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Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks
Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile beha...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8384857/ https://www.ncbi.nlm.nih.gov/pubmed/34429418 http://dx.doi.org/10.1038/s41467-021-25342-8 |
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author | Schwalbe-Koda, Daniel Tan, Aik Rui Gómez-Bombarelli, Rafael |
author_facet | Schwalbe-Koda, Daniel Tan, Aik Rui Gómez-Bombarelli, Rafael |
author_sort | Schwalbe-Koda, Daniel |
collection | PubMed |
description | Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification methods can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined with an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers, collective variables in molecules, and supramolecular chemistry in zeolite-molecule interactions, and can be extended to any NN potential architecture and materials system. |
format | Online Article Text |
id | pubmed-8384857 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83848572021-09-22 Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks Schwalbe-Koda, Daniel Tan, Aik Rui Gómez-Bombarelli, Rafael Nat Commun Article Neural network (NN) interatomic potentials provide fast prediction of potential energy surfaces, closely matching the accuracy of the electronic structure methods used to produce the training data. However, NN predictions are only reliable within well-learned training domains, and show volatile behavior when extrapolating. Uncertainty quantification methods can flag atomic configurations for which prediction confidence is low, but arriving at such uncertain regions requires expensive sampling of the NN phase space, often using atomistic simulations. Here, we exploit automatic differentiation to drive atomistic systems towards high-likelihood, high-uncertainty configurations without the need for molecular dynamics simulations. By performing adversarial attacks on an uncertainty metric, informative geometries that expand the training domain of NNs are sampled. When combined with an active learning loop, this approach bootstraps and improves NN potentials while decreasing the number of calls to the ground truth method. This efficiency is demonstrated on sampling of kinetic barriers, collective variables in molecules, and supramolecular chemistry in zeolite-molecule interactions, and can be extended to any NN potential architecture and materials system. Nature Publishing Group UK 2021-08-24 /pmc/articles/PMC8384857/ /pubmed/34429418 http://dx.doi.org/10.1038/s41467-021-25342-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Schwalbe-Koda, Daniel Tan, Aik Rui Gómez-Bombarelli, Rafael Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title | Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title_full | Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title_fullStr | Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title_full_unstemmed | Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title_short | Differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
title_sort | differentiable sampling of molecular geometries with uncertainty-based adversarial attacks |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8384857/ https://www.ncbi.nlm.nih.gov/pubmed/34429418 http://dx.doi.org/10.1038/s41467-021-25342-8 |
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