De Novo Drug Design with Joint Transformers

Adam Izdebski, Ewelina Weglarz-Tomczak, Ewa Szczurek, Jakub M. Tomczak

Abstract: De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.