def prepare_gnn_training(self):
if verbose:
print("\n\n==>> Clustering the graph and preparing dataloader....")
self.data = Data(x=self.x_data.float(), edge_index = self.edge_index_data.long(), edge_attr = self.edge_type_data, y=self.y_data)
new_num_nodes, _ = self.data.x.shape
self.data.train_mask = torch.FloatTensor(self.split_masks['train_mask'])
self.data.val_mask = torch.FloatTensor(self.split_masks['val_mask'])
self.data.representation_mask = torch.FloatTensor(self.split_masks['repr_mask'])
self.data.node2id = torch.tensor(list(self.node2id.values()))
# self.data.node_type = self.node_type
if not self.config['full_graph']:
if self.config['cluster'] :
cluster_data = ClusterData(self.data, num_parts=self.config['clusters'], recursive=False)
self.loader = ClusterLoader(cluster_data, batch_size=self.config['batch_size'], shuffle=self.config['shuffle'], num_workers=0)
elif self.config['saint'] == 'random_walk':
self.loader = GraphSAINTRandomWalkSampler(self.data, batch_size=6000, walk_length=2, num_steps=5, sample_coverage=100, num_workers=0)
elif self.config['saint'] == 'node':
self.loader = GraphSAINTNodeSampler(self.data, batch_size=6000, num_steps=5, sample_coverage=100, num_workers=0)
elif self.config['saint'] == 'edge':
self.loader = GraphSAINTEdgeSampler(self.data, batch_size=6000, num_steps=5, sample_coverage=100, num_workers=0)
else:
self.loader=None
return self.loader, self.vocab_size, self.data
def __init__(self, graph, model, args, criterion=None):
self.args = args
self.graph = graph
self.model = model.to(self.args.device)
#build data loader on cpu
self.loader = GraphSAINTRandomWalkSampler(graph,
batch_size=self.args.GraphSAINT['batch_size'],
walk_length=self.args.GraphSAINT['walk_length'],
num_steps=self.args.GraphSAINT['num_steps'])
print ('Data Loader created for learner . . .')
#Set loss function
if not criterion:
#BCEWithLogitsLoss is a class to use for individual or multiple binary prediction tasks
criterion = nn.BCEWithLogitsLoss()
self.criterion = criterion
#Set optimizer
self.optim = torch.optim.Adam(self.model.parameters(), lr=self.args.lr, weight_decay=self.args.w_decay)
self.train_loss = []
self.val_loss = []
self.train_complete = False
def build_sampler(args, data, save_dir):
if args.sampler == 'rw-my':
msg = 'Use GraphSaint randomwalk sampler(mysaint sampler)'
loader = MySAINTSampler(data, batch_size=args.batch_size, sample_type='random_walk',
walk_length=2, sample_coverage=1000, save_dir=save_dir)
elif args.sampler == 'node-my':
msg = 'Use random node sampler(mysaint sampler)'
loader = MySAINTSampler(data, sample_type='node', batch_size=args.batch_size * 3,
walk_length=2, sample_coverage=1000, save_dir=save_dir)
elif args.sampler == 'rw':
msg = 'Use GraphSaint randomwalk sampler'
loader = GraphSAINTRandomWalkSampler(data, batch_size=args.batch_size, walk_length=2,
num_steps=5, sample_coverage=1000,
save_dir=save_dir)
elif args.sampler == 'node':
msg = 'Use GraphSaint node sampler'
loader = GraphSAINTNodeSampler(data, batch_size=args.batch_size * 3,
num_steps=5, sample_coverage=1000, num_workers=0, save_dir=save_dir)
elif args.sampler == 'edge':
msg = 'Use GraphSaint edge sampler'
loader = GraphSAINTEdgeSampler(data, batch_size=args.batch_size,
num_steps=5, sample_coverage=1000,
save_dir=save_dir, num_workers=0)
elif args.sampler == 'cluster':
msg = 'Use cluster sampler'
cluster_data = ClusterData(data, num_parts=args.num_parts, save_dir=save_dir)
loader = ClusterLoader(cluster_data, batch_size=20, shuffle=True,
num_workers=0)
else:
raise KeyError('Sampler type error')
return loader, msg
def test_graph_saint():
adj = torch.tensor([
[1, 1, 1, 0, 1, 0],
[1, 1, 0, 1, 0, 1],
[1, 0, 1, 0, 1, 0],
[0, 1, 0, 1, 0, 1],
[1, 0, 1, 0, 1, 0],
[0, 1, 0, 1, 0, 1],
])
edge_index = adj.nonzero().t()
x = torch.Tensor([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
data = Data(edge_index=edge_index, x=x, num_nodes=6)
torch.manual_seed(12345)
loader = GraphSAINTNodeSampler(data,
batch_size=2,
num_steps=4,
sample_coverage=10,
log=False)
for sample in loader:
assert len(sample) == 4
assert sample.num_nodes <= 2
assert sample.num_edges <= 3 * 2
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
torch.manual_seed(12345)
loader = GraphSAINTEdgeSampler(data,
batch_size=2,
num_steps=4,
sample_coverage=10,
log=False)
for sample in loader:
assert len(sample) == 4
assert sample.num_nodes <= 4
assert sample.num_edges <= 3 * 4
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
torch.manual_seed(12345)
loader = GraphSAINTRandomWalkSampler(data,
batch_size=2,
walk_length=1,
num_steps=4,
sample_coverage=10,
log=False)
for sample in loader:
assert len(sample) == 4
assert sample.num_nodes <= 4
assert sample.num_edges <= 3 * 4
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
def sample_subgraph(whole_data):
data = whole_data.data
loader = GraphSAINTRandomWalkSampler(
data,
batch_size=self.sample_batch_size,
walk_length=self.sample_walk_length,
num_steps=self.subgraphs,
save_dir=whole_data.processed_dir,
)
results = []
for data in loader:
results.append(data)
return results
def build_sampler(args, data, save_dir):
if args.sampler == 'rw-my':
msg = 'Use GraphSaint randomwalk sampler(mysaint sampler)'
loader = MySAINTSampler(data,
batch_size=args.batch_size,
sample_type='random_walk',
walk_length=2,
sample_coverage=1000,
save_dir=save_dir)
elif args.sampler == 'node-my':
msg = 'Use random node sampler(mysaint sampler)'
loader = MySAINTSampler(data,
sample_type='node',
batch_size=args.batch_size * 3,
walk_length=2,
sample_coverage=1000,
save_dir=save_dir)
elif args.sampler == 'rw':
msg = 'Use GraphSaint randomwalk sampler'
loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch_size,
walk_length=2,
num_steps=5,
sample_coverage=1000,
save_dir=save_dir)
elif args.sampler == 'node':
msg = 'Use GraphSaint node sampler'
loader = GraphSAINTNodeSampler(data,
batch_size=args.batch_size * 3,
num_steps=5,
sample_coverage=1000,
num_workers=0,
save_dir=save_dir)
elif args.sampler == 'edge':
msg = 'Use GraphSaint edge sampler'
loader = GraphSAINTEdgeSampler(data,
batch_size=args.batch_size,
num_steps=5,
sample_coverage=1000,
save_dir=save_dir,
num_workers=0)
# elif args.sampler == 'cluster':
# logger.info('Use cluster sampler')
# cluster_data = ClusterData(data, num_parts=args.num_parts, save_dir=dataset.processed_dir)
# raise NotImplementedError('Cluster loader not implement yet')
else:
raise KeyError('Sampler type error')
return loader, msg
edge_attr=edge_type,
node_type=node_type,
local_node_idx=local_node_idx,
num_nodes=node_type.size(0))
homo_data.y = node_type.new_full((node_type.size(0), 1), -1)
homo_data.y[local2global['paper']] = data.y_dict['paper']
homo_data.train_mask = torch.zeros((node_type.size(0)), dtype=torch.bool)
homo_data.train_mask[local2global['paper'][split_idx['train']['paper']]] = True
print(homo_data)
train_loader = GraphSAINTRandomWalkSampler(homo_data,
batch_size=args.batch_size,
walk_length=args.num_layers,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
# Map informations to their canonical type.
x_dict = {}
for key, x in data.x_dict.items():
x_dict[key2int[key]] = x
num_nodes_dict = {}
for key, N in data.num_nodes_dict.items():
num_nodes_dict[key2int[key]] = N
class RGCNConv(MessagePassing):
def __init__(self, in_channels, out_channels, num_node_types,
def main():
parser = argparse.ArgumentParser(description='OGBN-Products (GraphSAINT)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=1)
parser.add_argument('--inductive', action='store_true')
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('--batch_size', type=int, default=20000)
parser.add_argument('--walk_length', type=int, default=3)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--num_steps', type=int, default=30)
parser.add_argument('--epochs', type=int, default=20)
parser.add_argument('--eval_steps', type=int, default=2)
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)
dataset = PygNodePropPredDataset(
name='ogbn-products', root='/srv/scratch/ogb/datasets/nodeproppred')
split_idx = dataset.get_idx_split()
data = dataset[0]
# Convert split indices to boolean masks and add them to `data`.
for key, idx in split_idx.items():
mask = torch.zeros(data.num_nodes, dtype=torch.bool)
mask[idx] = True
data[f'{key}_mask'] = mask
# We omit normalization factors here since those are only defined for the
# inductive learning setup.
sampler_data = data
if args.inductive:
sampler_data = to_inductive(data)
loader = GraphSAINTRandomWalkSampler(sampler_data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
model = SAGE(data.x.size(-1), args.hidden_channels, dataset.num_classes,
args.num_layers, args.dropout).to(device)
subgraph_loader = NeighborSampler(data.edge_index,
sizes=[-1],
batch_size=4096,
shuffle=False,
num_workers=12)
evaluator = Evaluator(name='ogbn-products')
logger = Logger(args.runs, args)
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):
loss = train(model, loader, optimizer, device)
if epoch % args.log_steps == 0:
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}')
if epoch > 9 and epoch % args.eval_steps == 0:
result = test(model, data, evaluator, subgraph_loader, device)
logger.add_result(run, result)
train_acc, valid_acc, test_acc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Train: {100 * train_acc:.2f}%, '
f'Valid: {100 * valid_acc:.2f}% '
f'Test: {100 * test_acc:.2f}%')
logger.add_result(run, result)
logger.print_statistics(run)
logger.print_statistics()
def main():
parser = argparse.ArgumentParser(description='OGBL-Citation2 (GraphSAINT)')
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=0.0)
parser.add_argument('--batch_size', type=int, default=16 * 1024)
parser.add_argument('--walk_length', type=int, default=3)
parser.add_argument('--lr', type=float, default=0.001)
parser.add_argument('--epochs', type=int, default=200)
parser.add_argument('--num_steps', type=int, default=100)
parser.add_argument('--eval_steps', type=int, default=10)
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)
dataset = PygLinkPropPredDataset(name='ogbl-citation2')
split_edge = dataset.get_edge_split()
data = dataset[0]
data.edge_index = to_undirected(data.edge_index, data.num_nodes)
loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
# We randomly pick some training samples that we want to evaluate on:
torch.manual_seed(12345)
idx = torch.randperm(split_edge['train']['source_node'].numel())[:86596]
split_edge['eval_train'] = {
'source_node': split_edge['train']['source_node'][idx],
'target_node': split_edge['train']['target_node'][idx],
'target_node_neg': split_edge['valid']['target_node_neg'],
}
model = GCN(data.x.size(-1), args.hidden_channels, args.hidden_channels,
args.num_layers, args.dropout).to(device)
predictor = LinkPredictor(args.hidden_channels, args.hidden_channels, 1,
args.num_layers, args.dropout).to(device)
evaluator = Evaluator(name='ogbl-citation2')
logger = Logger(args.runs, args)
run_idx = 0
while run_idx < args.runs:
model.reset_parameters()
predictor.reset_parameters()
optimizer = torch.optim.Adam(list(model.parameters()) +
list(predictor.parameters()),
lr=args.lr)
run_success = True
for epoch in range(1, 1 + args.epochs):
loss = train(model, predictor, loader, optimizer, device)
print(
f'Run: {run_idx + 1:02d}, Epoch: {epoch:02d}, Loss: {loss:.4f}'
)
if loss > 2.:
run_success = False
logger.reset(run_idx)
print('Learning failed. Rerun...')
break
if epoch > 49 and epoch % args.eval_steps == 0:
result = test(model,
predictor,
data,
split_edge,
evaluator,
batch_size=64 * 1024,
device=device)
logger.add_result(run_idx, result)
train_mrr, valid_mrr, test_mrr = result
print(f'Run: {run_idx + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}, '
f'Train: {train_mrr:.4f}, '
f'Valid: {valid_mrr:.4f}, '
f'Test: {test_mrr:.4f}')
print('GraphSAINT')
if run_success:
logger.print_statistics(run_idx)
run_idx += 1
print('GraphSAINT')
logger.print_statistics()
def train(epoch, model, optimizer):
global all_data, best_val_acc, best_embeddings, best_model, curr_hyperparameters, best_hyperparameters
# Save predictions
total_loss = 0
roc_val = []
ap_val = []
f1_val = []
acc_val = []
# Minibatches
if config.MINIBATCH == "NeighborSampler":
loader = NeighborSampler(all_data.edge_index,
sizes=[curr_hyperparameters['nb_size']],
batch_size=curr_hyperparameters['batch_size'],
shuffle=True)
elif config.MINIBATCH == "GraphSaint":
all_data.num_classes = torch.tensor([2])
loader = GraphSAINTRandomWalkSampler(
all_data,
batch_size=curr_hyperparameters['batch_size'],
walk_length=curr_hyperparameters['walk_length'],
num_steps=curr_hyperparameters['num_steps'])
# Iterate through minibatches
for data in loader:
if config.MINIBATCH == "NeighborSampler":
data = preprocess.set_data(data, all_data, config.MINIBATCH)
curr_train_pos = data.edge_index[:, data.train_mask]
curr_train_neg = negative_sampling(
curr_train_pos, num_neg_samples=curr_train_pos.size(1) // 4)
curr_train_total = torch.cat([curr_train_pos, curr_train_neg], dim=-1)
data.y = torch.zeros(curr_train_total.size(1)).float()
data.y[:curr_train_pos.size(1)] = 1.
# Perform training
data.to(device)
optimizer.zero_grad()
out = model(data.x, data.edge_index)
curr_dot_embed = utils.el_dot(out, curr_train_total)
loss = utils.calc_loss_both(data, curr_dot_embed)
if torch.isnan(loss) == False:
total_loss += loss
loss.backward()
optimizer.step()
curr_train_pos_mask = torch.zeros(curr_train_total.size(1)).bool()
curr_train_pos_mask[:curr_train_pos.size(1)] = 1
curr_train_neg_mask = (curr_train_pos_mask == 0)
roc_score, ap_score, train_acc, train_f1 = utils.calc_roc_score(
pred_all=curr_dot_embed.T[1],
pos_edges=curr_train_pos_mask,
neg_edges=curr_train_neg_mask)
print(">>>>>>Train: (ROC) ", roc_score, " (AP) ", ap_score, " (ACC) ",
train_acc, " (F1) ", train_f1)
curr_val_pos = data.edge_index[:, data.val_mask]
curr_val_neg = negative_sampling(
curr_val_pos, num_neg_samples=curr_val_pos.size(1) // 4)
curr_val_total = torch.cat([curr_val_pos, curr_val_neg], dim=-1)
curr_val_pos_mask = torch.zeros(curr_val_total.size(1)).bool()
curr_val_pos_mask[:curr_val_pos.size(1)] = 1
curr_val_neg_mask = (curr_val_pos_mask == 0)
val_dot_embed = utils.el_dot(out, curr_val_total)
data.y = torch.zeros(curr_val_total.size(1)).float()
data.y[:curr_val_pos.size(1)] = 1.
roc_score, ap_score, val_acc, val_f1 = utils.calc_roc_score(
pred_all=val_dot_embed.T[1],
pos_edges=curr_val_pos_mask,
neg_edges=curr_val_neg_mask)
roc_val.append(roc_score)
ap_val.append(ap_score)
acc_val.append(val_acc)
f1_val.append(val_f1)
res = "\t".join([
"Epoch: %04d" % (epoch + 1), "train_loss = {:.5f}".format(total_loss),
"val_roc = {:.5f}".format(np.mean(roc_val)),
"val_ap = {:.5f}".format(np.mean(ap_val)),
"val_f1 = {:.5f}".format(np.mean(f1_val)),
"val_acc = {:.5f}".format(np.mean(acc_val))
])
print(res)
log_f.write(res + "\n")
# Save best model and parameters
if best_val_acc <= np.mean(acc_val) + eps:
best_val_acc = np.mean(acc_val)
with open(str(config.DATASET_DIR / "best_model.pth"), 'wb') as f:
torch.save(model.state_dict(), f)
best_hyperparameters = curr_hyperparameters
best_model = model
return total_loss
def main():
parser = argparse.ArgumentParser(description='OGBN-Products (GraphSAINT)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--log_steps', type=int, default=5)
parser.add_argument('--use_sage', action='store_true')
parser.add_argument('--num_workers', type=int, default=0)
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('--batch_size', type=int, default=8000)
parser.add_argument('--walk_length', type=int, default=3)
parser.add_argument('--sample_coverage', type=int, default=1000)
parser.add_argument('--lr', type=float, default=0.001)
parser.add_argument('--num_steps', type=int, default=20)
parser.add_argument('--epochs', type=int, default=150)
parser.add_argument('--eval_steps', type=int, default=25)
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)
dataset = PygNodePropPredDataset(name='ogbn-products')
split_idx = dataset.get_idx_split()
data = dataset[0]
# Convert split indices to boolean masks and add them to `data`.
for key, idx in split_idx.items():
mask = torch.zeros(data.num_nodes, dtype=torch.bool)
mask[idx] = True
data[f'{key}_mask'] = mask
# Create "inductive" subgraph containing only train and validation nodes.
ind_data = to_inductive(copy.copy(data))
row, col = ind_data.edge_index
ind_data.edge_attr = 1. / degree(col, ind_data.num_nodes)[col]
loader = GraphSAINTRandomWalkSampler(ind_data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=args.sample_coverage,
save_dir=dataset.processed_dir,
num_workers=args.num_workers)
model = SAGE(ind_data.x.size(-1), args.hidden_channels,
dataset.num_classes, args.num_layers, args.dropout).to(device)
evaluator = Evaluator(name='ogbn-products')
logger = Logger(args.runs, args)
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):
loss = train(model, loader, optimizer, device)
if epoch % args.log_steps == 0:
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Loss: {loss:.4f}')
if epoch % args.eval_steps == 0:
result = test(model, data, evaluator)
logger.add_result(run, result)
train_acc, valid_acc, test_acc = result
print(f'Run: {run + 1:02d}, '
f'Epoch: {epoch:02d}, '
f'Train: {100 * train_acc:.2f}%, '
f'Valid: {100 * valid_acc:.2f}% '
f'Test: {100 * test_acc:.2f}%')
logger.add_result(run, result)
logger.print_statistics(run)
logger.print_statistics()
import torch
import torch.nn.functional as F
from torch_geometric.datasets import Flickr
from torch_geometric.data import GraphSAINTRandomWalkSampler
from torch_geometric.nn import SAGEConv
from torch_geometric.utils import degree
path = osp.join(osp.dirname(osp.realpath(__file__)), '..', 'data', 'Flickr')
dataset = Flickr(path)
data = dataset[0]
row, col = data.edge_index
data.edge_attr = 1. / degree(col, data.num_nodes)[col] # Norm by in-degree.
loader = GraphSAINTRandomWalkSampler(data, batch_size=6000, walk_length=2,
num_steps=5, sample_coverage=1000,
save_dir=dataset.processed_dir,
num_workers=4)
class Net(torch.nn.Module):
def __init__(self, hidden_channels):
super(Net, self).__init__()
in_channels = dataset.num_node_features
out_channels = dataset.num_classes
self.conv1 = SAGEConv(in_channels, hidden_channels, concat=True)
self.conv2 = SAGEConv(hidden_channels, hidden_channels, concat=True)
self.conv3 = SAGEConv(hidden_channels, hidden_channels, concat=True)
self.lin = torch.nn.Linear(3 * hidden_channels, out_channels)
def set_aggr(self, aggr):
self.conv1.aggr = aggr
def main():
parser = argparse.ArgumentParser(description='OGBN-Products (GraphSAINT)')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--inductive', action='store_true')
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('--batch_size', type=int, default=20000)
parser.add_argument('--walk_length', type=int, default=3)
parser.add_argument('--lr', type=float, default=0.01)
parser.add_argument('--num_steps', type=int, default=30)
parser.add_argument('--epochs', type=int, default=20)
parser.add_argument('--runs', type=int, default=10)
parser.add_argument('--step-size', type=float, default=8e-3)
parser.add_argument('-m', type=int, default=3)
parser.add_argument('--test-freq', type=int, default=2)
parser.add_argument('--attack', type=str, default='flag')
parser.add_argument('--amp', type=float, default=2)
args = parser.parse_args()
device = f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu'
device = torch.device(device)
dataset = PygNodePropPredDataset(name='ogbn-products')
split_idx = dataset.get_idx_split()
data = dataset[0]
# Convert split indices to boolean masks and add them to `data`.
for key, idx in split_idx.items():
mask = torch.zeros(data.num_nodes, dtype=torch.bool)
mask[idx] = True
data[f'{key}_mask'] = mask
# We omit normalization factors here since those are only defined for the
# inductive learning setup.
sampler_data = data
if args.inductive:
sampler_data = to_inductive(data)
loader = GraphSAINTRandomWalkSampler(sampler_data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
model = SAGE(data.x.size(-1), args.hidden_channels, dataset.num_classes,
args.num_layers, args.dropout).to(device)
subgraph_loader = NeighborSampler(data.edge_index,
sizes=[-1],
batch_size=4096,
shuffle=False,
num_workers=12)
evaluator = Evaluator(name='ogbn-products')
vals, tests = [], []
for run in range(args.runs):
best_val, final_test = 0, 0
model.reset_parameters()
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
for epoch in range(1, args.epochs + 1):
loss = train_flag(model, loader, optimizer, device, args)
if epoch > args.epochs / 2 and epoch % args.test_freq == 0 or epoch == args.epochs:
result = test(model, data, evaluator, subgraph_loader, device)
train, val, tst = result
if val > best_val:
best_val = val
final_test = tst
print(f'Run{run} val:{best_val}, test:{final_test}')
vals.append(best_val)
tests.append(final_test)
print('')
print(f"Average val accuracy: {np.mean(vals)} ± {np.std(vals)}")
print(f"Average test accuracy: {np.mean(tests)} ± {np.std(tests)}")
def test_graph_saint():
adj = torch.tensor([
[+1, +2, +3, +0, +4, +0],
[+5, +6, +0, +7, +0, +8],
[+9, +0, 10, +0, 11, +0],
[+0, 12, +0, 13, +0, 14],
[15, +0, 16, +0, 17, +0],
[+0, 18, +0, 19, +0, 20],
])
edge_index = adj.nonzero(as_tuple=False).t()
edge_type = adj[edge_index[0], edge_index[1]]
x = torch.Tensor([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
data = Data(edge_index=edge_index, x=x, edge_type=edge_type, num_nodes=6)
torch.manual_seed(12345)
loader = GraphSAINTNodeSampler(data, batch_size=3, num_steps=4,
sample_coverage=10, log=False)
sample = next(iter(loader))
assert sample.x.tolist() == [[2, 2], [4, 4], [5, 5]]
assert sample.edge_index.tolist() == [[0, 0, 1, 1, 2], [0, 1, 0, 1, 2]]
assert sample.edge_type.tolist() == [10, 11, 16, 17, 20]
assert len(loader) == 4
for sample in loader:
assert len(sample) == 5
assert sample.num_nodes <= 3
assert sample.num_edges <= 3 * 4
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
torch.manual_seed(12345)
loader = GraphSAINTEdgeSampler(data, batch_size=2, num_steps=4,
sample_coverage=10, log=False)
sample = next(iter(loader))
assert sample.x.tolist() == [[0, 0], [2, 2], [3, 3]]
assert sample.edge_index.tolist() == [[0, 0, 1, 1, 2], [0, 1, 0, 1, 2]]
assert sample.edge_type.tolist() == [1, 3, 9, 10, 13]
assert len(loader) == 4
for sample in loader:
assert len(sample) == 5
assert sample.num_nodes <= 4
assert sample.num_edges <= 4 * 4
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
torch.manual_seed(12345)
loader = GraphSAINTRandomWalkSampler(data, batch_size=2, walk_length=1,
num_steps=4, sample_coverage=10,
log=False)
sample = next(iter(loader))
assert sample.x.tolist() == [[1, 1], [2, 2], [4, 4]]
assert sample.edge_index.tolist() == [[0, 1, 1, 2, 2], [0, 1, 2, 1, 2]]
assert sample.edge_type.tolist() == [6, 10, 11, 16, 17]
assert len(loader) == 4
for sample in loader:
assert len(sample) == 5
assert sample.num_nodes <= 4
assert sample.num_edges <= 4 * 4
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
splitted_idx = dataset.get_idx_split()
data = dataset[0]
data.n_id = torch.arange(data.num_nodes)
data.node_species = None
data.y = data.y.float()
# Initialize features of nodes by aggregating edge features.
row, col = data.edge_index
#Set split indices to masks.
for split in ['train', 'valid', 'test']:
mask = torch.zeros(data.num_nodes, dtype=torch.bool)
mask[splitted_idx[split]] = True
data[f'{split}_mask'] = mask
train_loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
test_loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch_size,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
p_train_loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch_size * 2,
walk_length=args.walk_length,
num_steps=args.num_steps,
sample_coverage=0,
save_dir=dataset.processed_dir)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--device", type=str, default='0')
parser.add_argument('--model', type=str, default='GraphSAINT')
parser.add_argument('--dataset', type=str,
default='Reddit') # Reddit or Flickr
parser.add_argument('--batch', type=int,
default=2000) # Reddit:2000, Flickr:6000
parser.add_argument('--walk_length', type=int,
default=4) # Reddit:4, Flickr:2
parser.add_argument('--sample_coverage', type=int,
default=50) # Reddit:50, Flickr:100
parser.add_argument('--runs', type=int, default=10)
parser.add_argument('--epochs', type=int, default=100) # 100, 50
parser.add_argument('--lr', type=float, default=0.01) # 0.01, 0.001
parser.add_argument('--weight_decay', type=float, default=0.0005)
parser.add_argument('--hidden', type=int, default=256) # 128, 256
parser.add_argument('--dropout', type=float, default=0.1) # 0.1, 0.2
parser.add_argument('--use_normalization', action='store_true')
parser.add_argument('--binarize', action='store_true')
args = parser.parse_args()
assert args.model in ['GraphSAINT']
assert args.dataset in ['Flickr', 'Reddit']
path = '/home/wangjunfu/dataset/graph/' + str(args.dataset)
if args.dataset == 'Flickr':
dataset = Flickr(path)
else:
dataset = Reddit(path)
data = dataset[0]
row, col = data.edge_index
data.edge_weight = 1. / degree(col,
data.num_nodes)[col] # Norm by in-degree.
loader = GraphSAINTRandomWalkSampler(data,
batch_size=args.batch,
walk_length=args.walk_length,
num_steps=5,
sample_coverage=args.sample_coverage,
save_dir=dataset.processed_dir,
num_workers=0)
device = torch.device(
f'cuda:{args.device}' if torch.cuda.is_available() else 'cpu')
model = SAINT(data.num_node_features, args.hidden, dataset.num_classes,
args.dropout, args.binarize).to(device)
optimizer = torch.optim.Adam(model.parameters(), lr=args.lr)
val_f1s, test_f1s = [], []
for run in range(1, args.runs + 1):
best_val, best_test = 0, 0
model.reset_parameters()
start_time = time.time()
for epoch in range(1, args.epochs + 1):
loss = train(model, loader, optimizer, device,
args.use_normalization)
accs = test(model, data, device, args.use_normalization)
if accs[1] > best_val:
best_val = accs[1]
best_test = accs[2]
if args.runs == 1:
print(
f'Epoch: {epoch:02d}, Loss: {loss:.4f}, Train: {accs[0]:.4f}, '
f'Val: {accs[1]:.4f}, Test: {accs[2]:.4f}')
test_f1s.append(best_test)
print(
"Run: {:d}, best val: {:.4f}, best test: {:.4f}, time cost: {:d}s".
format(run, best_val, best_test, int(time.time() - start_time)))
test_f1s = torch.tensor(test_f1s)
print("{:.4f} ± {:.4f}".format(test_f1s.mean(), test_f1s.std()))
def test_graph_saint():
adj = torch.tensor([
[+1, +2, +3, +0, +4, +0],
[+5, +6, +0, +7, +0, +8],
[+9, +0, 10, +0, 11, +0],
[+0, 12, +0, 13, +0, 14],
[15, +0, 16, +0, 17, +0],
[+0, 18, +0, 19, +0, 20],
])
edge_index = adj.nonzero(as_tuple=False).t()
edge_id = adj[edge_index[0], edge_index[1]]
x = torch.Tensor([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
n_id = torch.arange(6)
data = Data(edge_index=edge_index,
x=x,
n_id=n_id,
edge_id=edge_id,
num_nodes=6)
loader = GraphSAINTNodeSampler(data,
batch_size=3,
num_steps=4,
sample_coverage=10,
log=False)
assert len(loader) == 4
for sample in loader:
assert sample.num_nodes <= data.num_nodes
assert sample.n_id.min() >= 0 and sample.n_id.max() < 6
assert sample.num_nodes == sample.n_id.numel()
assert sample.x.tolist() == x[sample.n_id].tolist()
assert sample.edge_index.min() >= 0
assert sample.edge_index.max() < sample.num_nodes
assert sample.edge_id.min() >= 1 and sample.edge_id.max() <= 21
assert sample.edge_id.numel() == sample.num_edges
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
loader = GraphSAINTEdgeSampler(data,
batch_size=2,
num_steps=4,
sample_coverage=10,
log=False)
assert len(loader) == 4
for sample in loader:
assert sample.num_nodes <= data.num_nodes
assert sample.n_id.min() >= 0 and sample.n_id.max() < 6
assert sample.num_nodes == sample.n_id.numel()
assert sample.x.tolist() == x[sample.n_id].tolist()
assert sample.edge_index.min() >= 0
assert sample.edge_index.max() < sample.num_nodes
assert sample.edge_id.min() >= 1 and sample.edge_id.max() <= 21
assert sample.edge_id.numel() == sample.num_edges
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges
loader = GraphSAINTRandomWalkSampler(data,
batch_size=2,
walk_length=1,
num_steps=4,
sample_coverage=10,
log=False)
assert len(loader) == 4
for sample in loader:
assert sample.num_nodes <= data.num_nodes
assert sample.n_id.min() >= 0 and sample.n_id.max() < 6
assert sample.num_nodes == sample.n_id.numel()
assert sample.x.tolist() == x[sample.n_id].tolist()
assert sample.edge_index.min() >= 0
assert sample.edge_index.max() < sample.num_nodes
assert sample.edge_id.min() >= 1 and sample.edge_id.max() <= 21
assert sample.edge_id.numel() == sample.num_edges
assert sample.node_norm.numel() == sample.num_nodes
assert sample.edge_norm.numel() == sample.num_edges