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Co-embedding of edges and nodes with deep graph convolutional neural networks
Graph neural networks (GNNs) have significant advantages in dealing with non-Euclidean data and have been widely used in various fields. However, most of the existing GNN models face two main challenges: (1) Most GNN models built upon the message-passing framework exhibit a shallow structure, which...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10560674/ https://www.ncbi.nlm.nih.gov/pubmed/37807013 http://dx.doi.org/10.1038/s41598-023-44224-1 |
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author | Zhou, Yuchen Huo, Hongtao Hou, Zhiwen Bu, Lingbin Mao, Jingyi Wang, Yifan Lv, Xiaojun Bu, Fanliang |
author_facet | Zhou, Yuchen Huo, Hongtao Hou, Zhiwen Bu, Lingbin Mao, Jingyi Wang, Yifan Lv, Xiaojun Bu, Fanliang |
author_sort | Zhou, Yuchen |
collection | PubMed |
description | Graph neural networks (GNNs) have significant advantages in dealing with non-Euclidean data and have been widely used in various fields. However, most of the existing GNN models face two main challenges: (1) Most GNN models built upon the message-passing framework exhibit a shallow structure, which hampers their ability to efficiently transmit information between distant nodes. To address this, we aim to propose a novel message-passing framework, enabling the construction of GNN models with deep architectures akin to convolutional neural networks (CNNs), potentially comprising dozens or even hundreds of layers. (2) Existing models often approach the learning of edge and node features as separate tasks. To overcome this limitation, we aspire to develop a deep graph convolutional neural network learning framework capable of simultaneously acquiring edge embeddings and node embeddings. By utilizing the learned multi-dimensional edge feature matrix, we construct multi-channel filters to more effectively capture accurate node features. To address these challenges, we propose the Co-embedding of Edges and Nodes with Deep Graph Convolutional Neural Networks (CEN-DGCNN). In our approach, we propose a novel message-passing framework that can fully integrate and utilize both node features and multi-dimensional edge features. Based on this framework, we develop a deep graph convolutional neural network model that prevents over-smoothing and obtains node non-local structural features and refined high-order node features by extracting long-distance dependencies between nodes and utilizing multi-dimensional edge features. Moreover, we propose a novel graph convolutional layer that can learn node embeddings and multi-dimensional edge embeddings simultaneously. The layer updates multi-dimensional edge embeddings across layers based on node features and an attention mechanism, which enables efficient utilization and fusion of both node and edge features. Additionally, we propose a multi-dimensional edge feature encoding method based on directed edges, and use the resulting multi-dimensional edge feature matrix to construct a multi-channel filter to filter the node information. Lastly, extensive experiments show that CEN-DGCNN outperforms a large number of graph neural network baseline methods, demonstrating the effectiveness of our proposed method. |
format | Online Article Text |
id | pubmed-10560674 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-105606742023-10-10 Co-embedding of edges and nodes with deep graph convolutional neural networks Zhou, Yuchen Huo, Hongtao Hou, Zhiwen Bu, Lingbin Mao, Jingyi Wang, Yifan Lv, Xiaojun Bu, Fanliang Sci Rep Article Graph neural networks (GNNs) have significant advantages in dealing with non-Euclidean data and have been widely used in various fields. However, most of the existing GNN models face two main challenges: (1) Most GNN models built upon the message-passing framework exhibit a shallow structure, which hampers their ability to efficiently transmit information between distant nodes. To address this, we aim to propose a novel message-passing framework, enabling the construction of GNN models with deep architectures akin to convolutional neural networks (CNNs), potentially comprising dozens or even hundreds of layers. (2) Existing models often approach the learning of edge and node features as separate tasks. To overcome this limitation, we aspire to develop a deep graph convolutional neural network learning framework capable of simultaneously acquiring edge embeddings and node embeddings. By utilizing the learned multi-dimensional edge feature matrix, we construct multi-channel filters to more effectively capture accurate node features. To address these challenges, we propose the Co-embedding of Edges and Nodes with Deep Graph Convolutional Neural Networks (CEN-DGCNN). In our approach, we propose a novel message-passing framework that can fully integrate and utilize both node features and multi-dimensional edge features. Based on this framework, we develop a deep graph convolutional neural network model that prevents over-smoothing and obtains node non-local structural features and refined high-order node features by extracting long-distance dependencies between nodes and utilizing multi-dimensional edge features. Moreover, we propose a novel graph convolutional layer that can learn node embeddings and multi-dimensional edge embeddings simultaneously. The layer updates multi-dimensional edge embeddings across layers based on node features and an attention mechanism, which enables efficient utilization and fusion of both node and edge features. Additionally, we propose a multi-dimensional edge feature encoding method based on directed edges, and use the resulting multi-dimensional edge feature matrix to construct a multi-channel filter to filter the node information. Lastly, extensive experiments show that CEN-DGCNN outperforms a large number of graph neural network baseline methods, demonstrating the effectiveness of our proposed method. Nature Publishing Group UK 2023-10-08 /pmc/articles/PMC10560674/ /pubmed/37807013 http://dx.doi.org/10.1038/s41598-023-44224-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Zhou, Yuchen Huo, Hongtao Hou, Zhiwen Bu, Lingbin Mao, Jingyi Wang, Yifan Lv, Xiaojun Bu, Fanliang Co-embedding of edges and nodes with deep graph convolutional neural networks |
title | Co-embedding of edges and nodes with deep graph convolutional neural networks |
title_full | Co-embedding of edges and nodes with deep graph convolutional neural networks |
title_fullStr | Co-embedding of edges and nodes with deep graph convolutional neural networks |
title_full_unstemmed | Co-embedding of edges and nodes with deep graph convolutional neural networks |
title_short | Co-embedding of edges and nodes with deep graph convolutional neural networks |
title_sort | co-embedding of edges and nodes with deep graph convolutional neural networks |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10560674/ https://www.ncbi.nlm.nih.gov/pubmed/37807013 http://dx.doi.org/10.1038/s41598-023-44224-1 |
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