---
title: "Fast Graph Representation Learning with PyTorch — Fey 2019"
description: "Graph neural networks are difficult to run efficiently: inputs are sparse, irregular and vary in size, which makes high GPU throughput hard to achieve."
authors: ["Matthias Fey", "Jan Eric Lenssen"]
year: 2019
venue: "arXiv:1903.02428"
source: "https://arxiv.org/abs/1903.02428"
doi: "10.48550/arxiv.1903.02428"
arxiv: "1903.02428"
licence: "arXiv — non-exclusive licence to distribute"
licence_url: "http://arxiv.org/licenses/nonexclusive-distrib/1.0/"
summary_licence: "Elamur Cosmic License"
canonical: "https://research.elamur.ai/free/en/papers/fey-2019-fast-graph-representation-learning-pytorch/"
---
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# Fast Graph Representation Learning with PyTorch Geometric

**Authors:** Matthias Fey, Jan Eric Lenssen · **Year:** 2019 · **Venue:** arXiv:1903.02428 · **Licence:** [arXiv — non-exclusive licence to distribute](http://arxiv.org/licenses/nonexclusive-distrib/1.0/)

**Links:** [Publisher's page](https://arxiv.org/abs/1903.02428) · [PDF](https://arxiv.org/pdf/1903.02428) · [DOI 10.48550/arxiv.1903.02428](https://doi.org/10.48550/arxiv.1903.02428) · [arXiv 1903.02428](https://arxiv.org/abs/1903.02428) · [OpenAlex](https://openalex.org/W2918342466)

**Citations:** 1132 citations (openalex-snapshot · 2026-10-14) · 281 in our library, of the 140673 papers whose bibliographies we read

## Summary
Graph neural networks are difficult to run efficiently: inputs are sparse, irregular and vary in size, which makes high GPU throughput hard to achieve. The authors present PyTorch Geometric (PyG), an open-source extension of PyTorch under the MIT license for deep learning on graphs, point clouds and manifolds. Its core is a generic MessagePassing abstraction. A user defines a message function, an update function and an aggregation (sum, mean or max), and the library runs them through custom CUDA gather/scatter kernels. Graphs of different sizes are batched by stacking them into one block-diagonal sparse adjacency matrix. PyG bundles many published convolution and pooling operators, along with loaders for common benchmark datasets. To check the implementations, the authors re-ran these methods under uniform settings on node, graph and point cloud classification. Most published results were reproduced, and PyG trained faster than DGL. This matters because researchers get one consistent and fast toolkit for both prototyping and fair comparison of GNN methods.

## Key points
- **Operators included:** GCN, SGC, ChebNet, ARMA, GraphSAGE, GAT, AGNN, GIN, APPNP, RGCN, PointNet++, PointCNN, MoNet, SplineCNN and EdgeCNN, plus pooling methods such as DiffPool, top-k, Graclus, Set2Set and SortPool.
- **Datasets:** automatic loaders cover over 60 graph kernel benchmarks (e.g., PROTEINS, IMDB-BINARY), Cora/CiteSeer/PubMed, QM9, ModelNet10/40, ShapeNet, FAUST, ICEWS and GDELT, among others.
- **Accuracy results:**
  - On semi-supervised node classification, APPNP scored best (Cora: 83.3% with the fixed split, 82.2% with random splits). Random splits lowered accuracy for every model.
  - DiffPool reached 92.1% on REDDIT-BINARY.
  - PointCNN reached 93.28% on ModelNet10.
- **Training speed vs. DGL:**
  - GAT on Cora took 0.80s in PyG, compared with 5.36s and 6.31s for the two DGL variants.
  - GCN on PubMed took 0.32s in PyG, compared with up to 12.91s in DGL.
- **Gather/scatter vs. sparse-matrix multiplication:** gather/scatter stays faster until the average node degree reaches roughly 128, and it does not require coalesced input. However, GPU scatter is non-deterministic, so training runs can differ even with the same seed.

*Our summary of the paper, in our own words — not its text. The work belongs to its authors; read it at the links above.*

Fields: [Other](https://md.research.elamur.ai/free/en/shelves/other/)

## Cite

The paper itself, not this page. BibTeX from the library's record of the work.

```bibtex
@misc{fey2019fast,
  title = {{Fast Graph Representation Learning with PyTorch Geometric}},
  author = {Fey, Matthias and Lenssen, Jan Eric},
  year = {2019},
  doi = {10.48550/arxiv.1903.02428},
  eprint = {1903.02428},
  archivePrefix = {arXiv},
  url = {https://doi.org/10.48550/arxiv.1903.02428}
}
```

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