AUTHOR=Shayakhmetov Rim , Kuznetsov Maksim , Zhebrak Alexander , Kadurin Artur , Nikolenko Sergey , Aliper Alexander , Polykovskiy Daniil 

TITLE=Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders

JOURNAL=Frontiers in Pharmacology

VOLUME=Volume 11 - 2020

YEAR=2020

URL=https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2020.00269

DOI=10.3389/fphar.2020.00269

ISSN=1663-9812

ABSTRACT=Gene expression profiles are useful for assessing drugs' efficacy and side-effects. In this paper, we propose a new generative model that infers drug molecules that could induce a desired change in gene expression. Our model—Bidirectional Adversarial Autoencoder—explicitly separates cellular processes captured in gene expression changes into two feature sets: related and unrelated to the drug incubation. The model uses related features to produce a drug hypothesis. We validate our model on the LINCS L1000 dataset by generating molecular structures in the SMILES format for the desired transcriptional response. In the experiments, we show that the proposed model can generate novel molecular structures that could induce a given gene expression change, or predict gene expression difference after incubation of a given molecular structure.