Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis

Abstract

MotivationThe transcriptomic data is being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are data harmonization and treatment outcome prediction. Both of them can be addressed via the style transfer approach. Either technical factors or any biological details about the samples which we would like to control (gender, biological state, treatment etc.) can be used as style components. ResultsThe proposed style transfer solution is based on Conditional Variational Autoencoders, Y-Autoencoders and adversarial feature decomposition. In order to quantitatively measure the quality of the style transfer, neural network classifiers which predict the style and semantics after training on real expression were used. Comparison with several existing style-transfer based approaches shows that proposed model has the highest style prediction accuracy on all considered datasets while having comparable or the best semantics prediction accuracy. Availabilityhttps://github.com/NRshka/stvae-source Contactantonec@novel-soft.com Supplementary informationFigShare.com (https://dx.doi.org/10.6084/m9.figshare.9925115)