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Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs
Having observed that gene expressions have a correlation, the Library of Integrated Network-based Cell-Signature program selects 1000 landmark genes to predict the remaining gene expression value. Further works have improved the prediction result by using deep learning models. However, these models...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9901809/ https://www.ncbi.nlm.nih.gov/pubmed/36745614 http://dx.doi.org/10.1371/journal.pone.0281286 |
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author | Li, Xuanyu Zhang, Xuan He, Wenduo Bu, Deliang Zhang, Sanguo |
author_facet | Li, Xuanyu Zhang, Xuan He, Wenduo Bu, Deliang Zhang, Sanguo |
author_sort | Li, Xuanyu |
collection | PubMed |
description | Having observed that gene expressions have a correlation, the Library of Integrated Network-based Cell-Signature program selects 1000 landmark genes to predict the remaining gene expression value. Further works have improved the prediction result by using deep learning models. However, these models ignore the latent structure of genes, limiting the accuracy of the experimental results. We therefore propose a novel neural network named Neighbour Connection Neural Network(NCNN) to utilize the gene interaction graph information. Comparing to the popular GCN model, our model incorperates the graph information in a better manner. We validate our model under two different settings and show that our model promotes prediction accuracy comparing to the other models. |
format | Online Article Text |
id | pubmed-9901809 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-99018092023-02-07 Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs Li, Xuanyu Zhang, Xuan He, Wenduo Bu, Deliang Zhang, Sanguo PLoS One Research Article Having observed that gene expressions have a correlation, the Library of Integrated Network-based Cell-Signature program selects 1000 landmark genes to predict the remaining gene expression value. Further works have improved the prediction result by using deep learning models. However, these models ignore the latent structure of genes, limiting the accuracy of the experimental results. We therefore propose a novel neural network named Neighbour Connection Neural Network(NCNN) to utilize the gene interaction graph information. Comparing to the popular GCN model, our model incorperates the graph information in a better manner. We validate our model under two different settings and show that our model promotes prediction accuracy comparing to the other models. Public Library of Science 2023-02-06 /pmc/articles/PMC9901809/ /pubmed/36745614 http://dx.doi.org/10.1371/journal.pone.0281286 Text en © 2023 Li et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Li, Xuanyu Zhang, Xuan He, Wenduo Bu, Deliang Zhang, Sanguo Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title | Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title_full | Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title_fullStr | Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title_full_unstemmed | Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title_short | Gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
title_sort | gene expression prediction based on neighbour connection neural network utilizing gene interaction graphs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9901809/ https://www.ncbi.nlm.nih.gov/pubmed/36745614 http://dx.doi.org/10.1371/journal.pone.0281286 |
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