Published online Sep 21, 2025. doi: 10.3748/wjg.v31.i35.109776
Revised: June 19, 2025
Accepted: September 1, 2025
Published online: September 21, 2025
Processing time: 120 Days and 13.2 Hours
Core Tip: There is substantial evidence indicating that stratification based on the gut microbiome could facilitate personalized interventions aimed at enhancing human health. It became essential to characterize the microbial ecosystems, resulting in a surge of various types of molecular profiling data, including metagenomics, metatranscriptomics, and metabolomics. In the analysis of such data, machine learning algorithms have proven to be effective in identifying crucial molecular signatures, uncovering potential patient stratifications, and especially in creating models that can reliably predict phenotypes. Machine learning may be supervised, unsupervised, semi-supervised or reinforcement type. Using a method for explaining individual classifier decisions for complex microbiota analysis may help in developing personalized treatment.
