How to validate a Bayesian evolutionary model.

IF 6.1 1区 生物学 Q1 EVOLUTIONARY BIOLOGY Systematic Biology Pub Date : 2024-11-07 DOI:10.1093/sysbio/syae064
Fábio K Mendes, Remco Bouckaert, Luiz M Carvalho, Alexei J Drummond
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Abstract

Biology has become a highly mathematical discipline in which probabilistic models play a central role. As a result, research in the biological sciences is now dependent on computational tools capable of carrying out complex analyses. These tools must be validated before they can be used, but what is understood as validation varies widely among methodological contributions. This may be a consequence of the still embryonic stage of the literature on statistical software validation for computational biology. Our manuscript aims to advance this literature. Here, we describe, illustrate and introduce new good practices for assessing the correctness of a model implementation, with an emphasis on Bayesian methods. We also introduce a suite of functionalities for automating validation protocols. It is our hope that the guidelines presented here help sharpen the focus of discussions on (as well as elevate) expected standards of statistical software for biology.

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如何验证贝叶斯进化模型。
生物学已成为一门高度数学化的学科,其中概率模型发挥着核心作用。因此,生物科学研究现在依赖于能够进行复杂分析的计算工具。这些工具在使用之前必须经过验证,但对验证的理解却因方法论的不同而大相径庭。这可能是计算生物学统计软件验证文献仍处于萌芽阶段的结果。我们的手稿旨在推动这一文献的发展。在这里,我们描述、说明并介绍了评估模型实现正确性的新的良好实践,重点是贝叶斯方法。我们还介绍了一套用于自动验证协议的功能。我们希望这里介绍的指导原则有助于使生物学统计软件预期标准的讨论重点更加突出(以及提高)。
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来源期刊
Systematic Biology
Systematic Biology 生物-进化生物学
CiteScore
13.00
自引率
7.70%
发文量
70
审稿时长
6-12 weeks
期刊介绍: Systematic Biology is the bimonthly journal of the Society of Systematic Biologists. Papers for the journal are original contributions to the theory, principles, and methods of systematics as well as phylogeny, evolution, morphology, biogeography, paleontology, genetics, and the classification of all living things. A Points of View section offers a forum for discussion, while book reviews and announcements of general interest are also featured.
期刊最新文献
How to validate a Bayesian evolutionary model. Evolution of Large Eyes in Stromboidea (Gastropoda): Impact of Photic Environment and Life History Traits. Rapid Evolution of Host Repertoire and Geographic Range in a Young and Diverse Genus of Montane Butterflies. Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation. Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation.
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