4.5 Loading OGB datasets using ogb package


Open Graph Benchmark (OGB) is a collection of benchmark datasets. The official OGB package ogb provides APIs for downloading and processing OGB datasets into dgl.data.DGLGraph objects. The section introduce their basic usage here.

First install ogb package using pip:

pip install ogb

The following code shows how to load datasets for Graph Property Prediction tasks.

# Load Graph Property Prediction datasets in OGB
import dgl
import torch
from ogb.graphproppred import DglGraphPropPredDataset
from torch.utils.data import DataLoader

def _collate_fn(batch):
    # batch is a list of tuple (graph, label)
    graphs = [e[0] for e in batch]
    g = dgl.batch(graphs)
    labels = [e[1] for e in batch]
    labels = torch.stack(labels, 0)
    return g, labels

# load dataset
dataset = DglGraphPropPredDataset(name='ogbg-molhiv')
split_idx = dataset.get_idx_split()
# dataloader
train_loader = DataLoader(dataset[split_idx["train"]], batch_size=32, shuffle=True, collate_fn=_collate_fn)
valid_loader = DataLoader(dataset[split_idx["valid"]], batch_size=32, shuffle=False, collate_fn=_collate_fn)
test_loader = DataLoader(dataset[split_idx["test"]], batch_size=32, shuffle=False, collate_fn=_collate_fn)

Loading Node Property Prediction datasets is similar, but note that there is only one graph object in this kind of dataset.

# Load Node Property Prediction datasets in OGB
from ogb.nodeproppred import DglNodePropPredDataset

dataset = DglNodePropPredDataset(name='ogbn-proteins')
split_idx = dataset.get_idx_split()

# there is only one graph in Node Property Prediction datasets
g, labels = dataset[0]
# get split labels
train_label = dataset.labels[split_idx['train']]
valid_label = dataset.labels[split_idx['valid']]
test_label = dataset.labels[split_idx['test']]

Link Property Prediction datasets also contain one graph per dataset.

# Load Link Property Prediction datasets in OGB
from ogb.linkproppred import DglLinkPropPredDataset

dataset = DglLinkPropPredDataset(name='ogbl-ppa')
split_edge = dataset.get_edge_split()

graph = dataset[0]