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自动参数探索与机器学习方法类似:为生命起源的进化建模提供动力。

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

机构信息

Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.

College of Computer Sciences, Wuhan University, Wuhan, China.

出版信息

PLoS Comput Biol. 2021 Dec 29;17(12):e1009761. doi: 10.1371/journal.pcbi.1009761. eCollection 2021 Dec.

Abstract

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.

摘要

生命的起源涉及复杂的进化过程。计算机建模是揭示相关机制的一种有前途的方法。然而,由于我们对前生物化学知识的限制,通常很难为建模设定参数。因此,研究通常以相反的方式进行:探索参数空间,以找到那些“支持”假设场景的参数值(也就是说,当有足够的知识时,将参数论证留到以后)。手动探索参数空间是一项艰巨的任务(特别是当建模变得复杂时),并且很难在论文中以常规的“方法”进行描述。在这里,我们表明可以采用类似于机器学习的方法来自动优化参数。通过这种高效的参数探索方法,生命起源的进化建模将变得更加强大。特别是,基于此,可以引入更接近现实(复杂)的模型,从而使理论研究更紧密地与该领域的实验研究相关联——有望在我们对生命起源的理解方面取得重大进展。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cbd3/8752021/af61445a44b6/pcbi.1009761.g001.jpg

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