def create_gconv_net(hparams):
dim = hparams["gconv"]["dim"]
gconv_model = GraphConvSequential(
GraphConvLayer(in_dim=75, out_dim=64), nn.BatchNorm1d(64), nn.ReLU(),
GraphPool(), GraphConvLayer(in_dim=64, out_dim=64), nn.BatchNorm1d(64),
nn.ReLU(), GraphPool(), nn.Linear(in_features=64, out_features=dim),
nn.BatchNorm1d(dim), nn.ReLU(), nn.Dropout(hparams["dprob"]),
GraphGather2D(activation='nonsat', batch_first=True))
model = nn.Sequential(gconv_model)
return model
def create_gconv_net(hparams):
dim = hparams["gconv"]["dim"]
gconv_model = GraphConvSequential(
GraphConvLayer(in_dim=75, out_dim=64), nn.BatchNorm1d(64), nn.ReLU(),
GraphPool(), GraphConvLayer(in_dim=64, out_dim=64), nn.BatchNorm1d(64),
nn.ReLU(), GraphPool(), nn.Linear(in_features=64, out_features=dim),
nn.BatchNorm1d(dim), nn.ReLU(), nn.Dropout(hparams["dprob"]),
GraphGather(activation='tanh'))
return nn.Sequential(gconv_model, nn.Linear(dim * 2,
hparams["latent_dim"]),
nn.BatchNorm1d(hparams["latent_dim"]), nn.ReLU())
def create_graph_conv_layers(gconv_args):
layers = []
for gc_arg in gconv_args:
gconv = GraphConvLayer(*gc_arg.args)
layers.append(gconv)
# Batch normalization
if gc_arg.use_batch_norm:
bn = nn.BatchNorm1d(gc_arg[1])
layers.append(bn)
# Dropout
if gc_arg.dropout > -1:
dr = nn.Dropout(gc_arg.dropout)
layers.append(dr)
# Pooling
if gc_arg.graph_pool:
p = GraphPool(gc_arg[2], gc_arg[3])
layers.append(p)
# Dense layer & normalization & dropout
layers.append(nn.Linear(gc_arg[1], gc_arg.dense_layer_size))
layers.append(nn.BatchNorm1d(gc_arg.dense_layer_size))
if gc_arg.dropout > -1:
layers.append(nn.Dropout(gc_arg.dropout))
# Gather
layers.append(GraphGather())
return layers
def create_gconv_net(hparams):
gconv_model = GraphConvSequential(GraphConvLayer(in_dim=75, out_dim=64),
nn.BatchNorm1d(64),
nn.ReLU(),
GraphPool(),
GraphConvLayer(in_dim=64, out_dim=64),
nn.BatchNorm1d(64),
nn.ReLU(),
GraphPool(),
nn.Linear(in_features=64, out_features=hparams["gconv"]["dim"]),
nn.BatchNorm1d(hparams["gconv"]["dim"]),
nn.ReLU(),
nn.Dropout(hparams["dprob"]),
GraphGather())
civ_dim = (hparams["gconv"]["dim"] * 2, hparams["prot"]["dim"])
return gconv_model, civ_dim
def create_integrated_net(hparams):
# segment 1 - graphconv
gconv_model = GraphConvSequential(
GraphConvLayer(in_dim=75, out_dim=64), nn.BatchNorm1d(64), nn.ReLU(),
GraphPool(), GraphConvLayer(in_dim=64, out_dim=64), nn.BatchNorm1d(64),
nn.ReLU(), GraphPool(),
nn.Linear(in_features=64, out_features=hparams["gconv_dim"]),
nn.BatchNorm1d(hparams["gconv_dim"]), nn.ReLU(),
nn.Dropout(hparams["dprob"]), GraphGather())
# segment 2 - fingerprint
fp_net = nn.Identity()
# segment 3 - protein
prot_net = nn.Identity()
civ_net = PairSequential(
(PairSequential(mod1=(gconv_model, ), mod2=(fp_net, )), ),
(prot_net, ))
civ_dim = hparams["prot_dim"] + hparams["gconv_dim"] * 2 + hparams["fp_dim"]
fcn_args = []
p = civ_dim
layers = hparams["hdims"]
if not isinstance(layers, list):
layers = [layers]
for dim in layers:
conf = FcnArgs(in_features=p,
out_features=dim,
activation='relu',
batch_norm=True,
dropout=hparams["dprob"])
fcn_args.append(conf)
p = dim
fcn_args.append(FcnArgs(in_features=p, out_features=hparams['output_dim']))
fcn_layers = create_fcn_layers(fcn_args)
model = nn.Sequential(civ_net, *fcn_layers)
return model
def test_graph_conv_layer(self):
feat_graph_conv = jova.feat.ConvMolFeaturizer()
mols = feat_graph_conv(self.mols)
self.assertEqual(len(mols), len(self.mols))
input_data = process_graph_conv_input(mols)
num_atom_feat = input_data[0][-1].shape[0]
gconv1 = GraphConvLayer(in_dim=num_atom_feat, out_dim=64)
# conv 1
out1 = gconv1(input_data)
self.assertIsNotNone(out1, msg="graph convolution 1 returned None")
out1 = torch.nn.BatchNorm1d(64)(out1)
print('\ngraph conv shape=', out1.shape)
# conv pool
gconvp1 = GraphPool()
input_data[0] = out1
out1 = gconvp1(input_data)
self.assertIsNotNone(out1, msg="graph pool 1 returned None")
print('conv pool shape=', out1.shape)
# conv gather
gconv_gather = GraphGather()
input_data[0] = out1
out_gathered = gconv_gather(input_data, len(mols))
self.assertIsNotNone(out_gathered, "Nothing was gathered")
print('out_gathered shape=', out_gathered.shape)
params = list(gconv1.parameters())
print('\n# of trainable parameters =', len(params))
for p in params:
print(p.size())
# backprop test
idx = 1 # np.random.randint(10)
self.assertIsNone(params[idx].grad, "Gradient property is not none")
c = 2
o = c * torch.sum(out_gathered)
o.backward()
self.assertIsNotNone(params[idx].grad, "Backprop failed")
for i in range(len(params)):
print('parameter-{} (shape={}) gradient = {}'.format(
i + 1, params[i].shape, params[i].grad))