""" This script demonstrate how to use dgl sparse library to sample on graph and train model. It trains and tests a GraphSAGE model using the sparse sample and compact operators to sample submatrix from the whole matrix. This flowchart describes the main functional sequence of the provided example. main │ ├───> Load and preprocess full dataset │ ├───> Instantiate SAGE model │ ├───> train │ │ │ └───> Training loop │ │ │ ├───> Sample submatrix │ │ │ └───> SAGE.forward └───> test │ ├───> Sample submatrix │ └───> Evaluate the model """ import argparse import dgl.sparse as dglsp import torch import torch.nn as nn import torch.nn.functional as F import torchmetrics.functional as MF from dgl.data import AsNodePredDataset from ogb.nodeproppred import DglNodePropPredDataset class SAGEConv(nn.Module): r"""GraphSAGE layer from `Inductive Representation Learning on Large Graphs `__ """ def __init__( self, in_feats, out_feats, ): super(SAGEConv, self).__init__() self._in_src_feats, self._in_dst_feats = in_feats, in_feats self._out_feats = out_feats self.fc_neigh = nn.Linear(self._in_src_feats, out_feats, bias=False) self.fc_self = nn.Linear(self._in_dst_feats, out_feats, bias=True) self.reset_parameters() def reset_parameters(self): gain = nn.init.calculate_gain("relu") nn.init.xavier_uniform_(self.fc_self.weight, gain=gain) nn.init.xavier_uniform_(self.fc_neigh.weight, gain=gain) def forward(self, A, feat): feat_src = feat feat_dst = feat[: A.shape[1]] # Aggregator type: mean. srcdata = self.fc_neigh(feat_src) # Divided by degree. D_hat = dglsp.diag(A.sum(0)) ** -1 A_div = A @ D_hat # Conv neighbors. dstdata = A_div.T @ srcdata rst = self.fc_self(feat_dst) + dstdata return rst class SAGE(nn.Module): def __init__(self, in_size, hid_size, out_size): super().__init__() self.layers = nn.ModuleList() # Three-layer GraphSAGE-gcn. self.layers.append(SAGEConv(in_size, hid_size)) self.layers.append(SAGEConv(hid_size, hid_size)) self.layers.append(SAGEConv(hid_size, out_size)) self.dropout = nn.Dropout(0.5) self.hid_size = hid_size self.out_size = out_size def forward(self, sampled_matrices, x): hidden_x = x for layer_idx, (layer, sampled_matrix) in enumerate( zip(self.layers, sampled_matrices) ): hidden_x = layer(sampled_matrix, hidden_x) if layer_idx != len(self.layers) - 1: hidden_x = F.relu(hidden_x) hidden_x = self.dropout(hidden_x) return hidden_x def multilayer_sample(A, fanouts, seeds, ndata): sampled_matrices = [] src = seeds ##################################################################### # (HIGHLIGHT) Using the sparse sample operator to preform random # sampling on the neighboring nodes of the seeds nodes. The sparse # compact operator is then employed to compact and relabel the sampled # matrix, resulting in the sampled matrix and the relabel index. ##################################################################### for fanout in fanouts: # Sample neighbors. sampled_matrix = A.sample(1, fanout, ids=src).coalesce() # Compact the sampled matrix. compacted_mat, row_ids = sampled_matrix.compact(0) sampled_matrices.insert(0, compacted_mat) src = row_ids x = ndata["feat"][src] y = ndata["label"][seeds] return sampled_matrices, x, y def evaluate(model, A, dataloader, ndata, num_classes): model.eval() ys = [] y_hats = [] fanouts = [10, 10, 10] for it, seeds in enumerate(dataloader): with torch.no_grad(): sampled_matrices, x, y = multilayer_sample(A, fanouts, seeds, ndata) ys.append(y) y_hats.append(model(sampled_matrices, x)) return MF.accuracy( torch.cat(y_hats), torch.cat(ys), task="multiclass", num_classes=num_classes, ) def validate(device, A, ndata, dataset, model, batch_size): inf_id = dataset.test_idx.to(device) inf_dataloader = torch.utils.data.DataLoader(inf_id, batch_size=batch_size) acc = evaluate(model, A, inf_dataloader, ndata, dataset.num_classes) return acc def train(device, A, ndata, dataset, model): # Create sampler & dataloader. train_idx = dataset.train_idx.to(device) val_idx = dataset.val_idx.to(device) train_dataloader = torch.utils.data.DataLoader( train_idx, batch_size=1024, shuffle=True ) val_dataloader = torch.utils.data.DataLoader(val_idx, batch_size=1024) optimizer = torch.optim.Adam(model.parameters(), lr=1e-3, weight_decay=5e-4) fanouts = [10, 10, 10] for epoch in range(10): model.train() total_loss = 0 for it, seeds in enumerate(train_dataloader): sampled_matrices, x, y = multilayer_sample(A, fanouts, seeds, ndata) y_hat = model(sampled_matrices, x) loss = F.cross_entropy(y_hat, y) optimizer.zero_grad() loss.backward() optimizer.step() total_loss += loss.item() acc = evaluate(model, A, val_dataloader, ndata, dataset.num_classes) print( "Epoch {:05d} | Loss {:.4f} | Accuracy {:.4f} ".format( epoch, total_loss / (it + 1), acc.item() ) ) if __name__ == "__main__": parser = argparse.ArgumentParser(description="GraphSAGE") parser.add_argument( "--mode", default="gpu", choices=["cpu", "gpu"], help="Training mode. 'cpu' for CPU training, 'gpu' for GPU training.", ) args = parser.parse_args() if not torch.cuda.is_available(): args.mode = "cpu" print(f"Training in {args.mode} mode.") ##################################################################### # (HIGHLIGHT) This example implements a graphSAGE algorithm by sparse # operators, which involves sampling a subgraph from a full graph and # conducting training. # # First, the whole graph is loaded onto the CPU or GPU and transformed # to sparse matrix. To obtain the training subgraph, it samples three # submatrices by seed nodes, which contains their randomly sampled # 1-hop, 2-hop, and 3-hop neighbors. Then, the features of the # subgraph are input to the network for training. ##################################################################### # Load and preprocess dataset. print("Loading data") device = torch.device("cpu" if args.mode == "cpu" else "cuda") dataset = AsNodePredDataset(DglNodePropPredDataset("ogbn-products")) g = dataset[0] g = g.to(device) # Create GraphSAGE model. in_size = g.ndata["feat"].shape[1] out_size = dataset.num_classes model = SAGE(in_size, 256, out_size).to(device) # Create sparse. indices = torch.stack(g.edges()) N = g.num_nodes() A = dglsp.spmatrix(indices, shape=(N, N)) # Model training. print("Training...") train(device, A, g.ndata, dataset, model) # Test the model. print("Testing...") acc = validate(device, A, g.ndata, dataset, model, batch_size=4096) print(f"Test accuracy {acc:.4f}")