def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, distance, distance_membership_i, distance_membership_j
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_features = in_layers[0].out_tensor
distance = in_layers[1].out_tensor
distance_membership_i = in_layers[2].out_tensor
distance_membership_j = in_layers[3].out_tensor
distance_hidden = tf.matmul(distance, self.W_df) + self.b_df
atom_features_hidden = tf.matmul(atom_features, self.W_cf) + self.b_cf
outputs = tf.multiply(
distance_hidden, tf.gather(atom_features_hidden, distance_membership_j))
# for atom i in a molecule m, this step multiplies together distance info of atom pair(i,j)
# and embeddings of atom j(both gone through a hidden layer)
outputs = tf.matmul(outputs, self.W_fc)
outputs = self.activation(outputs)
output_ii = tf.multiply(self.b_df, atom_features_hidden)
output_ii = tf.matmul(output_ii, self.W_fc)
output_ii = self.activation(output_ii)
# for atom i, sum the influence from all other atom j in the molecule
outputs = tf.segment_sum(outputs,
distance_membership_i) - output_ii + atom_features
out_tensor = outputs
if set_tensors:
self.trainable_variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Perform T steps of message passing """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Extract atom_features
atom_features = in_layers[0].out_tensor
pair_features = in_layers[1].out_tensor
atom_to_pair = in_layers[2].out_tensor
n_atom_features = atom_features.get_shape().as_list()[-1]
n_pair_features = pair_features.get_shape().as_list()[-1]
# Add trainable weights
self.build(pair_features, n_pair_features)
if n_atom_features < self.n_hidden:
pad_length = self.n_hidden - n_atom_features
out = tf.pad(atom_features, ((0, 0), (0, pad_length)), mode='CONSTANT')
elif n_atom_features > self.n_hidden:
raise ValueError("Too large initial feature vector")
else:
out = atom_features
for i in range(self.T):
message = self.message_function.forward(out, atom_to_pair)
out = self.update_function.forward(out, message)
out_tensor = out
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Perform T steps of message passing """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Extract atom_features
atom_features = in_layers[0].out_tensor
pair_features = in_layers[1].out_tensor
atom_to_pair = in_layers[2].out_tensor
n_atom_features = atom_features.get_shape().as_list()[-1]
n_pair_features = pair_features.get_shape().as_list()[-1]
# Add trainable weights
self.build(pair_features, n_pair_features)
if n_atom_features < self.n_hidden:
pad_length = self.n_hidden - n_atom_features
out = tf.pad(atom_features, ((0, 0), (0, pad_length)), mode='CONSTANT')
elif n_atom_features > self.n_hidden:
raise ValueError("Too large initial feature vector")
else:
out = atom_features
for i in range(self.T):
message = self.message_function.forward(out, atom_to_pair)
out = self.update_function.forward(out, message)
out_tensor = out
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
inputs = in_layers[0].out_tensor
K = self.K
outputs = []
for count in range(self.n_tasks):
# Similarity values
similarity = inputs[:, 2 * K * count:(2 * K * count + K)]
# Labels for all top K similar samples
ys = tf.cast(inputs[:, (2 * K * count + K):2 * K * (count + 1)], tf.int32)
R = self.b + self.W[0] * similarity + self.W[1] * tf.constant(
np.arange(K) + 1, dtype=tf.float32)
R = tf.sigmoid(R)
z = tf.reduce_sum(R * tf.gather(self.V, ys), axis=1) + self.b2
outputs.append(tf.reshape(z, shape=[-1, 1]))
out_tensor = tf.concat(outputs, axis=1)
if set_tensors:
self.trainable_variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
inputs = in_layers[0].out_tensor
K = self.K
outputs = []
for count in range(self.n_tasks):
# Similarity values
similarity = inputs[:, 2 * K * count:(2 * K * count + K)]
# Labels for all top K similar samples
ys = tf.cast(inputs[:, (2 * K * count + K):2 * K * (count + 1)],
tf.int32)
R = self.b + self.W[0] * similarity + self.W[1] * tf.constant(
np.arange(K) + 1, dtype=tf.float32)
R = tf.sigmoid(R)
z = tf.reduce_sum(R * tf.gather(self.V, ys), axis=1) + self.b2
outputs.append(tf.reshape(z, shape=[-1, 1]))
out_tensor = tf.concat(outputs, axis=1)
if set_tensors:
self.trainable_variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
A = in_layers[0].out_tensor
P = in_layers[1].out_tensor
self.out_tensor = [A, P]
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
d_cutoff = in_layers[0].out_tensor
d = in_layers[1].out_tensor
if self.atomic_number_differentiated:
atom_numbers = in_layers[2].out_tensor
atom_number_embedded = tf.nn.embedding_lookup(self.atom_number_embedding,
atom_numbers)
d_cutoff = tf.stack([d_cutoff] * self.length, axis=3)
d = tf.stack([d] * self.length, axis=3)
Rs = tf.reshape(self.Rs, (1, 1, 1, -1))
ita = tf.reshape(self.ita, (1, 1, 1, -1))
out_tensor = tf.exp(-ita * tf.square(d - Rs)) * d_cutoff
if self.atomic_number_differentiated:
out_tensors = []
for atom_type in self.atom_number_cases:
selected_atoms = tf.expand_dims(
tf.expand_dims(atom_number_embedded[:, :, atom_type], axis=1),
axis=3)
out_tensors.append(tf.reduce_sum(out_tensor * selected_atoms, axis=2))
self.out_tensor = tf.concat(out_tensors, axis=2)
else:
self.out_tensor = tf.reduce_sum(out_tensor, axis=2)
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, distance, distance_membership_i, distance_membership_j
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_features = in_layers[0].out_tensor
distance = in_layers[1].out_tensor
distance_membership_i = in_layers[2].out_tensor
distance_membership_j = in_layers[3].out_tensor
distance_hidden = tf.matmul(distance, self.W_df) + self.b_df
atom_features_hidden = tf.matmul(atom_features, self.W_cf) + self.b_cf
outputs = tf.multiply(
distance_hidden, tf.gather(atom_features_hidden, distance_membership_j))
# for atom i in a molecule m, this step multiplies together distance info of atom pair(i,j)
# and embeddings of atom j(both gone through a hidden layer)
outputs = tf.matmul(outputs, self.W_fc)
outputs = self.activation(outputs)
output_ii = tf.multiply(self.b_df, atom_features_hidden)
output_ii = tf.matmul(output_ii, self.W_fc)
output_ii = self.activation(output_ii)
# for atom i, sum the influence from all other atom j in the molecule
outputs = tf.segment_sum(outputs,
distance_membership_i) - output_ii + atom_features
out_tensor = outputs
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, atom_split
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
outputs = in_layers[0].out_tensor
atom_split = in_layers[1].out_tensor
if self.gaussian_expand:
outputs = self.gaussian_histogram(outputs)
output_molecules = tf.segment_sum(outputs, atom_split)
if self.gaussian_expand:
output_molecules = tf.matmul(output_molecules, self.W) + self.b
output_molecules = self.activation(output_molecules)
out_tensor = output_molecules
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
d_cutoff = in_layers[0].out_tensor
d = in_layers[1].out_tensor
if self.atomic_number_differentiated:
atom_numbers = in_layers[2].out_tensor
atom_number_embedded = tf.nn.embedding_lookup(
self.atom_number_embedding, atom_numbers)
d_cutoff = tf.stack([d_cutoff] * self.length, axis=3)
d = tf.stack([d] * self.length, axis=3)
Rs = tf.reshape(self.Rs, (1, 1, 1, -1))
ita = tf.reshape(self.ita, (1, 1, 1, -1))
out_tensor = tf.exp(-ita * tf.square(d - Rs)) * d_cutoff
if self.atomic_number_differentiated:
out_tensors = []
for atom_type in self.atom_number_cases:
selected_atoms = tf.expand_dims(tf.expand_dims(
atom_number_embedded[:, :, atom_type], axis=1),
axis=3)
out_tensors.append(
tf.reduce_sum(out_tensor * selected_atoms, axis=2))
out_tensor = tf.concat(out_tensors, axis=2)
else:
out_tensor = tf.reduce_sum(out_tensor, axis=2)
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Perform M steps of set2set gather,
detailed descriptions in: https://arxiv.org/abs/1511.06391 """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
# Extract atom_features
atom_features = in_layers[0].out_tensor
atom_split = in_layers[1].out_tensor
self.c = tf.zeros((self.batch_size, self.n_hidden))
self.h = tf.zeros((self.batch_size, self.n_hidden))
for i in range(self.M):
q_expanded = tf.gather(self.h, atom_split)
e = tf.reduce_sum(atom_features * q_expanded, 1)
e_mols = tf.dynamic_partition(e, atom_split, self.batch_size)
# Add another value(~-Inf) to prevent error in softmax
e_mols = [
tf.concat([e_mol, tf.constant([-1000.])], 0) for e_mol in e_mols
]
a = tf.concat([tf.nn.softmax(e_mol)[:-1] for e_mol in e_mols], 0)
r = tf.segment_sum(tf.reshape(a, [-1, 1]) * atom_features, atom_split)
# Model using this layer must set pad_batches=True
q_star = tf.concat([self.h, r], axis=1)
self.h, self.c = self.LSTMStep(q_star, self.c)
out_tensor = q_star
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Perform M steps of set2set gather,
detailed descriptions in: https://arxiv.org/abs/1511.06391 """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
# Extract atom_features
atom_features = in_layers[0].out_tensor
atom_split = in_layers[1].out_tensor
self.c = tf.zeros((self.batch_size, self.n_hidden))
self.h = tf.zeros((self.batch_size, self.n_hidden))
for i in range(self.M):
q_expanded = tf.gather(self.h, atom_split)
e = tf.reduce_sum(atom_features * q_expanded, 1)
e_mols = tf.dynamic_partition(e, atom_split, self.batch_size)
# Add another value(~-Inf) to prevent error in softmax
e_mols = [
tf.concat([e_mol, tf.constant([-1000.])], 0) for e_mol in e_mols
]
a = tf.concat([tf.nn.softmax(e_mol)[:-1] for e_mol in e_mols], 0)
r = tf.segment_sum(tf.reshape(a, [-1, 1]) * atom_features, atom_split)
# Model using this layer must set pad_batches=True
q_star = tf.concat([self.h, r], axis=1)
self.h, self.c = self.LSTMStep(q_star, self.c)
out_tensor = q_star
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, atom_split
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
outputs = in_layers[0].out_tensor
atom_split = in_layers[1].out_tensor
if self.gaussian_expand:
outputs = self.gaussian_histogram(outputs)
output_molecules = tf.segment_sum(outputs, atom_split)
if self.gaussian_expand:
output_molecules = tf.matmul(output_molecules, self.W) + self.b
output_molecules = self.activation(output_molecules)
out_tensor = output_molecules
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
out_tensor = in_layers[0].out_tensor[0]
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
output = in_layers[0].out_tensor
out_tensor = output[:, self.task_id:self.task_id + 1]
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
output = in_layers[0].out_tensor
out_tensor = output[:, self.task_id:self.task_id + 1]
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Angular Symmetry Function """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
max_atoms = self.max_atoms
d_cutoff = in_layers[0].out_tensor
d = in_layers[1].out_tensor
atom_coordinates = in_layers[2].out_tensor
if self.atomic_number_differentiated:
atom_numbers = in_layers[3].out_tensor
atom_number_embedded = tf.nn.embedding_lookup(self.atom_number_embedding,
atom_numbers)
vector_distances = tf.tile(tf.expand_dims(atom_coordinates, axis=2), (1, 1, max_atoms, 1)) - \
tf.tile(tf.expand_dims(atom_coordinates, axis=1), (1, max_atoms, 1, 1))
R_ij = tf.tile(tf.expand_dims(d, axis=3), (1, 1, 1, max_atoms))
R_ik = tf.tile(tf.expand_dims(d, axis=2), (1, 1, max_atoms, 1))
f_R_ij = tf.tile(tf.expand_dims(d_cutoff, axis=3), (1, 1, 1, max_atoms))
f_R_ik = tf.tile(tf.expand_dims(d_cutoff, axis=2), (1, 1, max_atoms, 1))
# Define angle theta = R_ij(Vector) dot R_ik(Vector)/R_ij(distance)/R_ik(distance)
theta = tf.reduce_sum(tf.tile(tf.expand_dims(vector_distances, axis=3), (1, 1, 1, max_atoms, 1)) * \
tf.tile(tf.expand_dims(vector_distances, axis=2), (1, 1, max_atoms, 1, 1)), axis=4)
theta = tf.div(theta, R_ij * R_ik + 1e-5)
R_ij = tf.stack([R_ij] * self.length, axis=4)
R_ik = tf.stack([R_ik] * self.length, axis=4)
f_R_ij = tf.stack([f_R_ij] * self.length, axis=4)
f_R_ik = tf.stack([f_R_ik] * self.length, axis=4)
theta = tf.stack([theta] * self.length, axis=4)
lambd = tf.reshape(self.lambd, (1, 1, 1, 1, -1))
zeta = tf.reshape(self.zeta, (1, 1, 1, 1, -1))
ita = tf.reshape(self.ita, (1, 1, 1, 1, -1))
Rs = tf.reshape(self.Rs, (1, 1, 1, 1, -1))
thetas = tf.reshape(self.thetas, (1, 1, 1, 1, -1))
out_tensor = tf.pow(1 + lambd * tf.cos(theta - thetas), zeta) * \
tf.exp(-ita * tf.square((R_ij + R_ik) / 2 - Rs)) * \
f_R_ij * f_R_ik * tf.pow(tf.constant(2.), 1 - zeta)
if self.atomic_number_differentiated:
out_tensors = []
for atom_type_j in self.atom_number_cases:
for atom_type_k in self.atom_number_cases:
selected_atoms = tf.stack([atom_number_embedded[:, :, atom_type_j]] * max_atoms, axis=2) * \
tf.stack([atom_number_embedded[:, :, atom_type_k]] * max_atoms, axis=1)
selected_atoms = tf.expand_dims(
tf.expand_dims(selected_atoms, axis=1), axis=4)
out_tensors.append(
tf.reduce_sum(out_tensor * selected_atoms, axis=[2, 3]))
self.out_tensor = tf.concat(out_tensors, axis=2)
else:
self.out_tensor = tf.reduce_sum(out_tensor, axis=[2, 3])
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Merge features together """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
out_tensor = in_layers[0].out_tensor
flags = in_layers[1].out_tensor
out_tensor = tf.reduce_sum(out_tensor * flags[:, :, 0:1], axis=1)
self.out_tensor = out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Merge features together """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
out_tensor = in_layers[0].out_tensor
flags = in_layers[1].out_tensor
out_tensor = tf.reduce_sum(out_tensor * flags[:, :, 0:1], axis=1)
self.out_tensor = out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""description and explanation refer to deepchem.nn.DTNNEmbedding
parent layers: atom_number
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_number = in_layers[0].out_tensor
atom_features = tf.nn.embedding_lookup(self.embedding_list, atom_number)
self.out_tensor = atom_features
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""Creates weave tensors.
parent layers: [atom_features, pair_features], pair_split, atom_to_pair
"""
activation = activations.get(self.activation) # Get activations
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_features = in_layers[0].out_tensor
pair_features = in_layers[1].out_tensor
pair_split = in_layers[2].out_tensor
atom_to_pair = in_layers[3].out_tensor
AA = tf.matmul(atom_features, self.W_AA) + self.b_AA
AA = activation(AA)
PA = tf.matmul(pair_features, self.W_PA) + self.b_PA
PA = activation(PA)
PA = tf.segment_sum(PA, pair_split)
A = tf.matmul(tf.concat([AA, PA], 1), self.W_A) + self.b_A
A = activation(A)
if self.update_pair:
AP_ij = tf.matmul(
tf.reshape(tf.gather(atom_features, atom_to_pair),
[-1, 2 * self.n_atom_input_feat]),
self.W_AP) + self.b_AP
AP_ij = activation(AP_ij)
AP_ji = tf.matmul(
tf.reshape(
tf.gather(atom_features, tf.reverse(atom_to_pair, [1])),
[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
AP_ji = activation(AP_ji)
PP = tf.matmul(pair_features, self.W_PP) + self.b_PP
PP = activation(PP)
P = tf.matmul(tf.concat([AP_ij + AP_ji, PP], 1),
self.W_P) + self.b_P
P = activation(P)
else:
P = pair_features
self.out_tensors = [A, P]
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = A
return self.out_tensors
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
slice_num = self.slice_num
axis = self.axis
inputs = in_layers[0].out_tensor
out_tensor = tf.slice(inputs, [0] * axis + [slice_num], [-1] * axis + [1])
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
slice_num = self.slice_num
axis = self.axis
inputs = in_layers[0].out_tensor
out_tensor = tf.slice(inputs, [0] * axis + [slice_num], [-1] * axis + [1])
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Angular Symmetry Function """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
max_atoms = self.max_atoms
d_cutoff = in_layers[0].out_tensor
d = in_layers[1].out_tensor
atom_coordinates = in_layers[2].out_tensor
vector_distances = tf.tile(tf.expand_dims(atom_coordinates, axis=2), (1, 1, max_atoms, 1)) - \
tf.tile(tf.expand_dims(atom_coordinates, axis=1), (1, max_atoms, 1, 1))
R_ij = tf.tile(tf.expand_dims(d, axis=3), (1, 1, 1, max_atoms))
R_ik = tf.tile(tf.expand_dims(d, axis=2), (1, 1, max_atoms, 1))
R_jk = tf.tile(tf.expand_dims(d, axis=1), (1, max_atoms, 1, 1))
f_R_ij = tf.tile(tf.expand_dims(d_cutoff, axis=3),
(1, 1, 1, max_atoms))
f_R_ik = tf.tile(tf.expand_dims(d_cutoff, axis=2),
(1, 1, max_atoms, 1))
f_R_jk = tf.tile(tf.expand_dims(d_cutoff, axis=1),
(1, max_atoms, 1, 1))
# Define angle theta = R_ij(Vector) dot R_ik(Vector)/R_ij(distance)/R_ik(distance)
theta = tf.reduce_sum(tf.tile(tf.expand_dims(vector_distances, axis=3), (1, 1, 1, max_atoms, 1)) * \
tf.tile(tf.expand_dims(vector_distances, axis=2), (1, 1, max_atoms, 1, 1)), axis=4)
theta = tf.div(theta, R_ij * R_ik + 1e-5)
R_ij = tf.stack([R_ij] * self.length, axis=4)
R_ik = tf.stack([R_ik] * self.length, axis=4)
R_jk = tf.stack([R_jk] * self.length, axis=4)
f_R_ij = tf.stack([f_R_ij] * self.length, axis=4)
f_R_ik = tf.stack([f_R_ik] * self.length, axis=4)
f_R_jk = tf.stack([f_R_jk] * self.length, axis=4)
theta = tf.stack([theta] * self.length, axis=4)
lambd = tf.reshape(self.lambd, (1, 1, 1, 1, -1))
zeta = tf.reshape(self.zeta, (1, 1, 1, 1, -1))
ita = tf.reshape(self.ita, (1, 1, 1, 1, -1))
out_tensor = tf.pow(1 + lambd * tf.cos(theta), zeta) * \
tf.exp(-ita * (tf.square(R_ij) + tf.square(R_ik) + tf.square(R_jk))) * \
f_R_ij * f_R_ik * f_R_jk
out_tensor = tf.reduce_sum(out_tensor, axis=[2, 3]) * \
tf.pow(tf.constant(2.), 1 - tf.reshape(self.zeta, (1, 1, -1)))
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""Creates weave tensors.
parent layers: [atom_features, pair_features], pair_split, atom_to_pair
"""
activation = activations.get(self.activation) # Get activations
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_features = in_layers[0].out_tensor
pair_features = in_layers[1].out_tensor
pair_split = in_layers[2].out_tensor
atom_to_pair = in_layers[3].out_tensor
AA = tf.matmul(atom_features, self.W_AA) + self.b_AA
AA = activation(AA)
PA = tf.matmul(pair_features, self.W_PA) + self.b_PA
PA = activation(PA)
PA = tf.segment_sum(PA, pair_split)
A = tf.matmul(tf.concat([AA, PA], 1), self.W_A) + self.b_A
A = activation(A)
if self.update_pair:
AP_ij = tf.matmul(
tf.reshape(
tf.gather(atom_features, atom_to_pair),
[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
AP_ij = activation(AP_ij)
AP_ji = tf.matmul(
tf.reshape(
tf.gather(atom_features, tf.reverse(atom_to_pair, [1])),
[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
AP_ji = activation(AP_ji)
PP = tf.matmul(pair_features, self.W_PP) + self.b_PP
PP = activation(PP)
P = tf.matmul(tf.concat([AP_ij + AP_ji, PP], 1), self.W_P) + self.b_P
P = activation(P)
else:
P = pair_features
self.out_tensors = [A, P]
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = A
return self.out_tensors
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Merge features together """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
atom_embedding = in_layers[0].out_tensor
radial_symmetry = in_layers[1].out_tensor
angular_symmetry = in_layers[2].out_tensor
atom_flags = in_layers[3].out_tensor
out_tensor = tf.concat(
[atom_embedding, radial_symmetry, angular_symmetry], axis=2)
self.out_tensor = out_tensor * atom_flags[:, :, 0:1]
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_number
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_number = in_layers[0].out_tensor
atom_features = tf.nn.embedding_lookup(self.embedding_list, atom_number)
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = atom_features
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" description and explanation refer to deepchem.nn.WeaveLayer
parent layers: [atom_features, pair_features], pair_split, atom_to_pair
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_features = in_layers[0].out_tensor[0]
pair_features = in_layers[0].out_tensor[1]
pair_split = in_layers[1].out_tensor
atom_to_pair = in_layers[2].out_tensor
AA = tf.matmul(atom_features, self.W_AA) + self.b_AA
AA = self.activation(AA)
PA = tf.matmul(pair_features, self.W_PA) + self.b_PA
PA = self.activation(PA)
PA = tf.segment_sum(PA, pair_split)
A = tf.matmul(tf.concat([AA, PA], 1), self.W_A) + self.b_A
A = self.activation(A)
if self.update_pair:
AP_ij = tf.matmul(
tf.reshape(tf.gather(atom_features, atom_to_pair),
[-1, 2 * self.n_atom_input_feat]),
self.W_AP) + self.b_AP
AP_ij = self.activation(AP_ij)
AP_ji = tf.matmul(
tf.reshape(
tf.gather(atom_features, tf.reverse(atom_to_pair, [1])),
[-1, 2 * self.n_atom_input_feat]), self.W_AP) + self.b_AP
AP_ji = self.activation(AP_ji)
PP = tf.matmul(pair_features, self.W_PP) + self.b_PP
PP = self.activation(PP)
P = tf.matmul(tf.concat([AP_ij + AP_ji, PP], 1),
self.W_P) + self.b_P
P = self.activation(P)
else:
P = pair_features
out_tensor = [A, P]
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_number
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
atom_number = in_layers[0].out_tensor
atom_features = tf.nn.embedding_lookup(self.embedding_list, atom_number)
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = atom_features
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Merge features together """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
atom_embedding = in_layers[0].out_tensor
radial_symmetry = in_layers[1].out_tensor
angular_symmetry = in_layers[2].out_tensor
atom_flags = in_layers[3].out_tensor
out_tensor = tf.concat(
[atom_embedding, radial_symmetry, angular_symmetry], axis=2)
self.out_tensor = out_tensor * atom_flags[:, :, 0:1]
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate distance matrix for BPSymmetryFunction with trainable cutoff """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
d = in_layers[0].out_tensor
d_flag = in_layers[1].out_tensor
# Cutoff with threshold Rc
d_flag = d_flag * tf.nn.relu(tf.sign(self.Rc - d))
d = 0.5 * (tf.cos(np.pi * d / self.Rc) + 1)
out_tensor = d * d_flag
out_tensor = out_tensor * tf.expand_dims((1 - tf.eye(self.max_atoms)), 0)
self.out_tensor = out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Angular Symmetry Function """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
max_atoms = self.max_atoms
d_cutoff = in_layers[0].out_tensor
d = in_layers[1].out_tensor
atom_coordinates = in_layers[2].out_tensor
vector_distances = tf.tile(tf.expand_dims(atom_coordinates, axis=2), (1, 1, max_atoms, 1)) - \
tf.tile(tf.expand_dims(atom_coordinates, axis=1), (1, max_atoms, 1, 1))
R_ij = tf.tile(tf.expand_dims(d, axis=3), (1, 1, 1, max_atoms))
R_ik = tf.tile(tf.expand_dims(d, axis=2), (1, 1, max_atoms, 1))
R_jk = tf.tile(tf.expand_dims(d, axis=1), (1, max_atoms, 1, 1))
f_R_ij = tf.tile(tf.expand_dims(d_cutoff, axis=3), (1, 1, 1, max_atoms))
f_R_ik = tf.tile(tf.expand_dims(d_cutoff, axis=2), (1, 1, max_atoms, 1))
f_R_jk = tf.tile(tf.expand_dims(d_cutoff, axis=1), (1, max_atoms, 1, 1))
# Define angle theta = R_ij(Vector) dot R_ik(Vector)/R_ij(distance)/R_ik(distance)
theta = tf.reduce_sum(tf.tile(tf.expand_dims(vector_distances, axis=3), (1, 1, 1, max_atoms, 1)) * \
tf.tile(tf.expand_dims(vector_distances, axis=2), (1, 1, max_atoms, 1, 1)), axis=4)
theta = tf.math.divide(theta, R_ij * R_ik + 1e-5)
R_ij = tf.stack([R_ij] * self.length, axis=4)
R_ik = tf.stack([R_ik] * self.length, axis=4)
R_jk = tf.stack([R_jk] * self.length, axis=4)
f_R_ij = tf.stack([f_R_ij] * self.length, axis=4)
f_R_ik = tf.stack([f_R_ik] * self.length, axis=4)
f_R_jk = tf.stack([f_R_jk] * self.length, axis=4)
theta = tf.stack([theta] * self.length, axis=4)
lambd = tf.reshape(self.lambd, (1, 1, 1, 1, -1))
zeta = tf.reshape(self.zeta, (1, 1, 1, 1, -1))
ita = tf.reshape(self.ita, (1, 1, 1, 1, -1))
out_tensor = tf.pow(1 + lambd * tf.cos(theta), zeta) * \
tf.exp(-ita * (tf.square(R_ij) + tf.square(R_ik) + tf.square(R_jk))) * \
f_R_ij * f_R_ik * f_R_jk
out_tensor = tf.reduce_sum(out_tensor, axis=[2, 3]) * \
tf.pow(tf.constant(2.), 1 - tf.reshape(self.zeta, (1, 1, -1)))
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
init_fn = initializations.get(self.init) # Set weight initialization
if self.activation == 'ani':
activation_fn = self.ani_activate
else:
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.cast(tf.cast(atom_numbers - atom_case, tf.bool),
tf.float32)
output = tf.reshape(output * tf.expand_dims(mask, 2),
(-1, self.max_atoms, self.out_channels))
outputs.append(output)
out_tensor = tf.add_n(outputs)
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, **kwargs):
"""description and explanation refer to deepchem.nn.DTNNGather
parent layers: atom_features, atom_membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
output = in_layers[0].out_tensor
atom_membership = in_layers[1].out_tensor
for i, W in enumerate(self.W_list):
output = tf.matmul(output, W) + self.b_list[i]
output = self.activation(output)
output = tf.segment_sum(output, atom_membership)
self.out_tensor = output
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate distance matrix for BPSymmetryFunction with trainable cutoff """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
max_atoms = self.max_atoms
atom_coordinates = in_layers[0].out_tensor
atom_flags = in_layers[1].out_tensor
tensor1 = tf.tile(
tf.expand_dims(atom_coordinates, axis=2), (1, 1, max_atoms, 1))
tensor2 = tf.tile(
tf.expand_dims(atom_coordinates, axis=1), (1, max_atoms, 1, 1))
# Calculate pairwise distance
d = tf.sqrt(tf.reduce_sum(tf.square(tensor1 - tensor2), axis=3))
# Masking for valid atom index
self.out_tensor = d * tf.to_float(atom_flags)
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate distance matrix for BPSymmetryFunction with trainable cutoff """
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
max_atoms = self.max_atoms
atom_coordinates = in_layers[0].out_tensor
atom_flags = in_layers[1].out_tensor
tensor1 = tf.tile(tf.expand_dims(atom_coordinates, axis=2),
(1, 1, max_atoms, 1))
tensor2 = tf.tile(tf.expand_dims(atom_coordinates, axis=1),
(1, max_atoms, 1, 1))
# Calculate pairwise distance
d = tf.sqrt(tf.reduce_sum(tf.square(tensor1 - tensor2), axis=3))
# Masking for valid atom index
self.out_tensor = d * tf.to_float(atom_flags)
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
init_fn = initializations.get(self.init) # Set weight initialization
if self.activation == 'ani':
activation_fn = self.ani_activate
else:
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.cast(tf.cast(atom_numbers - atom_case, tf.bool), tf.float32)
output = tf.reshape(output * tf.expand_dims(mask, 2),
(-1, self.max_atoms, self.out_channels))
outputs.append(output)
out_tensor = tf.add_n(outputs)
if set_tensors:
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, **kwargs):
"""description and explanation refer to deepchem.nn.DAGGather
parent layers: atom_features, membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Add trainable weights
self.build()
# Extract atom_features
atom_features = in_layers[0].out_tensor
membership = in_layers[1].out_tensor
# Extract atom_features
graph_features = tf.segment_sum(atom_features, membership)
# sum all graph outputs
outputs = self.DAGgraph_step(graph_features, self.W_list, self.b_list)
self.out_tensor = outputs
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self._build()
A_tilda_k = in_layers[0].out_tensor
X = in_layers[1].out_tensor
adp_fn_val = in_layers[2].out_tensor
attn_weights = tf.multiply(adp_fn_val, self.W)
wt_adjacency = attn_weights * A_tilda_k
out = tf.matmul(wt_adjacency, X) + tf.expand_dims(self.b, axis=1)
out_tensor = out
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self._build()
A_tilda_k = in_layers[0].out_tensor
X = in_layers[1].out_tensor
adp_fn_val = in_layers[2].out_tensor
attn_weights = tf.multiply(adp_fn_val, self.W)
wt_adjacency = attn_weights * A_tilda_k
out = tf.matmul(wt_adjacency, X) + tf.expand_dims(self.b, axis=1)
out_tensor = out
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
""" Generate Radial Symmetry Function """
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 = self.init(
[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):
output = self.activation(
tf.tensordot(inputs, self.W[i, :, :], [[2], [0]]) + 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 create_tensor(self, in_layers=None, **kwargs):
""" description and explanation refer to deepchem.nn.WeaveGather
parent layers: atom_features, atom_split
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
outputs = in_layers[0].out_tensor
atom_split = in_layers[1].out_tensor
if self.gaussian_expand:
outputs = self.gaussian_histogram(outputs)
output_molecules = tf.segment_sum(outputs, atom_split)
if self.gaussian_expand:
output_molecules = tf.matmul(output_molecules, self.W) + self.b
output_molecules = self.activation(output_molecules)
self.out_tensor = output_molecules
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
act_fn = activations.get('sigmoid')
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self._build()
A_tilda_k = in_layers[0].out_tensor
X = in_layers[1].out_tensor
if self.combine_method == "linear":
concatenated = tf.concat([A_tilda_k, X], axis=2)
adp_fn_val = act_fn(
tf.tensordot(concatenated, self.trainable_weights[0], axes=1))
else:
adp_fn_val = act_fn(tf.matmul(A_tilda_k, tf.tensordot(X, self.Q, axes=1)))
out_tensor = adp_fn_val
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, atom_membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
output = in_layers[0].out_tensor
atom_membership = in_layers[1].out_tensor
for i, W in enumerate(self.W_list[:-1]):
output = tf.matmul(output, W) + self.b_list[i]
output = self.activation(output)
output = tf.matmul(output, self.W_list[-1]) + self.b_list[-1]
if self.output_activation:
output = self.activation(output)
output = tf.segment_sum(output, atom_membership)
out_tensor = output
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
act_fn = activations.get('sigmoid')
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self._build()
A_tilda_k = in_layers[0].out_tensor
X = in_layers[1].out_tensor
if self.combine_method == "linear":
concatenated = tf.concat([A_tilda_k, X], axis=2)
adp_fn_val = act_fn(
tf.tensordot(concatenated, self.trainable_weights[0], axes=1))
else:
adp_fn_val = act_fn(
tf.matmul(A_tilda_k, tf.tensordot(X, self.Q, axes=1)))
out_tensor = adp_fn_val
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Add trainable weights
self.build()
# Extract atom_features
atom_features = in_layers[0].out_tensor
membership = in_layers[1].out_tensor
# Extract atom_features
graph_features = tf.segment_sum(atom_features, membership)
# sum all graph outputs
outputs = self.DAGgraph_step(graph_features, self.W_list, self.b_list)
out_tensor = outputs
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, atom_membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
self.build()
output = in_layers[0].out_tensor
atom_membership = in_layers[1].out_tensor
for i, W in enumerate(self.W_list[:-1]):
output = tf.matmul(output, W) + self.b_list[i]
output = self.activation(output)
output = tf.matmul(output, self.W_list[-1]) + self.b_list[-1]
if self.output_activation:
output = self.activation(output)
output = tf.segment_sum(output, atom_membership)
out_tensor = output
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, membership
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Add trainable weights
self.build()
# Extract atom_features
atom_features = in_layers[0].out_tensor
membership = in_layers[1].out_tensor
# Extract atom_features
graph_features = tf.segment_sum(atom_features, membership)
# sum all graph outputs
outputs = self.DAGgraph_step(graph_features, self.W_list, self.b_list,
**kwargs)
out_tensor = outputs
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, parents, calculation_orders, calculation_masks, n_atoms
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Add trainable weights
self.build()
atom_features = in_layers[0].out_tensor
# each atom corresponds to a graph, which is represented by the `max_atoms*max_atoms` int32 matrix of index
# each gragh include `max_atoms` of steps(corresponding to rows) of calculating graph features
parents = in_layers[1].out_tensor
# target atoms for each step: (batch_size*max_atoms) * max_atoms
calculation_orders = in_layers[2].out_tensor
calculation_masks = in_layers[3].out_tensor
n_atoms = in_layers[4].out_tensor
# initialize graph features for each graph
graph_features_initial = tf.zeros((self.max_atoms * self.batch_size,
self.max_atoms + 1, self.n_graph_feat))
# initialize graph features for each graph
# another row of zeros is generated for padded dummy atoms
graph_features = tf.Variable(graph_features_initial, trainable=False)
for count in range(self.max_atoms):
# `count`-th step
# extracting atom features of target atoms: (batch_size*max_atoms) * n_atom_features
mask = calculation_masks[:, count]
current_round = tf.boolean_mask(calculation_orders[:, count], mask)
batch_atom_features = tf.gather(atom_features, current_round)
# generating index for graph features used in the inputs
index = tf.stack(
[
tf.reshape(
tf.stack(
[tf.boolean_mask(tf.range(n_atoms), mask)] *
(self.max_atoms - 1),
axis=1), [-1]),
tf.reshape(tf.boolean_mask(parents[:, count, 1:], mask), [-1])
],
axis=1)
# extracting graph features for parents of the target atoms, then flatten
# shape: (batch_size*max_atoms) * [(max_atoms-1)*n_graph_features]
batch_graph_features = tf.reshape(
tf.gather_nd(graph_features, index),
[-1, (self.max_atoms - 1) * self.n_graph_feat])
# concat into the input tensor: (batch_size*max_atoms) * n_inputs
batch_inputs = tf.concat(
axis=1, values=[batch_atom_features, batch_graph_features])
# DAGgraph_step maps from batch_inputs to a batch of graph_features
# of shape: (batch_size*max_atoms) * n_graph_features
# representing the graph features of target atoms in each graph
batch_outputs = self.DAGgraph_step(batch_inputs, self.W_list, self.b_list,
**kwargs)
# index for targe atoms
target_index = tf.stack([tf.range(n_atoms), parents[:, count, 0]], axis=1)
target_index = tf.boolean_mask(target_index, mask)
# update the graph features for target atoms
graph_features = tf.scatter_nd_update(graph_features, target_index,
batch_outputs)
out_tensor = batch_outputs
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor
def create_tensor(self, in_layers=None, set_tensors=True, **kwargs):
"""
parent layers: atom_features, parents, calculation_orders, calculation_masks, n_atoms
"""
if in_layers is None:
in_layers = self.in_layers
in_layers = convert_to_layers(in_layers)
# Add trainable weights
self.build()
atom_features = in_layers[0].out_tensor
# each atom corresponds to a graph, which is represented by the `max_atoms*max_atoms` int32 matrix of index
# each gragh include `max_atoms` of steps(corresponding to rows) of calculating graph features
parents = in_layers[1].out_tensor
# target atoms for each step: (batch_size*max_atoms) * max_atoms
calculation_orders = in_layers[2].out_tensor
calculation_masks = in_layers[3].out_tensor
n_atoms = in_layers[4].out_tensor
# initialize graph features for each graph
graph_features_initial = tf.zeros((self.max_atoms * self.batch_size,
self.max_atoms + 1, self.n_graph_feat))
# initialize graph features for each graph
# another row of zeros is generated for padded dummy atoms
graph_features = tf.Variable(graph_features_initial, trainable=False)
for count in range(self.max_atoms):
# `count`-th step
# extracting atom features of target atoms: (batch_size*max_atoms) * n_atom_features
mask = calculation_masks[:, count]
current_round = tf.boolean_mask(calculation_orders[:, count], mask)
batch_atom_features = tf.gather(atom_features, current_round)
# generating index for graph features used in the inputs
index = tf.stack(
[
tf.reshape(
tf.stack(
[tf.boolean_mask(tf.range(n_atoms), mask)] *
(self.max_atoms - 1),
axis=1), [-1]),
tf.reshape(tf.boolean_mask(parents[:, count, 1:], mask), [-1])
],
axis=1)
# extracting graph features for parents of the target atoms, then flatten
# shape: (batch_size*max_atoms) * [(max_atoms-1)*n_graph_features]
batch_graph_features = tf.reshape(
tf.gather_nd(graph_features, index),
[-1, (self.max_atoms - 1) * self.n_graph_feat])
# concat into the input tensor: (batch_size*max_atoms) * n_inputs
batch_inputs = tf.concat(
axis=1, values=[batch_atom_features, batch_graph_features])
# DAGgraph_step maps from batch_inputs to a batch of graph_features
# of shape: (batch_size*max_atoms) * n_graph_features
# representing the graph features of target atoms in each graph
batch_outputs = self.DAGgraph_step(batch_inputs, self.W_list, self.b_list,
**kwargs)
# index for targe atoms
target_index = tf.stack([tf.range(n_atoms), parents[:, count, 0]], axis=1)
target_index = tf.boolean_mask(target_index, mask)
# update the graph features for target atoms
graph_features = tf.scatter_nd_update(graph_features, target_index,
batch_outputs)
out_tensor = batch_outputs
if set_tensors:
self.variables = self.trainable_weights
self.out_tensor = out_tensor
return out_tensor