Open AccessMachine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics
Author(s) -
Daniel Beck,
James A. Foster
Publication year - 2014
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0087830
Subject(s) - bacterial vaginosis , random forest , microbiome , artificial intelligence , machine learning , logistic regression , human microbiome , bacterial taxonomy , metagenomics , computer science , biology , computational biology , bioinformatics , microbiology and biotechnology , bacteria , genetics , 16s ribosomal rna , gene
Microbial communities are important to human health. Bacterial vaginosis (BV) is a disease associated with the vagina microbiome. While the causes of BV are unknown, the microbial community in the vagina appears to play a role. We use three different machine-learning techniques to classify microbial communities into BV categories. These three techniques include genetic programming (GP), random forests (RF), and logistic regression (LR). We evaluate the classification accuracy of each of these techniques on two different datasets. We then deconstruct the classification models to identify important features of the microbial community. We found that the classification models produced by the machine learning techniques obtained accuracies above 90% for Nugent score BV and above 80% for Amsel criteria BV. While the classification models identify largely different sets of important features, the shared features often agree with past research.