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Graph neural networks (GNNs) have been widely adopted in engineering applications such as social network analysis, chemical research and computer vision. However, their efficacy is severely compromised by the inherent homophily assumption,…

Machine Learning · Computer Science 2026-04-13 Yi Luo , Xu Sun , Guangchun Luo , Aiguo Chen

Graph neural networks have been extensively studied for learning with inter-connected data. Despite this, recent evidence has revealed GNNs' deficiencies related to over-squashing, heterophily, handling long-range dependencies, edge…

Machine Learning · Computer Science 2023-06-16 Qitian Wu , Wentao Zhao , Zenan Li , David Wipf , Junchi Yan

The Transformer architecture has gained growing attention in graph representation learning recently, as it naturally overcomes several limitations of graph neural networks (GNNs) by avoiding their strict structural inductive biases and…

Machine Learning · Statistics 2022-06-14 Dexiong Chen , Leslie O'Bray , Karsten Borgwardt

The dominant paradigm for machine learning on graphs uses Message Passing Graph Neural Networks (MP-GNNs), in which node representations are updated by aggregating information in their local neighborhood. Recently, there have been…

Machine Learning · Computer Science 2023-03-02 Daniel Glickman , Eran Yahav

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) show considerable potential in graph representation learning. The architecture of GTs typically integrates Graph Neural Networks (GNNs) with global attention mechanisms either in parallel or as a precursor to…

Machine Learning · Computer Science 2026-02-04 Gang Wu , Zhengwei Wang

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

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn…

Machine Learning · Computer Science 2020-02-06 Seongjun Yun , Minbyul Jeong , Raehyun Kim , Jaewoo Kang , Hyunwoo J. Kim

We introduce Attention Graphs, a new tool for mechanistic interpretability of Graph Neural Networks (GNNs) and Graph Transformers based on the mathematical equivalence between message passing in GNNs and the self-attention mechanism in…

Machine Learning · Computer Science 2025-02-26 Batu El , Deepro Choudhury , Pietro Liò , Chaitanya K. Joshi

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed…

Machine Learning · Computer Science 2021-06-14 Seongjun Yun , Minbyul Jeong , Sungdong Yoo , Seunghun Lee , Sean S. Yi , Raehyun Kim , Jaewoo Kang , Hyunwoo J. Kim

To alleviate the local receptive issue of GCN, Transformers have been exploited to capture the long range dependences of nodes for graph data representation and learning. However, existing graph Transformers generally employ regular…

Machine Learning · Computer Science 2023-05-15 Bo Jiang , Fei Xu , Ziyan Zhang , Jin Tang , Feiping Nie

Graph Transformers (GTs), which integrate message passing and self-attention mechanisms simultaneously, have achieved promising empirical results in graph prediction tasks. However, the design of scalable and topology-aware node…

Neural and Evolutionary Computing · Computer Science 2025-12-12 Huizhe Zhang , Jintang Li , Yuchang Zhu , Huazhen Zhong , Liang Chen

Graph Neural Networks (GNNs) are widely used in graph data mining tasks. Traditional GNNs follow a message passing scheme that can effectively utilize local and structural information. However, the phenomena of over-smoothing and…

Machine Learning · Computer Science 2025-04-14 Zijie Zhou , Zhaoqi Lu , Xuekai Wei , Rongqin Chen , Shenghui Zhang , Pak Lon Ip , Leong Hou U

Session-based recommendation systems suggest relevant items to users by modeling user behavior and preferences using short-term anonymous sessions. Existing methods leverage Graph Neural Networks (GNNs) that propagate and aggregate…

Information Retrieval · Computer Science 2022-01-10 Sai Mitheran , Abhinav Java , Surya Kant Sahu , Arshad Shaikh

Graph neural networks are powerful architectures for structured datasets. However, current methods struggle to represent long-range dependencies. Scaling the depth or width of GNNs is insufficient to broaden receptive fields as larger GNNs…

Machine Learning · Computer Science 2022-01-24 Zhanghao Wu , Paras Jain , Matthew A. Wright , Azalia Mirhoseini , Joseph E. Gonzalez , Ion Stoica

Graph Neural Networks (GNNs) have been highly successful for the node classification task. GNNs typically assume graphs are homophilic, i.e. neighboring nodes are likely to belong to the same class. However, a number of real-world graphs…

Machine Learning · Computer Science 2024-09-20 Yurui Lai , Taiyan Zhang , Rui Fan

Graph neural networks excel at graph representation learning but struggle with heterophilous data and long-range dependencies. And graph transformers address these issues through self-attention, yet face scalability and noise challenges on…

Machine Learning · Computer Science 2025-02-13 Xuanze Chen , Jiajun Zhou , Shanqing Yu , Qi Xuan

Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node…

Machine Learning · Computer Science 2024-10-29 Yuankai Luo , Lei Shi , Xiao-Ming Wu

Graph neural networks (GNNs) have been extensively studied for prediction tasks on graphs. As pointed out by recent studies, most GNNs assume local homophily, i.e., strong similarities in local neighborhoods. This assumption however limits…

Machine Learning · Computer Science 2021-10-04 Sean Li , Dongwoo Kim , Qing Wang

Node classification has gained significant importance in graph deep learning with real-world applications such as recommendation systems, drug discovery, and citation networks. Graph Convolutional Networks and Graph Transformers have…

Social and Information Networks · Computer Science 2025-04-04 Aman Singh , Shahid Shafi Dar , Ranveer Singh , Nagendra Kumar
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