# Generative Graph Pattern Machine

arXiv: https://arxiv.org/abs/2505.16130 · HTML: https://mlsanity.com/paper/2505.16130/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 68 of its 83 references that are in the map.
- First posted on arXiv 22 May 2025.

## Builds on (most cited first, 30 of 68)

- [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)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (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)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention](https://mlsanity.com/paper/2006.16236/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [SimMIM: A Simple Framework for Masked Image Modeling](https://mlsanity.com/paper/2111.09886/) (2021)
- [Visual Autoregressive Modeling: Scalable Image Generation via Next-Scale Prediction](https://mlsanity.com/paper/2404.02905/) (2024)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [Deep Graph Contrastive Representation Learning](https://mlsanity.com/paper/2006.04131/) (2020)
- [Graph Contrastive Learning with Adaptive Augmentation](https://mlsanity.com/paper/2010.14945/) (2020)
- [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)
- [GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training](https://mlsanity.com/paper/2006.09963/) (2020)

## Built on by (most cited first, 11 of 11)

- [Graph is a Substrate Across Data Modalities](https://mlsanity.com/paper/2601.22384/) (2026)
- [Semantic Refinement with LLMs for Graph Representations](https://mlsanity.com/paper/2512.21106/) (2025)
- [Molecular Representations in Implicit Functional Space via Hyper-Networks](https://mlsanity.com/paper/2601.22327/) (2026)
- [Temporal Graph Pattern Machine](https://mlsanity.com/paper/2601.22454/) (2026)
- [Learning Graph Foundation Models on Riemannian Graph-of-Graphs](https://mlsanity.com/paper/2605.09993/) (2026)
- [BHyGNN+: Unsupervised Representation Learning for Heterophilic Hypergraphs](https://mlsanity.com/paper/2602.14919/) (2026)
- [Generalizing GNNs with Tokenized Mixture of Experts](https://mlsanity.com/paper/2602.09258/) (2026)
- [Enhancing Graph Representations with Neighborhood-Contextualized Message-Passing](https://mlsanity.com/paper/2511.11046/) (2025)
- [On the Safety of Graph Representation Learning](https://mlsanity.com/paper/2605.06576/) (2026)
- [Hypergraph Pattern Machine: Compositional Tokenization for Higher-Order Interactions](https://mlsanity.com/paper/2605.16527/) (2026)
- [Are Common Substructures Transferable? Riemannian Graph Foundation Model with Neural Vector Bundles](https://mlsanity.com/paper/2606.03270/) (2026)

## Abstract (arXiv)

Graph neural networks (GNNs) have been predominantly driven by message-passing, where node representations are iteratively updated via local neighborhood aggregation. Despite their success, message-passing suffers from fundamental limitations -- including constrained expressiveness, over-smoothing, over-squashing, and limited capacity to model long-range dependencies. These issues hinder scalability: increasing data size or model size often fails to yield improved performance. To this end, we explore pathways beyond message-passing and introduce Generative Graph Pattern Machine (G2PM), a generative Transformer pre-training framework for graphs. G2PM represents graph instances (nodes, edges, or entire graphs) as sequences of substructures, and employs generative pre-training over the sequences to learn generalizable and transferable representations. Empirically, G2PM demonstrates strong scalability: on the ogbn-arxiv benchmark, it continues to improve with model sizes up to 60M parameters, outperforming prior generative approaches that plateau at significantly smaller scales (e.g., 3M). In addition, we systematically analyze the model design space, highlighting key architectural choices that contribute to its scalability and generalization. Across diverse tasks -- including node/link/graph classification, transfer learning, and cross-graph pretraining -- G2PM consistently outperforms strong baselines, establishing a compelling foundation for scalable graph learning. The code and dataset are available at https://github.com/Zehong-Wang/G2PM.