Behrang Shafei

Jose Pablo Folch, Robert M Lee, Behrang Shafei et al.

Bayesian Optimization is a useful tool for experiment design. Unfortunately, the classical, sequential setting of Bayesian Optimization does not translate well into laboratory experiments, for instance battery design, where measurements may come from different sources and their evaluations may require significant waiting times. Multi-fidelity Bayesian Optimization addresses the setting with measurements from different sources. Asynchronous batch Bayesian Optimization provides a framework to select new experiments before the results of the prior experiments are revealed. This paper proposes an algorithm combining multi-fidelity and asynchronous batch methods. We empirically study the algorithm behavior, and show it can outperform single-fidelity batch methods and multi-fidelity sequential methods. As an application, we consider designing electrode materials for optimal performance in pouch cells using experiments with coin cells to approximate battery performance.

Ben Tu, Axel Gandy, Nikolas Kantas et al.

Many real-world problems can be phrased as a multi-objective optimization problem, where the goal is to identify the best set of compromises between the competing objectives. Multi-objective Bayesian optimization (BO) is a sample efficient strategy that can be deployed to solve these vector-valued optimization problems where access is limited to a number of noisy objective function evaluations. In this paper, we propose a novel information-theoretic acquisition function for BO called Joint Entropy Search (JES), which considers the joint information gain for the optimal set of inputs and outputs. We present several analytical approximations to the JES acquisition function and also introduce an extension to the batch setting. We showcase the effectiveness of this new approach on a range of synthetic and real-world problems in terms of the hypervolume and its weighted variants.

Alexander Thebelt, Calvin Tsay, Robert M. Lee et al.

Tree ensembles can be well-suited for black-box optimization tasks such as algorithm tuning and neural architecture search, as they achieve good predictive performance with little or no manual tuning, naturally handle discrete feature spaces, and are relatively insensitive to outliers in the training data. Two well-known challenges in using tree ensembles for black-box optimization are (i) effectively quantifying model uncertainty for exploration and (ii) optimizing over the piece-wise constant acquisition function. To address both points simultaneously, we propose using the kernel interpretation of tree ensembles as a Gaussian Process prior to obtain model variance estimates, and we develop a compatible optimization formulation for the acquisition function. The latter further allows us to seamlessly integrate known constraints to improve sampling efficiency by considering domain-knowledge in engineering settings and modeling search space symmetries, e.g., hierarchical relationships in neural architecture search. Our framework performs as well as state-of-the-art methods for unconstrained black-box optimization over continuous/discrete features and outperforms competing methods for problems combining mixed-variable feature spaces and known input constraints.

Johannes P. Dürholt, Thomas S. Asche, Johanna Kleinekorte et al.

Our open-source Python package BoFire combines Bayesian Optimization (BO) with other design of experiments (DoE) strategies focusing on developing and optimizing new chemistry. Previous BO implementations, for example as they exist in the literature or software, require substantial adaptation for effective real-world deployment in chemical industry. BoFire provides a rich feature-set with extensive configurability and realizes our vision of fast-tracking research contributions into industrial use via maintainable open-source software. Owing to quality-of-life features like JSON-serializability of problem formulations, BoFire enables seamless integration of BO into RESTful APIs, a common architecture component for both self-driving laboratories and human-in-the-loop setups. This paper discusses the differences between BoFire and other BO implementations and outlines ways that BO research needs to be adapted for real-world use in a chemistry setting.

Becky Langdon, Gabriel D. Patrón, Chrysoula D. Kappatou et al.

The optimisation of fed-batch (bio)chemical process recipes is subject to inherent, underlying, and unmeasurable fluctuations across batches, whose trajectories are difficult to model and costly to measure. Bayesian Optimisation (BayesOpt) is a powerful tool for sampling and optimisation of expensive-to-measure functions. Gaussian Processes (GPs), the surrogate models used in BayesOpt, are static, forecast poorly, and lack generalisation across experiments, limiting their applicability to time-varying batch processes with stochastic parameters, i.e., process fluctuations. This work investigates System-Aware Neural ODE Processes (SANODEP) as a meta-learning model to overcome the limitations of GPs and increase few-shot optimisation performance in BayesOpt. Using a penicillin batch production case study, we find that SANODEP outperforms GP-based BayesOpt in the low-data regime, resulting in improved objectives when few experimental runs are performed. These improvements are observed in both on- and off-distribution batches, highlighting the generalisation capabilities of SANODEP. Using this approach, batch process operators can accelerate the initial optimisation steps in BayesOpt by deploying meta-learning or optimise the process with fewer experiments when the experimental cost is high.

Jose Pablo Folch, Calvin Tsay, Robert M Lee et al.

Bayesian optimization is a methodology to optimize black-box functions. Traditionally, it focuses on the setting where you can arbitrarily query the search space. However, many real-life problems do not offer this flexibility; in particular, the search space of the next query may depend on previous ones. Example challenges arise in the physical sciences in the form of local movement constraints, required monotonicity in certain variables, and transitions influencing the accuracy of measurements. Altogether, such transition constraints necessitate a form of planning. This work extends classical Bayesian optimization via the framework of Markov Decision Processes. We iteratively solve a tractable linearization of our utility function using reinforcement learning to obtain a policy that plans ahead for the entire horizon. This is a parallel to the optimization of an acquisition function in policy space. The resulting policy is potentially history-dependent and non-Markovian. We showcase applications in chemical reactor optimization, informative path planning, machine calibration, and other synthetic examples.

Toby Boyne, Jose Pablo Folch, Robert M Lee et al.

We perform Bayesian optimization using a Gaussian process perspective on Bayesian Additive Regression Trees (BART). Our BART Kernel (BARK) uses tree agreement to define a posterior over piecewise-constant functions, and we explore the space of tree kernels using a Markov chain Monte Carlo approach. Where BART only samples functions, the resulting BARK model obtains samples of Gaussian processes defining distributions over functions, which allow us to build acquisition functions for Bayesian optimization. Our tree-based approach enables global optimization over the surrogate, even for mixed-feature spaces. Moreover, where many previous tree-based kernels provide uncertainty quantification over function values, our sampling scheme captures uncertainty over the tree structure itself. Our experiments show the strong performance of BARK on both synthetic and applied benchmarks, due to the combination of our fully Bayesian surrogate and the optimization procedure.

Ben Tu, Nikolas Kantas, Robert M. Lee et al.

The goal of multi-objective optimisation is to identify the Pareto front surface which is the set obtained by connecting the best trade-off points. Typically this surface is computed by evaluating the objectives at different points and then interpolating between the subset of the best evaluated trade-off points. In this work, we propose to parameterise the Pareto front surface using polar coordinates. More precisely, we show that any Pareto front surface can be equivalently represented using a scalar-valued length function which returns the projected length along any positive radial direction. We then use this representation in order to rigorously develop the theory and applications of stochastic Pareto front surfaces. In particular, we derive many Pareto front surface statistics of interest such as the expectation, covariance and quantiles. We then discuss how these can be used in practice within a design of experiments setting, where the goal is to both infer and use the Pareto front surface distribution in order to make effective decisions. Our framework allows for clear uncertainty quantification and we also develop advanced visualisation techniques for this purpose. Finally we discuss the applicability of our ideas within multivariate extreme value theory and illustrate our methodology in a variety of numerical examples, including a case study with a real-world air pollution data set.

Ben Tu, Nikolas Kantas, Robert M. Lee et al.

Robust optimisation is a well-established framework for optimising functions in the presence of uncertainty. The inherent goal of this problem is to identify a collection of inputs whose outputs are both desirable for the decision maker, whilst also being robust to the underlying uncertainties in the problem. In this work, we study the multi-objective case of this problem. We identify that the majority of all robust multi-objective algorithms rely on two key operations: robustification and scalarisation. Robustification refers to the strategy that is used to account for the uncertainty in the problem. Scalarisation refers to the procedure that is used to encode the relative importance of each objective to a scalar-valued reward. As these operations are not necessarily commutative, the order that they are performed in has an impact on the resulting solutions that are identified and the final decisions that are made. The purpose of this work is to give a thorough exposition on the effects of these different orderings and in particular highlight when one should opt for one ordering over the other. As part of our analysis, we showcase how many existing risk concepts can be integrated into the specification and solution of a robust multi-objective optimisation problem. Besides this, we also demonstrate how one can principally define the notion of a robust Pareto front and a robust performance metric based on our ``robustify and scalarise'' methodology. To illustrate the efficacy of these new ideas, we present two insightful case studies which are based on real-world data sets.

Jixiang Qing, Becky D Langdon, Robert M Lee et al.

We consider the problem of optimizing initial conditions and termination time in dynamical systems governed by unknown ordinary differential equations (ODEs), where evaluating different initial conditions is costly and the state's value can not be measured in real-time but only with a delay while the measuring device processes the sample. To identify the optimal conditions in limited trials, we introduce a few-shot Bayesian Optimization (BO) framework based on the system's prior information. At the core of our approach is the System-Aware Neural ODE Processes (SANODEP), an extension of Neural ODE Processes (NODEP) designed to meta-learn ODE systems from multiple trajectories using a novel context embedding block. We further develop a two-stage BO framework to effectively incorporate search space constraints, enabling efficient optimization of both initial conditions and observation timings. We conduct extensive experiments showcasing SANODEP's potential for few-shot BO within dynamical systems. We also explore SANODEP's adaptability to varying levels of prior information, highlighting the trade-off between prior flexibility and model fitting accuracy.

Ben Tu, Nikolas Kantas, Robert M. Lee et al.

The goal of multi-objective optimisation is to identify a collection of points which describe the best possible trade-offs between the multiple objectives. In order to solve this vector-valued optimisation problem, practitioners often appeal to the use of scalarisation functions in order to transform the multi-objective problem into a collection of single-objective problems. This set of scalarised problems can then be solved using traditional single-objective optimisation techniques. In this work, we formalise this convention into a general mathematical framework. We show how this strategy effectively recasts the original multi-objective optimisation problem into a single-objective optimisation problem defined over sets. An appropriate class of objective functions for this new problem are the R2 utilities, which are utility functions that are defined as a weighted integral over the scalarised optimisation problems. As part of our work, we show that these utilities are monotone and submodular set functions which can be optimised effectively using greedy optimisation algorithms. We then analyse the performance of these greedy algorithms both theoretically and empirically. Our analysis largely focusses on Bayesian optimisation, which is a popular probabilistic framework for black-box optimisation.

Jose Pablo Folch, Shiqiang Zhang, Robert M Lee et al.

Bayesian Optimization is a very effective tool for optimizing expensive black-box functions. Inspired by applications developing and characterizing reaction chemistry using droplet microfluidic reactors, we consider a novel setting where the expense of evaluating the function can increase significantly when making large input changes between iterations. We further assume we are working asynchronously, meaning we have to select new queries before evaluating previous experiments. This paper investigates the problem and introduces 'Sequential Bayesian Optimization via Adaptive Connecting Samples' (SnAKe), which provides a solution by considering large batches of queries and preemptively building optimization paths that minimize input costs. We investigate some convergence properties and empirically show that the algorithm is able to achieve regret similar to classical Bayesian Optimization algorithms in both synchronous and asynchronous settings, while reducing input costs significantly. We show the method is robust to the choice of its single hyper-parameter and provide a parameter-free alternative.