Supervised machine learning for microbiomics: bridging the gap between current and best practices
This work addresses reproducibility and fairness gaps in microbiomics ML for clinical applications, though it is incremental as it synthesizes existing literature rather than proposing new methods.
The study analyzed 100 peer-reviewed articles in microbiomics from 2021-2022 to identify gaps in current machine learning practices, finding issues like small datasets (median 161.5 samples), limited demographic reporting, and high risks of data leakage (86% of studies). It provides guidance and an interactive tutorial to improve reproducibility and clinical applicability.
Machine learning (ML) is poised to drive innovations in clinical microbiomics, such as in disease diagnostics and prognostics. However, the successful implementation of ML in these domains necessitates the development of reproducible, interpretable models that meet the rigorous performance standards set by regulatory agencies. This study aims to identify key areas in need of improvement in current ML practices within microbiomics, with a focus on bridging the gap between existing methodologies and the requirements for clinical application. To do so, we analyze 100 peer-reviewed articles from 2021-2022. Within this corpus, datasets have a median size of 161.5 samples, with over one-third containing fewer than 100 samples, signaling a high potential for overfitting. Limited demographic data further raises concerns about generalizability and fairness, with 24% of studies omitting participants' country of residence, and attributes like race/ethnicity, education, and income rarely reported (11%, 2%, and 0%, respectively). Methodological issues are also common; for instance, for 86% of studies we could not confidently rule out test set omission and data leakage, suggesting a strong potential for inflated performance estimates across the literature. Reproducibility is also a concern, with 78% of studies abstaining from sharing their ML code publicly. Based on this analysis, we provide guidance to avoid common pitfalls that can hinder model performance, generalizability, and trustworthiness. An interactive tutorial on applying ML to microbiomics data accompanies the discussion, to help establish and reinforce best practices within the community.