Pitfalls and Remedies for Multi-Task Bayesian Optimization

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.

This paper extends safety guarantees for multi-task Bayesian optimization with uncertain co-regionalization matrices from intrinsic co-regionalization models to linear models of co-regionalization. The latter allows for more flexible modeling of the inter-task correlations by composing multiple features. We derive uniform error bounds for vector-valued functions sampled from a Gaussian process with a linear model of co-regionalization kernel. Furthermore, we show the potential performance gains of linear models of co-regionalization in a numerical comparison on a safe multi-task Bayesian optimization benchmark.

Existing methods for transfer learning struggle to deal with situations where the source datasets are limited and not guaranteed to be well-aligned with the target dataset. A typical strategy is to use the empirical loss minimizer on the source data as a prior mean for the target parameters. Our key conceptual contribution is to use a risk minimizer conditional on source parameters instead. This allows us to construct a single joint prior distribution for all parameters from the source datasets as well as the target dataset. As a consequence, we benefit from full Bayesian uncertainty quantification and can perform model averaging via Gibbs sampling over indicator variables governing the inclusion of each source dataset. We show how a particular instantiation of our prior leads to a Bayesian Lasso in a transformed coordinate system and discuss computational techniques to scale our approach to moderately sized datasets. We discuss connections between the Maximum a Posteriori estimate associated with our approach and the recently proposed Trans-Lasso method and demonstrate that the MAP estimator MSE-dominates the Trans-Lasso in the normal means setting when there is no regularization on the source datasets. Finally, we perform numerical experiments finding that full Bayesian inference provides superior predictive performance relative to Trans-Lasso on a genetics application, especially when the source data are limited.