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Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Machine Learning · Computer Science 2021-09-21 Vincent Mallet , Carlos G. Oliver , William L. Hamilton

Graph Neural Networks (GNNs) have become a popular approach for various applications, ranging from social network analysis to modeling chemical properties of molecules. While GNNs often show remarkable performance on public datasets, they…

Machine Learning · Computer Science 2022-02-03 Krzysztof Sadowski , Michał Szarmach , Eddie Mattia

Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that…

Machine Learning · Computer Science 2022-05-23 Davide Buffelli , Fabio Vandin

Graph neural networks (GNNs) are commonly divided into message-passing neural networks (MPNNs) and spectral graph neural networks, reflecting two largely separate research traditions in machine learning and signal processing. This paper…

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

Graph Neural Networks (GNNs) have led to state-of-the-art performance on a variety of machine learning tasks such as recommendation, node classification and link prediction. Graph neural network models generate node embeddings by merging…

Machine Learning · Computer Science 2020-11-04 Yunpeng Weng , Xu Chen , Liang Chen , Wei Liu

Graph embedding is an important approach for graph analysis tasks such as node classification and link prediction. The goal of graph embedding is to find a low dimensional representation of graph nodes that preserves the graph information.…

Machine Learning · Computer Science 2019-08-27 Mahsa Ghorbani , Mahdieh Soleymani Baghshah , Hamid R. Rabiee

Graph Neural Networks (GNNs) have become a dominant approach to learning graph representations, primarily because of their message-passing mechanisms. However, GNNs typically adopt a fixed aggregator function such as Mean, Max, or Sum…

Machine Learning · Computer Science 2025-07-29 Xuanting Xie , Bingheng Li , Erlin Pan , Zhao Kang , Wenyu Chen

Two architectures that generalize convolutional neural networks (CNNs) for the processing of signals supported on graphs are introduced. We start with the selection graph neural network (GNN), which replaces linear time invariant filters…

Signal Processing · Electrical Eng. & Systems 2019-01-30 Fernando Gama , Antonio G. Marques , Geert Leus , Alejandro Ribeiro

Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…

Machine Learning · Computer Science 2024-11-26 Hung-Chun Hsu , Bo-Jun Wu , Ming-Yi Hong , Che Lin , Chih-Yu Wang

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

Graph Neural Networks (GNNs) are popular deep learning models designed to process graph-structured data through recursive neighborhood aggregations in the message passing process. When applied to semi-supervised node classification, the…

Machine Learning · Computer Science 2025-01-13 Kevin Mancini , Islem Rekik

Graph Neural Networks (GNNs) have emerged as a dominant paradigm for graph classification. Specifically, most existing GNNs mainly rely on the message passing strategy between neighbor nodes, where the expressivity is limited by the…

Machine Learning · Computer Science 2025-12-12 Lin Du , Lu Bai , Jincheng Li , Lixin Cui , Hangyuan Du , Lichi Zhang , Yuting Chen , Zhao Li

Graph Neural Networks (GNNs) have significant advantages in handling non-Euclidean data and have been widely applied across various areas, thus receiving increasing attention in recent years. The framework of GNN models mainly includes the…

Machine Learning · Computer Science 2025-02-05 Shengda Zhuo , Jiwang Fang , Hongguang Lin , Yin Tang , Min Chen , Changdong Wang , Shuqiang Huang

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the…

Machine Learning · Computer Science 2024-12-03 Junchao Lin , Yuan Wan , Jingwen Xu , Xingchen Qi

In graph neural networks (GNNs), message passing iteratively aggregates nodes' information from their direct neighbors while neglecting the sequential nature of multi-hop node connections. Such sequential node connections e.g., metapaths,…

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive…

Machine Learning · Computer Science 2023-05-25 Francesco Di Giovanni , Lorenzo Giusti , Federico Barbero , Giulia Luise , Pietro Lio' , Michael Bronstein

Graph neural networks (GNNs) are known to be vulnerable to oversmoothing due to their implicit homophily assumption. We mitigate this problem with a novel scheme that regulates the aggregation of messages, modulating the type and extent of…

Machine Learning · Computer Science 2025-12-03 Haishan Wang , Arno Solin , Vikas Garg

We study the convergence of message passing graph neural networks on random graph models to their continuous counterpart as the number of nodes tends to infinity. Until now, this convergence was only known for architectures with aggregation…

Machine Learning · Statistics 2025-02-13 Matthieu Cordonnier , Nicolas Keriven , Nicolas Tremblay , Samuel Vaiter

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