Machine learning and Voronoi-based decision boundaries for Bacterial vaginosis to determine population- specific microbial interactions

In this study we utilize machine learning techniques to create predictive models and determine key bacterial interactions for the diagnosis of Bacterial vaginosis. Bacterial vaginosis (BV) is a common vaginal syndrome affecting reproductive-age women globally. It is associated with various adverse obstetric and gynecological out-comes including increased risk of sexually transmitted infections, HIV, cervical cancer, and pre-term birth. While it is known that BV is caused by a shift in abundance between Lactobacilli and anaerobic bacteria, it is unknown how gradual shifts in that balance lead towards BV status. Here we perform a rigorous comparison of machine learning architectures and feature selection methods used to train models on 16s rRNA data of patients presenting with BV. Using the highest-performing models, we employ explainable AI methods to determine the most important bacteria for BV diagnosis. Furthermore, we implement Voronoi-based decision boundaries to show how the relative abundances between pairs of these bacteria results in BV positive or BV negative outcomes. Results: We find that support vector machine and random forest models in combination with feature selection predict BV diagnosis with the most balanced accuracy. Using those models, we identify four Lactobacilli spp and six anaerobes to be key in to be key to the diagnosis of BV. The determination of key bacteria can inform BV diagnostics and pathogenesis research to species that have previously eluded scientific focus. Additionally, decision boundary plots offer a diagnostic point of reference for how the relative abundances of key vaginal flora are indicative of BV outcomes.