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Predicting DNA-protein binding is an important and classic problem in bioinformatics. Convolutional neural networks have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. However, none of the…

Genomics · Quantitative Biology 2021-06-04 Yuhang Guo , Xiao Luo , Liang Chen , Minghua Deng

Graph Neural Networks (GNNs), particularly Graph Convolutional Neural Networks (GCNNs), have emerged as pivotal instruments in machine learning and signal processing for processing graph-structured data. This paper proposes an analysis…

Machine Learning · Statistics 2024-11-04 Xinjue Wang , Esa Ollila , Sergiy A. Vorobyov

Graph Neural Networks (GNNs) are emerging as powerful tools for nonlinear Model Order Reduction (MOR) of time-dependent parameterized Partial Differential Equations (PDEs). However, existing methodologies struggle to combine geometric…

Machine Learning · Computer Science 2026-01-19 Lorenzo Tomada , Federico Pichi , Gianluigi Rozza

Jumping connections enable Graph Convolutional Networks (GCNs) to overcome over-smoothing, while graph sparsification reduces computational demands by selecting a sub-matrix of the graph adjacency matrix during neighborhood aggregation.…

Machine Learning · Computer Science 2025-07-09 Jiawei Sun , Hongkang Li , Meng Wang

Graph Convolutional Networks (GCNs) have shown very powerful for graph data representation and learning tasks. Existing GCNs usually conduct feature aggregation on a fixed neighborhood graph in which each node computes its representation by…

Computer Vision and Pattern Recognition · Computer Science 2019-11-21 Bo Jiang , Beibei Wang , Jin Tang , Bin Luo

Graph Neural Networks (GNNs) traditionally employ a message-passing mechanism that resembles diffusion over undirected graphs, which often leads to homogenization of node features and reduced discriminative power in tasks such as node…

Machine Learning · Computer Science 2025-03-04 Seong Ho Pahng , Sahand Hormoz

In this work, we aim to classify nodes of unstructured peer-to-peer networks with communication uncertainty, such as users of decentralized social networks. Graph Neural Networks (GNNs) are known to improve the accuracy of simple…

Machine Learning · Computer Science 2022-03-17 Emmanouil Krasanakis , Symeon Papadopoulos , Ioannis Kompatsiaris

We address two fundamental questions about graph neural networks (GNNs). First, we prove that several important graph properties cannot be computed by GNNs that rely entirely on local information. Such GNNs include the standard message…

Machine Learning · Computer Science 2020-02-17 Vikas K. Garg , Stefanie Jegelka , Tommi Jaakkola

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

In view of the huge success of convolution neural networks (CNN) for image classification and object recognition, there have been attempts to generalize the method to general graph-structured data. One major direction is based on spectral…

Machine Learning · Computer Science 2020-03-09 Feng Ji , Jielong Yang , Qiang Zhang , Wee Peng Tay

Graph convolutional networks (GCNs) are a powerful deep learning approach for graph-structured data. Recently, GCNs and subsequent variants have shown superior performance in various application areas on real-world datasets. Despite their…

Machine Learning · Computer Science 2020-07-07 Ming Chen , Zhewei Wei , Zengfeng Huang , Bolin Ding , Yaliang Li

Graph convolutional neural networks (GCNNs) have emerged as powerful tools for analyzing graph-structured data, achieving remarkable success across diverse applications. However, the theoretical understanding of the stability of these…

Machine Learning · Computer Science 2025-10-28 Ning Zhang , Henry Kenlay , Li Zhang , Mihai Cucuringu , Xiaowen Dong

Graph neural networks (GNN) has been demonstrated to be effective in classifying graph structures. To further improve the graph representation learning ability, hierarchical GNN has been explored. It leverages the differentiable pooling to…

Social and Information Networks · Computer Science 2019-12-19 Kaixiong Zhou , Qingquan Song , Xiao Huang , Daochen Zha , Na Zou , Xia Hu

Graphs serve as generic tools to encode the underlying relational structure of data. Often this graph is not given, and so the task of inferring it from nodal observations becomes important. Traditional approaches formulate a convex inverse…

Machine Learning · Computer Science 2024-06-24 Max Wasserman , Gonzalo Mateos

This paper aims at revisiting Graph Convolutional Neural Networks by bridging the gap between spectral and spatial design of graph convolutions. We theoretically demonstrate some equivalence of the graph convolution process regardless it is…

Machine Learning · Computer Science 2020-03-27 Muhammet Balcilar , Guillaume Renton , Pierre Heroux , Benoit Gauzere , Sebastien Adam , Paul Honeine

Graph Neural Networks (GNNs) rely on graph convolutions to exploit meaningful patterns in networked data. Based on matrix multiplications, convolutions incur in high computational costs leading to scalability limitations in practice. To…

Machine Learning · Computer Science 2022-10-28 Juan Cervino , Luana Ruiz , Alejandro Ribeiro

Graph neural networks (GNNs) are a class of neural networks that allow to efficiently perform inference on data that is associated to a graph structure, such as, e.g., citation networks or knowledge graphs. While several variants of GNNs…

Neural and Evolutionary Computing · Computer Science 2018-02-27 Simone Scardapane , Steven Van Vaerenbergh , Danilo Comminiello , Aurelio Uncini

Graph convolutional networks (GCNs) have been successfully applied in node classification tasks of network mining. However, most of these models based on neighborhood aggregation are usually shallow and lack the "graph pooling" mechanism,…

Social and Information Networks · Computer Science 2019-06-11 Fenyu Hu , Yanqiao Zhu , Shu Wu , Liang Wang , Tieniu Tan

Convolutional neural networks (CNNs) have achieved breakthrough performances in a wide range of applications including image classification, semantic segmentation, and object detection. Previous research on characterizing the generalization…

Machine Learning · Statistics 2019-10-04 Shan Lin , Jingwei Zhang

Skeleton-based human action recognition has attracted much attention with the prevalence of accessible depth sensors. Recently, graph convolutional networks (GCNs) have been widely used for this task due to their powerful capability to…

Computer Vision and Pattern Recognition · Computer Science 2021-08-23 Zhen Huang , Xu Shen , Xinmei Tian , Houqiang Li , Jianqiang Huang , Xian-Sheng Hua