MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods

• Published in: Microorganisms (Basel) Vol. 11; no. 11; p. 2816
• Main Authors: Kim, Jihun, Koh, Hyunwook
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.11.2023
• Subjects: Accuracy; Algorithms; Chatbots; classification and regression; Cloud computing; Computer programming; computer software; computers; Data mining; decision support systems; Decision trees; diagnostic techniques; Disease; human microbiome; humans; Internet; Learning algorithms; Machine learning; Medical microbiology; Methods; Microbiological research; microbiome; microbiome data analysis; Microbiomes; Microbiota (Symbiotic organisms); Next-generation sequencing; Observational studies; Open source software; prediction; Prediction models; Public health; Public software; Sparsity; Taxonomy; tree-based methods; Web applications; web cloud computing; South Korea
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms11112816

The advent of next-generation sequencing has greatly accelerated the field of human microbiome studies. Currently, investigators are seeking, struggling and competing to find new ways to diagnose, treat and prevent human diseases through the human microbiome. Machine learning is a promising approach to help such an effort, especially due to the high complexity of microbiome data. However, many of the current machine learning algorithms are in a “black box”, i.e., they are difficult to understand and interpret. In addition, clinicians, public health practitioners and biologists are not usually skilled at computer programming, and they do not always have high-end computing devices. Thus, in this study, we introduce a unified web cloud analytic platform, named MiTree, for user-friendly and interpretable microbiome data mining. MiTree employs tree-based learning methods, including decision tree, random forest and gradient boosting, that are well understood and suited to human microbiome studies. We also stress that MiTree can address both classification and regression problems through covariate-adjusted or unadjusted analysis. MiTree should serve as an easy-to-use and interpretable data mining tool for microbiome-based disease prediction modeling, and should provide new insights into microbiome-based diagnostics, treatment and prevention. MiTree is an open-source software that is available on our web server.