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

• Published in: Bioinformatics 2020-12, Vol.36 (20), p.5076-5085
• Main Authors: Russkikh, Nikolai, Antonets, Denis, Shtokalo, Dmitry, Makarov, Alexander, Vyatkin, Yuri, Zakharov, Alexey, Terentyev, Evgeny
• Format: Article
• Language: English
• Subjects: Exome Sequencing; Neural Networks, Computer; Original Papers; RNA-Seq; Semantics; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btaa624

Abstract Motivation The transcriptomic data are being frequently used in the research of biomarker genes of different diseases and biological states. The most common tasks there are the 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. Results The proposed style transfer solution is based on Conditional Variational Autoencoders, Y-Autoencoders and adversarial feature decomposition. 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. Availability and implementation https://github.com/NRshka/stvae-source. Supplementary information Supplementary data are available at Bioinformatics online.