], w[num_train:, :num_tasks]
ids_train, ids_valid = ids[:num_train], ids[num_train:]
if os.path.exists(train_dir):
shutil.rmtree(train_dir)
train_dataset = Dataset.from_numpy(train_dir, X_train, y_train,
w_train, ids_train, muv_tasks,
verbosity=verbosity)
if os.path.exists(valid_dir):
shutil.rmtree(valid_dir)
valid_dataset = Dataset.from_numpy(valid_dir, X_valid, y_valid,
w_valid, ids_valid, muv_tasks,
verbosity=verbosity)
# Fit Logistic Regression models
muv_task_types = {task: "classification" for task in muv_tasks}
classification_metric = Metric(metrics.roc_auc_score, np.mean,
verbosity=verbosity,
mode="classification")
def load_pcba(base_dir, reload=True):
"""Load PCBA datasets. Does not do train/test split"""
# Set some global variables up top
reload = True
verbosity = "high"
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 PCBA dataset
print("About to load PCBA dataset.")
dataset_file = os.path.join(
current_dir, "../../datasets/pcba.csv.gz")
dataset = load_from_disk(dataset_file)
print("Columns of dataset: %s" % str(dataset.columns.values))
print("Number of examples in dataset: %s" % str(dataset.shape[0]))
# Featurize PCBA dataset
print("About to featurize PCBA dataset.")
featurizer = CircularFingerprint(size=1024)
all_PCBA_tasks = [
'PCBA-1030','PCBA-1379','PCBA-1452','PCBA-1454','PCBA-1457',
'PCBA-1458','PCBA-1460','PCBA-1461','PCBA-1468','PCBA-1469',
'PCBA-1471','PCBA-1479','PCBA-1631','PCBA-1634','PCBA-1688',
'PCBA-1721','PCBA-2100','PCBA-2101','PCBA-2147','PCBA-2242',
'PCBA-2326','PCBA-2451','PCBA-2517','PCBA-2528','PCBA-2546',
'PCBA-2549','PCBA-2551','PCBA-2662','PCBA-2675','PCBA-2676',
'PCBA-411','PCBA-463254','PCBA-485281','PCBA-485290','PCBA-485294',
'PCBA-485297','PCBA-485313','PCBA-485314','PCBA-485341','PCBA-485349',
'PCBA-485353','PCBA-485360','PCBA-485364','PCBA-485367','PCBA-492947',
'PCBA-493208','PCBA-504327','PCBA-504332','PCBA-504333','PCBA-504339',
'PCBA-504444','PCBA-504466','PCBA-504467','PCBA-504706','PCBA-504842',
'PCBA-504845','PCBA-504847','PCBA-504891','PCBA-540276','PCBA-540317',
'PCBA-588342','PCBA-588453','PCBA-588456','PCBA-588579','PCBA-588590',
'PCBA-588591','PCBA-588795','PCBA-588855','PCBA-602179','PCBA-602233',
'PCBA-602310','PCBA-602313','PCBA-602332','PCBA-624170','PCBA-624171',
'PCBA-624173','PCBA-624202','PCBA-624246','PCBA-624287','PCBA-624288',
'PCBA-624291','PCBA-624296','PCBA-624297','PCBA-624417','PCBA-651635',
'PCBA-651644','PCBA-651768','PCBA-651965','PCBA-652025','PCBA-652104',
'PCBA-652105','PCBA-652106','PCBA-686970','PCBA-686978','PCBA-686979',
'PCBA-720504','PCBA-720532','PCBA-720542','PCBA-720551','PCBA-720553',
'PCBA-720579','PCBA-720580','PCBA-720707','PCBA-720708','PCBA-720709',
'PCBA-720711','PCBA-743255','PCBA-743266','PCBA-875','PCBA-881',
'PCBA-883','PCBA-884','PCBA-885','PCBA-887','PCBA-891','PCBA-899',
'PCBA-902','PCBA-903','PCBA-904','PCBA-912','PCBA-914','PCBA-915',
'PCBA-924','PCBA-925','PCBA-926','PCBA-927','PCBA-938','PCBA-995']
loader = DataLoader(tasks=all_PCBA_tasks,
smiles_field="smiles",
featurizer=featurizer,
verbosity=verbosity)
if not reload or not os.path.exists(data_dir):
dataset = loader.featurize(dataset_file, data_dir)
regen = True
else:
dataset = Dataset(data_dir, reload=True)
# Initialize transformers
transformers = [
BalancingTransformer(transform_w=True, dataset=dataset)]
if regen:
print("About to transform data")
for transformer in transformers:
transformer.transform(dataset)
return all_PCBA_tasks, dataset, transformers
def test_sklearn_transformed_regression(self):
"""Test that sklearn models can learn on simple transformed regression datasets."""
np.random.seed(123)
dataset = sklearn.datasets.load_diabetes()
X, y = dataset.data, dataset.target
frac_train = .7
n_samples = len(X)
X_train, y_train = X[:frac_train*n_samples], y[:frac_train*n_samples]
X_test, y_test = X[frac_train*n_samples:], y[frac_train*n_samples:]
train_dataset = Dataset.from_numpy(self.train_dir, X_train, y_train)
test_dataset = Dataset.from_numpy(self.test_dir, X_test, y_test)
# Eval model on train
input_transformers = [
NormalizationTransformer(transform_X=True, dataset=train_dataset),
ClippingTransformer(transform_X=True, dataset=train_dataset)]
output_transformers = [
NormalizationTransformer(transform_y=True, dataset=train_dataset)]
transformers = input_transformers + output_transformers
for transformer in transformers:
transformer.transform(train_dataset)
for transformer in transformers:
transformer.transform(test_dataset)
tasks = train_dataset.get_task_names()
task_types = {task: "regression" for task in tasks}
model_params = {
"batch_size": None,
"data_shape": train_dataset.get_data_shape()
}
verbosity = "high"
regression_metric = Metric(metrics.r2_score, verbosity=verbosity)
model = SklearnModel(tasks, task_types, model_params, self.model_dir,
mode="regression",
model_instance=LinearRegression())
# Fit trained model
model.fit(train_dataset)
model.save()
train_evaluator = Evaluator(model, train_dataset, transformers, verbosity=verbosity)
train_scores = train_evaluator.compute_model_performance([regression_metric])
print("train_scores")
print(train_scores)
assert train_scores[regression_metric.name] > .5
# Eval model on test
transformers = []
evaluator = Evaluator(model, test_dataset, transformers, verbosity=verbosity)
scores = evaluator.compute_model_performance([regression_metric])
print("scores")
print(scores)
assert scores[regression_metric.name] > .5
