Generative Graph Pattern Machine

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 (G$^2$PM), a generative Transformer pre-training framework for graphs. G$^2$PM 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, G$^2$PM 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---G$^2$PM 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.

Authors

• Zehong Wang
• Zheyuan Zhang
• Tianyi Ma
• Chuxu Zhang Brandeis University, Waltham, MA 02453
• Yanfang Ye University of Notre Dame Lucy Family Institute for Data & Society

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