Best practices for developing microbiome-based disease diagnostic classifiers through machine learning

P Li

doi:10.1080/19490976.2025.2489074

2025-04-04

DOI：10.1080/19490976.2025.2489074

原文链接

原文求助

摘要

En 中文

人类肠道微生物组在各种疾病中具有关键作用，可通过机器学习（ML）开发诊断模型。模型构建中使用的具体工具和参数，如数据预处理、批次效应去除和建模算法，会影响模型性能和泛化能力。为建立通用的流程，我们将ML过程分为上述三个步骤，并利用涵盖20种疾病的83个肠道微生物组队列对每个步骤进行顺序优化。我们测试了总计156种工具-参数-算法组合，并根据内部和外部AUC值进行基准评估。在数据预处理步骤中，我们确定了4种适用于回归型算法的数据预处理方法，以及1种适用于非回归型算法的方法。在批次效应去除步骤中，我们识别出sva R包中的ComBat函数为有效的批次效应去除方法，并比较了各种算法的性能。最后，在机器学习算法选择步骤中，我们发现Ridge和Random Forest表现最佳。我们优化的工作流程在疾病特异性优化方面与之前的详尽方法表现相似，因此具有通用性，可为构建多种疾病的诊断模型提供全面的指导，并有望成为未来医学诊断的有力工具。

Keyword:

Gut microbiome

machine learning

patient stratification

disease diagnostic models

optimal model construction workflow

期刊

Gut Microbes

IF:

论文数:

2.7K

被引数:

1.9W

机构

huazhong university of science and technology

学者数:

2.7W

论文数: 8.1K

被引数: 5

引用论文

The effect of host genetics on the gut microbiome 宿主遗传学对肠道微生物组的影响

NATURE GENETICS

IF31.8

2016-10-03

622

PREAI

Bonder, Marc Jan; Kurilshikov, Alexander; Tigchelaar, Ettje F.; Mujagic, Zlatan; Imhann, Floris; Vila, Arnau Vich; Deelen, Patrick; Vatanen, Tommi; Schirmer, Melanie; Smeekens, Sanne P.; Zhernakova, Dania V.; Jankipersadsing, Soesma A.; Jaeger, Martin; Oosting, Marije; Cenit, Maria Carmen; Masclee, Ad A. M.; Swertz, Morris A.; Li, Yang; Kumar, Vinod; Joosten, Leo; Harmsen, Hermie; Weersma, Rinse K.; Franke, Lude; Hofker, Marten H.; Xavier, Ramnik J.; Jonkers, Daisy; Netea, Mihai G.; Wijmenga, Cisca; Fu, Jingyuan; Zhernakova, Alexandra

Improved metagenomic analysis with Kraken 2 使用Kraken 2改进宏基因组分析

GENOME BIOLOGY

IF9.4

2019-11-28

2.4K

OAAI

Wood, Derrick E.; Lu, Jennifer; Langmead, Ben

Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers

GUT MICROBES

IF11

2023-05-04

OAAI

Li, Min; Liu, Jinxin; Zhu, Jiaying; Wang, Huarui; Sun, Chuqing; Gao, Na L.; Zhao, Xing-Ming; Chen, Wei-Hua

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis 肠道普雷沃氏菌的扩张与对关节炎的敏感性增强相关

ELIFE

IF0

2013-11-05

1.6K

OAAI

Scher, Jose U.; Sczesnak, Andrew; Longman, Randy S.; Segata, Nicola; Ubeda, Carles; Bielski, Craig; Rostron, Tim; Cerundolo, Vincenzo; Pamer, Eric G.; Abramson, Steven B.; Huttenhower, Curtis; Littman, Dan R.

Diet rapidly and reproducibly alters the human gut microbiome 饮食快速且可重复地改变人类肠道微生物组

Nature

IF0

2013-12-11

OAAI

Lawrence A. David; Corinne F. Maurice; Rachel N. Carmody; David B. Gootenberg; Julie E. Button; Benjamin E. Wolfe; Alisha V. Ling; A. Sloan Devlin; Yug Varma; Michael A. Fischbach; Sudha B. Biddinger; Rachel J. Dutton; Peter J. Turnbaugh

The Sequence Read Archive: a decade more of explosive growth Sequence Read Archive: 爆炸性增长的十年

NUCLEIC ACIDS RESEARCH

IF13.1

2021-11-24

151

OAAI

Katz, Kenneth; Shutov, Oleg; Lapoint, Richard; Kimelman, Michael; Brister, J. Rodney; O'Sullivan, Christopher

A Systematic Review of Mixed Studies Exploring the Effects of Probiotics on Gut-Microbiome to Modulate Therapy in Children With Autism Spectrum Disorder 混合研究系统评价：探究益生菌对自闭症谱系障碍儿童肠道微生物组以调节治疗的影响

Cureus

IF0

2022-12-08

OAAI

Maithily Patel; Lakshmi M Atluri; Natalie A Gonzalez; Navya Sakhamuri; Sreekartthik Athiyaman; Bhawna Randhi; Sai Dheeraj Gutlapalli; Jingxiong Pu; Maheen F Zaidi; Safeera Khan

Unveiling the Power of Gut Microbiome in Predicting Neoadjuvant Immunochemotherapy Responses in Esophageal Squamous Cell Carcinoma

RESEARCH

IF10.7

2024-11-14

OAAI

Liu, Le; Liang, Liping; Luo, Yingjie; Han, Jimin; Lu, Di; Cai, Ruijun; Sethi, Gautam; Mai, Shijie

Regularization and variable selection via the elastic net 基于弹性网的正则化和变量选择

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

IF3.6

2005-03-09

1.4W

OAAI