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Graph Neural Networks (GNNs) are key tools for graph representation learning, demonstrating strong results across diverse prediction tasks. In this paper, we present Convexified Message-Passing Graph Neural Networks (CGNNs), a novel and…

Machine Learning · Computer Science 2026-01-27 Saar Cohen , Noa Agmon , Uri Shaham

Deploying graph neural networks (GNNs) on whole-graph classification or regression tasks is known to be challenging: it often requires computing node features that are mindful of both local interactions in their neighbourhood and the global…

Machine Learning · Computer Science 2022-12-22 Andreea Deac , Marc Lackenby , Petar Veličković

Message passing neural networks (MPNNs) operate on graphs by exchanging information between neigbouring nodes. MPNNs have been successfully applied to various node-, edge-, and graph-level tasks in areas like molecular science, computer…

Machine Learning · Computer Science 2025-11-05 Lisi Qarkaxhija , Anatol E. Wegner , Ingo Scholtes

Message-passing has proved to be an effective way to design graph neural networks, as it is able to leverage both permutation equivariance and an inductive bias towards learning local structures in order to achieve good generalization.…

Machine Learning · Computer Science 2020-10-26 Clement Vignac , Andreas Loukas , Pascal Frossard

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various…

Machine Learning · Computer Science 2024-06-25 Zinan Zheng , Yang Liu , Jia Li , Jianhua Yao , Yu Rong

By conceiving physical systems as 3D many-body point clouds, geometric graph neural networks (GNNs), such as SE(3)/E(3) equivalent GNNs, have showcased promising performance. In particular, their effective message-passing mechanics make…

Machine Learning · Computer Science 2024-01-30 Weitao Du , Shengchao Liu , Xuecang Zhang

Compared to sequential learning models, graph-based neural networks exhibit excellent ability in capturing global information and have been used for semi-supervised learning tasks. Most Graph Convolutional Networks are designed with the…

Computation and Language · Computer Science 2022-04-12 Kunze Wang , Soyeon Caren Han , Siqu Long , Josiah Poon

Graph neural networks (GNNs) have shown considerable promise in computational chemistry. However, the limited availability of molecular data raises concerns regarding GNNs' ability to effectively capture the fundamental principles of…

Machine Learning · Computer Science 2025-03-12 Junyi An , Chao Qu , Yun-Fei Shi , XinHao Liu , Qianwei Tang , Fenglei Cao , Yuan Qi

Convolution Neural Networks on Graphs are important generalization and extension of classical CNNs. While previous works generally assumed that the graph structures of samples are regular with unified dimensions, in many applications, they…

Machine Learning · Computer Science 2017-08-17 Ruoyu Li , Junzhou Huang

Graph neural networks (GNNs) and message passing neural networks (MPNNs) have been proven to be expressive for subgraph structures in many applications. Some applications in heterogeneous graphs require explicit edge modeling, such as…

Machine Learning · Computer Science 2021-12-17 Xin Liu , Yangqiu Song

Message passing neural networks have become a method of choice for learning on graphs, in particular the prediction of chemical properties and the acceleration of molecular dynamics studies. While they readily scale to large training data…

Machine Learning · Computer Science 2021-06-08 Kristof T. Schütt , Oliver T. Unke , Michael Gastegger

Many scientific problems require to process data in the form of geometric graphs. Unlike generic graph data, geometric graphs exhibit symmetries of translations, rotations, and/or reflections. Researchers have leveraged such inductive bias…

Machine Learning · Computer Science 2022-02-23 Jiaqi Han , Yu Rong , Tingyang Xu , Wenbing Huang

Graph Neural Networks (GNNs) have achieved remarkable success across diverse applications, yet they remain limited by oversmoothing and poor performance on heterophilic graphs. To address these challenges, we introduce a novel framework…

Machine Learning · Computer Science 2025-11-19 Cristina López Amado , Tassilo Schwarz , Yu Tian , Renaud Lambiotte

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However,…

Machine Learning · Computer Science 2023-02-16 Peihao Wang , Shenghao Yang , Yunyu Liu , Zhangyang Wang , Pan Li

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in…

Machine Learning · Statistics 2024-01-31 Ilyes Batatia , Lars L. Schaaf , Huajie Chen , Gábor Csányi , Christoph Ortner , Felix A. Faber

We propose Embedding Propagation (EP), an unsupervised learning framework for graph-structured data. EP learns vector representations of graphs by passing two types of messages between neighboring nodes. Forward messages consist of label…

Machine Learning · Computer Science 2017-10-10 Alberto Garcia-Duran , Mathias Niepert

Message-passing graph neural networks (MPGNNs) dominate modern graph learning. Typical efforts enhance MPGNN's expressive power by enriching the adjacency-based aggregation. In contrast, we introduce an efficient aggregation over walk…

Machine Learning · Computer Science 2025-09-29 Marek Černý

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Machine Learning · Computer Science 2022-03-03 Tuan Le , Frank Noé , Djork-Arné Clevert

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of…

Machine Learning · Computer Science 2025-06-02 Guy Bar-Shalom , Yam Eitan , Fabrizio Frasca , Haggai Maron

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already…

Machine Learning · Computer Science 2017-06-14 Justin Gilmer , Samuel S. Schoenholz , Patrick F. Riley , Oriol Vinyals , George E. Dahl