# A Guide to Bayesian Optimization in Bioprocess Engineering

arXiv: https://arxiv.org/abs/2508.10642 · HTML: https://mlsanity.com/paper/2508.10642/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 40 of its 135 references that are in the map.
- First posted on arXiv 14 Aug 2025.

## Builds on (most cited first, 30 of 40)

- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration](https://mlsanity.com/paper/1809.11165/) (2018)
- [Deep Kernel Learning](https://mlsanity.com/paper/1511.02222/) (2015)
- [Scalable Global Optimization via Local Bayesian Optimization](https://mlsanity.com/paper/1910.01739/) (2019)
- [Predictive Entropy Search for Efficient Global Optimization of Black-box Functions](https://mlsanity.com/paper/1406.2541/) (2014)
- [Unexpected Improvements to Expected Improvement for Bayesian Optimization](https://mlsanity.com/paper/2310.20708/) (2023)
- [High-Dimensional Bayesian Optimization with Sparse Axis-Aligned Subspaces](https://mlsanity.com/paper/2103.00349/) (2021)
- [Maximizing acquisition functions for Bayesian optimization](https://mlsanity.com/paper/1805.10196/) (2018)
- [Batch Bayesian Optimization via Local Penalization](https://mlsanity.com/paper/1505.08052/) (2015)
- [Vanilla Bayesian Optimization Performs Great in High Dimensions](https://mlsanity.com/paper/2402.02229/) (2024)
- [Predictive Entropy Search for Multi-objective Bayesian Optimization](https://mlsanity.com/paper/1511.05467/) (2015)
- [Bayesian optimization for materials design](https://mlsanity.com/paper/1506.01349/) (2015)
- [A survey on high-dimensional Gaussian process modeling with application to Bayesian optimization](https://mlsanity.com/paper/2111.05040/) (2021)
- [Preferential Bayesian Optimization](https://mlsanity.com/paper/1704.03651/) (2017)
- [Dealing with Integer-valued Variables in Bayesian Optimization with Gaussian Processes](https://mlsanity.com/paper/1706.03673/) (2017)
- [Bayesian Optimisation over Multiple Continuous and Categorical Inputs](https://mlsanity.com/paper/1906.08878/) (2019)
- [BOSS: Bayesian Optimization over String Spaces](https://mlsanity.com/paper/2010.00979/) (2020)
- [Think Global and Act Local: Bayesian Optimisation over High-Dimensional Categorical and Mixed Search Spaces](https://mlsanity.com/paper/2102.07188/) (2021)
- [Benchmarking the Performance of Bayesian Optimization across Multiple Experimental Materials Science Domains](https://mlsanity.com/paper/2106.01309/) (2021)
- [GIBBON: General-purpose Information-Based Bayesian OptimisatioN](https://mlsanity.com/paper/2102.03324/) (2021)
- [Bayesian Optimization over Discrete and Mixed Spaces via Probabilistic Reparameterization](https://mlsanity.com/paper/2210.10199/) (2022)
- [Diversified Sampling for Batched Bayesian Optimization with Determinantal Point Processes](https://mlsanity.com/paper/2110.11665/) (2021)
- [Why Non-myopic Bayesian Optimization is Promising and How Far Should We Look-ahead? A Study via Rollout](https://mlsanity.com/paper/1911.01004/) (2019)
- [Spatial Mapping with Gaussian Processes and Nonstationary Fourier Features](https://mlsanity.com/paper/1711.05615/) (2017)
- [An Intuitive Tutorial to Gaussian Process Regression](https://mlsanity.com/paper/2009.10862/) (2020)
- [Combining Multi-Fidelity Modelling and Asynchronous Batch Bayesian Optimization](https://mlsanity.com/paper/2211.06149/) (2022)
- [Large-Scale Learning with Fourier Features and Tensor Decompositions](https://mlsanity.com/paper/2109.01545/) (2021)
- [New Paradigms for Exploiting Parallel Experiments in Bayesian Optimization](https://mlsanity.com/paper/2210.01071/) (2022)
- [Machine Learning-Assisted Discovery of Flow Reactor Designs](https://mlsanity.com/paper/2308.08841/) (2023)

## Built on by (most cited first, 1 of 1)

- [A Human-in-the-Loop Bayesian Optimization Framework for Constraint-Aware Bioprocess Development](https://mlsanity.com/paper/2606.19230/) (2026)

## Abstract (arXiv)

Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small datasets, and provide adaptive suggestions for sequential experimentation. While still in its infancy, Bayesian optimization has recently gained traction in bioprocess engineering. However, experimentation with biological systems is highly complex and the resulting experimental uncertainty requires specific extensions to classical Bayesian optimization. Moreover, current literature often targets readers with a strong statistical background, limiting its accessibility for practitioners. In light of these developments, this review has two aims: first, to provide an intuitive and practical introduction to Bayesian optimization; and second, to outline promising application areas and open algorithmic challenges, thereby highlighting opportunities for future research in machine learning.