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Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit

Predicting novel uses for drugs using their chemical, pharmacological, and indication information contributes to minimizing costs and development periods. Most previous prediction methods focused on integrating the similarity and association information of drugs and diseases. However, they tended to...

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Autores principales: Xuan, Ping, Zhao, Lianfeng, Zhang, Tiangang, Ye, Yilin, Zhang, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696443/
https://www.ncbi.nlm.nih.gov/pubmed/31349692
http://dx.doi.org/10.3390/molecules24152712
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author Xuan, Ping
Zhao, Lianfeng
Zhang, Tiangang
Ye, Yilin
Zhang, Yan
author_facet Xuan, Ping
Zhao, Lianfeng
Zhang, Tiangang
Ye, Yilin
Zhang, Yan
author_sort Xuan, Ping
collection PubMed
description Predicting novel uses for drugs using their chemical, pharmacological, and indication information contributes to minimizing costs and development periods. Most previous prediction methods focused on integrating the similarity and association information of drugs and diseases. However, they tended to construct shallow prediction models to predict drug-associated diseases, which make deeply integrating the information difficult. Further, path information between drugs and diseases is important auxiliary information for association prediction, while it is not deeply integrated. We present a deep learning-based method, CGARDP, for predicting drug-related candidate disease indications. CGARDP establishes a feature matrix by exploiting a variety of biological premises related to drugs and diseases. A novel model based on convolutional neural network (CNN) and gated recurrent unit (GRU) is constructed to learn the local and path representations for a drug-disease pair. The CNN-based framework on the left of the model learns the local representation of the drug-disease pair from their feature matrix. As the different paths have discriminative contributions to the drug-disease association prediction, we construct an attention mechanism at the path level to learn the informative paths. In the right part, a GRU-based framework learns the path representation based on path information between the drug and the disease. Cross-validation results indicate that CGARDP performs better than several state-of-the-art methods. Further, CGARDP retrieves more real drug-disease associations in the top part of the prediction result that are of concern to biologists. Case studies on five drugs demonstrate that CGARDP can discover potential drug-related disease indications.
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spelling pubmed-66964432019-09-05 Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit Xuan, Ping Zhao, Lianfeng Zhang, Tiangang Ye, Yilin Zhang, Yan Molecules Article Predicting novel uses for drugs using their chemical, pharmacological, and indication information contributes to minimizing costs and development periods. Most previous prediction methods focused on integrating the similarity and association information of drugs and diseases. However, they tended to construct shallow prediction models to predict drug-associated diseases, which make deeply integrating the information difficult. Further, path information between drugs and diseases is important auxiliary information for association prediction, while it is not deeply integrated. We present a deep learning-based method, CGARDP, for predicting drug-related candidate disease indications. CGARDP establishes a feature matrix by exploiting a variety of biological premises related to drugs and diseases. A novel model based on convolutional neural network (CNN) and gated recurrent unit (GRU) is constructed to learn the local and path representations for a drug-disease pair. The CNN-based framework on the left of the model learns the local representation of the drug-disease pair from their feature matrix. As the different paths have discriminative contributions to the drug-disease association prediction, we construct an attention mechanism at the path level to learn the informative paths. In the right part, a GRU-based framework learns the path representation based on path information between the drug and the disease. Cross-validation results indicate that CGARDP performs better than several state-of-the-art methods. Further, CGARDP retrieves more real drug-disease associations in the top part of the prediction result that are of concern to biologists. Case studies on five drugs demonstrate that CGARDP can discover potential drug-related disease indications. MDPI 2019-07-25 /pmc/articles/PMC6696443/ /pubmed/31349692 http://dx.doi.org/10.3390/molecules24152712 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Xuan, Ping
Zhao, Lianfeng
Zhang, Tiangang
Ye, Yilin
Zhang, Yan
Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title_full Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title_fullStr Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title_full_unstemmed Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title_short Inferring Drug-Related Diseases Based on Convolutional Neural Network and Gated Recurrent Unit
title_sort inferring drug-related diseases based on convolutional neural network and gated recurrent unit
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696443/
https://www.ncbi.nlm.nih.gov/pubmed/31349692
http://dx.doi.org/10.3390/molecules24152712
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