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Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the…

Machine Learning · Computer Science 2023-12-19 Vijay Prakash Dwivedi , Yozen Liu , Anh Tuan Luu , Xavier Bresson , Neil Shah , Tong Zhao

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. Recent studies have proposed…

Machine Learning · Computer Science 2025-02-28 Chaohao Yuan , Kangfei Zhao , Ercan Engin Kuruoglu , Liang Wang , Tingyang Xu , Wenbing Huang , Deli Zhao , Hong Cheng , Yu Rong

Graph Transformers (GTs) have shown strong empirical performance, yet current architectures vary widely in their use of attention mechanisms, positional embeddings (PEs), and expressivity. Existing expressivity results are often tied to…

Machine Learning · Computer Science 2025-11-12 Timo Stoll , Luis Müller , Christopher Morris

Graph Transformers (GTs) have significantly advanced the field of graph representation learning by overcoming the limitations of message-passing graph neural networks (GNNs) and demonstrating promising performance and expressive power.…

Machine Learning · Computer Science 2024-05-07 Wenhao Zhu , Guojie Song , Liang Wang , Shaoguo Liu

The design of Graph Transformers (GTs) generally neglects considerations for fairness, resulting in biased outcomes against certain sensitive subgroups. Since GTs encode graph information without relying on message-passing mechanisms,…

Machine Learning · Computer Science 2024-04-29 Renqiang Luo , Huafei Huang , Shuo Yu , Xiuzhen Zhang , Feng Xia

The paradigm of Transformers using the self-attention mechanism has manifested its advantage in learning graph-structured data. Yet, Graph Transformers are capable of modeling full range dependencies but are often deficient in extracting…

Machine Learning · Computer Science 2024-09-11 Minhong Zhu , Zhenhao Zhao , Weiran Cai

Graph learning has become essential in various domains, including recommendation systems and social network analysis. Graph Neural Networks (GNNs) have emerged as promising techniques for encoding structural information and improving…

Machine Learning · Computer Science 2024-10-10 Lianghao Xia , Ben Kao , Chao Huang

Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for graph-structured data. A key design choice in GTs is the use of Graph Neural Network…

Machine Learning · Computer Science 2026-05-29 Javier Porras-Valenzuela , Zhiyang Wang , Xiaotao Shang , Yusu Wang , Alejandro Ribeiro

Graph Neural Networks (GNNs) have emerged as the de facto standard for representation learning on graphs, owing to their ability to effectively integrate graph topology and node attributes. However, the inherent suboptimal nature of node…

Machine Learning · Computer Science 2023-12-27 Zhiyao Zhou , Sheng Zhou , Bochao Mao , Xuanyi Zhou , Jiawei Chen , Qiaoyu Tan , Daochen Zha , Yan Feng , Chun Chen , Can Wang

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of…

Machine Learning · Computer Science 2023-01-18 Ladislav Rampášek , Mikhail Galkin , Vijay Prakash Dwivedi , Anh Tuan Luu , Guy Wolf , Dominique Beaini

Transformers have attained outstanding performance across various modalities, owing to their simple but powerful scaled-dot-product (SDP) attention mechanisms. Researchers have attempted to migrate Transformers to graph learning, but most…

Machine Learning · Computer Science 2026-01-30 Liheng Ma , Soumyasundar Pal , Yingxue Zhang , Philip H. S. Torr , Mark Coates

Graphs are fundamental data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which involve predicting properties or labels for entire graphs,…

Machine Learning · Computer Science 2026-04-10 Haoyang Li , Yuming Xu , Alexander Zhou , Yongqi Zhang , Jason Chen Zhang , Lei Chen , Qing Li

Graph Transformer is a new architecture that surpasses GNNs in graph learning. While there emerge inspiring algorithm advancements, their practical adoption is still limited, particularly on real-world graphs involving up to millions of…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-07-22 Meng Zhang , Jie Sun , Qinghao Hu , Peng Sun , Zeke Wang , Yonggang Wen , Tianwei Zhang

Graph domain adaptation models are widely adopted in cross-network learning tasks, with the aim of transferring labeling or structural knowledge. Currently, there mainly exist two limitations in evaluating graph domain adaptation models. On…

Artificial Intelligence · Computer Science 2023-07-24 Boshen Shi , Yongqing Wang , Fangda Guo , Jiangli Shao , Huawei Shen , Xueqi Cheng

Recent studies have highlighted significant fairness issues in Graph Transformer (GT) models, particularly against subgroups defined by sensitive features. Additionally, GTs are computationally intensive and memory-demanding, limiting their…

Machine Learning · Computer Science 2025-01-03 Renqiang Luo , Huafei Huang , Ivan Lee , Chengpei Xu , Jianzhong Qi , Feng Xia

Recently, Transformer model, which has achieved great success in many artificial intelligence fields, has demonstrated its great potential in modeling graph-structured data. Till now, a great variety of Transformers has been proposed to…

Machine Learning · Computer Science 2022-02-18 Erxue Min , Runfa Chen , Yatao Bian , Tingyang Xu , Kangfei Zhao , Wenbing Huang , Peilin Zhao , Junzhou Huang , Sophia Ananiadou , Yu Rong

As the field of Graph Neural Networks (GNN) continues to grow, it experiences a corresponding increase in the need for large, real-world datasets to train and test new GNN models on challenging, realistic problems. Unfortunately, such graph…

Machine Learning · Computer Science 2023-06-12 Minji Yoon , Yue Wu , John Palowitch , Bryan Perozzi , Ruslan Salakhutdinov

Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them…

Machine Learning · Computer Science 2020-03-04 Ziniu Hu , Yuxiao Dong , Kuansan Wang , Yizhou Sun

Graph Transformers (GTs) have emerged as powerful architectures for graph-structured data, yet remain constrained by rigid designs and lack quantifiable interpretability. Current state-of-the-art GTs commit to fixed GNN types across all…

Machine Learning · Computer Science 2025-11-03 Shruti Sarika Chakraborty , Peter Minary

Graph pre-training has been concentrated on graph-level tasks involving small graphs (e.g., molecular graphs) or learning node representations on a fixed graph. Extending graph pre-trained models to web-scale graphs with billions of nodes…

Machine Learning · Computer Science 2025-11-07 Yufei He , Zhenyu Hou , Yukuo Cen , Jun Hu , Feng He , Xu Cheng , Jie Tang , Bryan Hooi
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