"""GCN using basic message passing References: - Semi-Supervised Classification with Graph Convolutional Networks - Paper: https://arxiv.org/abs/1609.02907 - Code: https://github.com/tkipf/gcn """ import argparse, time, math import numpy as np import torch import torch.nn as nn import torch.nn.functional as F from dgl import DGLGraph from dgl.data import register_data_args, load_data def gcn_msg(edge): msg = edge.src['h'] * edge.src['norm'] return {'m': msg} def gcn_reduce(node): accum = torch.sum(node.mailbox['m'], 1) * node.data['norm'] return {'h': accum} class NodeApplyModule(nn.Module): def __init__(self, out_feats, activation=None, bias=True): super(NodeApplyModule, self).__init__() if bias: self.bias = nn.Parameter(torch.Tensor(out_feats)) else: self.bias = None self.activation = activation self.reset_parameters() def reset_parameters(self): if self.bias is not None: stdv = 1. / math.sqrt(self.bias.size(0)) self.bias.data.uniform_(-stdv, stdv) def forward(self, nodes): h = nodes.data['h'] if self.bias is not None: h = h + self.bias if self.activation: h = self.activation(h) return {'h': h} class GCNLayer(nn.Module): def __init__(self, g, in_feats, out_feats, activation, dropout, bias=True): super(GCNLayer, self).__init__() self.g = g self.weight = nn.Parameter(torch.Tensor(in_feats, out_feats)) if dropout: self.dropout = nn.Dropout(p=dropout) else: self.dropout = 0. self.node_update = NodeApplyModule(out_feats, activation, bias) self.reset_parameters() def reset_parameters(self): stdv = 1. / math.sqrt(self.weight.size(1)) self.weight.data.uniform_(-stdv, stdv) def forward(self, h): if self.dropout: h = self.dropout(h) self.g.ndata['h'] = torch.mm(h, self.weight) self.g.update_all(gcn_msg, gcn_reduce, self.node_update) h = self.g.ndata.pop('h') return h class GCN(nn.Module): def __init__(self, g, in_feats, n_hidden, n_classes, n_layers, activation, dropout): super(GCN, self).__init__() self.layers = nn.ModuleList() # input layer self.layers.append(GCNLayer(g, in_feats, n_hidden, activation, dropout)) # hidden layers for i in range(n_layers - 1): self.layers.append(GCNLayer(g, n_hidden, n_hidden, activation, dropout)) # output layer self.layers.append(GCNLayer(g, n_hidden, n_classes, None, dropout)) def forward(self, features): h = features for layer in self.layers: h = layer(h) return h def evaluate(model, features, labels, mask): model.eval() with torch.no_grad(): logits = model(features) logits = logits[mask] labels = labels[mask] _, indices = torch.max(logits, dim=1) correct = torch.sum(indices == labels) return correct.item() * 1.0 / len(labels) def main(args): # load and preprocess dataset data = load_data(args) features = torch.FloatTensor(data.features) labels = torch.LongTensor(data.labels) train_mask = torch.ByteTensor(data.train_mask) val_mask = torch.ByteTensor(data.val_mask) test_mask = torch.ByteTensor(data.test_mask) in_feats = features.shape[1] n_classes = data.num_labels n_edges = data.graph.number_of_edges() print("""----Data statistics------' #Edges %d #Classes %d #Train samples %d #Val samples %d #Test samples %d""" % (n_edges, n_classes, train_mask.sum().item(), val_mask.sum().item(), test_mask.sum().item())) if args.gpu < 0: cuda = False else: cuda = True torch.cuda.set_device(args.gpu) features = features.cuda() labels = labels.cuda() train_mask = train_mask.cuda() val_mask = val_mask.cuda() test_mask = test_mask.cuda() # graph preprocess and calculate normalization factor g = data.graph g.remove_edges_from(g.selfloop_edges()) g = DGLGraph(g) # add self loop g.add_edges(g.nodes(), g.nodes()) n_edges = g.number_of_edges() # normalization degs = g.in_degrees().float() norm = torch.pow(degs, -0.5) norm[torch.isinf(norm)] = 0 if cuda: norm = norm.cuda() g.ndata['norm'] = norm.unsqueeze(1) # create GCN model model = GCN(g, in_feats, args.n_hidden, n_classes, args.n_layers, F.relu, args.dropout) if cuda: model.cuda() loss_fcn = torch.nn.CrossEntropyLoss() # use optimizer optimizer = torch.optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.weight_decay) # initialize graph dur = [] for epoch in range(args.n_epochs): model.train() if epoch >= 3: t0 = time.time() # forward logits = model(features) loss = loss_fcn(logits[train_mask], labels[train_mask]) optimizer.zero_grad() loss.backward() optimizer.step() if epoch >= 3: dur.append(time.time() - t0) acc = evaluate(model, features, labels, val_mask) print("Epoch {:05d} | Time(s) {:.4f} | Loss {:.4f} | Accuracy {:.4f} | " "ETputs(KTEPS) {:.2f}". format(epoch, np.mean(dur), loss.item(), acc, n_edges / np.mean(dur) / 1000)) print() acc = evaluate(model, features, labels, test_mask) print("Test Accuracy {:.4f}".format(acc)) if __name__ == '__main__': parser = argparse.ArgumentParser(description='GCN') register_data_args(parser) parser.add_argument("--dropout", type=float, default=0.5, help="dropout probability") parser.add_argument("--gpu", type=int, default=-1, help="gpu") parser.add_argument("--lr", type=float, default=1e-2, help="learning rate") parser.add_argument("--n-epochs", type=int, default=200, help="number of training epochs") parser.add_argument("--n-hidden", type=int, default=16, help="number of hidden gcn units") parser.add_argument("--n-layers", type=int, default=1, help="number of hidden gcn layers") parser.add_argument("--weight-decay", type=float, default=5e-4, help="Weight for L2 loss") args = parser.parse_args() print(args) main(args)