No More gdb7 (ee733230) · Commits · 钟慕尧 / deepchem

examples/benchmark.py

+8 −16

Original line number	Diff line number	Diff line
		@@ -17,7 +17,7 @@ on datasets: muv, pcba, tox21, sider, toxcast
		Giving regression performances of:
		MultitaskDNN(tf_regression),
		Graph convolution regression(graphconvreg)
		on datasets: delaney, nci, kaggle, pdbbind, gdb7, chembl
		on datasets: delaney, nci, kaggle, pdbbind, chembl

		time estimation listed in README file

		@@ -51,7 +51,7 @@ from delaney.delaney_datasets import load_delaney
		from nci.nci_datasets import load_nci
		from pdbbind.pdbbind_datasets import load_pdbbind_grid
		from chembl.chembl_datasets import load_chembl
		from gdb7.gdb7_datasets import load_gdb7
		from qm7.qm7_datasets import load_qm7
		from sampl.sampl_datasets import load_sampl
		from clintox.clintox_datasets import load_clintox

		@@ -80,7 +80,7 @@ def benchmark_loading_datasets(hyper_parameters,
		if dataset in ['muv', 'pcba', 'tox21', 'sider', 'toxcast', 'clintox']:
		mode = 'classification'
		elif dataset in ['kaggle', 'delaney', 'nci', 'pdbbind', 'chembl',
		'gdb7', 'sampl']:
		'sampl']:
		mode = 'regression'
		else:
		raise ValueError('Dataset not supported')
		@@ -112,18 +112,10 @@ def benchmark_loading_datasets(hyper_parameters,
		if not model in ['tf_regression']:
		return

		if dataset in ['gdb7']:
		featurizer = None
		if split in ['scaffold']: # gdb7 supports index, random and indice splitting
		return
		if not model in ['tf_regression']:
		return

		if split in ['year']:
		if not dataset in ['chembl']:
		return
		elif split in ['indice']:
		if not dataset in ['gdb7']:
		return
		elif not split in [None, 'index','random','scaffold']:
		raise ValueError('Splitter function not supported')
		@@ -133,7 +125,7 @@ def benchmark_loading_datasets(hyper_parameters,
		'sider': load_sider, 'toxcast': load_toxcast,
		'kaggle': load_kaggle, 'delaney': load_delaney,
		'pdbbind': load_pdbbind_grid,
		'chembl': load_chembl, 'gdb7': load_gdb7,
		'chembl': load_chembl,
		'sampl': load_sampl, 'clintox': load_clintox}

		print('-------------------------------------')
		@@ -152,7 +144,7 @@ def benchmark_loading_datasets(hyper_parameters,
		train_dataset, valid_dataset, test_dataset = all_dataset
		time_finish_loading = time.time()
		# time_finish_loading-time_start is the time(s) used for dataset loading
		if dataset in ['kaggle', 'pdbbind', 'gdb7']:
		if dataset in ['kaggle', 'pdbbind']:
		n_features = train_dataset.get_data_shape()[0]
		# dataset has customized features

		@@ -546,7 +538,7 @@ if __name__ == '__main__':
		'tf_regression, graphconvreg')
		parser.add_argument('-d', action='append', dest='dataset_args', default=[],
		help='Choice of dataset: tox21, sider, muv, toxcast, pcba, ' +
		'kaggle, delaney, nci, pdbbindi, chembl, gdb7, clintox')
		'kaggle, delaney, nci, pdbbindi, chembl, clintox')
		args = parser.parse_args()
		#Datasets and models used in the benchmark test
		splitters = args.splitter_args
		@@ -560,7 +552,7 @@ if __name__ == '__main__':
		'tf_regression', 'graphconvreg']
		if len(datasets) == 0:
		datasets = ['tox21', 'sider', 'muv', 'toxcast', 'pcba', 'clintox',
		'delaney', 'nci', 'kaggle', 'pdbbind', 'chembl', 'gdb7']
		'delaney', 'nci', 'kaggle', 'pdbbind', 'chembl']

		#input hyperparameters
		#tf: dropouts, learning rate, layer_sizes, weight initial stddev,penalty,

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