In machine learning and statistics, the penalized regression methods are the main tools for variable selection (or feature selection) in high-dimensional sparse data analysis. Due to the nonsmoothness of the associated thresholding operators of commonly used penalties such as the least absolute shrinkage and selection operator (LASSO), the smoothly clipped absolute deviation (SCAD), and the minimax concave penalty (MCP), the classical Newton-Raphson algorithm cannot be used. In this article, we propose a cubic Hermite interpolation penalty (CHIP) with a smoothing thresholding operator. Theoretically, we establish the nonasymptotic estimation error bounds for the global minimizer of the CHIP penalized high-dimensional linear regression. Moreover, we show that the estimated support coincides with the target support with a high probability. We derive the Karush-Kuhn-Tucker (KKT) condition for the CHIP penalized estimator and then develop a support detection-based Newton-Raphson (SDNR) algorithm to solve it. Simulation studies demonstrate that the proposed method performs well in a wide range of finite sample situations. We also illustrate the application of our method with a real data example.
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http://dx.doi.org/10.1109/TNNLS.2023.3251748 | DOI Listing |
BMC Bioinformatics
February 2024
Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
Background: Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been proposed for disease prediction. In this study, we evaluated the performance of several such methods for predicting asthma using the Korean Chip (KORV1.
View Article and Find Full Text PDFNat Commun
January 2024
Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
CRISPR-Cas13d cleaves RNA and is used in vivo and for diagnostics. However, a systematic understanding of its RNA binding and cleavage specificity is lacking. Here, we describe an RNA Chip-Hybridized Association-Mapping Platform (RNA-CHAMP) for measuring the binding affinity for > 10,000 RNAs containing structural perturbations and other alterations relative to the CRISPR RNA (crRNA).
View Article and Find Full Text PDFbioRxiv
March 2023
Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA.
Type VI CRISPR enzymes cleave target RNAs and are widely used for gene regulation, RNA tracking, and diagnostics. However, a systematic understanding of their RNA binding specificity and cleavage activation is lacking. Here, we describe RNA chip-hybridized association-mapping platform (RNA-CHAMP), a massively parallel platform that repurposes next-generation DNA sequencing chips to measure the binding affinity for over 10,000 RNA targets containing structural perturbations, mismatches, insertions, and deletions relative to the CRISPR RNA (crRNA).
View Article and Find Full Text PDFIEEE Trans Neural Netw Learn Syst
September 2024
In machine learning and statistics, the penalized regression methods are the main tools for variable selection (or feature selection) in high-dimensional sparse data analysis. Due to the nonsmoothness of the associated thresholding operators of commonly used penalties such as the least absolute shrinkage and selection operator (LASSO), the smoothly clipped absolute deviation (SCAD), and the minimax concave penalty (MCP), the classical Newton-Raphson algorithm cannot be used. In this article, we propose a cubic Hermite interpolation penalty (CHIP) with a smoothing thresholding operator.
View Article and Find Full Text PDFJ Gen Intern Med
September 2022
Maine Medical Center Research Institute, Scarborough, ME, USA.
The Affordable Care Act (2010) and Medicare Access and CHIP Reauthorization Act (2015) ushered in a new era of Medicare value-based payment programs. Five major mandatory pay-for-performance programs have been implemented since 2012 with increasing positive and negative payment adjustments over time. A growing body of evidence indicates that these programs are inequitable and financially penalize safety-net systems and systems that care for a higher proportion of racial and ethnic minority patients.
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