LRBmat: a novel gut microbial interaction and individual heterogeneity inference method for colorectal cancer

DOI10.1016/J.JTBI.2023.111538MaRDI QIDQ6136943zbMATH OpenOpenAlexFDO

Authors

Publication date 31 August 2023

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2303.07498

zbMATH Keywords

colorectal cancerindividual heterogeneityassociation rule mininggut microbiotabiomedical classificationgut microbial interactions

Mathematics Subject Classification ID

Pathology, pathophysiology (92C32) Microbiology (92C70)

Abstract: Many diseases are considered to be closely related to the changes in the gut microbial community, including colorectal cancer (CRC), which is one of the most common cancers in the world. The diagnostic classification and etiological analysis of CRC are two critical issues worthy of attention. Many methods adopt gut microbiota to solve it, but few of them simultaneously take into account the complex interactions and individual heterogeneity of gut microbiota, which are two common and important issues in genetics and intestinal microbiology, especially in high-dimensional cases. In this paper, a novel method with a Binary matrix based on Logistic Regression (LRBmat) is proposed to deal with the above problem. The binary matrix can directly weakened or avoided the influence of heterogeneity, and also contain the information about gut microbial interactions with any order. Moreover, LRBmat has a powerful generalization, it can combine with any machine learning method and enhance them. The real data analysis on CRC validates the proposed method, which has the best classification performance compared with the state-of-the-art. Furthermore, the association rules extracted from the binary matrix of the real data align well with the biological properties and existing literatures, which are helpful for the etiological analysis of CRC. The source codes for LRBmat are available at https://github.com/tsnm1/LRBmat.

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Cited in

(1)

• Feature selection based on Shapley additive explanations on metagenomic data for colorectal cancer diagnosis

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