Jixiang Qing

Victor Picheny, Joel Berkeley, Henry B. Moss et al. · berkeley

We present Trieste, an open-source Python package for Bayesian optimization and active learning benefiting from the scalability and efficiency of TensorFlow. Our library enables the plug-and-play of popular TensorFlow-based models within sequential decision-making loops, e.g. Gaussian processes from GPflow or GPflux, or neural networks from Keras. This modular mindset is central to the package and extends to our acquisition functions and the internal dynamics of the decision-making loop, both of which can be tailored and extended by researchers or engineers when tackling custom use cases. Trieste is a research-friendly and production-ready toolkit backed by a comprehensive test suite, extensive documentation, and available at https://github.com/secondmind-labs/trieste.

Jixiang Qing, Henry B. Moss, Tom Dhaene et al.

We present Parallel Feasible Pareto Frontier Entropy Search ($\{\text{PF}\}^2$ES) -- a novel information-theoretic acquisition function for multi-objective Bayesian optimization supporting unknown constraints and batch query. Due to the complexity of characterizing the mutual information between candidate evaluations and (feasible) Pareto frontiers, existing approaches must either employ crude approximations that significantly hamper their performance or rely on expensive inference schemes that substantially increase the optimization's computational overhead. By instead using a variational lower bound, $\{\text{PF}\}^2$ES provides a low-cost and accurate estimate of the mutual information. We benchmark $\{\text{PF}\}^2$ES against other information-theoretic acquisition functions, demonstrating its competitive performance for optimization across synthetic and real-world design problems.

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.

Jixiang Qing, Henry Moss, Matthias Sachs

We consider the active learning problem where the goal is to learn an unknown function with low prediction error under an unknown Boltzmann distribution induced by the function itself. This self-induced weighting arises naturally in problems such as potential energy surface (PES) modeling in computational chemistry, yet poses unique challenges as the target distribution is unknown and its partition function is intractable. We propose \texttt{AB-SID-iVAR}, a Gaussian Process-based acquisition function that approximates the intractable Bayesian target distribution in closed form while avoiding partition function estimation, and is applicable to both discrete and continuous input domains. We also analyze a Thompson sampling alternative (\texttt{TS-SID-iVAR}) as a higher variance Monte Carlo variant. Despite the unknown target, under mild conditions, we establish that the terminal prediction error vanishes with high probability, and provide a tighter average-case guarantee. We demonstrate consistent improvements over existing approaches in this setting on synthetic benchmarks and real-world PES modeling and drug discovery tasks.

Yilin Xie, Shiqiang Zhang, Jixiang Qing et al.

Graph Bayesian optimization (BO) has shown potential as a powerful and data-efficient tool for neural architecture search (NAS). Most existing graph BO works focus on developing graph surrogates models, i.e., metrics of networks and/or different kernels to quantify the similarity between networks. However, the acquisition optimization, as a discrete optimization task over graph structures, is not well studied due to the complexity of formulating the graph search space and acquisition functions. This paper presents explicit optimization formulations for graph input space including properties such as reachability and shortest paths, which are used later to formulate graph kernels and the acquisition function. We theoretically prove that the proposed encoding is an equivalent representation of the graph space and provide restrictions for the NAS domain with either node or edge labels. Numerical results over several NAS benchmarks show that our method efficiently finds the optimal architecture for most cases, highlighting its efficacy.

Toby Boyne, Juan S. Campos, Becky D. Langdon et al.

Machine learning has promised to change the landscape of laboratory chemistry, with impressive results in molecular property prediction and reaction retro-synthesis. However, chemical datasets are often inaccessible to the machine learning community as they tend to require cleaning, thorough understanding of the chemistry, or are simply not available. In this paper, we introduce a novel dataset for yield prediction, providing the first-ever transient flow dataset for machine learning benchmarking, covering over 1200 process conditions. While previous datasets focus on discrete parameters, our experimental set-up allow us to sample a large number of continuous process conditions, generating new challenges for machine learning models. We focus on solvent selection, a task that is particularly difficult to model theoretically and therefore ripe for machine learning applications. We showcase benchmarking for regression algorithms, transfer-learning approaches, feature engineering, and active learning, with important applications towards solvent replacement and sustainable manufacturing.

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.