Poster
in
Workshop: Machine Learning in Structural Biology Workshop

Designing Biological Sequences via Meta-Reinforcement Learning and Bayesian Optimization

Leo Feng · Padideh Nouri · Aneri Muni · Yoshua Bengio · Pierre-Luc Bacon

Abstract:

Designing functionally interesting biological sequences pose challenges due to the combinatorially large space of the problem. As such, the acceleration of exploration through this landscape can have a substantial impact on the progress of the medical field. Motivated by this, we propose MetaRLBO where we (1) train an autoregressive generative model via Meta-Reinforcement Learning augmented with surrogate reward functions and exploration bonus to navigate through the sequence space efficiently. The Meta-RL policy is trained over a distribution of beliefs (i.e., proxy oracles) of the objective function, encouraging the policy to generate diverse sequences. Due to the large-batch and low-round nature of the wet-lab evaluations (true function evaluation), we (2) perform a more targeted evaluation through Bayesian Optimization. Our in-silico experiments show that meta-learning over such ensembles provides robustness against reward misspecification and achieves competitive results compared to existing strong baselines.

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