""" 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 dgl import mxnet as mx import networkx as nx import numpy as np from dgl.data import ( CiteseerGraphDataset, CoraGraphDataset, PubmedGraphDataset, register_data_args, ) from dgl.nn.mxnet.conv import SAGEConv from mxnet import gluon, nd from mxnet.gluon import nn class GraphSAGE(nn.Block): def __init__( self, g, in_feats, n_hidden, n_classes, n_layers, activation, dropout, aggregator_type, ): super(GraphSAGE, self).__init__() self.g = g with self.name_scope(): self.layers = nn.Sequential() # input layer self.layers.add( SAGEConv( in_feats, n_hidden, aggregator_type, feat_drop=dropout, activation=activation, ) ) # hidden layers for i in range(n_layers - 1): self.layers.add( SAGEConv( n_hidden, n_hidden, aggregator_type, feat_drop=dropout, activation=activation, ) ) # output layer self.layers.add( SAGEConv( n_hidden, n_classes, aggregator_type, feat_drop=dropout, activation=None, ) ) # activation None def forward(self, features): h = features for layer in self.layers: h = layer(self.g, h) return h def evaluate(model, features, labels, mask): pred = model(features).argmax(axis=1) accuracy = ((pred == labels) * mask).sum() / mask.sum().asscalar() return accuracy.asscalar() def main(args): # load and preprocess dataset if args.dataset == "cora": data = CoraGraphDataset() elif args.dataset == "citeseer": data = CiteseerGraphDataset() elif args.dataset == "pubmed": data = PubmedGraphDataset() else: raise ValueError("Unknown dataset: {}".format(args.dataset)) g = data[0] if args.gpu < 0: cuda = False ctx = mx.cpu(0) else: cuda = True ctx = mx.gpu(args.gpu) g = g.int().to(ctx) features = g.ndata["feat"] labels = mx.nd.array(g.ndata["label"], dtype="float32", ctx=ctx) 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_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().asscalar(), val_mask.sum().asscalar(), test_mask.sum().asscalar(), ) ) # add self loop g = dgl.remove_self_loop(g) g = dgl.add_self_loop(g) n_edges = g.number_of_edges() # create GraphSAGE model model = GraphSAGE( g, in_feats, args.n_hidden, n_classes, args.n_layers, nd.relu, args.dropout, args.aggregator_type, ) model.initialize(ctx=ctx) n_train_samples = train_mask.sum().asscalar() loss_fcn = gluon.loss.SoftmaxCELoss() print(model.collect_params()) trainer = gluon.Trainer( model.collect_params(), "adam", {"learning_rate": args.lr, "wd": args.weight_decay}, ) # initialize graph dur = [] for epoch in range(args.n_epochs): if epoch >= 3: t0 = time.time() # forward with mx.autograd.record(): pred = model(features) loss = loss_fcn(pred, labels, mx.nd.expand_dims(train_mask, 1)) loss = loss.sum() / n_train_samples loss.backward() trainer.step(batch_size=1) if epoch >= 3: loss.asscalar() 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.asscalar(), acc, n_edges / np.mean(dur) / 1000, ) ) # test set accuracy acc = evaluate(model, features, labels, test_mask) print("Test accuracy {:.2%}".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)