sparse stuff (52761da8) · Commits · 钟慕尧 / deepchem

deepchem/datasets/tests/init.py

+16 −0

Original line number	Diff line number	Diff line
		@@ -73,3 +73,19 @@ class TestDatasetAPI(TestAPI):
		featurizer=featurizer,
		verbosity="low")
		return loader.featurize(input_file, self.data_dir)

		def load_sparse_multitask_dataset(self):
		"""Load sparse tox multitask data."""
		if os.path.exists(self.data_dir):
		shutil.rmtree(self.data_dir)
		featurizer = CircularFingerprint(size=1024)
		tasks = ["task1", "task2", "task3", "task4", "task5", "task6",
		"task7", "task8", "task9"]
		input_file = os.path.join(
		self.current_dir, "../../models/tests/sparse_multitask_example.csv")
		loader = DataLoader(
		tasks=tasks,
		smiles_field="smiles",
		featurizers=featurizer,
		verbosity="low")
		return loader.featurize(input_file, self.data_dir)

deepchem/models/tests/sparse_multitask_example.csv

0 → 100644

+601 −0

File added.

Preview size limit exceeded, changes collapsed.

deepchem/splits/init.py

+15 −0

Original line number	Diff line number	Diff line
		@@ -76,6 +76,21 @@ class Splitter(object):
		"""
		raise NotImplementedError

		class StratifiedSplitter(Splitter):
		"""
		Class for doing stratified splits -- where data is too sparse to do regular splits
		"""
		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):
		"""
		Overrides parent implementation to do stratified split
		"""
		numpyArrayList = dataset.to_numpy();
		print(numpyArrayList)
		return (False, False, False) #placeholder until rest of code is written

		class MolecularWeightSplitter(Splitter):
		"""
		Class for doing data splits by molecular weight.

deepchem/splits/tests/test_splitter.py

+18 −4

Original line number	Diff line number	Diff line
		@@ -19,8 +19,9 @@ class TestSplitters(TestDatasetAPI):
		"""
		Test some basic splitters.
		"""
		"""
		def test_singletask_random_split(self):
		"""Test singletask RandomSplitter class."""
		Test singletask RandomSplitter class.
		solubility_dataset = self.load_solubility_data()
		random_splitter = RandomSplitter()
		train_data, valid_data, test_data = \
		@@ -33,7 +34,7 @@ class TestSplitters(TestDatasetAPI):
		assert len(test_data) == 1

		def test_singletask_scaffold_split(self):
		"""Test singletask ScaffoldSplitter class."""
		Test singletask ScaffoldSplitter class.
		solubility_dataset = self.load_solubility_data()
		scaffold_splitter = ScaffoldSplitter()
		train_data, valid_data, test_data = \
		@@ -46,7 +47,7 @@ class TestSplitters(TestDatasetAPI):
		assert len(test_data) == 1

		def test_multitask_random_split(self):
		"""Test multitask RandomSplitter class."""
		Test multitask RandomSplitter class.
		multitask_dataset = self.load_multitask_data()
		random_splitter = RandomSplitter()
		train_data, valid_data, test_data = \
		@@ -59,7 +60,7 @@ class TestSplitters(TestDatasetAPI):
		assert len(test_data) == 1

		def test_multitask_scaffold_split(self):
		"""Test multitask ScaffoldSplitter class."""
		Test multitask ScaffoldSplitter class.
		multitask_dataset = self.load_multitask_data()
		scaffold_splitter = ScaffoldSplitter()
		train_data, valid_data, test_data = \
		@@ -70,3 +71,16 @@ class TestSplitters(TestDatasetAPI):
		assert len(train_data) == 8
		assert len(valid_data) == 1
		assert len(test_data) == 1
		"""
		def test_stratified_multitask_split(self):
		print("In stratified tester")
		sparse_dataset = self.load_sparse_multitask_dataset()
		stratified_splitter = StratifiedSplitter()
		train_data, valid_data, test_data = \
		stratified_splitter.train_valid_test_split(
		sparse_dataset,
		self.train_dir, self.valid_dir, self.test_dir,
		frac_train = 0.8, frac_valid = 0.1, frac_test = 0.1
		)
		print("end of stratified test")
		assert 1 == 1

Admin message