Biomarker selection and a prospective metabolite-based machine learning diagnostic for lyme disease
Eric Kehoe, Bryna L. Fitzgerald, Barbara Graham, M. Nurul Islam, Kartikay Sharma, Gary P. Wormser, John T. Belisle, Michael Kirby
Abstract
We provide a pipeline for data preprocessing, biomarker selection, and classification of liquid chromatography-mass spectrometry (LCMS) serum samples to generate a prospective diagnostic test for Lyme disease. We utilize tools of machine learning (ML), e.g., sparse support vector machines (SSVM), iterative feature removal (IFR), and k-fold feature ranking to select several biomarkers and build a discriminant model for Lyme disease. We report a 98.13% test balanced success rate (BSR) of our model based on a sequestered test set of LCMS serum samples. The methodology employed is general and can be readily adapted to other LCMS, or metabolomics, data sets.