Protein Sequence Design in a Latent Space via Model-based Reinforcement Learning

Minji Lee, Luiz Felipe Vecchietti, Hyunkyu Jung, Hyunjoo Ro, Meeyoung Cha, Ho Min Kim

Keywords: Biological sequence design, Model-based reinforcement learning, Protein design, Representation learning

TL;DR: This study investigates why many model-based biological sequence design methods produce results that empirically fail and proposes a novel optimization process that can efficiently traverse a latent representation space instead of the sequence space.

Abstract: Proteins are complex molecules responsible for different functions in the human body. Enhancing the functionality of a protein and/or cellular fitness can significantly impact various industries. However, their optimization remains challenging, and sequences generated by data-driven methods often fail in wet lab experiments. This study investigates the limitations of existing model-based sequence design methods and presents a novel optimization framework that can efficiently traverse the latent representation space instead of the protein sequence space. Our framework generates proteins with higher functionality and cellular fitness by modeling the sequence design task as a Markov decision process and applying model-based reinforcement learning. We discuss the results in a comprehensive evaluation of two distinct proteins, GPF and His3, along with the predicted structure of optimized sequences using deep learning-based structure prediction.

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