DORA: a dose-response autoencoder for interpretable transcriptome-to-viability prediction

Predicting the effect of drugs on cell viability is a central challenge in drug discovery. Artificial intelligence holds the promise to considerably accelerate this process by leveraging rich cellular data such as transcriptomics. Current models focus on either transcriptomes or inhibitory concentrations, but they fall short in integrating these sources of information. Here, we propose DORA (Dose-Response Autoencoder), a deep learning model that predicts changes in transcriptomes and viability in a dose-dependent manner, knowing the unperturbed cell state. By enforcing a latent space consistent with cumulative dose effects, DORA matches other methods at predicting transcriptomes and substantially outperforms existing latent representations at viability prediction. The transcriptome-viability relationship provided by the model further allows the recovery of known biomarkers of cell viability while suggesting novel ones. Overall, DORA provides a unified framework delivering actionable biological insights for phenotypic drug screening and personalized medicine.