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Graph neural networks (GNNs) have become increasingly popular for classification tasks on graph-structured data. Yet, the interplay between graph topology and feature evolution in GNNs is not well understood. In this paper, we focus on…

Machine Learning · Computer Science 2023-10-27 Vignesh Kothapalli , Tom Tirer , Joan Bruna

Graph Neural Networks (GNNs) have emerged as a promising tool to handle data exhibiting an irregular structure. However, most GNN architectures perform well on homophilic datasets, where the labels of neighboring nodes are likely to be the…

Machine Learning · Computer Science 2024-12-03 Victor M. Tenorio , Madeline Navarro , Samuel Rey , Santiago Segarra , Antonio G. Marques

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

Graph neural networks (GNNs) have achieved remarkable advances in graph-oriented tasks. However, real-world graphs invariably contain a certain proportion of heterophilous nodes, challenging the homophily assumption of traditional GNNs and…

Machine Learning · Computer Science 2025-02-04 Jiajun Zhou , Shengbo Gong , Xuanze Chen , Chenxuan Xie , Shanqing Yu , Qi Xuan , Xiaoniu Yang

Graph coarsening reduces the size of a graph while preserving certain properties. Most existing methods preserve either spectral or spatial characteristics. Recent research has shown that preserving topological features helps maintain the…

Machine Learning · Computer Science 2026-02-02 Xiang Wu , Rong-Hua Li , Xunkai Li , Kangfei Zhao , Hongchao Qin , Guoren Wang

While Graph Neural Networks (GNNs) have achieved enormous success in multiple graph analytical tasks, modern variants mostly rely on the strong inductive bias of homophily. However, real-world networks typically exhibit both homophilic and…

Machine Learning · Computer Science 2024-09-18 Jingwei Guo , Kaizhu Huang , Rui Zhang , Xinping Yi

Graph neural networks (GNNs) have shown great prowess in learning representations suitable for numerous graph-based machine learning tasks. When applied to semi-supervised node classification, GNNs are widely believed to work well due to…

Machine Learning · Computer Science 2023-07-24 Yao Ma , Xiaorui Liu , Neil Shah , Jiliang Tang

Learning useful node and graph representations with graph neural networks (GNNs) is a challenging task. It is known that deep GNNs suffer from over-smoothing where, as the number of layers increases, node representations become nearly…

Machine Learning · Computer Science 2022-02-28 Pantelis Elinas , Edwin V. Bonilla

The performance of graph neural nets (GNNs) is known to gradually decrease with increasing number of layers. This decay is partly attributed to oversmoothing, where repeated graph convolutions eventually make node embeddings…

Machine Learning · Computer Science 2020-02-14 Lingxiao Zhao , Leman Akoglu

Graph Neural Networks (GNNs) have been broadly applied in many urban applications upon formulating a city as an urban graph whose nodes are urban objects like regions or points of interest. Recently, a few enhanced GNN architectures have…

Machine Learning · Computer Science 2023-06-22 Congxi Xiao , Jingbo Zhou , Jizhou Huang , Tong Xu , Hui Xiong

Graph Neural Networks have become one of the indispensable tools to learn from graph-structured data, and their usefulness has been shown in wide variety of tasks. In recent years, there have been tremendous improvements in architecture…

Machine Learning · Statistics 2021-11-15 Sunil Kumar Maurya , Xin Liu , Tsuyoshi Murata

Graph Neural Networks (GNNs) have emerged as a cornerstone of deep learning, with most existing methods rooted in graph signal processing and diffusion equations to model message passing. However, these approaches inherently suffer from the…

Machine Learning · Computer Science 2026-05-26 Zexing Zhao , Guangsi Shi , Yu Gong , Tianyu Wang , Shirui Pan , Hongye Cheng , Yuxiao Li

Graph convolutional networks are a popular class of deep neural network algorithms which have shown success in a number of relational learning tasks. Despite their success, graph convolutional networks exhibit a number of peculiar features,…

Machine Learning · Computer Science 2022-08-22 Thomas Gebhart

Classifying Antimicrobial Peptides (AMPs) from the vast collection of peptides derived from metagenomic sequencing offers a promising avenue for combating antibiotic resistance. However, most existing AMP classification methods rely…

Quantitative Methods · Quantitative Biology 2026-01-15 Yingxu Wang , Victor Liang , Nan Yin , Siwei Liu , Eran Segal

In representation learning on the graph-structured data, under heterophily (or low homophily), many popular GNNs may fail to capture long-range dependencies, which leads to their performance degradation. To solve the above-mentioned issue,…

Machine Learning · Computer Science 2021-06-29 Mengying Jiang , Guizhong Liu , Yuanchao Su , Xinliang Wu

Sheaf Neural Networks (SNNs) represent a powerful generalization of Graph Neural Networks (GNNs) that significantly improve our ability to model complex relational data. While directionality has been shown to substantially boost performance…

Machine Learning · Computer Science 2025-06-04 Stefano Fiorini , Hakan Aktas , Iulia Duta , Stefano Coniglio , Pietro Morerio , Alessio Del Bue , Pietro Liò

Heterogeneous graphs, whose nodes and edges can belong to different types and feature spaces, arise in many real-world domains, including biology, recommendation, social networks, and computer systems. Existing heterogeneous graph neural…

Under circumstances of heterophily, where nodes with different labels tend to be connected based on semantic meanings, Graph Neural Networks (GNNs) often exhibit suboptimal performance. Current studies on graph heterophily mainly focus on…

Machine Learning · Computer Science 2024-11-13 Yilun Zheng , Jiahao Xu , Lihui Chen

Spectral features are widely incorporated within Graph Neural Networks (GNNs) to improve their expressive power, or their ability to distinguish among non-isomorphic graphs. One popular example is the usage of graph Laplacian eigenvectors…

Machine Learning · Computer Science 2025-09-29 Snir Hordan , Maya Bechler-Speicher , Gur Lifshitz , Nadav Dym

Graph Neural Networks (GNNs) have become the standard method for learning from networks across fields ranging from biology to social systems, yet a principled understanding of what enables them to extract meaningful representations, or why…

Machine Learning · Statistics 2026-03-19 Nil Ayday , Mahalakshmi Sabanayagam , Debarghya Ghoshdastidar