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Machine Learning of Coarse-Grained Models for Organic Molecules and Polymers: Progress, Opportunities, and Challenges
[Image: see text] Machine learning (ML) has emerged as one of the most powerful tools transforming all areas of science and engineering. The nature of molecular dynamics (MD) simulations, complex and time-consuming calculations, makes them particularly suitable for ML research. This review article f...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841771/ https://www.ncbi.nlm.nih.gov/pubmed/33521417 http://dx.doi.org/10.1021/acsomega.0c05321 |
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author | Ye, Huilin Xian, Weikang Li, Ying |
author_facet | Ye, Huilin Xian, Weikang Li, Ying |
author_sort | Ye, Huilin |
collection | PubMed |
description | [Image: see text] Machine learning (ML) has emerged as one of the most powerful tools transforming all areas of science and engineering. The nature of molecular dynamics (MD) simulations, complex and time-consuming calculations, makes them particularly suitable for ML research. This review article focuses on recent advancements in developing efficient and accurate coarse-grained (CG) models using various ML methods, in terms of regulating the coarse-graining process, constructing adequate descriptors/features, generating representative training data sets, and optimization of the loss function. Two classes of the CG models are introduced: bottom-up and top-down CG methods. To illustrate these methods and demonstrate the open methodological questions, we survey several important principles in constructing CG models and how these are incorporated into ML methods and improved with specific learning techniques. Finally, we discuss some key aspects of developing machine-learned CG models with high accuracy and efficiency. Besides, we describe how these aspects are tackled in state-of-the-art methods and which remain to be addressed in the near future. We expect that these machine-learned CG models can address thermodynamic consistent, transferable, and representative issues in classical CG models. |
format | Online Article Text |
id | pubmed-7841771 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-78417712021-01-29 Machine Learning of Coarse-Grained Models for Organic Molecules and Polymers: Progress, Opportunities, and Challenges Ye, Huilin Xian, Weikang Li, Ying ACS Omega [Image: see text] Machine learning (ML) has emerged as one of the most powerful tools transforming all areas of science and engineering. The nature of molecular dynamics (MD) simulations, complex and time-consuming calculations, makes them particularly suitable for ML research. This review article focuses on recent advancements in developing efficient and accurate coarse-grained (CG) models using various ML methods, in terms of regulating the coarse-graining process, constructing adequate descriptors/features, generating representative training data sets, and optimization of the loss function. Two classes of the CG models are introduced: bottom-up and top-down CG methods. To illustrate these methods and demonstrate the open methodological questions, we survey several important principles in constructing CG models and how these are incorporated into ML methods and improved with specific learning techniques. Finally, we discuss some key aspects of developing machine-learned CG models with high accuracy and efficiency. Besides, we describe how these aspects are tackled in state-of-the-art methods and which remain to be addressed in the near future. We expect that these machine-learned CG models can address thermodynamic consistent, transferable, and representative issues in classical CG models. American Chemical Society 2021-01-11 /pmc/articles/PMC7841771/ /pubmed/33521417 http://dx.doi.org/10.1021/acsomega.0c05321 Text en © 2021 The Authors. Published by American Chemical Society This is an open access article published under a Creative Commons Non-Commercial No Derivative Works (CC-BY-NC-ND) Attribution License (http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html) , which permits copying and redistribution of the article, and creation of adaptations, all for non-commercial purposes. |
spellingShingle | Ye, Huilin Xian, Weikang Li, Ying Machine Learning of Coarse-Grained Models for Organic Molecules and Polymers: Progress, Opportunities, and Challenges |
title | Machine Learning of Coarse-Grained Models for Organic
Molecules and Polymers: Progress, Opportunities, and Challenges |
title_full | Machine Learning of Coarse-Grained Models for Organic
Molecules and Polymers: Progress, Opportunities, and Challenges |
title_fullStr | Machine Learning of Coarse-Grained Models for Organic
Molecules and Polymers: Progress, Opportunities, and Challenges |
title_full_unstemmed | Machine Learning of Coarse-Grained Models for Organic
Molecules and Polymers: Progress, Opportunities, and Challenges |
title_short | Machine Learning of Coarse-Grained Models for Organic
Molecules and Polymers: Progress, Opportunities, and Challenges |
title_sort | machine learning of coarse-grained models for organic
molecules and polymers: progress, opportunities, and challenges |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841771/ https://www.ncbi.nlm.nih.gov/pubmed/33521417 http://dx.doi.org/10.1021/acsomega.0c05321 |
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