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Machine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics

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  • Daniel Beck
  • James A Foster

Abstract

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.

Suggested Citation

  • Daniel Beck & James A Foster, 2014. "Machine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-8, February.
    • Handle: RePEc:plo:pone00:0087830
    DOI: 10.1371/journal.pone.0087830
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    1. Ruth E. Ley & Peter J. Turnbaugh & Samuel Klein & Jeffrey I. Gordon, 2006. "Human gut microbes associated with obesity," Nature, Nature, vol. 444(7122), pages 1022-1023, December.
    2. Peter J. Turnbaugh & Ruth E. Ley & Michael A. Mahowald & Vincent Magrini & Elaine R. Mardis & Jeffrey I. Gordon, 2006. "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, Nature, vol. 444(7122), pages 1027-1031, December.
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