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Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders

Samuel Stanton · Wesley Maddox · Nate Gruver · Phillip Maffettone · Emily Delaney · Peyton Greenside · Andrew Wilson

Hall E #533

Keywords: [ PM: Bayesian Models and Methods ] [ OPT: Discrete and Combinatorial Optimization ] [ OPT: Multi-objective Optimization ] [ DL: Generative Models and Autoencoders ] [ PM: Gaussian Processes ] [ APP: Chemistry and Drug Discovery ] [ MISC: Online Learning, Active Learning and Bandits ]


Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous optimization. However, its adoption for drug design has been hindered by the discrete, high-dimensional nature of the decision variables. We develop a new approach (LaMBO) which jointly trains a denoising autoencoder with a discriminative multi-task Gaussian process head, allowing gradient-based optimization of multi-objective acquisition functions in the latent space of the autoencoder. These acquisition functions allow LaMBO to balance the explore-exploit tradeoff over multiple design rounds, and to balance objective tradeoffs by optimizing sequences at many different points on the Pareto frontier. We evaluate LaMBO on two small-molecule design tasks, and introduce new tasks optimizing in silico and in vitro properties of large-molecule fluorescent proteins. In our experiments LaMBO outperforms genetic optimizers and does not require a large pretraining corpus, demonstrating that BayesOpt is practical and effective for biological sequence design.

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