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Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging
[Image: see text] Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional—step-restricted second-order truncated expansion—molecular optimization methods....
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304864/ https://www.ncbi.nlm.nih.gov/pubmed/32374164 http://dx.doi.org/10.1021/acs.jctc.0c00257 |
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author | Raggi, Gerardo Galván, Ignacio Fdez. Ritterhoff, Christian L. Vacher, Morgane Lindh, Roland |
author_facet | Raggi, Gerardo Galván, Ignacio Fdez. Ritterhoff, Christian L. Vacher, Morgane Lindh, Roland |
author_sort | Raggi, Gerardo |
collection | PubMed |
description | [Image: see text] Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional—step-restricted second-order truncated expansion—molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In this paper, we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect, the GEK procedure will be used to mimic the behavior of a conventional second-order scheme but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimizations to facilitate restricted-variance optimizations. A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two: the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, full Baker-TS, and S22 test suites, at the density functional theory and second-order Møller–Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected. |
format | Online Article Text |
id | pubmed-7304864 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-73048642020-06-22 Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging Raggi, Gerardo Galván, Ignacio Fdez. Ritterhoff, Christian L. Vacher, Morgane Lindh, Roland J Chem Theory Comput [Image: see text] Machine learning techniques, specifically gradient-enhanced Kriging (GEK), have been implemented for molecular geometry optimization. GEK-based optimization has many advantages compared to conventional—step-restricted second-order truncated expansion—molecular optimization methods. In particular, the surrogate model given by GEK can have multiple stationary points, will smoothly converge to the exact model as the number of sample points increases, and contains an explicit expression for the expected error of the model function at an arbitrary point. Machine learning is, however, associated with abundance of data, contrary to the situation desired for efficient geometry optimizations. In this paper, we demonstrate how the GEK procedure can be utilized in a fashion such that in the presence of few data points, the surrogate surface will in a robust way guide the optimization to a minimum of a potential energy surface. In this respect, the GEK procedure will be used to mimic the behavior of a conventional second-order scheme but retaining the flexibility of the superior machine learning approach. Moreover, the expected error will be used in the optimizations to facilitate restricted-variance optimizations. A procedure which relates the eigenvalues of the approximate guessed Hessian with the individual characteristic lengths, used in the GEK model, reduces the number of empirical parameters to optimize to two: the value of the trend function and the maximum allowed variance. These parameters are determined using the extended Baker (e-Baker) and part of the Baker transition-state (Baker-TS) test suites as a training set. The so-created optimization procedure is tested using the e-Baker, full Baker-TS, and S22 test suites, at the density functional theory and second-order Møller–Plesset levels of approximation. The results show that the new method is generally of similar or better performance than a state-of-the-art conventional method, even for cases where no significant improvement was expected. American Chemical Society 2020-05-06 2020-06-09 /pmc/articles/PMC7304864/ /pubmed/32374164 http://dx.doi.org/10.1021/acs.jctc.0c00257 Text en Copyright © 2020 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Raggi, Gerardo Galván, Ignacio Fdez. Ritterhoff, Christian L. Vacher, Morgane Lindh, Roland Restricted-Variance Molecular Geometry Optimization Based on Gradient-Enhanced Kriging |
title | Restricted-Variance Molecular Geometry Optimization
Based on Gradient-Enhanced Kriging |
title_full | Restricted-Variance Molecular Geometry Optimization
Based on Gradient-Enhanced Kriging |
title_fullStr | Restricted-Variance Molecular Geometry Optimization
Based on Gradient-Enhanced Kriging |
title_full_unstemmed | Restricted-Variance Molecular Geometry Optimization
Based on Gradient-Enhanced Kriging |
title_short | Restricted-Variance Molecular Geometry Optimization
Based on Gradient-Enhanced Kriging |
title_sort | restricted-variance molecular geometry optimization
based on gradient-enhanced kriging |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7304864/ https://www.ncbi.nlm.nih.gov/pubmed/32374164 http://dx.doi.org/10.1021/acs.jctc.0c00257 |
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