def main():
parser = argparse.ArgumentParser(description='OGBN-MolHiv')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--num_workers', type=int, default=4)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--batch_size', type=int, default=64)
parser.add_argument('--num_layers', type=int, default=5)
parser.add_argument('--emb_dim', type=int, default=256)
parser.add_argument('--dropout', type=float, default=0.5)
parser.add_argument('--lr', type=float, default=0.001)
parser.add_argument('--epochs', type=int, default=50)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument('--eval',
action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument('--eval_batch_size', type=int, default=2048)
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = DglGraphPropPredDataset(name='ogbg-molhiv')
split_idx = dataset.get_idx_split()
evaluator = Evaluator(name='ogbg-molhiv')
train_loader = GraphDataLoader(dataset[split_idx["train"]],
batch_size=args.batch_size,
shuffle=True,
num_workers=args.num_workers)
val_loader = GraphDataLoader(dataset[split_idx["valid"]],
batch_size=args.eval_batch_size,
shuffle=True,
num_workers=0)
test_loader = GraphDataLoader(dataset[split_idx["test"]],
batch_size=args.eval_batch_size,
shuffle=True,
num_workers=0)
model = GCN(args.emb_dim,
num_classes=dataset.num_tasks,
num_layers=args.num_layers,
dropout=args.dropout).to(device)
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, args.epochs + 1):
t0 = time.time()
loss = train(model, device, train_loader, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
val_rocauc = test(model, device, val_loader,
evaluator)[dataset.eval_metric]
test_rocauc = test(model, device, test_loader,
evaluator)[dataset.eval_metric]
logger.add_result(run, (0.0, val_rocauc, test_rocauc))
if epoch % args.log_steps == 0:
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Valid: {val_rocauc:.4f} '
f'Test: {test_rocauc:.4f}')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='GraphSAGE')
parser.add_argument("--dataset", type=str, default='reddit')
parser.add_argument("--device", type=int, default=0)
parser.add_argument("--dropout",
type=float,
default=0.5,
help="dropout probability")
parser.add_argument("--lr", type=float, default=1e-2, help="learning rate")
parser.add_argument("--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("--aggr",
type=str,
choices=['sum', 'mean'],
default='mean',
help='Aggregation for messages')
parser.add_argument("--weight-decay",
type=float,
default=5e-4,
help="Weight for L2 loss")
parser.add_argument("--eval",
action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument("--runs", type=int, default=10)
args = parser.parse_args()
print(args)
# load and preprocess dataset
data = load_data(args)
features = torch.FloatTensor(data.features)
labels = torch.LongTensor(data.labels)
if hasattr(torch, 'BoolTensor'):
train_mask = torch.BoolTensor(data.train_mask)
val_mask = torch.BoolTensor(data.val_mask)
test_mask = torch.BoolTensor(data.test_mask)
else:
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()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes, train_mask.int().sum().item(),
val_mask.int().sum().item(), test_mask.int().sum().item()))
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
features = features.to(device)
labels = labels.to(device)
train_mask = train_mask.to(device)
val_mask = val_mask.to(device)
test_mask = test_mask.to(device)
# Remove duplicate edges
# In PyG, this is a default pre-processing step for Reddit, see
# https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/datasets/reddit.py#L58
g = data.graph
g = g.int().to(device)
# create GraphSAGE model
model = GraphSAGE(g, in_feats, args.n_hidden, n_classes, args.aggr, F.relu,
args.dropout).to(device)
loss_fcn = nn.CrossEntropyLoss()
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
for epoch in range(args.epochs):
model.train()
if epoch >= 3:
t0 = time.time()
# forward
logits = model(features)
loss = loss_fcn(logits[train_mask], labels[train_mask])
optimizer.zero_grad()
loss.backward()
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
train_acc, val_acc, test_acc = evaluate(model, features, labels,
train_mask, val_mask,
test_mask)
logger.add_result(run, (train_acc, val_acc, test_acc))
print(
"Run {:02d} | Epoch {:05d} | Loss {:.4f} | Train {:.4f} | Val {:.4f} | Test {:.4f}"
.format(run, epoch, loss.item(), train_acc, val_acc, test_acc))
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(
description='OGBN-Arxiv (GraphSAGE Full-Batch)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--num_layers', type=int, default=3)
parser.add_argument('--hidden_channels', type=int, default=256)
parser.add_argument('--dropout', type=float, default=0.5)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--epochs', type=int, default=500)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument("--eval",
action='store_true',
help='If not set, we will only do the training part.')
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = DglNodePropPredDataset(name='ogbn-arxiv')
split_idx = dataset.get_idx_split()
g, labels = dataset[0]
feats = g.ndata['feat']
g = dgl.to_bidirected(g)
g = g.int().to(device)
feats, labels = feats.to(device), labels.to(device)
train_idx = split_idx['train'].to(device)
model = GraphSAGE(in_feats=feats.size(-1),
hidden_feats=args.hidden_channels,
out_feats=dataset.num_classes,
num_layers=args.num_layers,
dropout=args.dropout).to(device)
evaluator = Evaluator(name='ogbn-arxiv')
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, 1 + args.epochs):
t0 = time.time()
loss = train(model, g, feats, labels, train_idx, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
result = test(model, g, feats, labels, split_idx, evaluator)
logger.add_result(run, result)
if epoch % args.log_steps == 0:
train_acc, valid_acc, test_acc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {100 * train_acc:.2f}%, '
f'Valid: {100 * valid_acc:.2f}% '
f'Test: {100 * test_acc:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='GAT')
parser.add_argument("--dataset", type=str)
parser.add_argument("--device", type=int, default=0)
parser.add_argument("--num-layers",
type=int,
default=3,
help="number of hidden layers")
parser.add_argument("--lr",
type=float,
default=0.005,
help="learning rate")
parser.add_argument('--weight-decay',
type=float,
default=5e-4,
help="weight decay")
parser.add_argument("--num-hidden",
type=int,
default=8,
help="number of hidden units")
parser.add_argument("--dropout",
type=float,
default=.6,
help="Dropout to use")
parser.add_argument('--epochs', type=int, default=200)
parser.add_argument("--eval",
action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument("--runs", type=int, default=10)
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
path = osp.join('dataset', args.dataset)
dataset = Planetoid(path, args.dataset, transform=T.NormalizeFeatures())
data = dataset[0]
features = data.x.to(device)
labels = data.y.to(device)
edge_index = data.edge_index.to(device)
adj = SparseTensor(row=edge_index[0], col=edge_index[1])
train_mask = torch.BoolTensor(data.train_mask).to(device)
val_mask = torch.BoolTensor(data.val_mask).to(device)
test_mask = torch.BoolTensor(data.test_mask).to(device)
model = GAT(num_layers=args.num_layers,
in_feats=features.size(-1),
num_hidden=args.num_hidden,
num_classes=dataset.num_classes,
heads=[8, 8, 1],
dropout=args.dropout).to(device)
loss_fcn = nn.CrossEntropyLoss()
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
for epoch in range(1, args.epochs + 1):
model.train()
if epoch >= 3:
t0 = time.time()
# forward
logits = model(features, adj)
loss = loss_fcn(logits[train_mask], labels[train_mask])
optimizer.zero_grad()
loss.backward()
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
train_acc, val_acc, test_acc = evaluate(model, features, adj,
labels, train_mask,
val_mask, test_mask)
logger.add_result(run, (train_acc, val_acc, test_acc))
print(
"Run {:02d} | Epoch {:05d} | Loss {:.4f} | Train {:.4f} | Val {:.4f} | Test {:.4f}"
.format(run, epoch, loss.item(), train_acc, val_acc, test_acc))
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main(args):
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
path = osp.join('dataset', 'Reddit')
dataset = Reddit(path)
data = dataset[0]
features = data.x.to(device)
labels = data.y.to(device)
edge_index = data.edge_index.to(device)
adj = SparseTensor(row=edge_index[0], col=edge_index[1])
train_mask = torch.BoolTensor(data.train_mask).to(device)
val_mask = torch.BoolTensor(data.val_mask).to(device)
test_mask = torch.BoolTensor(data.test_mask).to(device)
model = GraphSAGE(dataset.num_features, args.n_hidden, dataset.num_classes,
args.aggr, F.relu, args.dropout).to(device)
loss_fcn = nn.CrossEntropyLoss()
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
for epoch in range(1, args.epochs + 1):
model.train()
if epoch >= 3:
t0 = time.time()
# forward
logits = model(features, adj)
loss = loss_fcn(logits[train_mask], labels[train_mask])
optimizer.zero_grad()
loss.backward()
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
train_acc, val_acc, test_acc = evaluate(model, features, adj,
labels, train_mask,
val_mask, test_mask)
logger.add_result(run, (train_acc, val_acc, test_acc))
print(
"Run {:02d} | Epoch {:05d} | Loss {:.4f} | Train {:.4f} | Val {:.4f} | Test {:.4f}"
.format(run, epoch, loss.item(), train_acc, val_acc, test_acc))
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='ENZYMES')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--num_workers', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--batch_size', type=int, default=64)
parser.add_argument('--num_layers', type=int, default=4)
parser.add_argument('--hidden_size', type=int, default=128)
parser.add_argument('--dropout', type=float, default=0.5)
parser.add_argument('--lr', type=float, default=0.001)
parser.add_argument('--epochs', type=int, default=10)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument('--eval',
action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument('--eval_batch_size', type=int, default=2048)
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = LegacyTUDataset('ENZYMES')
num_samples = len(dataset)
indices = np.arange(num_samples)
np.random.seed(42)
np.random.shuffle(indices)
train_set = dgl.data.utils.Subset(dataset,
indices[:int(num_samples * 0.8)])
val_set = dgl.data.utils.Subset(
dataset, indices[int(num_samples * 0.8):int(num_samples * 0.9)])
test_set = dgl.data.utils.Subset(
dataset, indices[int(num_samples * 0.9):int(num_samples)])
train_loader = GraphDataLoader(train_set,
batch_size=args.batch_size,
shuffle=True,
num_workers=args.num_workers)
val_loader = GraphDataLoader(val_set,
batch_size=args.eval_batch_size,
shuffle=True,
num_workers=0)
test_loader = GraphDataLoader(test_set,
batch_size=args.eval_batch_size,
shuffle=True,
num_workers=0)
model = GCN(18,
args.hidden_size,
num_classes=int(dataset.num_labels),
num_layers=args.num_layers,
dropout=args.dropout).to(device)
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, args.epochs + 1):
t0 = time.time()
loss = train(model, device, train_loader, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
val_acc = test(model, device, val_loader)
test_acc = test(model, device, test_loader)
logger.add_result(run, (0.0, val_acc, test_acc))
if epoch % args.log_steps == 0:
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Valid: {val_acc * 100:.4f}% '
f'Test: {test_acc * 100:.4f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(
description='OGBN-Proteins (RGCN Full-Batch)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--num-layers', type=int, default=3)
parser.add_argument('--hidden-feats', type=int, default=32)
parser.add_argument('--dropout', type=float, default=0.)
parser.add_argument('--epochs', type=int, default=1000)
parser.add_argument('--eval_steps', type=int, default=5)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument("--eval",
action='store_true',
help='If not set, we will only do the training part.')
args = parser.parse_args()
print(args)
# OOM on a GPU of 16G
device = 'cpu'
device = torch.device(device)
dataset = PygNodePropPredDataset(name='ogbn-proteins')
data = dataset[0]
y_true = data.y.to(device)
node_feats = torch.ones((y_true.shape[0], 1)).to(device)
edge_index = data.edge_index.to(device)
edge_weights = data.edge_attr.to(device)
split_idx = dataset.get_idx_split()
train_idx = split_idx['train'].to(device)
adjs = []
for t in range(edge_weights.shape[-1]):
adjs.append(
SparseTensor(row=edge_index[0],
col=edge_index[1],
value=edge_weights[:, t]))
model = RGCN(num_layers=args.num_layers,
in_feats=node_feats.shape[-1],
hidden_feats=args.hidden_feats,
out_feats=y_true.shape[-1],
num_relations=edge_weights.shape[-1],
dropout=args.dropout).to(device)
evaluator = Evaluator(name='ogbn-proteins')
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, 1 + args.epochs):
t0 = time.time()
loss = train(model, node_feats, adjs, y_true, train_idx, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
if epoch % args.eval_steps == 0:
result = test(model, node_feats, adjs, y_true, split_idx,
evaluator)
logger.add_result(run, result)
if epoch % args.log_steps == 0:
train_rocauc, valid_rocauc, test_rocauc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {100 * train_rocauc:.2f}%, '
f'Valid: {100 * valid_rocauc:.2f}% '
f'Test: {100 * test_rocauc:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='GAT')
parser.add_argument("--dataset", type=str, default='reddit')
parser.add_argument("--device", type=int, default=0)
parser.add_argument("--num-layers",
type=int,
default=3,
help="number of hidden layers")
parser.add_argument("--lr",
type=float,
default=0.0029739421726400865,
help="learning rate")
parser.add_argument('--weight-decay',
type=float,
default=2.4222556964495987e-05,
help="weight decay")
parser.add_argument("--num-hidden",
type=int,
default=16,
help="number of hidden units")
parser.add_argument("--dropout",
type=float,
default=0.18074706609292976,
help="Dropout to use")
parser.add_argument('--epochs', type=int, default=500)
parser.add_argument("--eval",
action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument("--runs", type=int, default=10)
args = parser.parse_args()
print(args)
# load and preprocess dataset
data = load_data(args)
features = torch.FloatTensor(data.features)
labels = torch.LongTensor(data.labels)
if hasattr(torch, 'BoolTensor'):
train_mask = torch.BoolTensor(data.train_mask)
val_mask = torch.BoolTensor(data.val_mask)
test_mask = torch.BoolTensor(data.test_mask)
else:
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()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes, train_mask.int().sum().item(),
val_mask.int().sum().item(), test_mask.int().sum().item()))
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
# Remove duplicate edges
# In PyG, this is a default pre-processing step for Reddit, see
# https://github.com/rusty1s/pytorch_geometric/blob/master/torch_geometric/datasets/reddit.py#L58
g = data.graph
g = dgl.add_self_loop(g)
g = g.int().to(device)
features, labels = features.to(device), labels.to(device)
model = GAT(g=g,
num_layers=args.num_layers,
in_feats=in_feats,
num_hidden=args.num_hidden,
num_classes=n_classes,
heads=[1, 1, 1],
feat_drop=args.dropout,
attn_drop=args.dropout)
model = model.to(device)
loss_fcn = nn.CrossEntropyLoss()
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
for epoch in range(args.epochs):
model.train()
if epoch >= 3:
t0 = time.time()
# forward
logits = model(features)
loss = loss_fcn(logits[train_mask], labels[train_mask])
optimizer.zero_grad()
loss.backward()
optimizer.step()
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
train_acc, val_acc, test_acc = evaluate(model, features, labels,
train_mask, val_mask,
test_mask)
logger.add_result(run, (train_acc, val_acc, test_acc))
print(
"Run {:02d} | Epoch {:05d} | Loss {:.4f} | Train {:.4f} | Val {:.4f} | Test {:.4f}"
.format(run, epoch, loss.item(), train_acc, val_acc, test_acc))
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='OGBN-Arxiv (GAT Full-Batch)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument("--num-layers", type=int, default=3,
help="number of hidden layers")
parser.add_argument("--lr", type=float, default=0.0029739421726400865,
help="learning rate")
parser.add_argument('--weight-decay', type=float, default=2.4222556964495987e-05,
help="weight decay")
parser.add_argument("--num-hidden", type=int, default=16,
help="number of hidden units")
parser.add_argument("--dropout", type=float, default=0.18074706609292976,
help="Dropout to use")
parser.add_argument('--epochs', type=int, default=500)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument("--eval", action='store_true',
help='If not set, we will only do the training part.')
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = DglNodePropPredDataset(name='ogbn-arxiv')
split_idx = dataset.get_idx_split()
g, labels = dataset[0]
feats = g.ndata['feat'].to(device)
labels = labels.to(device)
train_idx = split_idx['train'].to(device)
g = dgl.to_bidirected(g)
g = dgl.add_self_loop(g)
g = g.int().to(device)
print(g)
model = GAT(num_layers=args.num_layers,
in_feats=feats.size(-1),
num_hidden=args.num_hidden,
num_classes=dataset.num_classes,
heads=[4, 4, 4],
feat_drop=args.dropout,
attn_drop=args.dropout).to(device)
evaluator = Evaluator(name='ogbn-arxiv')
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.weight_decay)
for epoch in range(1, 1 + args.epochs):
t0 = time.time()
loss = train(model, g, feats, labels, train_idx, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
result = test(model, g, feats, labels, split_idx, evaluator)
logger.add_result(run, result)
if epoch % args.log_steps == 0:
train_acc, valid_acc, test_acc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {100 * train_acc:.2f}%, '
f'Valid: {100 * valid_acc:.2f}% '
f'Test: {100 * test_acc:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='OGBN-Arxiv (GraphSAGE Full-Batch)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--num_layers', type=int, default=3)
parser.add_argument('--hidden_channels', type=int, default=256)
parser.add_argument('--dropout', type=float, default=0.5)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--epochs', type=int, default=500)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument("--eval", action='store_true',
help='If not set, we will only do the training part.')
args = parser.parse_args()
print(args)
dataset = DglNodePropPredDataset(name='ogbn-arxiv')
split_idx = dataset.get_idx_split()
g, labels = dataset[0]
feats = jax.device_put(
g.ndata['feat'],
jax.devices()[0]
)
g = g.to(jax.devices("cpu")[0])
g = dgl.to_bidirected(g)
g = g.int()
g = g.to(jax.devices()[0])
train_idx = split_idx['train'].numpy()
_model = GraphSAGE.partial(in_feats=feats.shape[-1],
hidden_feats=args.hidden_channels,
out_feats=dataset.num_classes,
num_layers=args.num_layers,
dropout=args.dropout)
_, initial_params = _model.init(jax.random.PRNGKey(0), g, feats)
model = nn.Model(_model, initial_params)
evaluator = Evaluator(name='ogbn-arxiv')
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
_, initial_params = _model.init(jax.random.PRNGKey(0), g, feats)
model = nn.Model(_model, initial_params)
optimizer = flax.optim.Adam(args.lr).create(model)
for epoch in range(1, 1 + args.epochs):
t0 = time.time()
optimizer, loss = train(model, g, feats, labels, train_idx, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
result = test(model, g, feats, labels, split_idx, evaluator)
logger.add_result(run, result)
if epoch % args.log_steps == 0:
train_acc, valid_acc, test_acc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {100 * train_acc:.2f}%, '
f'Valid: {100 * valid_acc:.2f}% '
f'Test: {100 * test_acc:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='OGBN-MolHiv')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--num_workers', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--batch_size', type=int, default=64)
parser.add_argument('--num_layers', type=int, default=4)
parser.add_argument('--hidden_size', type=int, default=128)
parser.add_argument('--dropout', type=float, default=0.5)
parser.add_argument('--lr', type=float, default=0.001)
parser.add_argument('--epochs', type=int, default=200)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument('--eval', action='store_true',
help='If not set, we will only do the training part.')
parser.add_argument('--eval_batch_size', type=int, default=2048)
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = TUDataset('dataset', name='ENZYMES', use_node_attr=True)
dataset = dataset.shuffle()
train_loader = DataLoader(dataset[:len(dataset) // 10 * 8], batch_size=args.batch_size, shuffle=True, num_workers=args.num_workers)
val_loader = DataLoader(dataset[len(dataset) // 10 * 8 : len(dataset) // 10 * 9], batch_size=args.eval_batch_size, shuffle=False, num_workers=0)
test_loader = DataLoader(dataset[len(dataset) // 10 * 9:], batch_size=args.eval_batch_size, shuffle=False, num_workers=0)
model = GCN(dataset.num_features,
args.hidden_size,
num_classes=dataset.num_classes,
num_layers=args.num_layers,
dropout=args.dropout).to(device)
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, args.epochs + 1):
t0 = time.time()
loss = train(model, device, train_loader, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
val_acc = test(model, device, val_loader)
test_acc = test(model, device, test_loader)
logger.add_result(run, (0.0, val_acc, test_acc))
if epoch % args.log_steps == 0:
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Valid: {val_acc * 100:.2f}% '
f'Test: {test_acc * 100:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()
def main():
parser = argparse.ArgumentParser('OGBN-Proteins (RGCN Full-Batch)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--num-layers', type=int, default=3)
parser.add_argument('--hidden-feats', type=int, default=32)
parser.add_argument('--dropout', type=float, default=0.)
parser.add_argument('--epochs', type=int, default=1000)
parser.add_argument('--eval_steps', type=int, default=5)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument("--eval", action='store_true',
help='If not set, we will only do the training part.')
args = parser.parse_args()
print(args)
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = DglNodePropPredDataset(name='ogbn-proteins')
graph, y_true = dataset[0]
graph = graph.int().to(device)
y_true = y_true.to(device)
node_feats = torch.ones((graph.number_of_nodes(), 1)).to(device)
split_idx = dataset.get_idx_split()
train_idx = split_idx['train'].to(device)
edge_weights = []
for t in range(graph.edata['feat'].shape[-1]):
edge_weights.append(graph.edata['feat'][:, t:t+1].to(device))
model = RGCN(num_layers=args.num_layers,
in_feats=node_feats.shape[-1],
hidden_feats=args.hidden_feats,
out_feats=y_true.shape[-1],
num_relations=len(edge_weights),
dropout=args.dropout).to(device)
evaluator = Evaluator(name='ogbn-proteins')
logger = Logger(args.runs, args)
dur = []
for run in range(args.runs):
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, 1 + args.epochs):
t0 = time.time()
loss = train(model, graph, node_feats, edge_weights,
y_true, train_idx, optimizer)
if epoch >= 3:
dur.append(time.time() - t0)
print('Training time/epoch {}'.format(np.mean(dur)))
if not args.eval:
continue
if epoch % args.eval_steps == 0:
result = test(model, graph, node_feats, edge_weights,
y_true, split_idx, evaluator)
logger.add_result(run, result)
if epoch % args.log_steps == 0:
train_rocauc, valid_rocauc, test_rocauc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {100 * train_rocauc:.2f}%, '
f'Valid: {100 * valid_rocauc:.2f}% '
f'Test: {100 * test_rocauc:.2f}%')
if args.eval:
logger.print_statistics(run)
if args.eval:
logger.print_statistics()