def __init__(self,
output_dim,
input_dim,
init='glorot_uniform',
inner_init='orthogonal',
forget_bias_init='one',
activation='tanh',
inner_activation='hard_sigmoid',
**kwargs):
warnings.warn(
"The dc.nn.LSTMStep is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by dc.models.tensorgraph.layers.LSTMStep",
DeprecationWarning)
super(LSTMStep, self).__init__(**kwargs)
self.output_dim = output_dim
self.init = initializations.get(init)
self.inner_init = initializations.get(inner_init)
# No other forget biases supported right now.
assert forget_bias_init == "one"
self.forget_bias_init = initializations.get(forget_bias_init)
self.activation = activations.get(activation)
self.inner_activation = activations.get(inner_activation)
self.input_dim = input_dim
def __init__(self,
n_test,
n_support,
max_depth,
init='glorot_uniform',
activation='linear',
**kwargs):
"""
Unlike the AttnLSTM model which only modifies the test vectors additively,
this model allows for an additive update to be performed to both test and
support using information from each other.
Parameters
----------
n_support: int
Size of support set.
n_test: int
Size of test set.
max_depth: int
Number of LSTM Embedding layers.
init: string
Type of weight initialization (from Keras)
activation: string
Activation type (ReLu/Linear/etc.)
"""
super(ResiLSTMEmbedding, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_depth = max_depth
self.n_test = n_test
self.n_support = n_support
def __init__(self,
n_test,
n_support,
n_feat,
max_depth,
init='glorot_uniform',
activation='linear',
dropout=None,
**kwargs):
"""
Parameters
----------
n_support: int
Size of support set.
n_test: int
Size of test set.
n_feat: int
Number of features per atom
max_depth: int
Number of "processing steps" used by sequence-to-sequence for sets model.
init: str, optional
Type of initialization of weights
activation: str, optional
Activation for layers.
dropout: float, optional
Dropout probability
"""
super(AttnLSTMEmbedding, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_depth = max_depth
self.n_test = n_test
self.n_support = n_support
self.n_feat = n_feat
def __init__(self,
nb_filter,
init='glorot_uniform',
activation='linear',
dropout=None,
max_deg=10,
min_deg=0,
**kwargs):
"""
Parameters
----------
nb_filter: int
Number of convolutional filters.
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied after convolution.
dropout: float, optional
Dropout probability.
max_deg: int, optional
Maximum degree of atoms in molecules.
min_deg: int, optional
Minimum degree of atoms in molecules.
"""
super(GraphConv, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.nb_filter = nb_filter # Save number of filters
self.dropout = dropout # Save dropout params
self.max_deg = max_deg
self.min_deg = min_deg
# TODO(rbharath): It's not clear where nb_affine comes from.
# Is there a solid explanation here?
self.nb_affine = 2 * max_deg + (1 - min_deg)
def __init__(self,
batch_size,
n_input=128,
gaussian_expand=False,
init='glorot_uniform',
activation='tanh',
epsilon=1e-3,
momentum=0.99,
**kwargs):
"""
Parameters
----------
batch_size: int
number of molecules in a batch
n_input: int, optional
number of features for each input molecule
gaussian_expand: boolean. optional
Whether to expand each dimension of atomic features by gaussian histogram
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
self.n_input = n_input
self.batch_size = batch_size
self.gaussian_expand = gaussian_expand
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.epsilon = epsilon
self.momentum = momentum
super(WeaveGather, self).__init__(**kwargs)
def __init__(self,
n_test,
n_support,
n_feat,
max_depth,
init='glorot_uniform',
activation='linear',
dropout=None,
**kwargs):
"""
Parameters
----------
n_support: int
Size of support set.
n_test: int
Size of test set.
n_feat: int
Number of features per atom
max_depth: int
Number of "processing steps" used by sequence-to-sequence for sets model.
init: str, optional
Type of initialization of weights
activation: str, optional
Activation for layers.
dropout: float, optional
Dropout probability
"""
super(AttnLSTMEmbedding, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_depth = max_depth
self.n_test = n_test
self.n_support = n_support
self.n_feat = n_feat
def __init__(self, output_dim,
init='glorot_uniform', inner_init='orthogonal',
forget_bias_init='one', activation='tanh',
inner_activation='hard_sigmoid', **kwargs):
super(LSTMStep, self).__init__(**kwargs)
self.output_dim = output_dim
self.init = initializations.get(init)
self.inner_init = initializations.get(inner_init)
# No other forget biases supported right now.
assert forget_bias_init == "one"
self.forget_bias_init = initializations.get(forget_bias_init)
self.activation = activations.get(activation)
self.inner_activation = activations.get(inner_activation)
def __init__(self, nb_filter, init='glorot_uniform', activation='linear',
dropout=None, max_deg=10, min_deg=0, **kwargs):
"""
Parameters
----------
nb_filter: int
Number of convolutional filters.
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied after convolution.
dropout: float, optional
Dropout probability.
max_deg: int, optional
Maximum degree of atoms in molecules.
min_deg: int, optional
Minimum degree of atoms in molecules.
"""
super(GraphConv, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.nb_filter = nb_filter # Save number of filters
self.dropout = dropout # Save dropout params
self.max_deg = max_deg
self.min_deg = min_deg
# TODO(rbharath): It's not clear where nb_affine comes from.
# Is there a solid explanation here?
self.nb_affine = 2*max_deg + (1-min_deg)
def __init__(self, n_test, n_support, max_depth, init='glorot_uniform',
activation='linear', **kwargs):
"""
Unlike the AttnLSTM model which only modifies the test vectors additively,
this model allows for an additive update to be performed to both test and
support using information from each other.
Parameters
----------
n_support: int
Size of support set.
n_test: int
Size of test set.
max_depth: int
Number of LSTM Embedding layers.
init: string
Type of weight initialization (from Keras)
activation: string
Activation type (ReLu/Linear/etc.)
"""
super(ResiLSTMEmbedding, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_depth = max_depth
self.n_test = n_test
self.n_support = n_support
def __init__(self,
batch_size,
n_atom_input_feat=50,
n_output=128,
init='glorot_uniform',
activation='tanh',
**kwargs):
"""
Parameters
----------
batch_size: int
number of molecules in a batch
n_atom_input_feat: int, optional
Number of features for each atom in input.
n_output: int, optional
Number of output features for each atom(concatenated)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
self.batch_size = batch_size
self.n_atom_input_feat = n_atom_input_feat
self.n_output = n_output
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(WeaveConcat, self).__init__(**kwargs)
def __init__(self,
output_dim,
init='glorot_uniform',
activation=None,
W_regularizer=None,
b_regularizer=None,
activity_regularizer=None,
W_constraint=None,
b_constraint=None,
bias=True,
input_dim=None,
**kwargs):
self.init = initializations.get(init)
self.activation = activations.get(activation)
self.output_dim = output_dim
self.input_dim = input_dim
self.W_regularizer = regularizers.get(W_regularizer)
self.b_regularizer = regularizers.get(b_regularizer)
self.activity_regularizer = regularizers.get(activity_regularizer)
self.W_constraint = constraints.get(W_constraint)
self.b_constraint = constraints.get(b_constraint)
self.bias = bias
self.input_spec = [InputSpec(ndim='2+')]
if self.input_dim:
kwargs['input_shape'] = (self.input_dim, )
super(Dense, self).__init__(**kwargs)
def __init__(self,
output_dim,
input_dim,
init='glorot_uniform',
activation="relu",
bias=True,
**kwargs):
self.init = initializations.get(init)
self.activation = activations.get(activation)
self.output_dim = output_dim
self.input_dim = input_dim
self.bias = bias
input_shape = (self.input_dim,)
if self.input_dim:
kwargs['input_shape'] = (self.input_dim,)
super(Dense, self).__init__(**kwargs)
self.input_dim = input_dim
self.W = self.add_weight(
(self.input_dim, self.output_dim),
initializer=self.init,
name='{}_W'.format(self.name))
self.b = self.add_weight(
(self.output_dim,), initializer='zero', name='{}_b'.format(self.name))
def __init__(self,
batch_size,
n_input=128,
gaussian_expand=False,
init='glorot_uniform',
activation='tanh',
epsilon=1e-3,
momentum=0.99,
**kwargs):
"""
Parameters
----------
batch_size: int
number of molecules in a batch
gaussian_expand: boolean. optional
Whether to expand each dimension of atomic features by gaussian histogram
"""
self.n_input = n_input
self.batch_size = batch_size
self.gaussian_expand = gaussian_expand
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.epsilon = epsilon
self.momentum = momentum
super(WeaveGather, self).__init__(**kwargs)
def __init__(self,
n_embedding=30,
n_distance=100,
n_hidden=60,
init='glorot_uniform',
activation='tanh',
**kwargs):
"""
Parameters
----------
n_embedding: int, optional
Number of features for each atom
n_distance: int, optional
granularity of distance matrix
n_hidden: int, optional
Number of nodes in hidden layer
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
self.n_embedding = n_embedding
self.n_distance = n_distance
self.n_hidden = n_hidden
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNStep, self).__init__(**kwargs)
def __init__(self,
n_embedding=30,
n_distance=100,
n_hidden=60,
init='glorot_uniform',
activation='tanh',
**kwargs):
"""
Parameters
----------
n_embedding: int, optional
Number of features for each atom
n_distance: int, optional
granularity of distance matrix
n_hidden: int, optional
Number of nodes in hidden layer
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
warnings.warn(
"The dc.nn.DTNNStep is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by "
"dc.models.tensorgraph.graph_layers.DTNNStep", DeprecationWarning)
self.n_embedding = n_embedding
self.n_distance = n_distance
self.n_hidden = n_hidden
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNStep, self).__init__(**kwargs)
def __init__(self,
n_embedding=30,
n_outputs=100,
layer_sizes=[100],
init='glorot_uniform',
activation='tanh',
**kwargs):
"""
Parameters
----------
n_embedding: int, optional
Number of features for each atom
n_outputs: int, optional
Number of features for each molecule(output)
layer_sizes: list of int, optional(default=[1000])
Structure of hidden layer(s)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
self.n_embedding = n_embedding
self.n_outputs = n_outputs
self.layer_sizes = layer_sizes
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNGather, self).__init__(**kwargs)
def __init__(self,
max_atoms,
n_atom_input_feat=75,
n_pair_input_feat=14,
n_atom_output_feat=50,
n_pair_output_feat=50,
n_hidden_AA=50,
n_hidden_PA=50,
n_hidden_AP=50,
n_hidden_PP=50,
update_pair=True,
init='glorot_uniform',
activation='relu',
dropout=None,
**kwargs):
"""
Parameters
----------
max_atoms: int
Maximum number of atoms in a molecule, should be defined based on dataset
n_atom_input_feat: int, optional
Number of features for each atom in input.
n_pair_input_feat: int, optional
Number of features for each pair of atoms in input.
n_atom_output_feat: int, optional
Number of features for each atom in output.
n_pair_output_feat: int, optional
Number of features for each pair of atoms in output.
n_hidden_XX: int, optional
Number of units(convolution depths) in corresponding hidden layer
update_pair: bool, optional
Whether to calculate for pair features,
could be turned off for last layer
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported here
"""
super(WeaveLayer, self).__init__(**kwargs)
self.max_atoms = max_atoms
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.update_pair = update_pair # last weave layer does not need to update
self.n_hidden_AA = n_hidden_AA
self.n_hidden_PA = n_hidden_PA
self.n_hidden_AP = n_hidden_AP
self.n_hidden_PP = n_hidden_PP
self.n_hidden_A = n_hidden_AA + n_hidden_PA
self.n_hidden_P = n_hidden_AP + n_hidden_PP
self.n_atom_input_feat = n_atom_input_feat
self.n_pair_input_feat = n_pair_input_feat
self.n_atom_output_feat = n_atom_output_feat
self.n_pair_output_feat = n_pair_output_feat
def __init__(self,
output_dim,
init='glorot_uniform',
inner_init='orthogonal',
forget_bias_init='one',
activation='tanh',
inner_activation='hard_sigmoid',
**kwargs):
super(LSTMStep, self).__init__(**kwargs)
self.output_dim = output_dim
self.init = initializations.get(init)
self.inner_init = initializations.get(inner_init)
# No other forget biases supported right now.
assert forget_bias_init == "one"
self.forget_bias_init = initializations.get(forget_bias_init)
self.activation = activations.get(activation)
self.inner_activation = activations.get(inner_activation)
def __init__(self, batch_size, activation='linear', **kwargs):
"""
Parameters
----------
batch_size: int
Number of elements in batch of data.
"""
super(GraphGather, self).__init__(**kwargs)
self.activation = activations.get(activation) # Get activations
self.batch_size = batch_size
def __init__(self, batch_size, activation='linear', **kwargs):
"""
Parameters
----------
batch_size: int
Number of elements in batch of data.
"""
super(GraphGather, self).__init__(**kwargs)
self.activation = activations.get(activation) # Get activations
self.batch_size = batch_size
def __init__(self,
n_embedding=20,
layer_sizes=[100],
init='glorot_uniform',
activation='tanh',
**kwargs):
self.n_embedding = n_embedding
self.layer_sizes = layer_sizes
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNGather, self).__init__(**kwargs)
def __init__(self,
n_embedding=20,
layer_sizes=[100],
init='glorot_uniform',
activation='tanh',
**kwargs):
self.n_embedding = n_embedding
self.layer_sizes = layer_sizes
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNGather, self).__init__(**kwargs)
def __init__(self,
max_atoms,
out_channels,
atom_number_cases=[1, 6, 7, 8],
init='glorot_uniform',
activation='relu',
**kwargs):
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_atoms = max_atoms
self.out_channels = out_channels
self.atom_number_cases = atom_number_cases
super(AtomicDifferentiatedDense, self).__init__(**kwargs)
def __init__(self,
max_atoms,
n_atom_input_feat=75,
n_pair_input_feat=14,
n_atom_output_feat=50,
n_pair_output_feat=50,
n_hidden_AA=50,
n_hidden_PA=50,
n_hidden_AP=50,
n_hidden_PP=50,
init='glorot_uniform',
activation='relu',
dropout=None,
**kwargs):
"""
Parameters
----------
n_atom_input_feat: int
Number of features for each atom in input.
n_pair_input_feat: int
Number of features for each pair of atoms in input.
n_atom_output_feat: int
Number of features for each atom in output.
n_pair_output_feat: int
Number of features for each pair of atoms in output.
n_hidden_XX: int
Number of units(convolution depths) in corresponding hidden layer
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported here
"""
super(WeaveLayer, self).__init__(**kwargs)
self.max_atoms = max_atoms
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.n_hidden_AA = n_hidden_AA
self.n_hidden_PA = n_hidden_PA
self.n_hidden_AP = n_hidden_AP
self.n_hidden_PP = n_hidden_PP
self.n_hidden_A = n_hidden_AA + n_hidden_PA
self.n_hidden_P = n_hidden_AP + n_hidden_PP
self.n_atom_input_feat = n_atom_input_feat
self.n_pair_input_feat = n_pair_input_feat
self.n_atom_output_feat = n_atom_output_feat
self.n_pair_output_feat = n_pair_output_feat
def __init__(self,
n_embedding=20,
n_distance=100,
n_hidden=20,
init='glorot_uniform',
activation='tanh',
**kwargs):
self.n_embedding = n_embedding
self.n_distance = n_distance
self.n_hidden = n_hidden
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNStep, self).__init__(**kwargs)
def __init__(self,
n_embedding=20,
n_distance=100,
n_hidden=20,
init='glorot_uniform',
activation='tanh',
**kwargs):
self.n_embedding = n_embedding
self.n_distance = n_distance
self.n_hidden = n_hidden
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNStep, self).__init__(**kwargs)
def __init__(self,
n_graph_feat=30,
n_atom_feat=75,
max_atoms=50,
layer_sizes=[100],
init='glorot_uniform',
activation='relu',
dropout=None,
batch_size=64,
**kwargs):
"""
Parameters
----------
n_graph_feat: int, optional
Number of features for each node(and the whole grah).
n_atom_feat: int, optional
Number of features listed per atom.
max_atoms: int, optional
Maximum number of atoms in molecules.
layer_sizes: list of int, optional(default=[1000])
Structure of hidden layer(s)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported here
batch_size: int, optional
number of molecules in a batch
"""
warnings.warn(
"The dc.nn.DAGLayer is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by "
"dc.models.tensorgraph.graph_layers.DAGLayer", DeprecationWarning)
super(DAGLayer, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.layer_sizes = layer_sizes
self.dropout = dropout
self.max_atoms = max_atoms
self.batch_size = batch_size
self.n_inputs = n_atom_feat + (self.max_atoms - 1) * n_graph_feat
# number of inputs each step
self.n_graph_feat = n_graph_feat
self.n_outputs = n_graph_feat
self.n_atom_feat = n_atom_feat
def __init__(self, batch_size, activation='linear', **kwargs):
"""
Parameters
----------
batch_size: int
Number of elements in batch of data.
"""
warnings.warn(
"The dc.nn.GraphGather is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by dc.models.tensorgraph.layers.GraphGather",
DeprecationWarning)
super(GraphGather, self).__init__(**kwargs)
self.activation = activations.get(activation) # Get activations
self.batch_size = batch_size
def __init__(self,
nb_filter,
n_atom_features,
batch_size,
init='glorot_uniform',
activation='linear',
dropout=None,
max_deg=10,
min_deg=0,
**kwargs):
"""
Parameters
----------
nb_filter: int
Number of convolutional filters.
n_atom_features: int
Number of features listed per atom.
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied after convolution.
dropout: float, optional
Dropout probability.
max_deg: int, optional
Maximum degree of atoms in molecules.
min_deg: int, optional
Minimum degree of atoms in molecules.
"""
warnings.warn("The dc.nn.GraphConv is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by dc.models.tensorgraph.layers.GraphConv",
DeprecationWarning)
super(Gather1, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.nb_filter = nb_filter # Save number of filters
self.dropout = dropout # Save dropout params
self.max_deg = max_deg
self.min_deg = min_deg
self.batch_size = batch_size
# Is there a solid explanation here?
self.nb_affine = max_deg + (1 - min_deg)
self.n_atom_features = n_atom_features
def __init__(self,
output_dim,
input_dim,
init='glorot_uniform',
activation="relu",
bias=True,
**kwargs):
self.init = initializations.get(init)
self.activation = activations.get(activation)
self.output_dim = output_dim
self.input_dim = input_dim
self.bias = bias
input_shape = (self.input_dim,)
if self.input_dim:
kwargs['input_shape'] = (self.input_dim,)
super(Dense, self).__init__(**kwargs)
self.input_dim = input_dim
def __init__(self,
n_test,
n_support,
n_feat,
max_depth,
init='glorot_uniform',
activation='linear',
**kwargs):
"""
Unlike the AttnLSTM model which only modifies the test vectors additively,
this model allows for an additive update to be performed to both test and
support using information from each other.
Parameters
----------
n_support: int
Size of support set.
n_test: int
Size of test set.
n_feat: int
Number of input atom features
max_depth: int
Number of LSTM Embedding layers.
init: string
Type of weight initialization (from Keras)
activation: string
Activation type (ReLu/Linear/etc.)
"""
warnings.warn(
"The dc.nn.ResiLSTMEmbedding is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by "
"dc.models.tensorgraph.layers.IterRefLSTM", DeprecationWarning)
super(ResiLSTMEmbedding, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.max_depth = max_depth
self.n_test = n_test
self.n_support = n_support
self.n_feat = n_feat
def __init__(self,
n_graph_feat=30,
n_atom_features=75,
layer_sizes=[100],
init='glorot_uniform',
activation='relu',
dropout=None,
max_atoms=50,
**kwargs):
"""
Parameters
----------
n_graph_feat: int
Number of features for each node(and the whole grah).
n_atom_features: int
Number of features listed per atom.
layer_sizes: list of int, optional(default=[1000])
Structure of hidden layer(s)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported here
max_atoms: int, optional
Maximum number of atoms in molecules.
"""
super(DAGLayer, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.layer_sizes = layer_sizes
self.dropout = dropout
self.max_atoms = max_atoms
self.n_inputs = n_atom_features + (self.max_atoms - 1) * n_graph_feat
# number of inputs each step
self.n_graph_feat = n_graph_feat
self.n_outputs = n_graph_feat
self.n_atom_features = n_atom_features
def __init__(self,
n_graph_feat=30,
n_atom_features=75,
layer_sizes=[100],
init='glorot_uniform',
activation='relu',
dropout=None,
max_atoms=50,
**kwargs):
"""
Parameters
----------
n_graph_feat: int
Number of features for each node(and the whole grah).
n_atom_features: int
Number of features listed per atom.
layer_sizes: list of int, optional(default=[1000])
Structure of hidden layer(s)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported here
max_atoms: int, optional
Maximum number of atoms in molecules.
"""
super(DAGLayer, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.layer_sizes = layer_sizes
self.dropout = dropout
self.max_atoms = max_atoms
self.n_inputs = n_atom_features + (self.max_atoms - 1) * n_graph_feat
# number of inputs each step
self.n_graph_feat = n_graph_feat
self.n_outputs = n_graph_feat
self.n_atom_features = n_atom_features
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
init_fn = initializations.get(self.init) # Set weight initialization
activation_fn = activations.get(self.activation)
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
inputs = in_layers[0].out_tensor
atom_numbers = in_layers[1].out_tensor
in_channels = inputs.get_shape().as_list()[-1]
self.W = init_fn(
[len(self.atom_number_cases), in_channels, self.out_channels])
self.b = model_ops.zeros(
(len(self.atom_number_cases), self.out_channels))
outputs = []
for i, atom_case in enumerate(self.atom_number_cases):
# optimization to allow for tensorcontraction/broadcasted mmul
# using a reshape trick. Note that the np and tf matmul behavior
# differs when dealing with broadcasts
a = inputs # (i,j,k)
b = self.W[i, :, :] # (k, l)
ai = tf.shape(a)[0]
aj = tf.shape(a)[1]
ak = tf.shape(a)[2]
bl = tf.shape(b)[1]
output = activation_fn(
tf.reshape(tf.matmul(tf.reshape(a, [ai * aj, ak]), b),
[ai, aj, bl]) + self.b[i, :])
mask = 1 - tf.to_float(tf.cast(atom_numbers - atom_case, tf.bool))
output = tf.reshape(output * tf.expand_dims(mask, 2),
(-1, self.max_atoms, self.out_channels))
outputs.append(output)
self.out_tensor = tf.add_n(outputs)
def __init__(self, output_dim, init='glorot_uniform',
activation=None,
W_regularizer=None, b_regularizer=None, activity_regularizer=None,
W_constraint=None, b_constraint=None,
bias=True, input_dim=None, **kwargs):
self.init = initializations.get(init)
self.activation = activations.get(activation)
self.output_dim = output_dim
self.input_dim = input_dim
self.W_regularizer = regularizers.get(W_regularizer)
self.b_regularizer = regularizers.get(b_regularizer)
self.activity_regularizer = regularizers.get(activity_regularizer)
self.W_constraint = constraints.get(W_constraint)
self.b_constraint = constraints.get(b_constraint)
self.bias = bias
self.input_spec = [InputSpec(ndim='2+')]
if self.input_dim:
kwargs['input_shape'] = (self.input_dim,)
super(Dense, self).__init__(**kwargs)
def __init__(self,
n_graph_feat=30,
n_outputs=30,
max_atoms=50,
layer_sizes=[100],
init='glorot_uniform',
activation='relu',
dropout=None,
**kwargs):
"""
Parameters
----------
n_graph_feat: int, optional
Number of features for each atom
n_outputs: int, optional
Number of features for each molecule.
max_atoms: int, optional
Maximum number of atoms in molecules.
layer_sizes: list of int, optional
Structure of hidden layer(s)
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
dropout: float, optional
Dropout probability, not supported
"""
super(DAGGather, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.layer_sizes = layer_sizes
self.dropout = dropout
self.max_atoms = max_atoms
self.n_graph_feat = n_graph_feat
self.n_outputs = n_outputs
def __init__(self,
n_embedding=30,
n_outputs=100,
layer_sizes=[100],
output_activation=True,
init='glorot_uniform',
activation='tanh',
**kwargs):
"""
Parameters
----------
n_embedding: int, optional
Number of features for each atom
layer_sizes: list of int, optional(default=[1000])
Structure of hidden layer(s)
n_tasks: int, optional
Number of final summed outputs
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied
"""
warnings.warn(
"The dc.nn.DTNNGather is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by "
"dc.models.tensorgraph.graph_layers.DTNNGather",
DeprecationWarning)
self.n_embedding = n_embedding
self.layer_sizes = layer_sizes
self.n_outputs = n_outputs
self.output_activation = output_activation
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
super(DTNNGather, self).__init__(**kwargs)
def __init__(self,
nb_filter,
n_atom_features,
batch_size,
init='glorot_uniform',
activation='linear',
dropout=None,
max_deg=10,
min_deg=0,
**kwargs):
"""
Parameters
----------
nb_filter: int
Number of convolutional filters.
n_atom_features: int
Number of features listed per atom.
init: str, optional
Weight initialization for filters.
activation: str, optional
Activation function applied after convolution.
dropout: float, optional
Dropout probability.
max_deg: int, optional
Maximum degree of atoms in molecules.
min_deg: int, optional
Minimum degree of atoms in molecules.
"""
warnings.warn("The dc.nn.GraphConv is "
"deprecated. Will be removed in DeepChem 1.4. "
"Will be replaced by dc.models.tensorgraph.layers.GraphConv",
DeprecationWarning)
super(GraphConv_and_gather, self).__init__(**kwargs)
self.init = initializations.get(init) # Set weight initialization
self.activation = activations.get(activation) # Get activations
self.nb_filter = nb_filter # Save number of filters
self.dropout = dropout # Save dropout params
self.max_deg = max_deg
self.min_deg = min_deg
self.batch_size = batch_size
# Is there a solid explanation here?
self.nb_affine = 3 * max_deg + (2 - min_deg)
self.n_atom_features = n_atom_features
n_atom_features = self.n_atom_features
self.beta_init = initializations.get('zero')
self.gamma_init = initializations.get('one')
self.epsilon = 1e-5
self.momentum = 0.99
self.gamma_regularizer = regularizers.get(None)
self.beta_regularizer = regularizers.get(None)
# Generate the nb_affine weights and biases
self.W_list = [
self.init([n_atom_features, self.nb_filter])
for k in range(self.nb_affine)
]
self.b_list = [
model_ops.zeros(shape=[
self.nb_filter,
]) for k in range(self.nb_affine)
]
self.trainable_weights = self.W_list + self.b_list