Zaixiang Tang1,2,3, Yueping Shen1,2, Xinyan Zhang3, Nengjun Yi3. 1. Department of Biostatistics, School of Public Health. 2. Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, and Center for Genetic Epidemiology and Genomics, Medical College of Soochow University, Suzhou 215123, China. 3. Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Abstract
MOTIVATION: Large-scale molecular profiling data have offered extraordinary opportunities to improve survival prediction of cancers and other diseases and to detect disease associated genes. However, there are considerable challenges in analyzing large-scale molecular data. RESULTS: We propose new Bayesian hierarchical Cox proportional hazards models, called the spike-and-slab lasso Cox, for predicting survival outcomes and detecting associated genes. We also develop an efficient algorithm to fit the proposed models by incorporating Expectation-Maximization steps into the extremely fast cyclic coordinate descent algorithm. The performance of the proposed method is assessed via extensive simulations and compared with the lasso Cox regression. We demonstrate the proposed procedure on two cancer datasets with censored survival outcomes and thousands of molecular features. Our analyses suggest that the proposed procedure can generate powerful prognostic models for predicting cancer survival and can detect associated genes. AVAILABILITY AND IMPLEMENTATION: The methods have been implemented in a freely available R package BhGLM ( http://www.ssg.uab.edu/bhglm/ ). CONTACT: nyi@uab.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Large-scale molecular profiling data have offered extraordinary opportunities to improve survival prediction of cancers and other diseases and to detect disease associated genes. However, there are considerable challenges in analyzing large-scale molecular data. RESULTS: We propose new Bayesian hierarchical Cox proportional hazards models, called the spike-and-slab lasso Cox, for predicting survival outcomes and detecting associated genes. We also develop an efficient algorithm to fit the proposed models by incorporating Expectation-Maximization steps into the extremely fast cyclic coordinate descent algorithm. The performance of the proposed method is assessed via extensive simulations and compared with the lasso Cox regression. We demonstrate the proposed procedure on two cancer datasets with censored survival outcomes and thousands of molecular features. Our analyses suggest that the proposed procedure can generate powerful prognostic models for predicting cancer survival and can detect associated genes. AVAILABILITY AND IMPLEMENTATION: The methods have been implemented in a freely available R package BhGLM ( http://www.ssg.uab.edu/bhglm/ ). CONTACT: nyi@uab.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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