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核心技术专利:CN118964589B侵权必究
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一种用于微生物组数据分析的新型狄利克雷-多项混合回归模型。

A New Dirichlet-Multinomial Mixture Regression Model for the Analysis of Microbiome Data.

作者信息

Ascari Roberto, Migliorati Sonia, Ongaro Andrea

机构信息

Department of Economics, Management and Statistics (DEMS), University of Milano-Bicocca, Milano, Italy.

出版信息

Stat Med. 2025 Aug;44(18-19):e70220. doi: 10.1002/sim.70220.


DOI:10.1002/sim.70220
PMID:40772811
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12330782/
Abstract

Motivated by the challenges in analyzing gut microbiome and metagenomic data, this paper introduces a novel mixture distribution for multivariate counts and a regression model built upon it. The flexibility and interpretability of the proposed distribution accommodate both negative and positive dependence among taxa and are accompanied by numerous theoretical properties, including explicit expressions for inter- and intraclass correlations, thereby providing a powerful tool for understanding complex microbiome interactions. Furthermore, the regression model based on this distribution facilitates the clear identification and interpretation of relationships between taxa and covariates by modeling the marginal mean of the multivariate response (i.e., taxa counts). Inference is performed using a tailored Hamiltonian Monte Carlo estimation method combined with a spike-and-slab variable selection procedure. Extensive simulation studies and an application to a human gut microbiome dataset highlight the proposed model's substantial improvements over competing models in terms of fit, interpretability, and predictive performance.

摘要

受分析肠道微生物组和宏基因组数据挑战的驱动,本文介绍了一种用于多变量计数的新型混合分布以及基于该分布构建的回归模型。所提出分布的灵活性和可解释性兼顾了分类群之间的负相关和正相关,并伴随着众多理论特性,包括类间和类内相关性的显式表达式,从而为理解复杂的微生物组相互作用提供了一个强大的工具。此外,基于此分布的回归模型通过对多变量响应(即分类群计数)的边际均值进行建模,有助于清晰地识别和解释分类群与协变量之间的关系。使用定制的哈密顿蒙特卡罗估计方法结合尖峰和平板变量选择程序进行推断。广泛的模拟研究以及对人类肠道微生物组数据集的应用突出了所提出模型在拟合、可解释性和预测性能方面相对于竞争模型的显著改进。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/ecaee8a0dc19/SIM-44-0-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/2c3d15eb8482/SIM-44-0-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/8b191e3c844e/SIM-44-0-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/731311c238be/SIM-44-0-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/83d4242ee939/SIM-44-0-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/7447de21879d/SIM-44-0-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/ecaee8a0dc19/SIM-44-0-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/2c3d15eb8482/SIM-44-0-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/8b191e3c844e/SIM-44-0-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/731311c238be/SIM-44-0-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/83d4242ee939/SIM-44-0-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/7447de21879d/SIM-44-0-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9b44/12330782/ecaee8a0dc19/SIM-44-0-g001.jpg

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A New Dirichlet-Multinomial Mixture Regression Model for the Analysis of Microbiome Data.

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[8]
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本文引用的文献

[1]
A Bayesian zero-inflated Dirichlet-multinomial regression model for multivariate compositional count data.

Biometrics. 2023-12

[2]
Stan: A Probabilistic Programming Language.

J Stat Softw. 2017

[3]
A new regression model for overdispersed binomial data accounting for outliers and an excess of zeros.

Stat Med. 2021-7-30

[4]
Naught all zeros in sequence count data are the same.

Comput Struct Biotechnol J. 2020-9-28

[5]
Dirichlet-multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data.

Mol Ecol Resour. 2020-1-29

[6]
An adaptive independence test for microbiome community data.

Biometrics. 2020-6

[7]
Intraclass correlation - A discussion and demonstration of basic features.

PLoS One. 2019-7-22

[8]
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Nature. 2019-5-29

[9]
Scalable estimation and regularization for the logistic normal multinomial model.

Biometrics. 2019-12

[10]
The role of the microbiota in infectious diseases.

Nat Microbiol. 2018-12-13

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