arXiv Machine Learning

Communicability-Inspired Positional Encoding (CIPE)

arXiv:2606. 25293v1 Announce Type: new Abstract: Positional encodings (PEs) are essential for Transformers.

arXiv Machine Learning
Aug 28

Plain Transformers Can be Powerful Graph Learners

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 AI
Jun 26

Rotary Position Encodings for Graphs

arXiv:2509. 22259v4 Announce Type: replace-cross Abstract: We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data.

By Isaac Reid, Arijit Sehanobish, Cederik H\"ofs, Bruno Mlodozeniec, Leonhard Vulpius, Federico Barbero, Adrian Weller, Krzysztof Choromanski, Richard E. Turner, Petar Veli\v{c}kovi\'c
arXiv Machine Learning
Aug 19

HyPE-GT: where Graph Transformers meet Hyperbolic Positional Encodings

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 AI
Jul 28

A Survey of Graph Transformers: Architectures, Theories and Applications

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 AI
Jun 4

A Unified Geometric Space for Topological Alignment Between Transformer-Based Models and Human Brain Networks

arXiv:2510. 24342v2 Announce Type: replace Abstract: Prior brain-AI alignment studies are typically constrained by specific inputs and tasks, limiting their ability to capture organizational properties across models with different modalities.

By Silin Chen, Yuzhong Chen, Caiwei Wang, Zifan Wang, Junhao Wang, Zifeng Jia, Keith M Kendrick, Tuo Zhang, Lin Zhao, Dezhong Yao, Tianming Liu, Xi Jiang
arXiv AI
Jun 24

Mind the Heads: Topological Representation Alignment for Multimodal LLMs

arXiv:2606. 23885v1 Announce Type: cross Abstract: Representation alignment has emerged as an effective approach to improve Multimodal Large Language Models (MLLMs) by regularizing their internal representations toward those of an external vision encoder.

By Davide Caffagni, Alberto Compagnoni, Federico Melis, Sara Sarto, Pier Luigi Dovesi, Mark Granroth-Wilding, Marcella Cornia, Lorenzo Baraldi