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.
© The Author(s) 2021. Published by Oxford University Press.