""" Inductive Representation Learning on Large Graphs Paper: http://papers.nips.cc/paper/6703-inductive-representation-learning-on-large-graphs.pdf Code: https://github.com/williamleif/graphsage-simple Simple reference implementation of GraphSAGE. """ import argparse import time import numpy as np import networkx as nx import torch import torch.nn as nn import torch.nn.functional as F import dgl from dgl import DGLGraph from dgl.data import register_data_args, load_data from dgl.nn.pytorch.conv import SAGEConv class GraphSAGE(nn.Module): def __init__(self, in_feats, n_hidden, n_classes, n_layers, activation, dropout, aggregator_type): super(GraphSAGE, self).__init__() self.layers = nn.ModuleList() self.dropout = nn.Dropout(dropout) self.activation = activation # input layer self.layers.append(SAGEConv(in_feats, n_hidden, aggregator_type)) # hidden layers for i in range(n_layers - 1): self.layers.append(SAGEConv(n_hidden, n_hidden, aggregator_type)) # output layer self.layers.append(SAGEConv(n_hidden, n_classes, aggregator_type)) # activation None def forward(self, graph, inputs): h = self.dropout(inputs) for l, layer in enumerate(self.layers): h = layer(graph, h) if l != len(self.layers) - 1: h = self.activation(h) h = self.dropout(h) return h def evaluate(model, graph, features, labels, nid): model.eval() with torch.no_grad(): logits = model(graph, features) logits = logits[nid] labels = labels[nid] _, 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) g = data[0] features = g.ndata['feat'] labels = g.ndata['label'] train_mask = g.ndata['train_mask'] val_mask = g.ndata['val_mask'] test_mask = g.ndata['test_mask'] in_feats = features.shape[1] n_classes = data.num_classes 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.int().sum().item(), val_mask.int().sum().item(), test_mask.int().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() print("use cuda:", args.gpu) train_nid = train_mask.nonzero().squeeze() val_nid = val_mask.nonzero().squeeze() test_nid = test_mask.nonzero().squeeze() # graph preprocess and calculate normalization factor g = dgl.remove_self_loop(g) n_edges = g.number_of_edges() if cuda: g = g.int().to(args.gpu) # create GraphSAGE model model = GraphSAGE(in_feats, args.n_hidden, n_classes, args.n_layers, F.relu, args.dropout, args.aggregator_type) if cuda: model.cuda() # 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(g, features) loss = F.cross_entropy(logits[train_nid], labels[train_nid]) optimizer.zero_grad() loss.backward() optimizer.step() if epoch >= 3: dur.append(time.time() - t0) acc = evaluate(model, g, features, labels, val_nid) 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, g, features, labels, test_nid) print("Test Accuracy {:.4f}".format(acc)) if __name__ == '__main__': parser = argparse.ArgumentParser(description='GraphSAGE') 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") parser.add_argument("--aggregator-type", type=str, default="gcn", help="Aggregator type: mean/gcn/pool/lstm") args = parser.parse_args() print(args) main(args)