yapf (fd0766bd) · Commits · 钟慕尧 / deepchem

deepchem/models/tensorflow_models/IRV.py

+17 −22

Original line number	Diff line number	Diff line
		@@ -12,15 +12,13 @@ from deepchem.models.tensorgraph.layers import Layer, SigmoidCrossEntropy, \
		from deepchem.models.tensorgraph.layers import convert_to_layers
		from deepchem.trans import undo_transforms


		class IRVLayer(Layer):
		""" Core layer of IRV classifier, architecture described in:
		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750043/
		"""

		def __init__(self,
		n_tasks,
		K,
		**kwargs):
		def __init__(self, n_tasks, K, **kwargs):
		"""
		Parameters
		----------
		@@ -79,14 +77,13 @@ class IRVLayer(Layer):
		def set_tensors(self, tensor):
		self.V, self.W, self.b, self.b2, self.out_tensor, self.trainable_weights, self.variables = tensor


		class IRVRegularize(Layer):
		""" This Layer extracts the trainable weights in IRVLayer
		and return the their L2-norm
		"""
		def __init__(self,
		IRVLayer,
		penalty=0.0,
		**kwargs):

		def __init__(self, IRVLayer, penalty=0.0, **kwargs):
		self.IRVLayer = IRVLayer
		self.penalty = penalty
		super(IRVRegularize, self).__init__(**kwargs)
		@@ -101,14 +98,12 @@ class IRVRegularize(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class Slice(Layer):
		""" Choose a slice of input given axis and order
		"""

		def __init__(self,
		slice_num,
		axis=1,
		**kwargs):
		def __init__(self, slice_num, axis=1, **kwargs):
		"""
		Parameters
		----------
		@@ -135,6 +130,7 @@ class Slice(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class TensorflowMultiTaskIRVClassifier(TensorGraph):

		def __init__(self,
		@@ -163,7 +159,6 @@ class TensorflowMultiTaskIRVClassifier(TensorGraph):
		super(TensorflowMultiTaskIRVClassifier, self).__init__(**kwargs)
		self.build_graph()


		def build_graph(self):
		"""Constructs the graph architecture of IRV as described in:

deepchem/models/tensorgraph/layers.py

+6 −2

Original line number	Diff line number	Diff line
		@@ -1183,6 +1183,7 @@ class SoftMax(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class Sigmoid(Layer):

		def __init__(self, in_layers=None, **kwargs):
		@@ -1202,6 +1203,7 @@ class Sigmoid(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class Concat(Layer):

		def __init__(self, in_layers=None, axis=1, **kwargs):
		@@ -1548,6 +1550,7 @@ class SoftMaxCrossEntropy(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class SigmoidCrossEntropy(Layer):

		def __init__(self, in_layers=None, **kwargs):
		@@ -1568,6 +1571,7 @@ class SigmoidCrossEntropy(Layer):
		self.out_tensor = out_tensor
		return out_tensor


		class ReduceMean(Layer):

		def __init__(self, in_layers=None, axis=None, **kwargs):

deepchem/molnet/run_benchmark_models.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -151,8 +151,10 @@ def benchmark_classification(train_dataset,
		# Building scikit logistic regression model
		def model_builder(model_dir_logreg):
		sklearn_model = LogisticRegression(
		penalty=penalty_type, C=1./penalty,
		class_weight="balanced", n_jobs=-1)
		penalty=penalty_type,
		C=1. / penalty,
		class_weight="balanced",
		n_jobs=-1)
		return deepchem.models.sklearn_models.SklearnModel(
		sklearn_model, model_dir_logreg)

Admin message