def forward(self, batch_graph):
node_feat, edge_feat, labels = MOLLIB.PrepareFeatureLabel(batch_graph)
if cmd_args.mode == 'gpu':
node_feat = node_feat.cuda()
edge_feat = edge_feat.cuda()
labels = labels.cuda()
embed = self.s2v(batch_graph, node_feat, edge_feat)
return self.mlp(embed, labels)
val_list[3] = ctypes.c_void_p(subg_vals.numpy().ctypes.data)
self.lib.PrepareLoopyBP(self.batch_graph_handle,
ctypes.cast(idx_list, ctypes.c_void_p),
ctypes.cast(val_list, ctypes.c_void_p))
n2e_sp = torch.sparse.FloatTensor(n2e_idxes, n2e_vals, torch.Size([total_num_edges * 2, total_num_nodes]))
e2e_sp = torch.sparse.FloatTensor(e2e_idxes, e2e_vals, torch.Size([total_num_edges * 2, total_num_edges * 2]))
e2n_sp = torch.sparse.FloatTensor(e2n_idxes, e2n_vals, torch.Size([total_num_nodes, total_num_edges * 2]))
subg_sp = torch.sparse.FloatTensor(subg_idxes, subg_vals, torch.Size([len(graph_list), total_num_nodes]))
return n2e_sp, e2e_sp, e2n_sp, subg_sp
dll_path = '%s/build/dll/libs2v.so' % os.path.dirname(os.path.realpath(__file__))
if os.path.exists(dll_path):
S2VLIB = _s2v_lib(sys.argv)
else:
S2VLIB = None
if __name__ == '__main__':
sys.path.append('%s/../harvard_cep' % os.path.dirname(os.path.realpath(__file__)))
from util import resampling_idxes, load_raw_data
from mol_lib import MOLLIB, MolGraph
raw_data_dict = load_raw_data()
test_data = MOLLIB.LoadMolGraph('test', raw_data_dict['test'])
batch_graph = test_data[0:10]
S2VLIB.PrepareLoopyBP(batch_graph)
regressor = Regressor()
if cmd_args.mode == 'gpu':
regressor = regressor.cuda()
if cmd_args.saved_model is not None and cmd_args.saved_model != '':
if os.path.isfile(cmd_args.saved_model):
print('loading model from %s' % cmd_args.saved_model)
if cmd_args.mode == 'cpu':
regressor.load_state_dict(
torch.load(cmd_args.saved_model,
map_location=lambda storage, loc: storage))
else:
regressor.load_state_dict(torch.load(cmd_args.saved_model))
if cmd_args.phase == 'test':
test_data = MOLLIB.LoadMolGraph('test', raw_data_dict['test'])
test_loss = loop_dataset(test_data, regressor,
list(range(len(test_data))))
print('\033[93maverage test loss: mae %.5f rmse %.5f\033[0m' %
(test_loss[0], test_loss[1]))
sys.exit()
train_idxes = resampling_idxes(raw_data_dict)
cooked_data_dict = {}
for d in raw_data_dict:
cooked_data_dict[d] = MOLLIB.LoadMolGraph(d, raw_data_dict[d])
optimizer = optim.Adam(regressor.parameters(), lr=cmd_args.learning_rate)
iter_train = (len(train_idxes) +
(cmd_args.batch_size - 1)) // cmd_args.batch_size