Transfer Learning Architectures for Scalable Multi-Fidelity Bayesian Optimization
Authors: Jaewook Lee, Ethan Errington, Christian D. Lorenz, Miao Guo
Organizations: Department of Engineering, King’s College London, London, WC2R 2LS, United Kingdom.
Abstract
Self-driving laboratories increasingly rely on multi-fidelity Bayesian optimization (MFBO) to balance cheap, approximate evaluations against scarce, expensive ones, with a predictive surrogate at its core. Gaussian processes (GPs) are the default choice, but they scale poorly as data accumulate and assume a smooth landscape that molecular and materials search spaces routinely violate. Transfer learning offers an alternative suited to this regime: it learns a representation from abundant cheap data and adapts it to sparse expensive data. Despite its use in property prediction, transfer learning has not been tested as the engine of a closed-loop optimization. Here we benchmark eleven transfer-learning surrogates against four GP methods under an identical selection rule, fidelity budget, and model size, across nine tasks spanning synthetic functions to real chemistry and materials problems. GPs win on smooth, low-dimensional functions but perform worst on molecular and materials problems, where transfer-learning surrogates reach substantially better solutions using far less computation. Because acquisition policy is held fixed across surrogates, this advantage is attributable to the surrogate itself. Uncertainty-driven exploration is not reliably beneficial, and calibration does not predict optimization performance, so greedy exploitation of the transfer-learned mean is the more robust default. Transfer learning is therefore the surrogate of choice for molecular and materials MFBO.
Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance. Here we present a systematic, compute-aware study of BO that evaluates surrogate models along two axes: optimization quality and computational frugality. Across eight benchmark functions and nine real-world datasets spanning materials science, mechanics, robotics, chemistry, and machine learning, we benchmark four surrogate models: Gaussian Processes, Random Forests, NGBoost, and Bayesian Adaptive Spline Surfaces. We show that Gaussian Process-based BO consistently incurs the highest time and memory overhead without delivering superior optimization or sample efficiency. In contrast, scalable alternatives achieve equal or better performance at a fraction of the computational cost. Motivated by these findings, we introduce a surrogate-recommendation framework that predicts the most suitable BO surrogate from inexpensive dataset characteristics. Together, these results establish FruBO as a reproducible, compute-aware baseline for Bayesian Optimization and provide practical guidance for surrogate selection under limited computational and experimental budgets.
Bayesian optimization routinely warm-starts a target experiment with data from related source tasks, and the multi-task Gaussian process is the textbook surrogate for the job. We revisit this default in a controlled setting and find that it misestimates the cross-task correlation even in the simplest non-trivial case, affinely related source and target tasks, where a working transfer learning method should obviously succeed. We trace the failure to two independent structural mechanisms. Per-task standardization, the textbook fix for the affine slice ambiguity, propagates a finite-sample alignment error into the recovered correlation. The marginal likelihood itself identifies the correlation only at a per-sample rate that a Gaussian process at non-overlapping designs further dilutes. We propose three conservative remedies that follow from the analysis: promoting per-task means and scales to model parameters, restricting the task covariance to non-negative correlations, and co-locating part of the source and target designs. Across synthetic multi-task problems and surrogate-based hyperparameter tuning transfer, these remedies recover the target-only baseline on the simple instances, while the broader failure persists on harder instances and across most rank-based and latent-context variants.
Black-box optimization is a ubiquitous problem in science and engineering, often dealing with expensive objective functions with cheaper lower-fidelity proxies available. Multi-fidelity Bayesian optimization (MF-BO) is a principled approach to this problem, leveraging correlations across different fidelities when querying the objective. However, for many important MF-BO tasks, the true highest-fidelity function is prohibitively expensive to be part of the optimization loop. Nevertheless, practitioners often have gold standard data (observations of the highest-fidelity function) obtained from previous experiments that might provide information for the current task. For instance, in molecular optimization, chemists often pick the top-k candidate molecules using various computer simulations, and later reveal their true objective function values. In this work, we demonstrate the suboptimality of standard MF-BO algorithms in the real-world scenarios above, even under ideal assumptions. Next, we mitigate this problem by incorporating historical high-fidelity data accompanied by task descriptors---which can be explicitly given or extracted from unstructured metadata. We demonstrate the effectiveness of our methods on synthetic functions, as well as real-world problems in chemistry and hyperparameter optimization.
Gustavo Sutter, Hao Wang, Luis Ricardez-Sandoval +2