+docstrings (ed0c5ebf) · Commits · 钟慕尧 / deepchem

AUTHORS

deleted100644 → 0

+0 −78

Original line number	Diff line number	Diff line
		Alexander Rose <alexander.rose@weirdbyte.de>
		Aneesh <apappu97@gmail.com>
		Aneesh Pappu <apappu97@gmail.com>
		Anthony Gitter <agitter@users.noreply.github.com>
		Bharath <rbharath@stanford.edu>
		Bharath Ramsundar <bharath.ramsundar@gmail.com>
		Bharath Ramsundar <rbharath@gpu-15-5.local>
		Bharath Ramsundar <rbharath@gpu-19-2.local>
		Bharath Ramsundar <rbharath@gpu-9-10.local>
		Bharath Ramsundar <rbharath@gpu-9-7.local>
		Bharath Ramsundar <rbharath@sherlock-ln01.stanford.edu>
		Bharath Ramsundar <rbharath@sherlock-ln02.stanford.edu>
		Bharath Ramsundar <rbharath@stanford.edu>
		Bharath Ramsundar <rbharath@vsp-compute-38.stanford.edu>
		Bowen Liu <bowen@bowenliu.net>
		Bowen Liu <bowenliu16@users.noreply.github.com>
		Bowen Liu <liubowen@sherlock-ln02.stanford.edu>
		CCXD <c.c.lam.2@umail.leidenuniv.nl>
		Carlos Hernandez <cxh@stanford.edu>
		DorisMai <huanghao@stanford.edu>
		Evan N. Feinberg <evan.n.feinberg@gmail.com>
		Franklin Lee <flee2@stanford.edu>
		Hai Nguyen <hainm.comp@gmail.com>
		Hai Nguyen <hainm@users.noreply.github.com>
		Han Raut Altae-Tran <hraut@sherlock-ln02.stanford.edu>
		Haozhen Wu <hwu84@wisc.edu>
		J <sha0lin@alumni.carnegiemellon.edu>
		Joe Gomes <jgomes@berkeley.edu>
		Joe Gomes <joegomes@sherlock-ln02.stanford.edu>
		Joe Gomes <joegomes@stanford.edu>
		John Chodera <john.chodera@choderalab.org>
		Joseph Gomes <joegomes@stanford.edu>
		Joseph Heenan <jheenan@greenkeytech.com>
		Juan Eiros <j.eiros-zamora14@imperial.ac.uk>
		Karl Leswing <karl.leswing@gmail.com>
		Karl Leswing <lilleswing@gmail.com>
		Levi Pierce <lpierce@relaytx.com>
		Maciej Wójcikowski <mwojcikowski@users.noreply.github.com>
		Nate Stanley <dr-nate@users.noreply.github.com>
		Patrick Hop <hop.patrick1@gmail.com>
		Patrick Hop <patrickhop@ph-dev.local>
		Peter Eastman <peter.eastman@gmail.com>
		Prasad Kawthekar <prasadkawthekar1@gmail.com>
		Steven Kearnes <skearnes@users.noreply.github.com>
		Ubuntu <ubuntu@ip-172-31-5-2.us-west-1.compute.internal>
		Ubuntu <ubuntu@ip-172-31-55-121.ec2.internal>
		Yutong Zhao <proteneer@gmail.com>
		ZHENQIN WU <zqwu@gpu-17-35.local>
		ZHENQIN WU <zqwu@gpu-9-1.local>
		ZHENQIN WU <zqwu@gpu-9-2.local>
		ZHENQIN WU <zqwu@sh-5-36.local>
		ZHENQIN WU <zqwu@sherlock-ln01.stanford.edu>
		ZHENQIN WU <zqwu@sherlock-ln02.stanford.edu>
		ZHENQIN WU <zqwu@sherlock-ln03.stanford.edu>
		ZHENQIN WU <zqwu@sherlock-ln04.stanford.edu>
		Zheng Xu <xuzheng1111@gmail.com>
		Zhenqin Wu <zhenqin.wu2@gmail.com>
		Zhenqin Wu <zqwu@stanford.edu>
		calebgeniesse <calebgeniesse@gmail.com>
		cc <c.c.lam.2@umail.leidenuniv.nl>
		cfperez <christian.f.perez@gmail.com>
		cxh <cxh@liberty.stanford.edu>
		dibya <dibyadeep@gmail.com>
		dibyadeeppaul <dibyadeep@gmail.com>
		evanfeinberg <enf@vsp-compute-01.stanford.edu>
		evanfeinberg <evan.n.feinberg@gmail.com>
		haozhenWu <hwu84@wisc.edu>
		jchodera <john.chodera@choderalab.org>
		joegomes <jgomes@berkeley.edu>
		ktaneishi <ktaneishi@users.noreply.github.com>
		leswing <Karl>
		leswing <lilleswing@gmail.com>
		miaecle <zqwu@stanford.edu>
		patrickhop <hop.patrick1@gmail.com>
		peastman <peastman@stanford.edu>
		unknown <Zhenqin Wu@DESKTOP-DULN7K0.stanford.edu>
		unknown <吴桢钦>
		vipulraheja <vipul.raheja@human.x.ai>

ChangeLog

deleted100644 → 0

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File deleted.

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deepchem/models/tensorgraph/models/graph_models.py

+18 −1

Original line number	Diff line number	Diff line
		@@ -609,7 +609,19 @@ class GraphConvTensorGraph(TensorGraph):
		labels=self.my_labels,
		weights=[self.my_task_weights])

		def bayesian_predict(self, X, transformers=[], n_passes=4, untransform=False):
		def bayesian_predict(self,
		dataset,
		transformers=[],
		n_passes=4,
		untransform=False):
		"""Generates predictions and confidences on a dataset object
		https://arxiv.org/pdf/1506.02142.pdf

		# Returns:
		mu: numpy ndarray of shape (n_samples, n_tasks)
		sigma: numpy ndarray of shape (n_samples, n_tasks)
		"""
		X = dataset.X
		max_index = X.shape[0] - 1
		num_batches = (max_index // self.batch_size) + 1

		@@ -634,6 +646,11 @@ class GraphConvTensorGraph(TensorGraph):
		return mu[:max_index + 1], sigma[:max_index + 1]

		def predict_on_smiles(self, smiles, transformers=[], untransform=False):
		"""Generates predictions on a numpy array of smile strings

		# Returns:
		y_: numpy ndarray of shape (n_samples, n_tasks)
		"""
		max_index = len(smiles) - 1
		n_tasks = len(self.outputs)
		num_batches = (max_index // self.batch_size) + 1

deepchem/models/tensorgraph/tensor_graph.py

+4 −0

Original line number	Diff line number	Diff line
		@@ -306,6 +306,10 @@ class TensorGraph(Model):
		featurizer,
		n_tasks,
		transformers=[]):
		"""
		# Returns:
		A numpy ndarray of shape (n_samples, n_tasks)
		"""
		convmols = featurize_smiles_np(smiles, featurizer)

		dataset = NumpyDataset(X=convmols, y=None, n_tasks=len(self.outputs))

examples/delaney/delaney_graphconv_error_bars.py

+0 −1

Original line number	Diff line number	Diff line
		@@ -48,7 +48,6 @@ print(mu[:4])
		print(sigma[:4])

		target = undo_transforms(valid_dataset.y, transformers)
		#target = valid_dataset.y

		print(r2_score(target, mu))

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