Di Wang1, Zheng Jing2, Kevin He1, Lana X Garmire3. 1. Department of Biostatistics, University of Michigan, Ann Arbor, MI. 2. Department of Statistics, University of Michigan, Ann Arbor, MI. 3. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.
Abstract
SUMMARY: Cox-nnet is a neural-network based prognosis prediction method, originally applied to genomics data. Here we propose the version 2 of Cox-nnet, with significant improvement on efficiency and interpretability, making it suitable to predict prognosis based on large-scale population data, including those electronic medical records (EMR) datasets. We also add permutation-based feature importance scores and the direction of feature coefficients. When applied on a kidney transplantation dataset, Cox-nnet v2.0 reduces the training time of Cox-nnet up to 32 folds (n = 10,000) and achieves better prediction accuracy than Cox-PH (p < 0.05). It also achieves similarly superior performance on a publicly available SUPPORT data (n = 8,000). The high efficiency and accuracy make Cox-nnet v2.0 a desirable method for survival prediction in large-scale EMR data. AVAILABILITY AND IMPLEMENTATION: Cox-nnet v2.0 is freely available to the public at https://github.com/lanagarmire/Cox-nnet-v2.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Cox-nnet is a neural-network based prognosis prediction method, originally applied to genomics data. Here we propose the version 2 of Cox-nnet, with significant improvement on efficiency and interpretability, making it suitable to predict prognosis based on large-scale population data, including those electronic medical records (EMR) datasets. We also add permutation-based feature importance scores and the direction of feature coefficients. When applied on a kidney transplantation dataset, Cox-nnet v2.0 reduces the training time of Cox-nnet up to 32 folds (n = 10,000) and achieves better prediction accuracy than Cox-PH (p < 0.05). It also achieves similarly superior performance on a publicly available SUPPORT data (n = 8,000). The high efficiency and accuracy make Cox-nnet v2.0 a desirable method for survival prediction in large-scale EMR data. AVAILABILITY AND IMPLEMENTATION: Cox-nnet v2.0 is freely available to the public at https://github.com/lanagarmire/Cox-nnet-v2.0. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Benjamin A Goldstein; Ann Marie Navar; Michael J Pencina; John P A Ioannidis Journal: J Am Med Inform Assoc Date: 2016-05-17 Impact factor: 4.497