main.py

"""
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 mxnet as mx
from mxnet import nd, gluon
from mxnet.gluon import nn
import dgl
from dgl.data import register_data_args
from dgl.data import CoraGraphDataset, CiteseerGraphDataset, PubmedGraphDataset
from dgl.nn.mxnet.conv import SAGEConv


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.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)