torch-geometric

PyTorch Geometric (PyG)

PyG is the standard library for Graph Neural Networks built on PyTorch. It provides data structures for graphs, 60+ GNN layer implementations, scalable mini-batch training, and support for heterogeneous graphs.

Install: uv add torch_geometric (or uv pip install torch_geometric; requires PyTorch). Optional: pyg-lib, torch-scatter, torch-sparse, torch-cluster for accelerated ops.

Core Concepts

Graph Data: Data and HeteroData

A graph lives in a Data object. The key attributes:

from torch_geometric.data import Data

data = Data(
    x=node_features,          # [num_nodes, num_node_features]
    edge_index=edge_index,     # [2, num_edges] — COO format, dtype=torch.long
    edge_attr=edge_features,   # [num_edges, num_edge_features]
    y=labels,                  # node-level [num_nodes, *] or graph-level [1, *]
    pos=positions,             # [num_nodes, num_dimensions] (for point clouds/spatial)
)

edge_index format is critical: it's a [2, num_edges] tensor where edge_index[0] = source nodes, edge_index[1] = target nodes. It is NOT a list of tuples. If you have edge pairs as rows, transpose and call .contiguous():

# If edges are [[src1, dst1], [src2, dst2], ...] — transpose first:
edge_index = edge_pairs.t().contiguous()

For undirected graphs, include both directions: edge (0,1) needs both [0,1] and [1,0] in edge_index.

For heterogeneous graphs, use HeteroData — see the Heterogeneous Graphs section below.

Datasets

PyG bundles many standard datasets that auto-download and preprocess:

from torch_geometric.datasets import Planetoid, TUDataset

# Single-graph node classification (Cora, Citeseer, Pubmed)
dataset = Planetoid(root='./data', name='Cora')
data = dataset[0]  # single graph with train/val/test masks

# Multi-graph classification (ENZYMES, MUTAG, IMDB-BINARY, etc.)
dataset = TUDataset(root='./data', name='ENZYMES')
# dataset[0], dataset[1], ... are individual graphs