entity_classify_mb.py

"""Modeling Relational Data with Graph Convolutional Networks
Paper: https://arxiv.org/abs/1703.06103
Reference Code: https://github.com/tkipf/relational-gcn
"""
import argparse
import itertools
import time

import dgl

import numpy as np
import torch as th
import torch.nn.functional as F
from dgl.data.rdf import AIFBDataset, AMDataset, BGSDataset, MUTAGDataset
from model import EntityClassify, RelGraphEmbed


def extract_embed(node_embed, input_nodes):
    emb = {}
    for ntype, nid in input_nodes.items():
        nid = input_nodes[ntype]
        emb[ntype] = node_embed[ntype][nid]
    return emb


def evaluate(model, loader, node_embed, labels, category, device):
    model.eval()
    total_loss = 0
    total_acc = 0
    count = 0
    with loader.enable_cpu_affinity():
        for input_nodes, seeds, blocks in loader:
            blocks = [blk.to(device) for blk in blocks]
            seeds = seeds[category]
            emb = extract_embed(node_embed, input_nodes)
            emb = {k: e.to(device) for k, e in emb.items()}
            lbl = labels[seeds].to(device)
            logits = model(emb, blocks)[category]
            loss = F.cross_entropy(logits, lbl)
            acc = th.sum(logits.argmax(dim=1) == lbl).item()
            total_loss += loss.item() * len(seeds)
            total_acc += acc
            count += len(seeds)
    return total_loss / count, total_acc / count


def main(args):
    # check cuda
    device = "cpu"
    use_cuda = args.gpu >= 0 and th.cuda.is_available()
    if use_cuda:
        th.cuda.set_device(args.gpu)
        device = "cuda:%d" % args.gpu

    # load graph data
    if args.dataset == "aifb":
        dataset = AIFBDataset()
    elif args.dataset == "mutag":
        dataset = MUTAGDataset()
    elif args.dataset == "bgs":
        dataset = BGSDataset()
    elif args.dataset == "am":
        dataset = AMDataset()
    else:
        raise ValueError()

    g = dataset[0]
    category = dataset.predict_category
    num_classes = dataset.num_classes
    train_mask = g.nodes[category].data.pop("train_mask")
    test_mask = g.nodes[category].data.pop("test_mask")
    train_idx = th.nonzero(train_mask, as_tuple=False).squeeze()
    test_idx = th.nonzero(test_mask, as_tuple=False).squeeze()
    labels = g.nodes[category].data.pop("labels")

    # split dataset into train, validate, test
    if args.validation:
        val_idx = train_idx[: len(train_idx) // 5]
        train_idx = train_idx[len(train_idx) // 5 :]
    else:
        val_idx = train_idx

    # create embeddings
    embed_layer = RelGraphEmbed(g, args.n_hidden)

    if not args.data_cpu:
        labels = labels.to(device)
        embed_layer = embed_layer.to(device)

    if args.num_workers <= 0:
        raise ValueError(
            "The '--num_workers' parameter value is expected "
            "to be >0, but got {}.".format(args.num_workers)
        )

    node_embed = embed_layer()
    # create model
    model = EntityClassify(
        g,
        args.n_hidden,
        num_classes,
        num_bases=args.n_bases,
        num_hidden_layers=args.n_layers - 2,
        dropout=args.dropout,
        use_self_loop=args.use_self_loop,
    )

    if use_cuda:
        model.cuda()

    # train sampler
    sampler = dgl.dataloading.MultiLayerNeighborSampler(
        [args.fanout] * args.n_layers
    )
    loader = dgl.dataloading.DataLoader(
        g,
        {category: train_idx},
        sampler,
        batch_size=args.batch_size,
        shuffle=True,
        num_workers=args.num_workers,
    )

    # validation sampler
    # we do not use full neighbor to save computation resources
    val_sampler = dgl.dataloading.MultiLayerNeighborSampler(
        [args.fanout] * args.n_layers
    )
    val_loader = dgl.dataloading.DataLoader(
        g,
        {category: val_idx},
        val_sampler,
        batch_size=args.batch_size,
        shuffle=True,
        num_workers=args.num_workers,
    )

    # optimizer
    all_params = itertools.chain(model.parameters(), embed_layer.parameters())
    optimizer = th.optim.Adam(all_params, lr=args.lr, weight_decay=args.l2norm)

    # training loop
    print("start training...")
    mean = 0
    for epoch in range(args.n_epochs):
        model.train()
        optimizer.zero_grad()
        if epoch > 3:
            t0 = time.time()

        with loader.enable_cpu_affinity():
            for i, (input_nodes, seeds, blocks) in enumerate(loader):
                blocks = [blk.to(device) for blk in blocks]
                seeds = seeds[
                    category
                ]  # we only predict the nodes with type "category"
                batch_tic = time.time()
                emb = extract_embed(node_embed, input_nodes)
                lbl = labels[seeds]
                if use_cuda:
                    emb = {k: e.cuda() for k, e in emb.items()}
                    lbl = lbl.cuda()
                logits = model(emb, blocks)[category]
                loss = F.cross_entropy(logits, lbl)
                loss.backward()
                optimizer.step()

                train_acc = th.sum(logits.argmax(dim=1) == lbl).item() / len(
                    seeds
                )
                print(
                    f"Epoch {epoch:05d} | Batch {i:03d} | Train Acc: "
                    "{train_acc:.4f} | Train Loss: {loss.item():.4f} | Time: "
                    "{time.time() - batch_tic:.4f}"
                )

        if epoch > 3:
            mean = (mean * (epoch - 3) + (time.time() - t0)) / (epoch - 2)

            val_loss, val_acc = evaluate(
                model, val_loader, node_embed, labels, category, device
            )
            print(
                f"Epoch {epoch:05d} | Valid Acc: {val_acc:.4f} | Valid loss: "
                "{val_loss:.4f} | Time: {mean:.4f}"
            )
    print()
    if args.model_path is not None:
        th.save(model.state_dict(), args.model_path)

    output = model.inference(
        g,
        args.batch_size,
        "cuda" if use_cuda else "cpu",
        args.num_workers,
        node_embed,
    )
    test_pred = output[category][test_idx]
    test_labels = labels[test_idx].to(test_pred.device)
    test_acc = (test_pred.argmax(1) == test_labels).float().mean()
    print("Test Acc: {:.4f}".format(test_acc))
    print()


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="RGCN")
    parser.add_argument(
        "--dropout", type=float, default=0, help="dropout probability"
    )
    parser.add_argument(
        "--n-hidden", type=int, default=16, help="number of hidden units"
    )
    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-bases",
        type=int,
        default=-1,
        help="number of filter weight matrices, default: -1 [use all]",
    )
    parser.add_argument(
        "--n-layers", type=int, default=2, help="number of propagation rounds"
    )
    parser.add_argument(
        "-e",
        "--n-epochs",
        type=int,
        default=20,
        help="number of training epochs",
    )
    parser.add_argument(
        "-d", "--dataset", type=str, required=True, help="dataset to use"
    )
    parser.add_argument(
        "--model_path", type=str, default=None, help="path for save the model"
    )
    parser.add_argument("--l2norm", type=float, default=0, help="l2 norm coef")
    parser.add_argument(
        "--use-self-loop",
        default=False,
        action="store_true",
        help="include self feature as a special relation",
    )
    parser.add_argument(
        "--batch-size",
        type=int,
        default=100,
        help="Mini-batch size. If -1, use full graph training.",
    )
    parser.add_argument(
        "--fanout", type=int, default=4, help="Fan-out of neighbor sampling."
    )
    parser.add_argument(
        "--data-cpu",
        action="store_true",
        help="By default the script puts all node features and labels "
        "on GPU when using it to save time for data copy. This may "
        "be undesired if they cannot fit in GPU memory at once. "
        "This flag disables that.",
    )
    parser.add_argument(
        "--num_workers", type=int, default=4, help="Number of node dataloader"
    )

    fp = parser.add_mutually_exclusive_group(required=False)
    fp.add_argument("--validation", dest="validation", action="store_true")
    fp.add_argument("--testing", dest="validation", action="store_false")
    parser.set_defaults(validation=True)

    args = parser.parse_args()
    print(args)
    main(args)