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The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life

The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the stud...

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Detalles Bibliográficos
Autores principales: Liang, Yuzhen, Yu, Chunwu, Ma, Wentao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8752021/
https://www.ncbi.nlm.nih.gov/pubmed/34965249
http://dx.doi.org/10.1371/journal.pcbi.1009761
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author Liang, Yuzhen
Yu, Chunwu
Ma, Wentao
author_facet Liang, Yuzhen
Yu, Chunwu
Ma, Wentao
author_sort Liang, Yuzhen
collection PubMed
description The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the studies were conducted in a reverse way: the parameter-space was explored to find those parameter values “supporting” a hypothetical scene (that is, leaving the parameter-justification a later job when sufficient knowledge is available). Exploring the parameter-space manually is an arduous job (especially when the modeling becomes complicated) and additionally, difficult to characterize as regular “Methods” in a paper. Here we show that a machine-learning-like approach may be adopted, automatically optimizing the parameters. With this efficient parameter-exploring approach, the evolutionary modeling on the origin of life would become much more powerful. In particular, based on this, it is expected that more near-reality (complex) models could be introduced, and thereby theoretical research would be more tightly associated with experimental investigation in this field–hopefully leading to significant steps forward in respect to our understanding on the origin of life.
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spelling pubmed-87520212022-01-12 The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life Liang, Yuzhen Yu, Chunwu Ma, Wentao PLoS Comput Biol Research Article The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the studies were conducted in a reverse way: the parameter-space was explored to find those parameter values “supporting” a hypothetical scene (that is, leaving the parameter-justification a later job when sufficient knowledge is available). Exploring the parameter-space manually is an arduous job (especially when the modeling becomes complicated) and additionally, difficult to characterize as regular “Methods” in a paper. Here we show that a machine-learning-like approach may be adopted, automatically optimizing the parameters. With this efficient parameter-exploring approach, the evolutionary modeling on the origin of life would become much more powerful. In particular, based on this, it is expected that more near-reality (complex) models could be introduced, and thereby theoretical research would be more tightly associated with experimental investigation in this field–hopefully leading to significant steps forward in respect to our understanding on the origin of life. Public Library of Science 2021-12-29 /pmc/articles/PMC8752021/ /pubmed/34965249 http://dx.doi.org/10.1371/journal.pcbi.1009761 Text en © 2021 Liang et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Liang, Yuzhen
Yu, Chunwu
Ma, Wentao
The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title_full The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title_fullStr The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title_full_unstemmed The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title_short The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life
title_sort automatic parameter-exploration with a machine-learning-like approach: powering the evolutionary modeling on the origin of life
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8752021/
https://www.ncbi.nlm.nih.gov/pubmed/34965249
http://dx.doi.org/10.1371/journal.pcbi.1009761
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