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Transition1x - a dataset for building generalizable reactive machine learning potentials
Machine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. This is primarily because available datasets for training ML models on small molecular systems almost exclusively contain configu...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9789978/ https://www.ncbi.nlm.nih.gov/pubmed/36566281 http://dx.doi.org/10.1038/s41597-022-01870-w |
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author | Schreiner, Mathias Bhowmik, Arghya Vegge, Tejs Busk, Jonas Winther, Ole |
author_facet | Schreiner, Mathias Bhowmik, Arghya Vegge, Tejs Busk, Jonas Winther, Ole |
author_sort | Schreiner, Mathias |
collection | PubMed |
description | Machine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. This is primarily because available datasets for training ML models on small molecular systems almost exclusively contain configurations at or near equilibrium. In this work, we present the dataset Transition1x containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the ωB97x/6–31 G(d) level of theory. The data was generated by running Nudged Elastic Band (NEB) with DFT on 10k organic reactions of various types while saving intermediate calculations. We train equivariant graph message-passing neural network models on Transition1x and cross-validate on the popular ANI1x and QM9 datasets. We show that ML models cannot learn features in transition state regions solely by training on hitherto popular benchmark datasets. Transition1x is a new challenging benchmark that will provide an important step towards developing next-generation ML force fields that also work far away from equilibrium configurations and reactive systems. |
format | Online Article Text |
id | pubmed-9789978 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-97899782022-12-26 Transition1x - a dataset for building generalizable reactive machine learning potentials Schreiner, Mathias Bhowmik, Arghya Vegge, Tejs Busk, Jonas Winther, Ole Sci Data Data Descriptor Machine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. This is primarily because available datasets for training ML models on small molecular systems almost exclusively contain configurations at or near equilibrium. In this work, we present the dataset Transition1x containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the ωB97x/6–31 G(d) level of theory. The data was generated by running Nudged Elastic Band (NEB) with DFT on 10k organic reactions of various types while saving intermediate calculations. We train equivariant graph message-passing neural network models on Transition1x and cross-validate on the popular ANI1x and QM9 datasets. We show that ML models cannot learn features in transition state regions solely by training on hitherto popular benchmark datasets. Transition1x is a new challenging benchmark that will provide an important step towards developing next-generation ML force fields that also work far away from equilibrium configurations and reactive systems. Nature Publishing Group UK 2022-12-24 /pmc/articles/PMC9789978/ /pubmed/36566281 http://dx.doi.org/10.1038/s41597-022-01870-w Text en © The Author(s) 2022 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 | Data Descriptor Schreiner, Mathias Bhowmik, Arghya Vegge, Tejs Busk, Jonas Winther, Ole Transition1x - a dataset for building generalizable reactive machine learning potentials |
title | Transition1x - a dataset for building generalizable reactive machine learning potentials |
title_full | Transition1x - a dataset for building generalizable reactive machine learning potentials |
title_fullStr | Transition1x - a dataset for building generalizable reactive machine learning potentials |
title_full_unstemmed | Transition1x - a dataset for building generalizable reactive machine learning potentials |
title_short | Transition1x - a dataset for building generalizable reactive machine learning potentials |
title_sort | transition1x - a dataset for building generalizable reactive machine learning potentials |
topic | Data Descriptor |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9789978/ https://www.ncbi.nlm.nih.gov/pubmed/36566281 http://dx.doi.org/10.1038/s41597-022-01870-w |
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