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A deep ensemble model to predict miRNA-disease association

Cumulative evidence from biological experiments has confirmed that microRNAs (miRNAs) are related to many types of human diseases through different biological processes. It is anticipated that precise miRNA-disease association prediction could not only help infer potential disease-related miRNA but...

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Detalles Bibliográficos
Autores principales: Fu, Laiyi, Peng, Qinke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670180/
https://www.ncbi.nlm.nih.gov/pubmed/29101378
http://dx.doi.org/10.1038/s41598-017-15235-6
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author Fu, Laiyi
Peng, Qinke
author_facet Fu, Laiyi
Peng, Qinke
author_sort Fu, Laiyi
collection PubMed
description Cumulative evidence from biological experiments has confirmed that microRNAs (miRNAs) are related to many types of human diseases through different biological processes. It is anticipated that precise miRNA-disease association prediction could not only help infer potential disease-related miRNA but also boost human diagnosis and disease prevention. Considering the limitations of previous computational models, a more effective computational model needs to be implemented to predict miRNA-disease associations. In this work, we first constructed a human miRNA-miRNA similarity network utilizing miRNA-miRNA functional similarity data and heterogeneous miRNA Gaussian interaction profile kernel similarities based on the assumption that similar miRNAs with similar functions tend to be associated with similar diseases, and vice versa. Then, we constructed disease-disease similarity using disease semantic information and heterogeneous disease-related interaction data. We proposed a deep ensemble model called DeepMDA that extracts high-level features from similarity information using stacked autoencoders and then predicts miRNA-disease associations by adopting a 3-layer neural network. In addition to five-fold cross-validation, we also proposed another cross-validation method to evaluate the performance of the model. The results show that the proposed model is superior to previous methods with high robustness.
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spelling pubmed-56701802017-11-15 A deep ensemble model to predict miRNA-disease association Fu, Laiyi Peng, Qinke Sci Rep Article Cumulative evidence from biological experiments has confirmed that microRNAs (miRNAs) are related to many types of human diseases through different biological processes. It is anticipated that precise miRNA-disease association prediction could not only help infer potential disease-related miRNA but also boost human diagnosis and disease prevention. Considering the limitations of previous computational models, a more effective computational model needs to be implemented to predict miRNA-disease associations. In this work, we first constructed a human miRNA-miRNA similarity network utilizing miRNA-miRNA functional similarity data and heterogeneous miRNA Gaussian interaction profile kernel similarities based on the assumption that similar miRNAs with similar functions tend to be associated with similar diseases, and vice versa. Then, we constructed disease-disease similarity using disease semantic information and heterogeneous disease-related interaction data. We proposed a deep ensemble model called DeepMDA that extracts high-level features from similarity information using stacked autoencoders and then predicts miRNA-disease associations by adopting a 3-layer neural network. In addition to five-fold cross-validation, we also proposed another cross-validation method to evaluate the performance of the model. The results show that the proposed model is superior to previous methods with high robustness. Nature Publishing Group UK 2017-11-03 /pmc/articles/PMC5670180/ /pubmed/29101378 http://dx.doi.org/10.1038/s41598-017-15235-6 Text en © The Author(s) 2017 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Fu, Laiyi
Peng, Qinke
A deep ensemble model to predict miRNA-disease association
title A deep ensemble model to predict miRNA-disease association
title_full A deep ensemble model to predict miRNA-disease association
title_fullStr A deep ensemble model to predict miRNA-disease association
title_full_unstemmed A deep ensemble model to predict miRNA-disease association
title_short A deep ensemble model to predict miRNA-disease association
title_sort deep ensemble model to predict mirna-disease association
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5670180/
https://www.ncbi.nlm.nih.gov/pubmed/29101378
http://dx.doi.org/10.1038/s41598-017-15235-6
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