Accelerated Discovery of Cryoprotectant Cocktails via Multi-Objective Bayesian Optimization

Abstract

Designing cryoprotectant agent (CPA) cocktails for vitrification is challenging because formulations must be concentrated enough to suppress ice formation yet non-toxic enough to preserve cell viability. This tradeoff creates a large, multi-objective design space in which traditional discovery is slow, often relying on expert intuition or exhaustive experimentation. We present a data-efficient framework that accelerates CPA cocktail design by combining high-throughput screening with an active-learning loop based on multi-objective Bayesian optimization. From an initial set of measured cocktails, we train probabilistic surrogate models to predict concentration and viability and quantify uncertainty across candidate formulations. We then iteratively select the next experiments by prioritizing cocktails expected to improve the Pareto front, maximizing expected Pareto improvement under uncertainty, and update the models as new assay results are collected. Wet-lab validation shows that our approach efficiently discovers cocktails that simultaneously achieve high CPA concentrations and high post-exposure viability. Relative to a naive strategy and a strong baseline, our method improves dominated hypervolume by 9.5\% and 4.5\%, respectively, while reducing the number of experiments needed to reach high-quality solutions. In complementary synthetic studies, it recovers a comparably strong set of Pareto-optimal solutions using only 30\% of the evaluations required by the prior state-of-the-art multi-objective approach, which amounts to saving approximately 10 weeks of experimental time. Because the framework assumes only a suitable assay and defined formulation space, it can be adapted to different CPA libraries, objective definitions, and cell lines to accelerate cryopreservation development.