import argparse, time, math import numpy as np import torch import torch.nn as nn import torch.nn.functional as F import dgl import dgl.function as fn from dgl import DGLGraph from dgl.data import register_data_args, load_data class NodeUpdate(nn.Module): def __init__(self, layer_id, in_feats, out_feats, dropout, activation=None, test=False, concat=False): super(NodeUpdate, self).__init__() self.layer_id = layer_id self.linear = nn.Linear(in_feats, out_feats) self.dropout = None if dropout != 0: self.dropout = nn.Dropout(p=dropout) self.activation = activation self.concat = concat self.test = test def forward(self, node): h = node.data['h'] if self.test: norm = node.data['norm'] h = h * norm else: agg_history_str = 'agg_h_{}'.format(self.layer_id-1) agg_history = node.data[agg_history_str] # control variate h = h + agg_history if self.dropout: h = self.dropout(h) h = self.linear(h) if self.concat: h = torch.cat((h, self.activation(h)), dim=1) elif self.activation: h = self.activation(h) return {'activation': h} class GCNSampling(nn.Module): def __init__(self, in_feats, n_hidden, n_classes, n_layers, activation, dropout): super(GCNSampling, self).__init__() self.n_layers = n_layers self.dropout = None if dropout != 0: self.dropout = nn.Dropout(p=dropout) self.activation = activation # input layer self.linear = nn.Linear(in_feats, n_hidden) self.layers = nn.ModuleList() # hidden layers for i in range(1, n_layers): skip_start = (i == n_layers-1) self.layers.append(NodeUpdate(i, n_hidden, n_hidden, dropout, activation, concat=skip_start)) # output layer self.layers.append(NodeUpdate(n_layers, 2*n_hidden, n_classes, dropout)) def forward(self, nf): h = nf.layers[0].data['preprocess'] if self.dropout: h = self.dropout(h) h = self.linear(h) skip_start = (0 == self.n_layers-1) if skip_start: h = torch.cat((h, self.activation(h)), dim=1) else: h = self.activation(h) for i, layer in enumerate(self.layers): new_history = h.clone().detach() history_str = 'h_{}'.format(i) history = nf.layers[i].data[history_str] h = h - history nf.layers[i].data['h'] = h nf.block_compute(i, fn.copy_src(src='h', out='m'), lambda node : {'h': node.mailbox['m'].mean(dim=1)}, layer) h = nf.layers[i+1].data.pop('activation') # update history if i < nf.num_layers-1: nf.layers[i].data[history_str] = new_history return h class GCNInfer(nn.Module): def __init__(self, in_feats, n_hidden, n_classes, n_layers, activation): super(GCNInfer, self).__init__() self.n_layers = n_layers self.activation = activation # input layer self.linear = nn.Linear(in_feats, n_hidden) self.layers = nn.ModuleList() # hidden layers for i in range(1, n_layers): skip_start = (i == n_layers-1) self.layers.append(NodeUpdate(i, n_hidden, n_hidden, 0, activation, True, concat=skip_start)) # output layer self.layers.append(NodeUpdate(n_layers, 2*n_hidden, n_classes, 0, None, True)) def forward(self, nf): h = nf.layers[0].data['preprocess'] h = self.linear(h) skip_start = (0 == self.n_layers-1) if skip_start: h = torch.cat((h, self.activation(h)), dim=1) else: h = self.activation(h) for i, layer in enumerate(self.layers): nf.layers[i].data['h'] = h nf.block_compute(i, fn.copy_src(src='h', out='m'), fn.sum(msg='m', out='h'), layer) h = nf.layers[i+1].data.pop('activation') return h def main(args): # load and preprocess dataset data = load_data(args) if args.self_loop and not args.dataset.startswith('reddit'): data.graph.add_edges_from([(i,i) for i in range(len(data.graph))]) train_nid = np.nonzero(data.train_mask)[0].astype(np.int64) test_nid = np.nonzero(data.test_mask)[0].astype(np.int64) 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() n_train_samples = train_mask.sum().item() n_val_samples = val_mask.sum().item() n_test_samples = test_mask.sum().item() print("""----Data statistics------' #Edges %d #Classes %d #Train samples %d #Val samples %d #Test samples %d""" % (n_edges, n_classes, n_train_samples, n_val_samples, n_test_samples)) # create GCN model g = DGLGraph(data.graph, readonly=True) norm = 1. / g.in_degrees().float().unsqueeze(1) 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() norm = norm.cuda() g.ndata['features'] = features num_neighbors = args.num_neighbors n_layers = args.n_layers g.ndata['norm'] = norm g.update_all(fn.copy_src(src='features', out='m'), fn.sum(msg='m', out='preprocess'), lambda node : {'preprocess': node.data['preprocess'] * node.data['norm']}) for i in range(n_layers): g.ndata['h_{}'.format(i)] = torch.zeros(features.shape[0], args.n_hidden).to(device=features.device) g.ndata['h_{}'.format(n_layers-1)] = torch.zeros(features.shape[0], 2*args.n_hidden).to(device=features.device) model = GCNSampling(in_feats, args.n_hidden, n_classes, n_layers, F.relu, args.dropout) loss_fcn = nn.CrossEntropyLoss() infer_model = GCNInfer(in_feats, args.n_hidden, n_classes, n_layers, F.relu) if cuda: model.cuda() infer_model.cuda() # use optimizer optimizer = torch.optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.weight_decay) for epoch in range(args.n_epochs): for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size, num_neighbors, neighbor_type='in', shuffle=True, num_workers=32, num_hops=n_layers, seed_nodes=train_nid): for i in range(n_layers): agg_history_str = 'agg_h_{}'.format(i) g.pull(nf.layer_parent_nid(i+1).long(), fn.copy_src(src='h_{}'.format(i), out='m'), fn.sum(msg='m', out=agg_history_str), lambda node : {agg_history_str: node.data[agg_history_str] * node.data['norm']}) node_embed_names = [['preprocess', 'h_0']] for i in range(1, n_layers): node_embed_names.append(['h_{}'.format(i), 'agg_h_{}'.format(i-1)]) node_embed_names.append(['agg_h_{}'.format(n_layers-1)]) nf.copy_from_parent(node_embed_names=node_embed_names) model.train() # forward pred = model(nf) batch_nids = nf.layer_parent_nid(-1).to(device=pred.device).long() batch_labels = labels[batch_nids] loss = loss_fcn(pred, batch_labels) optimizer.zero_grad() loss.backward() optimizer.step() node_embed_names = [['h_{}'.format(i)] for i in range(n_layers)] node_embed_names.append([]) nf.copy_to_parent(node_embed_names=node_embed_names) for infer_param, param in zip(infer_model.parameters(), model.parameters()): infer_param.data.copy_(param.data) num_acc = 0. for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size, g.number_of_nodes(), neighbor_type='in', num_workers=32, num_hops=n_layers, seed_nodes=test_nid): node_embed_names = [['preprocess']] for i in range(n_layers): node_embed_names.append(['norm']) nf.copy_from_parent(node_embed_names=node_embed_names) infer_model.eval() with torch.no_grad(): pred = infer_model(nf) batch_nids = nf.layer_parent_nid(-1).to(device=pred.device).long() batch_labels = labels[batch_nids] num_acc += (pred.argmax(dim=1) == batch_labels).sum().cpu().item() print("Test Accuracy {:.4f}". format(num_acc/n_test_samples)) 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=3e-2, help="learning rate") parser.add_argument("--n-epochs", type=int, default=200, help="number of training epochs") parser.add_argument("--batch-size", type=int, default=1000, help="train batch size") parser.add_argument("--test-batch-size", type=int, default=1000, help="test batch size") parser.add_argument("--num-neighbors", type=int, default=2, help="number of neighbors to be sampled") 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("--self-loop", action='store_true', help="graph self-loop (default=False)") parser.add_argument("--weight-decay", type=float, default=5e-4, help="Weight for L2 loss") args = parser.parse_args() print(args) main(args)