Improving the accuracy and internal consistency of regression-based clustering of high-dimensional datasets

Zhang Bo, He Jianghua, Hu Jinxiang, Chalise Prabhakar and Koestler Devin C. ()
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Zhang Bo: Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
He Jianghua: Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
Hu Jinxiang: Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
Chalise Prabhakar: Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
Koestler Devin C.: Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA

Statistical Applications in Genetics and Molecular Biology, 2023, vol. 22, issue 1, 15

Abstract: Component-wise Sparse Mixture Regression (CSMR) is a recently proposed regression-based clustering method that shows promise in detecting heterogeneous relationships between molecular markers and a continuous phenotype of interest. However, CSMR can yield inconsistent results when applied to high-dimensional molecular data, which we hypothesize is in part due to inherent limitations associated with the feature selection method used in the CSMR algorithm. To assess this hypothesis, we explored whether substituting different regularized regression methods (i.e. Lasso, Elastic Net, Smoothly Clipped Absolute Deviation (SCAD), Minmax Convex Penalty (MCP), and Adaptive-Lasso) within the CSMR framework can improve the clustering accuracy and internal consistency (IC) of CSMR in high-dimensional settings. We calculated the true positive rate (TPR), true negative rate (TNR), IC and clustering accuracy of our proposed modifications, benchmarked against the existing CSMR algorithm, using an extensive set of simulation studies and real biological datasets. Our results demonstrated that substituting Adaptive-Lasso within the existing feature selection method used in CSMR led to significantly improved IC and clustering accuracy, with strong performance even in high-dimensional scenarios. In conclusion, our modifications of the CSMR method resulted in improved clustering performance and may thus serve as viable alternatives for the regression-based clustering of high-dimensional datasets.

Keywords: disease heterogeneity; mixture modeling; supervised learning (search for similar items in EconPapers)
Date: 2023
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DOI: 10.1515/sagmb-2022-0031

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