import argparse import torch import torch.nn as nn import torch.nn.functional as F from dgl.data import CoraGraphDataset, CiteseerGraphDataset, PubmedGraphDataset from dgl import AddSelfLoop from torch.nn import init from dgl.mock_sparse import create_from_coo, diag, identity class GraphConv(nn.Module): def __init__(self, in_size, out_size, activation=None): super(GraphConv, self).__init__() self.W = nn.Parameter(torch.Tensor(in_size, out_size)) self.activation = activation self.bias = nn.Parameter(torch.Tensor(out_size)) self.reset_parameters() def forward(self, A, x): h = x @ self.W # Dense mm, pytorch op h = A @ h # SpMM h += self.bias if self.activation: h = self.activation(h) return h def reset_parameters(self): init.xavier_uniform_(self.W) init.zeros_(self.bias) class GCN(nn.Module): def __init__(self, in_size, hid_size, out_size): super().__init__() self.layers = nn.ModuleList() # two-layer GCN self.layers.append(GraphConv(in_size, hid_size, activation=F.relu)) self.layers.append(GraphConv(hid_size, out_size)) self.dropout = nn.Dropout(0.5) def forward(self, A, features): h = features for i, layer in enumerate(self.layers): if i != 0: h = self.dropout(h) h = layer(A, h) return h def gcn_norm(A): # normalization I = identity(A.shape) # create an identity matrix A_hat = A + I # add self-loop to A D = diag(A_hat.sum(0)) # diagonal degree matrix of A_hat # FIXME DiagMatrix does not have power() method D_hat = D D_hat.val = D_hat.val**-0.5 A_hat = D_hat @ A_hat @ D_hat return A_hat def evaluate(A, features, labels, mask, model): model.eval() with torch.no_grad(): logits = model(A, 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 train(A, features, labels, masks, model): # define train/val samples, loss function and optimizer train_mask = masks[0] val_mask = masks[1] loss_fcn = nn.CrossEntropyLoss() optimizer = torch.optim.Adam(model.parameters(), lr=1e-2, weight_decay=5e-4) # training loop for epoch in range(200): model.train() logits = model(A, features) loss = loss_fcn(logits[train_mask], labels[train_mask]) optimizer.zero_grad() loss.backward() optimizer.step() acc = evaluate(A, features, labels, val_mask, model) print( "Epoch {:05d} | Loss {:.4f} | Accuracy {:.4f} ".format( epoch, loss.item(), acc ) ) if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument( "--dataset", type=str, default="cora", help="Dataset name ('cora', 'citeseer', 'pubmed', 'synthetic).", ) args = parser.parse_args() print(f"Training with DGL SparseMatrix GraphConv module.") # load and preprocess dataset transform = ( AddSelfLoop() ) # by default, it will first remove self-loops to prevent duplication if args.dataset == "cora": data = CoraGraphDataset(transform=transform) elif args.dataset == "citeseer": data = CiteseerGraphDataset(transform=transform) elif args.dataset == "pubmed": data = PubmedGraphDataset(transform=transform) else: raise ValueError("Unknown dataset: {}".format(args.dataset)) g = data[0].int() features = g.ndata["feat"] labels = g.ndata["label"] masks = g.ndata["train_mask"], g.ndata["val_mask"], g.ndata["test_mask"] row, col = g.adj_sparse("coo") A = create_from_coo( row, col, shape=(g.number_of_nodes(), g.number_of_nodes()) ) A = gcn_norm(A) # create GCN model in_size = features.shape[1] out_size = data.num_classes model = GCN(in_size, 16, out_size) # model training print("Training...") train(A, features, labels, masks, model) # test the model print("Testing...") acc = evaluate(A, features, labels, masks[2], model) print("Test accuracy {:.4f}".format(acc))