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Given a graph $G$, the graph $[G]$ obtained by adding, for each pair of vertices of $G$, a unique vertex adjacent to both vertices is called the binding graph of $G$. In this work, we show that the class of binding graphs is…

Combinatorics · Mathematics 2024-08-27 Rui Xue

This work generalizes graph neural networks (GNNs) beyond those based on the Weisfeiler-Lehman (WL) algorithm, graph Laplacians, and diffusions. Our approach, denoted Relational Pooling (RP), draws from the theory of finite partial…

Machine Learning · Computer Science 2019-05-16 Ryan L. Murphy , Balasubramaniam Srinivasan , Vinayak Rao , Bruno Ribeiro

Applying machine learning to molecules is challenging because of their natural representation as graphs rather than vectors.Several architectures have been recently proposed for deep learning from molecular graphs, but they suffer from…

Machine Learning · Statistics 2020-09-15 Jaak Simm , Adam Arany , Edward De Brouwer , Yves Moreau

Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs)…

Social and Information Networks · Computer Science 2020-02-06 Xiaoxiao Li , Joao Saude

Graph neural networks (GNNs) have emerged as powerful models for learning representations of graph data showing state of the art results in various tasks. Nevertheless, the superiority of these methods is usually supported by either…

Machine Learning · Computer Science 2024-11-22 Tianqi Zhao , Megha Khosla

Subgraph counting is a fundamental task for analyzing structural patterns in graph-structured data, with important applications in domains such as computational biology and social network analysis, where recurring motifs reveal functional…

Machine Learning · Computer Science 2025-12-02 Shubhajit Roy , Shrutimoy Das , Binita Maity , Anant Kumar , Anirban Dasgupta

Graph Neural Networks (GNNs) are recently proposed neural network structures for the processing of graph-structured data. Due to their employed neighbor aggregation strategy, existing GNNs focus on capturing node-level information and…

Machine Learning · Computer Science 2022-01-05 Xing Ai , Chengyu Sun , Zhihong Zhang , Edwin R Hancock

Graph isomorphism, a classical algorithmic problem, determines whether two input graphs are structurally identical or not. Interestingly, it is one of the few problems that is not yet known to belong to either the P or NP-complete…

Data Structures and Algorithms · Computer Science 2024-10-01 Sourav Dutta , Arnab Bhattacharya

Graph Neural Networks (GNNs) have emerged as a powerful category of learning architecture for handling graph-structured data. However, existing GNNs typically ignore crucial structural characteristics in node-induced subgraphs, which thus…

Machine Learning · Computer Science 2023-06-13 Kaixuan Chen , Shunyu Liu , Tongtian Zhu , Tongya Zheng , Haofei Zhang , Zunlei Feng , Jingwen Ye , Mingli Song

Rethink convolution-based graph neural networks (GNN) -- they characteristically suffer from limited expressiveness, over-smoothing, and over-squashing, and require specialized sparse kernels for efficient computation. Here, we design a…

Machine Learning · Computer Science 2024-10-01 Yuanqing Wang , Kyunghyun Cho

The Weisfeiler-Lehman (WL) test is a classical procedure for graph isomorphism testing. The WL test has also been widely used both for designing graph kernels and for analyzing graph neural networks. In this paper, we propose the…

Machine Learning · Computer Science 2022-02-08 Samantha Chen , Sunhyuk Lim , Facundo Mémoli , Zhengchao Wan , Yusu Wang

Most Graph Neural Networks (GNNs) propagate messages by treating node embeddings as holistic feature vectors, implicitly assuming uniform relevance across feature dimensions. This limits their ability to selectively transmit informative…

Machine Learning · Computer Science 2025-12-24 Longlong Li , Mengyang Zhao , Guanghui Wang , Cunquan Qu

Representational limits of message-passing graph neural networks (MP-GNNs), e.g., in terms of the Weisfeiler-Leman (WL) test for isomorphism, are well understood. Augmenting these graph models with topological features via persistent…

Machine Learning · Computer Science 2023-11-13 Johanna Immonen , Amauri H. Souza , Vikas Garg

Graph Neural Networks (GNNs) have achieved remarkable performance in modeling graphs for various applications. However, most existing GNNs assume the graphs exhibit strong homophily in node labels, i.e., nodes with similar labels are…

Machine Learning · Computer Science 2023-02-20 Enyan Dai , Shijie Zhou , Zhimeng Guo , Suhang Wang

Aligning users across networks using graph representation learning has been found effective where the alignment is accomplished in a low-dimensional embedding space. Yet, achieving highly precise alignment is still challenging, especially…

Social and Information Networks · Computer Science 2023-01-02 Li Liu , Penggang Chen , Xin Li , William K. Cheung , Youmin Zhang , Qun Liu , Guoyin Wang

The Weisfeiler-Leman (WL) dimension of a graph is a measure for the inherent descriptive complexity of the graph. While originally derived from a combinatorial graph isomorphism test called the Weisfeiler-Leman algorithm, the WL dimension…

Discrete Mathematics · Computer Science 2019-04-16 Martin Grohe , Sandra Kiefer

The Weisfeiler--Lehman (WL) test and its simplicial extension (SWL) characterize the combinatorial expressivity of message passing networks, but they are blind to geometry, i.e., meshes with identical connectivity but different embeddings…

Machine Learning · Computer Science 2026-05-08 Elena Xinyi Wang , Bastian Rieck

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

Despite significant advances in Graph Neural Networks (GNNs), their limited expressivity remains a fundamental challenge. Research on GNN expressivity has produced many expressive architectures, leading to architecture hierarchies with…

Machine Learning · Computer Science 2025-10-06 Yam Eitan , Moshe Eliasof , Yoav Gelberg , Fabrizio Frasca , Guy Bar-Shalom , Haggai Maron

Graph Neural Networks (GNNs) require a relatively large number of labeled nodes and a reliable/uncorrupted graph connectivity structure in order to obtain good performance on the semi-supervised node classification task. The performance of…

Machine Learning · Computer Science 2021-07-01 Abdullah Alchihabi , Yuhong Guo