def build_weights(self, model_params):
initializer = chainer.initializers.HeNormal()
setattr(
self,
'model_params',
model_params,
)
num_hidden_features = [self.model_params['conv_width']
] * self.model_params['fp_depth']
all_layer_sizes = [num_atom_features()] + num_hidden_features
'''
for i in range(len(all_layer_sizes)):
all_layer_sizes[i] = 1
'''
'''output weights'''
for layer in range(len(all_layer_sizes)):
setattr(
self, 'layer_output_weights_' + str(layer),
L.Linear(all_layer_sizes[layer],
self.model_params['fp_length'],
initialW=initializer))
'''hidden weights'''
in_and_out_sizes = zip(all_layer_sizes[:-1], all_layer_sizes[1:])
for layer, (N_prev, N_cur) in enumerate(in_and_out_sizes):
setattr(self, 'layer_' + str(layer) + '_self_filter',
L.Linear(N_prev, N_cur, initialW=initializer))
for degree in degrees:
name = weights_name(layer, degree)
setattr(
self, name,
L.Linear(N_prev + num_bond_features(),
N_cur,
initialW=initializer))
def graph_from_edgelist(edgelist):
graph = MolGraph()
atoms_by_rd_idx = {}
edges = []
with open(edgelist) as f:
for line in f.readlines():
line = line.strip('\n')
if '#' not in line:
edges.append(re.findall('\d+', 'xyz123abc456def789'))
for edge in edges:
node_1 = graph.new_node('atom',
features=np.random.uniform(
low=0,
high=1,
size=(num_atom_features(), )),
rdkit_ix=int(edge[0]))
node_2 = graph.new_node('atom',
features=np.random.uniform(
low=0,
high=1,
size=(num_atom_features(), )),
rdkit_ix=int(edge[1]))
node_1.add_neighbors((node_2, ))
edge = graph.new_node('bond',
features=np.random.uniform(
low=0, high=1, size=(num_bond_features(), )))
edge.add_neighbors((node_1, node_2))
mol_node = graph.new_node('molecule')
mol_node.add_neighbors(graph.nodes['atom'])
return graph
def build_convnet_fingerprint_fun(num_hidden_features=[100, 100],
fp_length=512,
normalize=True,
activation_function=relu,
return_atom_activations=False):
"""Sets up functions to compute convnets over all molecules in a minibatch together."""
# Specify weight shapes.
parser = WeightsParser()
all_layer_sizes = [num_atom_features()] + num_hidden_features
for layer in range(len(all_layer_sizes)):
parser.add_weights(('layer output weights', layer),
(all_layer_sizes[layer], fp_length))
parser.add_weights(('layer output bias', layer), (1, fp_length))
in_and_out_sizes = zip(all_layer_sizes[:-1], all_layer_sizes[1:])
for layer, (N_prev, N_cur) in enumerate(in_and_out_sizes):
parser.add_weights(("layer", layer, "biases"), (1, N_cur))
parser.add_weights(("layer", layer, "self filter"), (N_prev, N_cur))
for degree in degrees:
parser.add_weights(weights_name(layer, degree),
(N_prev + num_bond_features(), N_cur))
def update_layer(weights,
layer,
atom_features,
bond_features,
array_rep,
normalize=False):
def get_weights_func(degree):
return parser.get(weights, weights_name(layer, degree))
layer_bias = parser.get(weights, ("layer", layer, "biases"))
layer_self_weights = parser.get(weights,
("layer", layer, "self filter"))
self_activations = np.dot(atom_features, layer_self_weights)
neighbor_activations = matmult_neighbors(array_rep, atom_features,
bond_features,
get_weights_func)
total_activations = neighbor_activations + self_activations + layer_bias
if normalize:
total_activations = batch_normalize(total_activations)
return activation_function(total_activations)
def output_layer_fun_and_atom_activations(weights, smiles):
"""Computes layer-wise convolution, and returns a fixed-size output."""
array_rep = array_rep_from_smiles(tuple(smiles))
atom_features = array_rep['atom_features']
bond_features = array_rep['bond_features']
all_layer_fps = []
atom_activations = []
def write_to_fingerprint(atom_features, layer):
cur_out_weights = parser.get(weights,
('layer output weights', layer))
cur_out_bias = parser.get(weights, ('layer output bias', layer))
atom_outputs = softmax(cur_out_bias +
np.dot(atom_features, cur_out_weights),
axis=1)
atom_activations.append(atom_outputs)
# Sum over all atoms within a moleclue:
layer_output = sum_and_stack(atom_outputs, array_rep['atom_list'])
all_layer_fps.append(layer_output)
num_layers = len(num_hidden_features)
for layer in xrange(num_layers):
write_to_fingerprint(atom_features, layer)
atom_features = update_layer(weights,
layer,
atom_features,
bond_features,
array_rep,
normalize=normalize)
write_to_fingerprint(atom_features, num_layers)
return sum(all_layer_fps), atom_activations, array_rep
def output_layer_fun(weights, smiles):
output, _, _ = output_layer_fun_and_atom_activations(weights, smiles)
return output
def compute_atom_activations(weights, smiles):
_, atom_activations, array_rep = output_layer_fun_and_atom_activations(
weights, smiles)
return atom_activations, array_rep
if return_atom_activations:
return output_layer_fun, parser, compute_atom_activations
else:
return output_layer_fun, parser
def build_convnet_fingerprint_fun(num_hidden_features=[100, 100], fp_length=512,
normalize=True, activation_function=relu,
return_atom_activations=False):
"""Sets up functions to compute convnets over all molecules in a minibatch together."""
#import pdb; pdb.set_trace()
# Specify weight shapes.
parser = WeightsParser()
all_layer_sizes = [num_atom_features()] + num_hidden_features # """ V:Concatinating 2 lists OUT: [62,20,20, 20, 20] """
print("num_atom_features ",num_atom_features())
for layer in range(len(all_layer_sizes)):
parser.add_weights(('layer output weights', layer), (all_layer_sizes[layer], fp_length))
parser.add_weights(('layer output bias', layer), (1, fp_length))
in_and_out_sizes = zip(all_layer_sizes[:-1], all_layer_sizes[1:]) #""" V :OUT: [(62,20), (20,20), (20,20), (20,20)]"""
print("in_and_out_sizes ",in_and_out_sizes)
for layer, (N_prev, N_cur) in enumerate(in_and_out_sizes):
parser.add_weights(("layer", layer, "biases"), (1, N_cur))
parser.add_weights(("layer", layer, "self filter"), (N_prev, N_cur))
for degree in degrees: ################## V: I Dont know what a degree is ########################## degrees = [0, 1, 2, 3, 4, 5]
parser.add_weights(weights_name(layer, degree), (N_prev + num_bond_features(), N_cur))
def update_layer(weights, layer, atom_features, bond_features, array_rep, normalize=False):
# import pdb; pdb.set_trace()
def get_weights_func(degree):
return parser.get(weights, weights_name(layer, degree))
layer_bias = parser.get(weights, ("layer", layer, "biases"))
layer_self_weights = parser.get(weights, ("layer", layer, "self filter"))
self_activations = np.dot(atom_features, layer_self_weights)
neighbour_activations = matmult_neighbors(
array_rep, atom_features, bond_features, get_weights_func)
# import pdb; pdb.set_trace()
total_activations = neighbour_activations + self_activations + layer_bias ### DOUBT : if i check the atom features here for visualisation, it is 1370
# import pdb; pdb.set_trace()
# print("Total activations", np.shape(total_activations))
if normalize:
total_activations = batch_normalize(total_activations)
return activation_function(total_activations)
def output_layer_fun_and_atom_activations(weights, smiles): # V: Came here from line # 108 def output_layer_fun(weights, smiles)
"""Computes layer-wise convolution, and returns a fixed-size output."""
import pdb; pdb.set_trace()
array_rep = array_rep_from_smiles(tuple(smiles))
atom_features = array_rep['atom_features'] # V: (1370,62)
bond_features = array_rep['bond_features'] # V: (1416,6)
all_layer_fps = []
atom_activations = []
def write_to_fingerprint(atom_features, layer):
# import pdb; pdb.set_trace()
cur_out_weights = parser.get(weights, ('layer output weights', layer))
cur_out_bias = parser.get(weights, ('layer output bias', layer))
# import pdb; pdb.set_trace()
atom_outputs = softmax(cur_out_bias + np.dot(atom_features, cur_out_weights), axis=1) #V: Smooth all the atom features and then find the softmax, i.e the FP
atom_activations.append(atom_outputs) # V: Not needed for neural fingerprint, needed for visualization in neural FP
# Sum over all atoms within a moleclue:
layer_output = sum_and_stack(atom_outputs, array_rep['atom_list']) #V: array_rep['atom_list'] stores the indexes of atoms in each smile size: (100,)
all_layer_fps.append(layer_output)
num_layers = len(num_hidden_features) #V: (num_layers = 4) , num_hidden_features = [20, 20, 20, 20]
for layer in xrange(num_layers):
write_to_fingerprint(atom_features, layer)
atom_features = update_layer(weights, layer, atom_features, bond_features, array_rep,
normalize=normalize)
write_to_fingerprint(atom_features, num_layers)
return sum(all_layer_fps), atom_activations, array_rep
def output_layer_fun(weights, smiles): # V: Came here from line # 80 in build_vanilla_net.py
#import pdb; pdb.set_trace()
output, _, _ = output_layer_fun_and_atom_activations(weights, smiles)
return output
def compute_atom_activations(weights, smiles):
_, atom_activations, array_rep = output_layer_fun_and_atom_activations(weights, smiles)
return atom_activations, array_rep
if return_atom_activations:
#import pdb; pdb.set_trace()
return output_layer_fun, parser, compute_atom_activations
else:
#import pdb; pdb.set_trace()
return output_layer_fun, parser
def tensorize_smiles_job(smiles, max_degree=5, max_atoms=None):
'''Takes a list of smiles and turns the graphs in tensor representation.
# Arguments:
smiles: a list (or iterable) of smiles representations
max_atoms: the maximum number of atoms per molecule (to which all
molecules will be padded), use `None` for auto
max_degree: max_atoms: the maximum number of neigbour per atom that each
molecule can have (to which all molecules will be padded), use `None`
for auto
**NOTE**: It is not recommended to set max_degree to `None`/auto when
using `NeuralGraph` layers. Max_degree determines the number of
trainable parameters and is essentially a hyperparameter.
While models can be rebuilt using different `max_atoms`, they cannot
be rebuild for different values of `max_degree`, as the architecture
will be different.
For organic molecules `max_degree=5` is a good value (Duvenaud et. al, 2015)
# Returns:
atoms: np.array, An atom feature np.array of size `(molecules, max_atoms, atom_features)`
bonds: np.array, A bonds np.array of size `(molecules, max_atoms, max_neighbours)`
edges: np.array, A connectivity array of size `(molecules, max_atoms, max_neighbours, bond_features)`
TODO:
* Arguments for sparse vector encoding
'''
# import sizes
n = len(smiles)
n_atom_features = features.num_atom_features()
n_bond_features = features.num_bond_features()
# preallocate atom tensor with 0's and bond tensor with -1 (because of 0 index)
# If max_degree or max_atoms is set to None (auto), initialise dim as small
# as possible (1)
atom_tensor = np.zeros((n, max_atoms or 1, n_atom_features),
dtype=np.float32)
bond_tensor = np.zeros(
(n, max_atoms or 1, max_degree or 1, n_bond_features),
dtype=np.float32)
edge_tensor = -np.ones((n, max_atoms or 1, max_degree or 1), dtype=np.int8)
for mol_ix, s in enumerate(smiles):
#load mol, atoms and bonds
sio = sys.stderr = StringIO()
mol = Chem.MolFromSmiles(s)
assert mol is not None, 'Could not parse smiles {}, error: {}'.format(
s, sio.getvalue())
atoms = mol.GetAtoms()
bonds = mol.GetBonds()
# If max_atoms is exceeded, resize if max_atoms=None (auto), else raise
if len(atoms) > atom_tensor.shape[1]:
assert max_atoms is None, 'too many atoms ({0}) in molecule: {1}'.format(
len(atoms), s)
atom_tensor = padaxis(atom_tensor, len(atoms), axis=1)
bond_tensor = padaxis(bond_tensor, len(atoms), axis=1)
edge_tensor = padaxis(edge_tensor,
len(atoms),
axis=1,
pad_value=-1)
rdkit_ix_lookup = {}
connectivity_mat = {}
for atom_ix, atom in enumerate(atoms):
# write atom features
atom_tensor[mol_ix,
atom_ix, :n_atom_features] = features.atom_features(
atom)
# store entry in idx
rdkit_ix_lookup[atom.GetIdx()] = atom_ix
# preallocate array with neighbour lists (indexed by atom)
connectivity_mat = [[] for _ in atoms]
for bond in bonds:
# lookup atom ids
a1_ix = rdkit_ix_lookup[bond.GetBeginAtom().GetIdx()]
a2_ix = rdkit_ix_lookup[bond.GetEndAtom().GetIdx()]
# lookup how many neighbours are encoded yet
a1_neigh = len(connectivity_mat[a1_ix])
a2_neigh = len(connectivity_mat[a2_ix])
# If max_degree is exceeded, resize if max_degree=None (auto), else raise
new_degree = max(a1_neigh, a2_neigh) + 1
if new_degree > bond_tensor.shape[2]:
assert max_degree is None, 'too many neighours ({0}) in molecule: {1}'.format(
new_degree, s)
bond_tensor = padaxis(bond_tensor, new_degree, axis=2)
edge_tensor = padaxis(edge_tensor,
new_degree,
axis=2,
pad_value=-1)
# store bond features
bond_features = np.array(features.bond_features(bond), dtype=int)
bond_tensor[mol_ix, a1_ix, a1_neigh, :] = bond_features
bond_tensor[mol_ix, a2_ix, a2_neigh, :] = bond_features
#add to connectivity matrix
connectivity_mat[a1_ix].append(a2_ix)
connectivity_mat[a2_ix].append(a1_ix)
#store connectivity matrix
for a1_ix, neighbours in enumerate(connectivity_mat):
degree = len(neighbours)
edge_tensor[mol_ix, a1_ix, :degree] = neighbours
return atom_tensor, bond_tensor, edge_tensor