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Graph neural networks (GNNs) have demonstrated success in modeling relational data primarily under the assumption of homophily. However, many real-world graphs exhibit heterophily, where linked nodes belong to different categories or…

Computation and Language · Computer Science 2025-03-10 Shujie Li , Yuxia Wu , Chuan Shi , Yuan Fang

Graph Neural Networks (GNNs) have been generalized to process the heterogeneous graphs by various approaches. Unfortunately, these approaches usually model the heterogeneity via various complicated modules. This paper aims to propose a…

Machine Learning · Computer Science 2023-11-23 Junfu Wang , Yuanfang Guo , Liang Yang , Yunhong Wang

Graph Neural Networks (GNNs) have proven to be highly effective for node classification tasks across diverse graph structural patterns. Traditionally, GNNs employ a uniform global filter, typically a low-pass filter for homophilic graphs…

Machine Learning · Computer Science 2024-06-06 Haoyu Han , Juanhui Li , Wei Huang , Xianfeng Tang , Hanqing Lu , Chen Luo , Hui Liu , Jiliang Tang

Graph-Convolution-based methods have been successfully applied to representation learning on homophily graphs where nodes with the same label or similar attributes tend to connect with one another. Due to the homophily assumption of Graph…

Machine Learning · Computer Science 2022-06-29 Di Jin , Rui Wang , Meng Ge , Dongxiao He , Xiang Li , Wei Lin , Weixiong Zhang

Graph Neural Networks (GNNs) are widely used on a variety of graph-based machine learning tasks. For node-level tasks, GNNs have strong power to model the homophily property of graphs (i.e., connected nodes are more similar) while their…

Machine Learning · Computer Science 2022-04-26 Lun Du , Xiaozhou Shi , Qiang Fu , Xiaojun Ma , Hengyu Liu , Shi Han , Dongmei Zhang

Current graph neural networks (GNNs) lack generalizability with respect to scales (graph sizes, graph diameters, edge weights, etc..) when solving many graph analysis problems. Taking the perspective of synthesizing graph theory programs,…

Machine Learning · Computer Science 2020-10-27 Hao Tang , Zhiao Huang , Jiayuan Gu , Bao-Liang Lu , Hao Su

Graph Neural Networks have emerged as the most popular architecture for graph-level learning, including graph classification and regression tasks, which frequently arise in areas such as biochemistry and drug discovery. Achieving good…

Machine Learning · Computer Science 2025-03-04 Lukas Fesser , Melanie Weber

Graph neural networks (GNNs) have shown significant success in learning graph representations. However, recent studies reveal that GNNs often fail to outperform simple MLPs on heterophilous graph tasks, where connected nodes may differ in…

Machine Learning · Computer Science 2025-04-10 Songwei Zhao , Yuan Jiang , Zijing Zhang , Yang Yu , Hechang Chen

Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data but often struggle on heterophilous graphs, where connected nodes differ in features or class labels. This limitation arises from…

Machine Learning · Computer Science 2025-09-30 Zhongtian Sun , Anoushka Harit , Alexandra Cristea , Christl A. Donnelly , Pietro Liò

Physics-informed Graph Neural Networks have achieved remarkable performance in learning through graph-structured data by mitigating common GNN challenges such as over-smoothing, over-squashing, and heterophily adaption. Despite these…

Machine Learning · Computer Science 2024-06-13 Dai Shi , Andi Han , Lequan Lin , Yi Guo , Zhiyong Wang , Junbin Gao

Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of…

Machine Learning · Computer Science 2025-12-03 Haishan Wang , Arno Solin , Vikas Garg

Graphs are ubiquitous for modeling complex relationships between objects across various fields. Graph neural networks (GNNs) have become a mainstream technique for graph-based applications, but their performance heavily relies on abundant…

Machine Learning · Computer Science 2025-02-27 Xingtong Yu , Jie Zhang , Yuan Fang , Renhe Jiang

Graph neural networks (GNN) have been ubiquitous in graph node classification tasks. Most of GNN methods update the node embedding iteratively by aggregating its neighbors' information. However, they often suffer from negative disturbance,…

Machine Learning · Computer Science 2022-02-02 Jie Chen , Shouzhen Chen , Mingyuan Bai , Jian Pu , Junping Zhang , Junbin Gao

Graph neural networks (GNNs) excel in modeling relational data such as biological, social, and transportation networks, but the underpinnings of their success are not well understood. Traditional complexity measures from statistical…

Machine Learning · Computer Science 2024-01-24 Cheng Shi , Liming Pan , Hong Hu , Ivan Dokmanić

Graphs with heterophily have been regarded as challenging scenarios for Graph Neural Networks (GNNs), where nodes are connected with dissimilar neighbors through various patterns. In this paper, we present theoretical understandings of the…

Machine Learning · Computer Science 2024-06-05 Junfu Wang , Yuanfang Guo , Liang Yang , Yunhong Wang

Heterogeneous graphs (HGs) are common in real-world scenarios and often exhibit heterophily. However, most existing studies focus on either heterogeneity or heterophily in isolation, overlooking the prevalence of heterophilic HGs in…

Machine Learning · Computer Science 2025-08-11 Qin Chen , Guojie Song

Heterogeneous graph neural networks (GNNs) achieve strong performance on node classification tasks in a semi-supervised learning setting. However, as in the simpler homogeneous GNN case, message-passing-based heterogeneous GNNs may struggle…

Machine Learning · Computer Science 2022-10-24 Hongjoon Ahn , Yongyi Yang , Quan Gan , Taesup Moon , David Wipf

Graph neural networks (GNNs) have achieved remarkable success in node classification. Building on this progress, heterogeneous graph neural networks (HGNNs) integrate relation types and node and edge semantics to leverage heterogeneous…

Machine Learning · Computer Science 2025-10-08 Xiao Yang , Xuejiao Zhao , Zhiqi Shen

In recent years, Graph Neural Networks (GNNs) have been popular in graph representation learning which assumes the homophily property, i.e., the connected nodes have the same label or have similar features. However, they may fail to…

Machine Learning · Computer Science 2022-11-22 Lanning Wei , Zhiqiang He , Huan Zhao , Quanming Yao

While graph heterophily has been extensively studied in recent years, a fundamental research question largely remains nascent: How and to what extent will graph heterophily affect the prediction performance of graph neural networks (GNNs)?…

Machine Learning · Computer Science 2023-06-27 Shuaicheng Zhang , Haohui Wang , Si Zhang , Dawei Zhou