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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

Recent progress in Graph Neural Networks (GNNs) has greatly enhanced the ability to model complex molecular structures for predicting properties. Nevertheless, molecular data encompasses more than just graph structures, including textual…

Machine Learning · Computer Science 2024-06-04 Junjie Xu , Zongyu Wu , Minhua Lin , Xiang Zhang , Suhang Wang

We propose and study Hierarchical Ego Graph Neural Networks (HEGNNs), an expressive extension of graph neural networks (GNNs) with hierarchical node individualization, inspired by the Individualization-Refinement paradigm for isomorphism…

Machine Learning · Computer Science 2026-01-26 Arie Soeteman , Balder ten Cate

Graph Neural Networks (GNNs) have become the standard approach for learning and reasoning over relational data, leveraging the message-passing mechanism that iteratively propagates node embeddings through graph structures. While GNNs have…

Machine Learning · Computer Science 2025-01-14 Xiaoyu Li , Yingyu Liang , Zhenmei Shi , Zhao Song , Wei Wang , Jiahao Zhang

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by additionally making use of graph structure based on the relational inductive bias (edge bias), rather than treating the nodes as collections of independent and identically…

Machine Learning · Computer Science 2023-11-07 Sitao Luan , Chenqing Hua , Qincheng Lu , Jiaqi Zhu , Xiao-Wen Chang , Doina Precup

Graph neural networks (GNNs) have achieved tremendous success in graph mining. However, the inability of GNNs to model substructures in graphs remains a significant drawback. Specifically, message-passing GNNs (MPGNNs), as the prevailing…

Machine Learning · Computer Science 2021-04-08 Qingqing Long , Yilun Jin , Yi Wu , Guojie Song

Neural networks efficiently encode learned information within their parameters. Consequently, many tasks can be unified by treating neural networks themselves as input data. When doing so, recent studies demonstrated the importance of…

Machine Learning · Computer Science 2024-01-02 Derek Lim , Haggai Maron , Marc T. Law , Jonathan Lorraine , James Lucas

Hypergraph, an expressive structure with flexibility to model the higher-order correlations among entities, has recently attracted increasing attention from various research domains. Despite the success of Graph Neural Networks (GNNs) for…

Machine Learning · Computer Science 2021-05-04 Jing Huang , Jie Yang

Graph neural networks (GNNs) rely on graph convolutions to extract local features from network data. These graph convolutions combine information from adjacent nodes using coefficients that are shared across all nodes. Since these…

Machine Learning · Computer Science 2020-10-22 Luana Ruiz , Luiz F. O. Chamon , Alejandro Ribeiro

In recent years, graph neural networks (GNNs) have emerged as a promising tool for solving machine learning problems on graphs. Most GNNs are members of the family of message passing neural networks (MPNNs). There is a close connection…

Machine Learning · Computer Science 2023-03-01 Giannis Nikolentzos , Michail Chatzianastasis , Michalis Vazirgiannis

The expressive power of graph neural networks is usually measured by comparing how many pairs of graphs or nodes an architecture can possibly distinguish as non-isomorphic to those distinguishable by the $k$-dimensional Weisfeiler-Leman…

Machine Learning · Computer Science 2024-04-02 Arjun Subramonian , Adina Williams , Maximilian Nickel , Yizhou Sun , Levent Sagun

Graph Neural Networks (GNNs) have emerged as a promising approach for ``learning to branch'' in Mixed-Integer Linear Programming (MILP). While standard Message-Passing GNNs (MPNNs) are efficient, they theoretically lack the expressive power…

Machine Learning · Computer Science 2025-12-11 Junru Zhou , Yicheng Wang , Pan Li

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of…

Information Retrieval · Computer Science 2023-09-19 Xuheng Cai , Lianghao Xia , Xubin Ren , Chao Huang

Robustness in complex systems is of significant engineering and economic importance. However, conventional attack-based a posteriori robustness assessments incur prohibitive computational overhead. Recently, deep learning methods, such as…

Machine Learning · Computer Science 2025-12-29 Chengyu Tian , Wenbin Pei

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

Current GNN architectures use a vertex neighborhood aggregation scheme, which limits their discriminative power to that of the 1-dimensional Weisfeiler-Lehman (WL) graph isomorphism test. Here, we propose a novel graph convolution operator…

Machine Learning · Computer Science 2020-09-22 Clemens Damke , Vitalik Melnikov , Eyke Hüllermeier

Graph Neural Networks (GNNs) excel in handling graph-structured data but often underperform in link prediction tasks compared to classical methods, mainly due to the limitations of the commonly used message-passing principle. Notably, their…

Machine Learning · Computer Science 2025-02-18 Niloofar Azizi , Nils Kriege , Horst Bischof

We define a generic class of functions that captures most conceivable aggregations for Message-Passing Graph Neural Networks (MP-GNNs), and prove that any MP-GNN model with such aggregations induces only a polynomial number of equivalence…

Machine Learning · Computer Science 2026-03-24 Eran Rosenbluth

Subgraph representation learning based on Graph Neural Network (GNN) has exhibited broad applications in scientific advancements, such as predictions of molecular structure-property relationships and collective cellular function. In…

Machine Learning · Computer Science 2022-10-17 Yili Shen , Xiao Liu , Cheng-Wei Ju , Jiaxu Yan , Jun Yi , Zhou Lin , Hui Guan

Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means…

Machine Learning · Computer Science 2021-02-08 Jiaxuan You , Jonathan Gomes-Selman , Rex Ying , Jure Leskovec