Bioprocesses are central to modern biotechnology, enabling sustainable production in pharmaceuticals, specialty chemicals, cosmetics, and food. However, developing high-performing processes is costly and complex, requiring iterative, multi-scale experimentation from microtiter plates to pilot reactors. Conventional Design of Experiments (DoE) approaches often struggle to address process scale-up and the joint optimization of reaction conditions and biocatalyst selection. We propose a multi-fidelity batch Bayesian optimization framework to accelerate bioprocess development and reduce experimental costs. The method integrates Gaussian Processes tailored for multi-fidelity modeling and mixed-variable optimization, guiding experiment selection across scales and biocatalysts. A custom simulation of a Chinese Hamster Ovary bioprocess, capturing non-linear and coupled scale-up dynamics, is used for benchmarking against multiple simulated industrial DoE baselines. Multiple case studies show how the proposed workflow can achieve a reduction in experimental costs and increased yield. This work provides a data-efficient strategy for bioprocess optimization and highlights future opportunities
Data scarcity and sparsity in bio-manufacturing poses challenges for accurate model development, process monitoring, and optimization. We aim to replicate and capture the complex dynamics of industrial bioprocesses by proposing the use of a Quantum Wasserstein Generative Adversarial Network with Gradient Penalty (QWGAN-GP) to generate synthetic time series data for industrially relevant processes. The generator within our GAN is comprised of a Parameterized Quantum Circuit (PQC). This methodology offers potential advantages in process monitoring, modeling, forecasting, and optimization, enabling more efficient bioprocess management by reducing the dependence on scarce experimental data. Our results demonstrate acceptable performance in capturing the temporal dynamics of real bioprocess data. We focus on Optical Density, a key measurement for Dry Biomass estimation. The data generated showed high fidelity to the actual historical experimental data. This intersection of quantum computing and machine learning has opened new frontiers in data analysis and generation, particularly in computationally intensive fields, for use cases such as increasing prediction accuracy for soft sensor d
Efficient implementation of nonlinear model predictive control (NMPC) for bioprocesses remains challenging because large nonlinear models are difficult to organize, simulate, and embed within optimization and control workflows. This difficulty is particularly pronounced for large-scale and multiscale systems that require hierarchical model construction and customized simulation strategies. To address this issue, we present GlycoPy, a CasADi-based Python framework for hierarchical modeling, optimization, and control of bioprocesses. GlycoPy combines an equation-oriented, object-oriented modeling architecture with CasADi's symbolic and differentiable computational capabilities, enabling hierarchical model composition, numerical and symbolic simulation, parameter estimation, dynamic optimization, and NMPC within a unified workflow. A key feature of the framework is its support for customized differentiable simulation algorithms that can be embedded directly in gradient-based optimization and control. GlycoPy is demonstrated on a multiscale monoclonal antibody glycosylation process in Chinese hamster ovary cell culture, where it is used for hierarchical model construction, quasi-steady
This work presents an extension to Pareto Front Guided Sampling (PFGS), a Human-in-the-Loop (HitL) Bayesian Optimization (BO) framework in which Gaussian process (GP) surrogate-derived quantities are reformulated as objectives of a multi-objective optimization problem, and the resulting Pareto front is exposed to a domain expert for interactive candidate selection rather than returning a single automated recommendation. The framework is extended in two directions: constrained optimization is addressed by incorporating the posterior probability of satisfying output specification limits as an explicit Pareto objective, computed analytically from the GP posterior distribution; robust optimization is addressed by a Monte Carlo sampling strategy that estimates expected lower-confidence performance over a user-defined variability of input perturbations, capturing performance degradation under likely implementation deviations. The resulting multi-dimensional Pareto representation renders trade-offs between predicted performance, model uncertainty, probabilistic constraint satisfaction, and input robustness simultaneously visible through pairwise two-dimensional projections on an interacti
Efficient and robust bioprocess control is essential for maximizing performance and adaptability in advanced biotechnological systems. In this work, we present a reinforcement-learning framework for multi-setpoint and multi-trajectory tracking. Tracking multiple setpoints and time-varying trajectories in reinforcement learning is challenging due to the complexity of balancing multiple objectives, a difficulty further exacerbated by system uncertainties such as uncertain initial conditions and stochastic dynamics. This challenge is relevant, e.g., in bioprocesses involving microbial consortia, where precise control over population compositions is required. We introduce a novel return function based on multiplicative reciprocal saturation functions, which explicitly couples reward gains to the simultaneous satisfaction of multiple references. Through a case study involving light-mediated cybergenetic growth control in microbial consortia, we demonstrate via computational experiments that our approach achieves faster convergence, improved stability, and superior control compliance compared to conventional quadratic-cost-based return functions. Moreover, our method enables tuning of th
The inherent complexity of living cells as production units creates major challenges for maintaining stable and optimal bioprocess conditions, especially in open Photobioreactors (PBRs) exposed to fluctuating environments. To address this, we propose a Reinforcement Learning (RL) control approach, combined with Behavior Cloning (BC), for pH regulation in open PBR systems. This represents, to the best of our knowledge, the first application of an RL-based control strategy to such a nonlinear and disturbance-prone bioprocess. Our method begins with an offline training stage in which the RL agent learns from trajectories generated by a nominal Proportional-Integral-Derivative (PID) controller, without direct interaction with the real system. This is followed by a daily online fine-tuning phase, enabling adaptation to evolving process dynamics and stronger rejection of fast, transient disturbances. This hybrid offline-online strategy allows deployment of an adaptive control policy capable of handling the inherent nonlinearities and external perturbations in open PBRs. Simulation studies highlight the advantages of our method: the Integral of Absolute Error (IAE) was reduced by 8% compa
Data is crucial for machine learning (ML) applications, yet acquiring large datasets can be costly and time-consuming, especially in complex, resource-intensive fields like biopharmaceuticals. A key process in this industry is upstream bioprocessing, where living cells are cultivated and optimised to produce therapeutic proteins and biologics. The intricate nature of these processes, combined with high resource demands, often limits data collection, resulting in smaller datasets. This comprehensive review explores ML methods designed to address the challenges posed by small data and classifies them into a taxonomy to guide practical applications. Furthermore, each method in the taxonomy was thoroughly analysed, with a detailed discussion of its core concepts and an evaluation of its effectiveness in tackling small data challenges, as demonstrated by application results in the upstream bioprocessing and other related domains. By analysing how these methods tackle small data challenges from different perspectives, this review provides actionable insights, identifies current research gaps, and offers guidance for leveraging ML in data-constrained environments.
While deep learning has accelerated drug discovery, its impact on biomanufacturing has been considerably more limited. The reason is data scarcity. Bioreactor experiments are high-cost, take days to weeks, and are rarely shared in public form, leaving each research work with only a handful of experiments. The domain itself, however, is rich in prior knowledge. Biokinetic ordinary differential equation (ODE) models have described microbial growth for decades, yet how to inject this knowledge into a neural network has not been studied systematically. We present the first systematic study of how to inject this ODE knowledge into a neural network, comparing a data-level prior that pre-trains a generic decoder on simulated ODE curves against an architecture-level prior that embeds the ODE inside the decoder. Both consistently outperform no-prior baselines across 11 datasets and 7 microbial species. Our central finding is that the two are substitutable. A generic decoder pre-trained on simulation matches a fully bio-structured decoder trained on real data. Simulation pre-training therefore offers a simple, data-efficient recipe for deep learning under bioprocess data scarcity.
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental data. This paper introduces a symbolic and statistical learning framework to identify key regulatory mechanisms and quantify model uncertainty. Bioprocess dynamics is formulated with stochastic differential equations characterizing intrinsic process variability, with a predefined set of candidate regulatory mechanisms constructed from biological knowledge. A Bayesian learning approach is developed, which is based on a joint learning of kinetic parameters and regulatory structure through a formulation of the mixture model. To enhance computational efficiency, a Metropolis-adjusted Langevin algorithm with adjoint sensitivity analysis is developed for posterior exploration. Compared to state-of-the-art Bayesian inference approaches, the proposed framework achieves improved sample efficiency and robust model selection. An empirical study demonstrates its ability to recover missing regulatory mechanisms and improve model fidelity under data-limited condi
Biotechnology can benefit from dynamic control to improve production efficiency. In this context, optogenetics enables modulation of gene expression using light as an external input, allowing fine-tuning of protein levels to unlock dynamic metabolic control and regulation of cell growth. Optogenetic systems can be actuated by light intensity. However, relying solely on intensity-driven control (i.e., signal amplitude) may fail to properly tune optogenetic bioprocesses when the dose-response relationship (i.e., light intensity versus gene-expression strength) is steep. In these cases, tunability is effectively constrained to either fully active or fully repressed gene expression, with little intermediate regulation. Pulse-width modulation can alleviate this issue by alternating between fully ON and OFF light intensity within forcing periods, thereby smoothing the average response and enhancing process controllability. Optimizing pulse-width-modulated optogenetics entails a switching-time optimal control problem with a binary input over multiple forcing periods. While this can be formulated as a mixed-integer optimization problem on a refined control grid with monotonic input constra
Motivated by the pressing challenges in the digital twin development for biomanufacturing systems, we introduce an adjoint sensitivity analysis (SA) approach to expedite the learning of mechanistic model parameters. In this paper, we consider enzymatic stochastic reaction networks representing a multi-scale bioprocess mechanistic model that allows us to integrate disparate data from diverse production processes and leverage the information from existing macro-kinetic and genome-scale models. To support forward prediction and backward reasoning, we develop a convergent adjoint SA algorithm studying how the perturbations of model parameters and inputs (e.g., initial state) propagate through enzymatic reaction networks and impact on output trajectory predictions. This SA can provide a sample efficient and interpretable way to assess the sensitivities between inputs and outputs accounting for their causal dependencies. Our empirical study underscores the resilience of these sensitivities and illuminates a deeper comprehension of the regulatory mechanisms behind bioprocess through sensitivities.
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.
This study presents a collection of physical devices and software services that fully automate Raman spectra measurements for liquid samples within a robotic facility. This method is applicable to various fields, with demonstrated efficacy in biotechnology, where Raman spectroscopy monitors substrates, metabolites, and product-related concentrations. Our system specifically measures 50 $\micro L$ samples using a liquid handling robot capable of taking 8 samples simultaneously. We record multiple Raman spectra for 10s each. Furthermore, our system takes around 20s for sample handling, cleaning, and preparation of the next measurement. All spectra and metadata are stored in a database, and we use a machine learning model to estimate concentrations from the spectra. This automated approach enables gathering spectra for various applications under uniform conditions in high-throughput fermentation processes, calibration procedures, and offline evaluations. This allows data to be combined to train sophisticated machine learning models with improved generalization. Consequently, we can develop accurate models more quickly for new applications by reusing data from prior applications, there
This paper introduces a novel fractional-order chemostat model (FOCM) incorporating Caputo fractional derivative with sliding memory (CFDS) to capture microbial memory effects in biological water treatment, addressing limitations of integer-order models that overlook time-dependent behaviors and fail to capture microbial memory such as delayed growth responses to past nutrient availability, history-dependent adaptation to inflow fluctuations, and persistent historical effects over hours to days, which are biologically critical in wastewater treatment. By optimizing periodic dilution rate control, we minimize the average pollutant output, constrained by treatment capacity and periodic boundaries. Key contributions include: (1) a rigorous fractional framework linking microbial kinetics to memory-driven control; (2) reduction to a 1D fractional-order differential equation (FDE) for computational efficiency; (3) proofs of optimal periodic solution (OPS) existence/uniqueness via Schauder's theorem and convexity; (4) bang-bang control derivation using fractional Pontryagin maximum principle (PMP) and Fourier-Gegenbauer pseudospectral (FG-PS) method with a specialized edge-detection techn
Fostered by novel analytical techniques, digitalization and automation, modern bioprocess development provides high amounts of heterogeneous experimental data, containing valuable process information. In this context, data-driven methods like machine learning (ML) approaches have a high potential to rationally explore large design spaces while exploiting experimental facilities most efficiently. The aim of this review is to demonstrate how ML methods have been applied so far in bioprocess development, especially in strain engineering and selection, bioprocess optimization, scale-up, monitoring and control of bioprocesses. For each topic, we will highlight successful application cases, current challenges and point out domains that can potentially benefit from technology transfer and further progress in the field of ML.
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics datasets, guiding feature selection and dimensionality reduction for dynamic modeling. Continuous and differentiable machine-learning functions can be trained to link the reduced omics feature set to key components of the dynamic model, resulting in a hybrid model. As proof of concept, we apply this framework to a high-dimensional proteomics dataset of $\textit{Saccharomyces cerevisiae}$. After identifying key intracellular proteins that correlate with cell growth, targeted dynamic experiments are designed, and key model parameters are captured as functions of the selected proteins using Gaussian processes. This approach captures the dynamic behavior of yeast strains under varying proteome profiles while estimating the uncertainty in the hybrid model's predictions. The outlined modeling framework is adaptable to other scenarios, such as integrating additional layers of omics data for more advanced multiscale biological systems, or employing alterna
Precision fermentation relies on microbial cell factories to produce sustainable food, pharmaceuticals, chemicals, and biofuels. Specialized laboratories such as biofoundries are advancing these processes using high-throughput bioreactor platforms, which generate vast datasets. However, the lack of community standards limits data accessibility and interoperability, preventing integration across platforms. In order to address this, we introduce PREFER, an open-source ontology designed to establish a unified standard for bioprocess data. Built in alignment with the widely adopted Basic Formal Ontology (BFO) and connecting with several other community ontologies, PREFER ensures consistency and cross-domain compatibility and covers the whole precision fermentation process. Integrating PREFER into high-throughput bioprocess development workflows enables structured metadata that supports automated cross-platform execution and high-fidelity data capture. Furthermore, PREFER's standardization has the potential to bridge disparate data silos, generating machine-actionable datasets critical for training predictive, robust machine learning models in synthetic biology. This work provides the f
Biopharmaceutical manufacturing is vital to public health but lacks the agility for rapid, on-demand production of biotherapeutics due to the complexity and variability of bioprocesses. To overcome this, we introduce RApid PosTeriOR GENerator (RAPTOR-GEN), a mechanism-informed Bayesian learning framework designed to accelerate intelligent digital twin development from sparse and heterogeneous experimental data. This framework is built on a multi-scale probabilistic knowledge graph (pKG), formulated as a stochastic differential equation (SDE)-based foundational model that captures the nonlinear dynamics of bioprocesses. RAPTOR-GEN consists of two ingredients: (i) an interpretable metamodel integrating linear noise approximation (LNA) that exploits the structural information of bioprocessing mechanisms and a sequential learning strategy to fuse heterogeneous and sparse data, enabling inference of latent state variables and explicit approximation of the intractable likelihood function; and (ii) an efficient Bayesian posterior sampling method that utilizes Langevin diffusion (LD) to accelerate posterior exploration by exploiting the gradients of the derived likelihood. It generalizes t
In this study, deep learning is used to estimate kinetic parameters for modeling itaconic acid production based on real batch experiments conducted at different agitation speeds and reactor scales. Two deep learning strategies, namely direct deep learning (DDL) and generative conditional flow matching (CFM) are compared and benchmarked against nonlinear regression as a reference method. Compared with DDL, CFM consistently yields more accurate results. The concentration profiles predicted by CFM closely match those obtained from nonlinear regression, whereas DDL results in larger deviations. Similar behavior is observed in the scale-up experiments, where the CFM model again generalizes better and is more robust than the direct approach. These findings demonstrate that CFM can reliably predict system behavior across different operating conditions and scales, offering a flexible and data-efficient framework for parameter estimation in dynamic bioprocess models.
Dynamic metabolic control allows key metabolic fluxes to be modulated in real time, enhancing bioprocess flexibility and expanding available optimization degrees of freedom. This is achieved, e.g., via targeted modulation of metabolic enzyme expression. However, identifying optimal dynamic control policies is challenging due to the generally high-dimensional solution space and the need to manage metabolic burden and cytotoxic effects arising from inducible enzyme expression. The task is further complicated by stochastic dynamics, which reduce bioprocess reproducibility. We propose a reinforcement learning framework} to derive optimal policies by allowing an agent (the controller) to interact with a surrogate dynamic model. To promote robustness, we apply domain randomization, enabling the controller to generalize across uncertainties. When transferred to an experimental system, the agent can in principle continue fine-tuning the policy. Our framework provides an alternative to conventional model-based control such as model predictive control, which requires model differentiation with respect to decision variables; often impractical for complex stochastic, nonlinear, stiff, and piec