# Attending to Graph Transformers

arXiv: https://arxiv.org/abs/2302.04181 · HTML: https://mlsanity.com/paper/2302.04181/

## Key facts

- Cited by 83 papers in the map (data through 14 Oct 2026).
- Builds on 73 of its 95 references that are in the map.
- First posted on arXiv 8 Feb 2023.

## Builds on (most cited first, 30 of 73)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [A Primer in BERTology: What we know about how BERT works](https://mlsanity.com/paper/2002.12327/) (2020)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [A Survey on Visual Transformer](https://mlsanity.com/paper/2012.12556/) (2020)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [Heterogeneous Graph Transformer](https://mlsanity.com/paper/2003.01332/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [A Survey of Transformers](https://mlsanity.com/paper/2106.04554/) (2021)
- [Provably Powerful Graph Networks](https://mlsanity.com/paper/1905.11136/) (2019)
- [GemNet: Universal Directional Graph Neural Networks for Molecules](https://mlsanity.com/paper/2106.08903/) (2021)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting](https://mlsanity.com/paper/2006.09252/) (2020)
- [Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs](https://mlsanity.com/paper/1704.02901/) (2017)

## Built on by (most cited first, 30 of 83)

- [Large Language Models on Graphs: A Comprehensive Survey](https://mlsanity.com/paper/2312.02783/) (2023)
- [Talk like a Graph: Encoding Graphs for Large Language Models](https://mlsanity.com/paper/2310.04560/) (2023)
- [Graph Foundation Models: Concepts, Opportunities and Challenges](https://mlsanity.com/paper/2310.11829/) (2023)
- [Position: Graph Foundation Models are Already Here](https://mlsanity.com/paper/2402.02216/) (2024)
- [Graph Mamba: Towards Learning on Graphs with State Space Models](https://mlsanity.com/paper/2402.08678/) (2024)
- [Classic GNNs are Strong Baselines: Reassessing GNNs for Node Classification](https://mlsanity.com/paper/2406.08993/) (2024)
- [Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights](https://mlsanity.com/paper/2406.10727/) (2024)
- [Transformers are Universal In-context Learners](https://mlsanity.com/paper/2408.01367/) (2024)
- [On the Scalability of GNNs for Molecular Graphs](https://mlsanity.com/paper/2404.11568/) (2024)
- [VCR-Graphormer: A Mini-batch Graph Transformer via Virtual Connections](https://mlsanity.com/paper/2403.16030/) (2024)
- [Relational Graph Transformer](https://mlsanity.com/paper/2505.10960/) (2025)
- [Graph Transformers: A Survey](https://mlsanity.com/paper/2407.09777/) (2024)
- [Learning Probabilistic Symmetrization for Architecture Agnostic Equivariance](https://mlsanity.com/paper/2306.02866/) (2023)
- [Probabilistically Rewired Message-Passing Neural Networks](https://mlsanity.com/paper/2310.02156/) (2023)
- [Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence](https://mlsanity.com/paper/2502.09263/) (2025)
- [Adaptive Message Passing: A General Framework to Mitigate Oversmoothing, Oversquashing, and Underreaching](https://mlsanity.com/paper/2312.16560/) (2023)
- [Exposition on over-squashing problem on GNNs: Current Methods, Benchmarks and Challenges](https://mlsanity.com/paper/2311.07073/) (2023)
- [Graph Meets LLMs: Towards Large Graph Models](https://mlsanity.com/paper/2308.14522/) (2023)
- [Comparing Graph Transformers via Positional Encodings](https://mlsanity.com/paper/2402.14202/) (2024)
- [Distinguished In Uniform: Self Attention Vs. Virtual Nodes](https://mlsanity.com/paper/2405.11951/) (2024)
- [Learning Graph Quantized Tokenizers](https://mlsanity.com/paper/2410.13798/) (2024)
- [GraphGPT: Generative Pre-trained Graph Eulerian Transformer](https://mlsanity.com/paper/2401.00529/) (2023)
- [Dynamic Graph Representation Learning with Neural Networks: A Survey](https://mlsanity.com/paper/2304.05729/) (2023)
- [Expressive Sign Equivariant Networks for Spectral Geometric Learning](https://mlsanity.com/paper/2312.02339/) (2023)
- [Probabilistic Graph Rewiring via Virtual Nodes](https://mlsanity.com/paper/2405.17311/) (2024)
- [A Survey of Graph Transformers: Architectures, Theories and Applications](https://mlsanity.com/paper/2502.16533/) (2025)
- [Even Sparser Graph Transformers](https://mlsanity.com/paper/2411.16278/) (2024)
- [Towards Mechanistic Interpretability of Graph Transformers via Attention Graphs](https://mlsanity.com/paper/2502.12352/) (2025)
- [MANTRA: The Manifold Triangulations Assemblage](https://mlsanity.com/paper/2410.02392/) (2024)
- [Graph Convolutions Enrich the Self-Attention in Transformers!](https://mlsanity.com/paper/2312.04234/) (2023)

## Abstract (arXiv)

Recently, transformer architectures for graphs emerged as an alternative to established techniques for machine learning with graphs, such as (message-passing) graph neural networks. So far, they have shown promising empirical results, e.g., on molecular prediction datasets, often attributed to their ability to circumvent graph neural networks' shortcomings, such as over-smoothing and over-squashing. Here, we derive a taxonomy of graph transformer architectures, bringing some order to this emerging field. We overview their theoretical properties, survey structural and positional encodings, and discuss extensions for important graph classes, e.g., 3D molecular graphs. Empirically, we probe how well graph transformers can recover various graph properties, how well they can deal with heterophilic graphs, and to what extent they prevent over-squashing. Further, we outline open challenges and research direction to stimulate future work. Our code is available at https://github.com/luis-mueller/probing-graph-transformers.