A General Framework for Constrained Bayesian Optimization using Information-based Search

We present an information-theoretic framework for solving global black-box optimization problems that also have black-box constraints. Of particular interest to us is to efficiently solve problems with $\textit{decoupled}$ constraints, in which subsets of the objective and constraint functions may be evaluated independently. For example, when the objective is evaluated on a CPU and the constraints are evaluated independently on a GPU. These problems require an acquisition function that can be separated into the contributions of the individual function evaluations. We develop one such acquisition function and call it Predictive Entropy Search with Constraints (PESC). PESC is an approximation to the expected information gain criterion and it compares favorably to alternative approaches based on improvement in several synthetic and real-world problems. In addition to this, we consider problems with a mix of functions that are fast and slow to evaluate. These problems require balancing the amount of time spent in the meta-computation of PESC and in the actual evaluation of the target objective. We take a bounded rationality approach and develop a partial update for PESC which trades off accuracy against speed. We then propose a method for adaptively switching between the partial and full updates for PESC. This allows us to interpolate between versions of PESC that are efficient in terms of function evaluations and those that are efficient in terms of wall-clock time. Overall, we demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.Rafael del Pino Foundation, Google Focused Research Award, Engineering and Physical Sciences Research Council (Grant IDs: EP/I036575/1, EP/J012300/1

A General Framework for Constrained Bayesian Optimization using Information-based Search

This is the author accepted manuscript. The final version is available from MIT Press via https://dl.acm.org/citation.cfm?id=2946645.3053442.We present an information-theoretic framework for solving global black-box optimization problems that also have black-box constraints. Of particular interest to us is to efficiently solve problems with decoupled constraints, in which subsets of the objective and constraint functions may be evaluated independently. For example, when the objective is evaluated on a CPU and the constraints are evaluated independently on a GPU. These problems require an acquisition function that can be separated into the contributions of the individual function evaluations. We develop one such acquisition function and call it Predictive Entropy Search with Constraints (PESC). PESC is an approximation to the expected information gain criterion and it compares favorably to alternative approaches based on improvement in several synthetic and real-world problems. In addition to this, we consider problems with a mix of functions that are fast and slow to evaluate. These problems require balancing the amount of time spent in the meta-computation of PESC and in the actual evaluation of the target objective. We take a bounded rationality approach and develop a partial update for PESC which trades off accuracy against speed. We then propose a method for adaptively switching between the partial and full updates for PESC. This allows us to interpolate between versions of PESC that are efficient in terms of function evaluations and those that are efficient in terms of wall-clock time. Overall, we demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.José Miguel Hernández-Lobato acknowledges support from the Rafael del Pino Foundation. Zoubin Ghahramani acknowledges support from Google Focused Research Award and EPSRC grant EP/I036575/1. Matthew W. Hoffman acknowledges support from EPSRC grant EP/J012300/1

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

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.Comment: 9 pages, 7 figures. Submitted to NeurIPS 2022 AI4Science Worksho

Advances in Bayesian Optimization with Applications in Aerospace Engineering

Optimization requires the quantities of interest that define objective functions and constraints to be evaluated a large number of times. In aerospace engineering, these quantities of interest can be expensive to compute (e.g., numerically solving a set of partial differential equations), leading to a challenging optimization problem. Bayesian optimization (BO) is a class of algorithms for the global optimization of expensive-to-evaluate functions. BO leverages all past evaluations available to construct a surrogate model. This surrogate model is then used to select the next design to evaluate. This paper reviews two recent advances in BO that tackle the challenges of optimizing expensive functions and thus can enrich the optimization toolbox of the aerospace engineer. The first method addresses optimization problems subject to inequality constraints where a finite budget of evaluations is available, a common situation when dealing with expensive models (e.g., a limited time to conduct the optimization study or limited access to a supercomputer). This challenge is addressed via a lookahead BO algorithm that plans the sequence of designs to evaluate in order to maximize the improvement achieved, not only at the next iteration, but once the total budget is consumed. The second method demonstrates how sensitivity information, such as gradients computed with adjoint methods, can be incorporated into a BO algorithm. This algorithm exploits sensitivity information in two ways: first, to enhance the surrogate model, and second, to improve the selection of the next design to evaluate by accounting for future gradient evaluations. The benefits of the two methods are demonstrated on aerospace examples