PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design

• URL: http://arxiv.org/abs/2210.04096v1
• Date: Sat, 8 Oct 2022 19:42:16 GMT
• Title: PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design
• Authors: Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra and Kyunghyun Cho
• Abstract summary: We present PropertyDAG, a framework that operates on top of the traditional multi-objective BO to impose this desired ordering on the objectives. We demonstrate its performance over multiple simulated active learning iterations on a penicillin production task, toy numerical problem, and a real-world antibody design task.
• Score: 42.92794039060737
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences. Whereas it is possible to optimize the various properties of interest jointly using a multi-objective acquisition function, such as the expected hypervolume improvement (EHVI), this approach does not account for objectives with a hierarchical dependency structure. We consider a common use case where some regions of the Pareto frontier are prioritized over others according to a specified $\textit{partial ordering}$ in the objectives. For instance, when designing antibodies, we would like to maximize the binding affinity to a target antigen only if it can be expressed in live cell culture -- modeling the experimental dependency in which affinity can only be measured for antibodies that can be expressed and thus produced in viable quantities. In general, we may want to confer a partial ordering to the properties such that each property is optimized conditioned on its parent properties satisfying some feasibility condition. To this end, we present PropertyDAG, a framework that operates on top of the traditional multi-objective BO to impose this desired ordering on the objectives, e.g. expression $\rightarrow$ affinity. We demonstrate its performance over multiple simulated active learning iterations on a penicillin production task, toy numerical problem, and a real-world antibody design task.

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