# Pre-training with Graph Transformers

arXiv: https://arxiv.org/abs/2609.13844 · HTML: https://mlsanity.com/paper/2609.13844/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 22 references that are in the map.
- First posted on arXiv 12 Sep 2026.

## Builds on (most cited first, 13 of 13)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Graph Transformer Networks](https://mlsanity.com/paper/1911.06455/) (2019)
- [Inductive Representation Learning on Temporal Graphs](https://mlsanity.com/paper/2002.07962/) (2020)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)
- [Dynamic Graph Representation Learning via Self-Attention Networks](https://mlsanity.com/paper/1812.09430/) (2018)
- [Bi-Level Attention Graph Neural Networks](https://mlsanity.com/paper/2304.11533/) (2023)

## Abstract (arXiv)

This article investigates pre-training strategies for graph transformers in the biochemistry domain. By conducting comprehensive experiments, the study reveals that supervised pre-training using computed properties as labels provides the highest performance gain on downstream tasks. The results also highlight the importance of constraining model capacity to mitigate overfitting in graph transformers.