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While Graph Neural Networks (GNNs) are powerful models for learning representations on graphs, most state-of-the-art models do not have significant accuracy gain beyond two to three layers. Deep GNNs fundamentally need to address: 1).…

Recent works have investigated the role of graph bottlenecks in preventing long-range information propagation in message-passing graph neural networks, causing the so-called `over-squashing' phenomenon. As a remedy, graph rewiring…

Machine Learning · Computer Science 2022-12-14 Domenico Tortorella , Alessio Micheli

As a randomized learner model, SCNs are remarkable that the random weights and biases are assigned employing a supervisory mechanism to ensure universal approximation and fast learning. However, the randomness makes SCNs more likely to…

Machine Learning · Computer Science 2022-05-27 Wei Dai , Chuanfeng Ning , Shiyu Pei , Song Zhu , Xuesong Wang

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this…

Machine Learning · Computer Science 2024-09-27 Yusong Wang , Chaoran Cheng , Shaoning Li , Yuxuan Ren , Bin Shao , Ge Liu , Pheng-Ann Heng , Nanning Zheng

Graph neural networks (GNNs) have exhibited state-of-the-art performance across wide-range of domains such as recommender systems, material design, and drug repurposing. Yet message-passing GNNs suffer from over-squashing -- exponential…

Machine Learning · Computer Science 2025-08-14 Danial Saber , Amirali Salehi-Abari

Most state-of-the-art Graph Neural Networks (GNNs) can be defined as a form of graph convolution which can be realized by message passing between direct neighbors or beyond. To scale such GNNs to large graphs, various neighbor-, layer-, or…

Machine Learning · Computer Science 2021-10-28 Mucong Ding , Kezhi Kong , Jingling Li , Chen Zhu , John P Dickerson , Furong Huang , Tom Goldstein

Message Passing Neural Networks (MPNNs) are a class of Graph Neural Networks (GNNs) that propagate information across the graph via local neighborhoods. The scheme gives rise to two key challenges: over-smoothing and over-squashing. While…

Machine Learning · Computer Science 2025-05-30 Jasraj Singh , Keyue Jiang , Brooks Paige , Laura Toni

Message passing is the dominant paradigm in Graph Neural Networks (GNNs). The efficiency of message passing, however, can be limited by the topology of the graph. This happens when information is lost during propagation due to being…

Machine Learning · Computer Science 2024-11-05 Floriano Tori , Vincent Holst , Vincent Ginis

Graph Neural Networks (GNNs) perform computations on graphs by routing the signal between graph regions using a graph shift operator or a message passing scheme. Often, the propagation of the signal leads to a loss of information, where the…

Machine Learning · Computer Science 2026-05-14 Eden Nagar , Ya-Wei Eileen Lin , Ron Levie

Graph Neural Networks (GNNs) struggle to balance heterophily and homophily in representation learning, a challenge further amplified in self-supervised settings. We propose H$^3$GNNs, an end-to-end self-supervised learning framework that…

Machine Learning · Computer Science 2025-04-17 Rui Xue , Tianfu Wu

Most graph neural networks (GNNs) are prone to the phenomenon of over-squashing in which node features become insensitive to information from distant nodes in the graph. Recent works have shown that the topology of the graph has the…

Machine Learning · Computer Science 2023-11-30 Julia Balla

Graph Neural Networks (GNNs) are the subject of intense focus by the machine learning community for problems involving relational reasoning. GNNs can be broadly divided into spatial and spectral approaches. Spatial approaches use a form of…

Machine Learning · Statistics 2021-01-05 Kimberly Stachenfeld , Jonathan Godwin , Peter Battaglia

Graph Neural Networks learn on graph-structured data by iteratively aggregating local neighborhood information. While this local message passing paradigm imparts a powerful inductive bias and exploits graph sparsity, it also yields three…

Machine Learning · Computer Science 2025-11-07 Ryien Hosseini , Filippo Simini , Venkatram Vishwanath , Rebecca Willett , Henry Hoffmann

Graph neural networks (GNNs) have received tremendous attention due to their superiority in learning node representations. These models rely on message passing and feature transformation functions to encode the structural and feature…

Machine Learning · Computer Science 2021-12-02 Kai Guo , Kaixiong Zhou , Xia Hu , Yu Li , Yi Chang , Xin Wang

Graph neural networks (GNNs) are a powerful solution for various structure learning applications due to their strong representation capabilities for graph data. However, traditional GNNs, relying on message-passing mechanisms that gather…

Machine Learning · Computer Science 2024-03-19 Wei Duan , Jie Lu , Yu Guang Wang , Junyu Xuan

Long-range interactions are essential for the correct description of complex systems in many scientific fields. The price to pay for including them in the calculations, however, is a dramatic increase in the overall computational costs.…

In recent years, Graph Neural Networks (GNNs) have been popular in the graph classification task. Currently, shallow GNNs are more common due to the well-known over-smoothing problem facing deeper GNNs. However, they are sub-optimal without…

Machine Learning · Computer Science 2023-02-20 Lanning Wei , Zhiqiang He , Huan Zhao , Quanming Yao

Graph neural networks (GNNs) are emerging machine learning models on graphs. Permutation-equivariance and proximity-awareness are two important properties highly desirable for GNNs. Both properties are needed to tackle some challenging…

Machine Learning · Computer Science 2022-02-23 Ziwei Zhang , Chenhao Niu , Peng Cui , Jian Pei , Bo Zhang , Wenwu Zhu

While Graph Neural Networks (GNNs) have been successfully leveraged for learning on graph-structured data across domains, several potential pitfalls have been described recently. Those include the inability to accurately leverage…

Machine Learning · Computer Science 2024-03-21 Lukas Fesser , Melanie Weber

Message Passing Neural Networks (MPNNs) are a common type of Graph Neural Network (GNN), in which each node's representation is computed recursively by aggregating representations (messages) from its immediate neighbors akin to a…

Machine Learning · Computer Science 2022-04-22 Lingxiao Zhao , Wei Jin , Leman Akoglu , Neil Shah