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基于观测生物时间序列的数据分析因果关系。

Data-driven causal analysis of observational biological time series.

机构信息

Molecular and Cellular Biology PhD program, University of Washington, Seattle, United States.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.

出版信息

Elife. 2022 Aug 19;11:e72518. doi: 10.7554/eLife.72518.


DOI:10.7554/eLife.72518
PMID:35983746
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9391047/
Abstract

Complex systems are challenging to understand, especially when they defy manipulative experiments for practical or ethical reasons. Several fields have developed parallel approaches to infer causal relations from observational time series. Yet, these methods are easy to misunderstand and often controversial. Here, we provide an accessible and critical review of three statistical causal discovery approaches (pairwise correlation, Granger causality, and state space reconstruction), using examples inspired by ecological processes. For each approach, we ask what it tests for, what causal statement it might imply, and when it could lead us astray. We devise new ways of visualizing key concepts, describe some novel pathologies of existing methods, and point out how so-called 'model-free' causality tests are not assumption-free. We hope that our synthesis will facilitate thoughtful application of methods, promote communication across different fields, and encourage explicit statements of assumptions. A video walkthrough is available (Video 1 or https://youtu.be/AIV0ttQrjK8).

摘要

复杂系统难以理解,尤其是当出于实际或伦理原因而无法进行操纵性实验时。有几个领域已经开发出了从观测时间序列中推断因果关系的并行方法。然而,这些方法很容易被误解,而且常常存在争议。在这里,我们使用受生态过程启发的示例,对三种统计因果发现方法(成对相关、格兰杰因果关系和状态空间重构)进行了易于理解和批判性的回顾。对于每种方法,我们都会询问它测试的是什么,它可能暗示的因果陈述是什么,以及何时可能导致我们产生误解。我们设计了新的可视化关键概念的方法,描述了现有方法的一些新的病理,并指出了所谓的“无模型”因果检验并非无假设。我们希望我们的综合能促进方法的深思熟虑的应用,促进不同领域之间的交流,并鼓励明确陈述假设。视频讲解(视频 1 或 https://youtu.be/AIV0ttQrjK8)可用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/baf4/9391047/82cf22328d71/elife-72518-app4-fig6.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/baf4/9391047/2db0d2f9c2f3/elife-72518-app2-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/baf4/9391047/51d6e9509c0c/elife-72518-app2-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/baf4/9391047/a8fc54601499/elife-72518-app3-fig1.jpg
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本文引用的文献

[1]
Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities.

Nat Commun. 2021-11-23

[2]
Estimating Transfer Entropy in Continuous Time Between Neural Spike Trains or Other Event-Based Data.

PLoS Comput Biol. 2021-4

[3]
Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions.

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[4]
Refined nonuniform embedding for coupling detection in multivariate time series.

Phys Rev E. 2020-6

[5]
Partial cross mapping eliminates indirect causal influences.

Nat Commun. 2020-5-26

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Sci Adv. 2019-11-27

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Causality analysis and prediction of 2-methylisoborneol production in a reservoir using empirical dynamic modeling.

Water Res. 2019-7-16

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ISME J. 2019-6-28

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