update performance chart (4df9fe23) · Commits · 钟慕尧 / deepchem

README.md

+293 −186

File changed.

Preview size limit exceeded, changes collapsed.

+3 −3

Original line number	Diff line number	Diff line
		@@ -100,9 +100,9 @@ CheckFeaturizer = {
		}

		CheckSplit = {
		'bace_c': ['index', 'random'],
		'bace_r': ['index', 'random'],
		'bbbp': ['index', 'random', 'scaffold'],
		'bace_c': ['random', 'scaffold'],
		'bace_r': ['random', 'scaffold'],
		'bbbp': ['random', 'scaffold'],
		'chembl': ['index', 'random', 'scaffold', 'year'],
		'clearance': ['index', 'random', 'scaffold'],
		'clintox': ['index', 'random', 'scaffold'],

+5 −3

Original line number	Diff line number	Diff line
		@@ -54,7 +54,8 @@ def load_bace_regression(featurizer=None, split='random'):

		splitters = {
		'index': deepchem.splits.IndexSplitter(),
		'random': deepchem.splits.RandomSplitter()
		'random': deepchem.splits.RandomSplitter(),
		'scaffold': deepchem.splits.ScaffoldSplitter()
		}
		splitter = splitters[split]
		train, valid, test = splitter.train_valid_test_split(dataset)
		@@ -104,7 +105,8 @@ def load_bace_classification(featurizer=None, split='random'):

		splitters = {
		'index': deepchem.splits.IndexSplitter(),
		'random': deepchem.splits.RandomSplitter()
		'random': deepchem.splits.RandomSplitter(),
		'scaffold': deepchem.splits.ScaffoldSplitter()
		}
		splitter = splitters[split]
		train, valid, test = splitter.train_valid_test_split(dataset)

+7 −7

Original line number	Diff line number	Diff line
		@@ -71,15 +71,15 @@ hps['tf_regression'] = {
		'learning_rate': 0.0008
		}
		hps['tf_regression_ft'] = {
		'layer_sizes': [1000, 1000],
		'weight_init_stddevs': [0.02, 0.02],
		'bias_init_consts': [1., 1.],
		'dropouts': [0.25, 0.25],
		'penalty': 0.0005,
		'layer_sizes': [400, 100, 100],
		'weight_init_stddevs': [0.05, 0.1, 0.1],
		'bias_init_consts': [0., 0., 0.],
		'dropouts': [0.01, 0.01, 0.01],
		'penalty': 0.,
		'penalty_type': 'l2',
		'batch_size': 128,
		'batch_size': 25,
		'nb_epoch': 50,
		'learning_rate': 0.0008,
		'learning_rate': 0.001,
		'fit_transformers': deepchem.trans.CoulombFitTransformer
		}
		hps['rf_regression'] = {'n_estimators': 500}

+1 −1

Original line number	Diff line number	Diff line
		@@ -43,7 +43,7 @@ class TestMolnet(unittest.TestCase):
		def test_qm7_multitask(self):
		"""Tests molnet benchmarking on qm7 with multitask network."""
		datasets = ['qm7']
		model = 'tf_regressioni_ft'
		model = 'tf_regression_ft'
		split = 'random'
		out_path = tempfile.mkdtemp()
		dc.molnet.run_benchmark(