Current methods of finding optimal experimental conditions, Edisonian systematic searches, often inefficiently evaluate suboptimal design points and require fine resolution to identify near optimal conditions. For expensive experimental campaigns or those with large design spaces, the shortcomings of the status quo approaches are more significant. Here, we extend Bayesian optimization (BO) and introduce a chemically-informed data-driven optimization (ChIDDO) approach. This approach uses inexpensive and low-fidelity information obtained from physical models of chemical processes and subsequently combines it with expensive and high-fidelity experimental data to optimize a common objective function. Using common optimization benchmark objective functions, we describe scenarios in which the ChIDDO algorithm outperforms the traditional BO approach, and then implement the algorithm on a simulated electrochemical engineering optimization problem.
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Batched Stochastic Bayesian Optimization via Combinatorial Constraints Design
In many high-throughput experimental design settings, such as those common in biochemical engineering, batched queries are often more cost effective than one-by-one sequential queries. Furthermore, it is often not possible to directly choose items to query. Instead, the experimenter specifies a set of constraints that generates a library of possible items, which are then selected stochastically. Motivated by these considerations, we investigate Batched Stochastic Bayesian Optimization (BSBO), a novel Bayesian optimization scheme for choosing the constraints in order to guide exploration towards items with greater utility. We focus on site saturation mutagenesis, a prototypical setting of BSBO in biochemical engineering, and propose a natural objective function for this problem. Importantly, we show that our objective function can be efficiently decomposed as a difference of submodular functions (DS), which allows us to employ DS optimization tools to greedily identify sets of constraints that increase the likelihood of finding items with high utility. Our experimental results show that our algorithm outperforms common heuristics on both synthetic and two real protein datasets.
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- Award ID(s):
- 1645832
- NSF-PAR ID:
- 10207052
- Editor(s):
- Chaudhuri, K
- Date Published:
- Journal Name:
- Proceedings of Machine Learning Research
- Volume:
- 89
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
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