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Most graph neural networks follow the message passing mechanism. However, it faces the over-smoothing problem when multiple times of message passing is applied to a graph, causing indistinguishable node representations and prevents the…

Machine Learning · Computer Science 2023-02-06 Yunchong Song , Chenghu Zhou , Xinbing Wang , Zhouhan Lin

Many complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into…

Social and Information Networks · Computer Science 2023-01-06 Xue Gong , Desmond J. Higham , Konstantinos Zygalakis

Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph…

Social and Information Networks · Computer Science 2019-09-13 Palash Goyal , Di Huang , Sujit Rokka Chhetri , Arquimedes Canedo , Jaya Shree , Evan Patterson

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

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Machine Learning · Computer Science 2021-09-21 Vincent Mallet , Carlos G. Oliver , William L. Hamilton

The irreducible complexity of natural phenomena has led Graph Neural Networks to be employed as a standard model to perform representation learning tasks on graph-structured data. While their capacity to capture local and global patterns is…

Machine Learning · Computer Science 2024-02-13 Lorenzo Giusti

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

Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can suffer from information flow bottlenecks.…

Computational Physics · Physics 2025-02-21 Alessandro Caruso , Jacopo Venturin , Lorenzo Giambagli , Edoardo Rolando , Frank Noé , Cecilia Clementi

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 Transformer shows remarkable potential in brain network analysis due to its ability to model graph structures and complex node relationships. Most existing methods typically model the brain as a flat network, ignoring its modular…

Machine Learning · Computer Science 2025-11-25 Jiajun Ma , Yongchao Zhang , Chao Zhang , Zhao Lv , Shengbing Pei

Hypergraphs are crucial for modelling higher-order interactions in real-world data. Hypergraph neural networks (HNNs) effectively utilise these structures by message passing to generate informative node features for various downstream tasks…

Machine Learning · Computer Science 2025-03-12 Bohan Tang , Zexi Liu , Keyue Jiang , Siheng Chen , Xiaowen Dong

Modelling long-range dependencies is critical for scene understanding tasks in computer vision. Although CNNs have excelled in many vision tasks, they are still limited in capturing long-range structured relationships as they typically…

Computer Vision and Pattern Recognition · Computer Science 2022-09-16 Li Zhang , Dan Xu , Anurag Arnab , Philip H. S. Torr

Real-world graphs are typically complex, exhibiting heterogeneity in the global structure, as well as strong heterophily within local neighborhoods. While a growing body of literature has revealed the limitations of common graph neural…

Machine Learning · Computer Science 2023-10-19 Jintang Li , Zheng Wei , Jiawang Dan , Jing Zhou , Yuchang Zhu , Ruofan Wu , Baokun Wang , Zhang Zhen , Changhua Meng , Hong Jin , Zibin Zheng , Liang Chen

Graph-based environments pose unique challenges to multi-agent reinforcement learning. In decentralized approaches, agents operate within a given graph and make decisions based on partial or outdated observations. The size of the observed…

Multiagent Systems · Computer Science 2024-06-05 Jannis Weil , Zhenghua Bao , Osama Abboud , Tobias Meuser

In the semi-supervised setting where labeled data are largely limited, it remains to be a big challenge for message passing based graph neural networks (GNNs) to learn feature representations for the nodes with the same class label that is…

Machine Learning · Computer Science 2023-05-09 Acong Zhang , Ping Li , Guanrong Chen

Dynamic interactions between entities are prevalent in domains like social platforms, financial systems, healthcare, and e-commerce. These interactions can be effectively represented as time-evolving graphs, where predicting future…

Machine Learning · Computer Science 2026-01-21 Sidharth Agarwal , Tanishq Dubey , Shubham Gupta , Srikanta Bedathur

Previous studies have demonstrated the strong performance of Graph Neural Networks (GNNs) in node classification. However, most existing GNNs adopt a node-centric perspective and rely on global message passing, leading to high computational…

Machine Learning · Computer Science 2026-01-14 Qian Zeng , Xin Lin , Jingyi Gao , Yang Yu

In real-world scenarios, texts in a graph are often linked by multiple semantic relations (e.g., papers in an academic graph are referenced by other publications, written by the same author, or published in the same venue), where text…

Computation and Language · Computer Science 2024-07-16 Bowen Jin , Wentao Zhang , Yu Zhang , Yu Meng , Han Zhao , Jiawei Han

Graph neural networks (GNNs) have recently received significant attention. Learning node-wise message propagation in GNNs aims to set personalized propagation steps for different nodes in the graph. Despite the success, existing methods…

Machine Learning · Computer Science 2023-11-07 Yao Cheng , Minjie Chen , Xiang Li , Caihua Shan , Ming Gao

Hypergraph Convolutional Neural Networks (HGCNNs) have demonstrated their potential in modeling high-order relations preserved in graph-structured data. However, most existing convolution filters are localized and determined by the…

Machine Learning · Computer Science 2022-04-15 Jiying Zhang , Yuzhao Chen , Xi Xiao , Runiu Lu , Shu-Tao Xia
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