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A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach

DNA (Deoxyribonucleic Acid) N4-methylcytosine (4mC), a kind of epigenetic modification of DNA, is important for modifying gene functions, such as protein interactions, conformation, and stability in DNA, as well as for the control of gene expression throughout cell development and genomic imprinting...

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Autores principales: Halder, Rajib Kumar, Uddin, Mohammed Nasir, Uddin, Md. Ashraf, Aryal, Sunil, Islam, Md. Aminul, Hossain, Fahima, Jahan, Nusrat, Khraisat, Ansam, Alazab, Ammar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048346/
https://www.ncbi.nlm.nih.gov/pubmed/36980853
http://dx.doi.org/10.3390/genes14030582
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author Halder, Rajib Kumar
Uddin, Mohammed Nasir
Uddin, Md. Ashraf
Aryal, Sunil
Islam, Md. Aminul
Hossain, Fahima
Jahan, Nusrat
Khraisat, Ansam
Alazab, Ammar
author_facet Halder, Rajib Kumar
Uddin, Mohammed Nasir
Uddin, Md. Ashraf
Aryal, Sunil
Islam, Md. Aminul
Hossain, Fahima
Jahan, Nusrat
Khraisat, Ansam
Alazab, Ammar
author_sort Halder, Rajib Kumar
collection PubMed
description DNA (Deoxyribonucleic Acid) N4-methylcytosine (4mC), a kind of epigenetic modification of DNA, is important for modifying gene functions, such as protein interactions, conformation, and stability in DNA, as well as for the control of gene expression throughout cell development and genomic imprinting. This simply plays a crucial role in the restriction–modification system. To further understand the function and regulation mechanism of 4mC, it is essential to precisely locate the 4mC site and detect its chromosomal distribution. This research aims to design an efficient and high-throughput discriminative intelligent computational system using the natural language processing method “word2vec” and a multi-configured 1D convolution neural network (1D CNN) to predict 4mC sites. In this article, we propose a grid search-based multi-layer dynamic ensemble system (GS-MLDS) that can enhance existing knowledge of each level. Each layer uses a grid search-based weight searching approach to find the optimal accuracy while minimizing computation time and additional layers. We have used eight publicly available benchmark datasets collected from different sources to test the proposed model’s efficiency. Accuracy results in test operations were obtained as follows: 0.978, 0.954, 0.944, 0.961, 0.950, 0.973, 0.948, 0.952, 0.961, and 0.980. The proposed model has also been compared to 16 distinct models, indicating that it can accurately predict 4mC.
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spelling pubmed-100483462023-03-29 A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach Halder, Rajib Kumar Uddin, Mohammed Nasir Uddin, Md. Ashraf Aryal, Sunil Islam, Md. Aminul Hossain, Fahima Jahan, Nusrat Khraisat, Ansam Alazab, Ammar Genes (Basel) Article DNA (Deoxyribonucleic Acid) N4-methylcytosine (4mC), a kind of epigenetic modification of DNA, is important for modifying gene functions, such as protein interactions, conformation, and stability in DNA, as well as for the control of gene expression throughout cell development and genomic imprinting. This simply plays a crucial role in the restriction–modification system. To further understand the function and regulation mechanism of 4mC, it is essential to precisely locate the 4mC site and detect its chromosomal distribution. This research aims to design an efficient and high-throughput discriminative intelligent computational system using the natural language processing method “word2vec” and a multi-configured 1D convolution neural network (1D CNN) to predict 4mC sites. In this article, we propose a grid search-based multi-layer dynamic ensemble system (GS-MLDS) that can enhance existing knowledge of each level. Each layer uses a grid search-based weight searching approach to find the optimal accuracy while minimizing computation time and additional layers. We have used eight publicly available benchmark datasets collected from different sources to test the proposed model’s efficiency. Accuracy results in test operations were obtained as follows: 0.978, 0.954, 0.944, 0.961, 0.950, 0.973, 0.948, 0.952, 0.961, and 0.980. The proposed model has also been compared to 16 distinct models, indicating that it can accurately predict 4mC. MDPI 2023-02-25 /pmc/articles/PMC10048346/ /pubmed/36980853 http://dx.doi.org/10.3390/genes14030582 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Halder, Rajib Kumar
Uddin, Mohammed Nasir
Uddin, Md. Ashraf
Aryal, Sunil
Islam, Md. Aminul
Hossain, Fahima
Jahan, Nusrat
Khraisat, Ansam
Alazab, Ammar
A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title_full A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title_fullStr A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title_full_unstemmed A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title_short A Grid Search-Based Multilayer Dynamic Ensemble System to Identify DNA N4—Methylcytosine Using Deep Learning Approach
title_sort grid search-based multilayer dynamic ensemble system to identify dna n4—methylcytosine using deep learning approach
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10048346/
https://www.ncbi.nlm.nih.gov/pubmed/36980853
http://dx.doi.org/10.3390/genes14030582
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