update (54efe778) · Commits · 钟慕尧 / deepchem

deepchem/molnet/check_availability.py

+5 −1

Original line number	Diff line number	Diff line
		@@ -120,6 +120,7 @@ CheckFeaturizer = {
		('delaney', 'graphconvreg'): ['GraphConv', 75],
		('delaney', 'dag_regression'): ['GraphConv', 75],
		('delaney', 'weave_regression'): ['Weave', 75],
		('delaney', 'mpnn'): ['Weave', [75, 14]],
		('hopv', 'tf_regression'): ['ECFP', 1024],
		('hopv', 'rf_regression'): ['ECFP', 1024],
		('hopv', 'krr'): ['ECFP', 1024],
		@@ -134,6 +135,7 @@ CheckFeaturizer = {
		('lipo', 'graphconvreg'): ['GraphConv', 75],
		('lipo', 'dag_regression'): ['GraphConv', 75],
		('lipo', 'weave_regression'): ['Weave', 75],
		('lipo', 'mpnn'): ['Weave', [75, 14]],
		('nci', 'tf_regression'): ['ECFP', 1024],
		('nci', 'rf_regression'): ['ECFP', 1024],
		('nci', 'krr'): ['ECFP', 1024],
		@@ -154,11 +156,13 @@ CheckFeaturizer = {
		('sampl', 'graphconvreg'): ['GraphConv', 75],
		('sampl', 'dag_regression'): ['GraphConv', 75],
		('sampl', 'weave_regression'): ['Weave', 75],
		('sampl', 'mpnn'): ['Weave', [75, 14]],
		('kaggle', 'tf_regression'): [None, 14293],
		('kaggle', 'rf_regression'): [None, 14293],
		('kaggle', 'krr'): [None, 14293],
		('pdbbind', 'tf_regression'): ['grid', 2052],
		('pdbbind', 'rf_regression'): ['grid', 2052],
		('pdbbind', 'krr'): ['grid', 2052],
		('qm7', 'tf_regression'): ['ECFP', 1024],
		('qm7', 'rf_regression'): ['ECFP', 1024],
		('qm7', 'krr'): ['ECFP', 1024],
		@@ -205,7 +209,7 @@ CheckSplit = {
		'muv': ['index', 'random', 'scaffold', 'task'],
		'nci': ['index', 'random', 'scaffold'],
		'pcba': ['index', 'random', 'scaffold'],
		'pdbbind': ['index', 'random'],
		'pdbbind': ['index', 'random', 'time'],
		'ppb': ['index', 'random', 'scaffold'],
		'qm7': ['index', 'random', 'stratified'],
		'qm7b': ['index', 'random', 'stratified'],

deepchem/molnet/run_benchmark_models.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -452,6 +452,7 @@ def benchmark_regression(train_dataset,
		'dtnn', 'dag_regression', 'xgb_regression', 'weave_regression', 'krr',
		'ani', 'krr_ft', 'mpnn'
		]
		import xgboost
		if hyper_parameters is None:
		hyper_parameters = hps[model]
		model_name = model

examples/delaneympnn.pkl

0 → 100644

+20 −0

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		(dp0
		S'nb_epoch'
		p1
		I50
		sS'M'
		p2
		I2
		sS'batch_size'
		p3
		I32
		sS'seed'
		p4
		I123
		sS'T'
		p5
		I1
		sS'learning_rate'
		p6
		F0.003183415042748088
		s.
		No newline at end of file

examples/delaneyxgb_regression.pkl

0 → 100644

+47 −0

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		(dp0
		S'reg_alpha'
		p1
		I0
		sS'colsample_bylevel'
		p2
		I1
		sS'scale_pos_weight'
		p3
		I1
		sS'learning_rate'
		p4
		F0.05507631674959027
		sS'max_delta_step'
		p5
		I1
		sS'base_score'
		p6
		F0.5
		sS'n_estimators'
		p7
		I5669
		sS'seed'
		p8
		I2016
		sS'early_stopping_rounds'
		p9
		I97
		sS'colsample_bytree'
		p10
		F0.66
		sS'min_child_weight'
		p11
		I5
		sS'subsample'
		p12
		F0.53
		sS'reg_lambda'
		p13
		I1
		sS'max_depth'
		p14
		I8
		sS'gamma'
		p15
		F0.0
		s.
		No newline at end of file

examples/lipompnn.pkl

0 → 100644

+20 −0

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		(dp0
		S'nb_epoch'
		p1
		I50
		sS'M'
		p2
		I8
		sS'batch_size'
		p3
		I51
		sS'seed'
		p4
		I123
		sS'T'
		p5
		I1
		sS'learning_rate'
		p6
		F0.0018902288949438869
		s.
		No newline at end of file

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