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Designing expressive Graph Neural Networks (GNNs) is a central topic in learning graph-structured data. While numerous approaches have been proposed to improve GNNs in terms of the Weisfeiler-Lehman (WL) test, generally there is still a…

Machine Learning · Computer Science 2024-02-13 Bohang Zhang , Shengjie Luo , Liwei Wang , Di He

Graph neural networks (GNNs) are one of the most popular research topics for deep learning. GNN methods typically have been designed on top of the graph signal processing theory. In particular, diffusion equations have been widely used for…

Machine Learning · Computer Science 2023-06-16 Jeongwhan Choi , Seoyoung Hong , Noseong Park , Sung-Bae Cho

Graph Convolutional Networks (GCNs) suffer from performance degradation when models go deeper. However, earlier works only attributed the performance degeneration to over-smoothing. In this paper, we conduct theoretical and experimental…

Machine Learning · Computer Science 2024-01-24 Weigang Lu , Yibing Zhan , Binbin Lin , Ziyu Guan , Liu Liu , Baosheng Yu , Wei Zhao , Yaming Yang , Dacheng Tao

Existing Graph Neural Network (GNN) methods that learn inductive unsupervised graph representations focus on learning node and edge representations by predicting observed edges in the graph. Although such approaches have shown advances in…

Machine Learning · Computer Science 2020-10-12 Leonardo Cotta , Carlos H. C. Teixeira , Ananthram Swami , Bruno Ribeiro

Message-passing neural networks (MPNNs) have been successfully applied to representation learning on graphs in a variety of real-world applications. However, two fundamental weaknesses of MPNNs' aggregators limit their ability to represent…

Machine Learning · Computer Science 2020-02-17 Hongbin Pei , Bingzhe Wei , Kevin Chen-Chuan Chang , Yu Lei , Bo Yang

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this…

Machine Learning · Computer Science 2023-06-06 Omri Puny , Derek Lim , Bobak T. Kiani , Haggai Maron , Yaron Lipman

Recent work shows that the expressive power of Graph Neural Networks (GNNs) in distinguishing non-isomorphic graphs is exactly the same as that of the Weisfeiler-Lehman (WL) graph test. In particular, they show that the WL test can be…

Over-smoothing in Graph Neural Networks (GNNs) causes collapse in distinct node features, particularly on heterophilic graphs where adjacent nodes often have dissimilar labels. Although sheaf neural networks partially mitigate this problem,…

Machine Learning · Computer Science 2025-11-11 Yoonhyuk Choi , Jiho Choi , Chong-Kwon Kim

Graph limit models, like graphons for limits of dense graphs, have recently been used to study size transferability of graph neural networks (GNNs). While most literature focuses on message passing GNNs (MPNNs), in this work we attend to…

Machine Learning · Computer Science 2025-05-20 Daniel Herbst , Stefanie Jegelka

Numerous subgraph-enhanced graph neural networks (GNNs) have emerged recently, provably boosting the expressive power of standard (message-passing) GNNs. However, there is a limited understanding of how these approaches relate to each other…

Machine Learning · Computer Science 2022-10-18 Chendi Qian , Gaurav Rattan , Floris Geerts , Christopher Morris , Mathias Niepert

Oversmoothing is a common phenomenon observed in graph neural networks (GNNs), in which an increase in the network depth leads to a deterioration in their performance. Graph contrastive learning (GCL) is emerging as a promising way of…

Machine Learning · Computer Science 2024-02-26 Jintang Li , Wangbin Sun , Ruofan Wu , Yuchang Zhu , Liang Chen , Zibin Zheng

Graph neural networks (GNNs) have achieved success in various inference tasks on graph-structured data. However, common challenges faced by many GNNs in the literature include the problem of graph node embedding under various geometries and…

Machine Learning · Computer Science 2023-03-03 Qiyu Kang , Kai Zhao , Yang Song , Sijie Wang , Rui She , Wee Peng Tay

In node classification tasks, graph convolutional neural networks (GCNs) have demonstrated competitive performance over traditional methods on diverse graph data. However, it is known that the performance of GCNs degrades with increasing…

Machine Learning · Computer Science 2022-11-29 Yujun Yan , Milad Hashemi , Kevin Swersky , Yaoqing Yang , Danai Koutra

Graph Neural Networks (GNNs) have become essential in high-stakes domains such as drug discovery, yet their black-box nature remains a significant barrier to trustworthiness. While self-explainable GNNs attempt to bridge this gap, they…

Machine Learning · Computer Science 2026-02-25 Chuqin Geng , Li Zhang , Haolin Ye , Ziyu Zhao , Yuhe Jiang , Tara Saba , Xinyu Wang , Xujie Si

The vanilla Graph Convolutional Network (GCN) uses a low-pass filter to extract low-frequency signals from graph topology, which may lead to the over-smoothing problem when GCN goes deep. To this end, various methods have been proposed to…

Machine Learning · Computer Science 2024-02-13 Chen Huang , Haoyang Li , Yifan Zhang , Wenqiang Lei , Jiancheng Lv

Mesh-based graph neural networks (GNNs) have become effective surrogates for PDE simulations, yet their deep message passing incurs high cost and over-smoothing on large, long-range meshes; hierarchical GNNs shorten propagation paths but…

Machine Learning · Computer Science 2025-09-16 Bo Lei , Victor M. Castillo , Yeping Hu

Graph Neural Networks (GNNs) have achieved significant success in addressing node classification tasks. However, the effectiveness of traditional GNNs degrades on heterophilic graphs, where connected nodes often belong to different labels…

Machine Learning · Computer Science 2025-11-11 Asela Hevapathige , Asiri Wijesinghe , Ahad N. Zehmakan

In order to better understand manifold neural networks (MNNs), we introduce Manifold Filter-Combine Networks (MFCNs). The filter-combine framework parallels the popular aggregate-combine paradigm for graph neural networks (GNNs) and…

In recent years, there has been a significant amount of research focused on expanding the expressivity of Graph Neural Networks (GNNs) beyond the Weisfeiler-Lehman (1-WL) framework. While many of these studies have yielded advancements in…

Machine Learning · Computer Science 2024-03-12 Shouheng Li , Dongwoo Kim , Qing Wang

Message passing graph neural networks (GNNs) are known to have their expressiveness upper-bounded by 1-dimensional Weisfeiler-Leman (1-WL) algorithm. To achieve more powerful GNNs, existing attempts either require ad hoc features, or…

Machine Learning · Computer Science 2024-01-24 Meng Liu , Haiyang Yu , Shuiwang Ji