Dcmd: Distance-based classification using mixture distributions on microbiome data

Konstantin Shestopaloff, Mei Dong, Fan Gao and Wei Xu

PLOS Computational Biology, 2021, vol. 17, issue 3, 1-18

Abstract: Current advances in next-generation sequencing techniques have allowed researchers to conduct comprehensive research on the microbiome and human diseases, with recent studies identifying associations between the human microbiome and health outcomes for a number of chronic conditions. However, microbiome data structure, characterized by sparsity and skewness, presents challenges to building effective classifiers. To address this, we present an innovative approach for distance-based classification using mixture distributions (DCMD). The method aims to improve classification performance using microbiome community data, where the predictors are composed of sparse and heterogeneous count data. This approach models the inherent uncertainty in sparse counts by estimating a mixture distribution for the sample data and representing each observation as a distribution, conditional on observed counts and the estimated mixture, which are then used as inputs for distance-based classification. The method is implemented into a k-means classification and k-nearest neighbours framework. We develop two distance metrics that produce optimal results. The performance of the model is assessed using simulated and human microbiome study data, with results compared against a number of existing machine learning and distance-based classification approaches. The proposed method is competitive when compared to the other machine learning approaches, and shows a clear improvement over commonly used distance-based classifiers, underscoring the importance of modelling sparsity for achieving optimal results. The range of applicability and robustness make the proposed method a viable alternative for classification using sparse microbiome count data. The source code is available at https://github.com/kshestop/DCMD for academic use.Author summary: The uneven performance of conventional distanced-based classifiers when using microbiome profiles to predict disease status has motivated us to develop a novel distance-based method that accounts for uncertainty when modeling sparse counts. We propose a classification algorithm that uses mixture distributions to measure normed distances between microbiome distributions, which better models the underlying structure by handling excess zeros and sparsity inherent in microbial abundance counts. Applications of DCMD have shown improved classification performance and robustness, making the proposed method an improved alternative for classification using microbiome data.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1008799

DOI: 10.1371/journal.pcbi.1008799

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