The paper shows that a plain Transformer can serve as an effective graph learner by adding three lightweight modifications: simplified L₂ attention, adaptive RMS normalization, and an MLP-based positional encoding stem. These changes preserve token magnitude and enable the model to achieve high expressivity on graph benchmarks, outperforming more complex graph transformer variants. The results suggest that plain Transformers can act as a unified backbone for multimodal learning across language, vision, and graph domains.
By Liheng Ma, Soumyasundar Pal, Yingxue Zhang, Philip H. S. Torr, Mark Coates
arXiv:2604. 17324v2 Announce Type: replace-cross Abstract: Global self-attention drives modern graph transformers, yet the softmax at its core imposes a structural constraint rarely examined directly: every attention row is non-negative and sums to one, so each per-head output is a mass-conserving convex combination of value vectors.
By Yang Liu, Dongxin Guo, Tom Zheng, Siu Ming Yiu, Liam Ning, Jikun Wu
arXiv:2602. 01553v3 Announce Type: replace-cross Abstract: Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies.
By Quang Truong, Yu Song, Donald Loveland, Mingxuan Ju, Tong Zhao, Neil Shah, Jiliang Tang
arXiv:2607. 17272v1 Announce Type: new Abstract: Node representation learning has advanced rapidly, yet most existing methods rely on per-dataset training and hyperparameter tuning.
By Dooho Lee, Jaemin Yoo
arXiv:2502. 16533v3 Announce Type: replace-cross Abstract: Graph Transformers (GTs) have demonstrated a strong capability in modeling graph structures by addressing the intrinsic limitations of graph neural networks (GNNs), such as over-smoothing and over-squashing.
By Chaohao Yuan, Kangfei Zhao, Ercan Engin Kuruoglu, Liang Wang, Tingyang Xu, Wenbing Huang, Deli Zhao, Hong Cheng, Yu Rong
arXiv:2602.15239v3 Announce Type: replace
Abstract: Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for...
By Javier Porras-Valenzuela, Zhiyang Wang, Teresa Shang, Yusu Wang, Alejandro Ribeiro
The paper investigates how the choice of graph tokenization affects transformer expressivity. It analyzes three tokenization families—spectral, random‑walk, and adjacency—showing that each induces different depth requirements and that some tokenizations are inherently lossy or ill‑conditioned for certain tasks. The authors prove lower bounds and impossibility results for converting between tokenizations and validate these findings with experiments on synthetic and real‑world data.
By Maya Bechler-Speicher, Gilad Yehudai, Gil Harari, Clayton Sanford, Amir Globerson, Joan Bruna
HyPE-GT introduces a framework that generates learnable hyperbolic positional encodings for Graph Transformers, enabling the capture of complex hierarchical relationships in graph-structured data. Unlike traditional Euclidean encodings, HyPE’s hyperbolic encodings can be selected to suit specific downstream tasks and help mitigate oversmoothing in deep Graph Neural Networks. Experiments on molecular benchmarks and large-scale Open Graph Benchmark datasets demonstrate improved performance, while additional tests on Coauthor and Copurchase networks confirm HyPE’s effectiveness in controlling oversmoothing.
By Kushal Bose, Swagatam Das
arXiv:2608. 04381v1 Announce Type: cross Abstract: Self-supervised learning on graphs is largely shaped by contrastive methods that depend on carefully designed augmentations, and by generative methods that reconstruct node attributes in the input space.
By Tinghe Zhang, Jian Xu, Jiaheng Chen, Jiaxing Li, Yucheng Xiao, Qiang Wang
arXiv:2607. 17570v1 Announce Type: new Abstract: Graph foundation models (GFMs) with global attention are increasingly used to represent mixed-integer linear programs (MILPs), aiming to capture structure beyond the locality of standard graph neural networks.
By Md Abrar Jahin, Craig A. Knoblock, Jay Pujara
Positional encodings (PEs) are essential for Transformers. Yet designing effective PEs for non-Euclidean graphs remains challenging.
arXiv:2609.05955v1 Announce Type: new
Abstract: Tabular foundation models have become powerful graph learners. Systems such as G2T-FM and GraphPFN encode each node as a feature row and make predictio...
By Mingqi Yang, Zidong Guo, Jihui Yang, Wenming Zuo