Model Validation Procedures

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Pharmaceutical Processes".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 21148

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Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany
Interests: charged objects in solution: polyelectrolytes and ions; dynamic and structural properties of complex electrolyte solutions; molecular theories of solvation: solvation principles and thermodynamic effects; co-solute and specific ion effects and their influence on macromolecular folding equilibria
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Special Issue Information

Dear Colleagues,

Over the last decades, various computational, statistical, or machine-learning based models have been developed for research in life sciences as well as for process engineering. Standard approaches include, but are not limited to, mechanistic models, hybrid mechanistic-machine learning models, statistical approaches, computational fluid dynamics and lattice-Boltzmann methods, molecular models, and ab-initio and atomistic/coarse-grained molecular dynamic simulations. Besides academic research, nowadays, industrial manufacturing, development, and research also explore the potential of these methods for the development of processes and novel products like active pharmaceutical ingredients. Despite the ongoing success, crucial and non-trivial challenges are the calibration and the validation procedure of the chosen model. Hence, it is often not obvious how to calibrate the model parameters with regard to the experimental data. Even more importantly, reliable validation criteria to verify the outcomes of the calculations are often missing. Such standards are of the utmost importance in order to support process development and product characterization in industry, as well as scientific validation in academic research. This Special Issue aims to establish a collection of articles on reliable model validation and calibration procedures in order to define novel standards. We welcome research articles on novel methods, but also review papers, in order to give an overview about the current state-of-the-art. Topics include, but are not limited to, the following:

  • Novel and scientifically sound calibration and validation procedures for computational, statistical, and machine-learning based models in life sciences and process engineering;
  • Novel statistical approaches for experimental data;
  • Criteria to define the validity of model outcomes, specifically, machine learning-based methods;
  • Calibration protocols for coarse-grained and molecular models;
  • Reliable calibration and validation procedures for mechanistic, hybrid, statistical, computational fluid dynamics, and lattice-Boltzmann simulations, as well as neural network approaches for the study of unit operation behavior in bioprocesses;
  • Validation and calibration protocols for integrated processed and coupled unit operation models.

Dr. Jens Smiatek
Guest Editor

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Keywords

  • Model validation
  • Model calibration
  • Mechanistic and hybrid models
  • Statistical methods and approaches
  • Validation of machine-learning based methods
  • Process models
  • Biopharmaceutical engineering
  • Life sciences
  • Molecular and homology models

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Published Papers (5 papers)

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Research

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18 pages, 896 KiB  
Article
Holistic Process Models: A Bayesian Predictive Ensemble Method for Single and Coupled Unit Operation Models
by Liliana Montano Herrera, Tobias Eilert, I-Ting Ho, Milena Matysik, Michael Laussegger, Ralph Guderlei, Bernhard Schrantz, Alexander Jung, Erich Bluhmki and Jens Smiatek
Processes 2022, 10(4), 662; https://doi.org/10.3390/pr10040662 - 29 Mar 2022
Cited by 4 | Viewed by 2395
Abstract
The coupling of individual models in terms of end-to-end calculations for unit operations in manufacturing processes is a challenging task. We present a probability distribution-based approach for the combined outcomes of parametric and non-parametric models. With this so-called Bayesian predictive ensemble, the statistical [...] Read more.
The coupling of individual models in terms of end-to-end calculations for unit operations in manufacturing processes is a challenging task. We present a probability distribution-based approach for the combined outcomes of parametric and non-parametric models. With this so-called Bayesian predictive ensemble, the statistical moments such as mean value and standard deviation can be accurately computed without any further approximation. It is shown that the ensemble of different model predictions leads to an uninformed prior distribution, which can be transformed into a predictive posterior distribution using Bayesian inference and numerical Markov Chain Monte Carlo calculations. We demonstrate the advantages of our method using several numerical examples. Our approach is not restricted to certain unit operations, and can also be used for the more robust interpretation and assessment of model predictions in general. Full article
(This article belongs to the Special Issue Model Validation Procedures)
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16 pages, 4512 KiB  
Article
Validation of Novel Lattice Boltzmann Large Eddy Simulations (LB LES) for Equipment Characterization in Biopharma
by Maike Kuschel, Jürgen Fitschen, Marko Hoffmann, Alexandra von Kameke, Michael Schlüter and Thomas Wucherpfennig
Processes 2021, 9(6), 950; https://doi.org/10.3390/pr9060950 - 27 May 2021
Cited by 32 | Viewed by 5933
Abstract
Detailed process and equipment knowledge is crucial for the successful production of biopharmaceuticals. An essential part is the characterization of equipment for which Computational Fluid Dynamics (CFD) is an important tool. While the steady, Reynolds-averaged Navier–Stokes (RANS) k − ε approach has been [...] Read more.
Detailed process and equipment knowledge is crucial for the successful production of biopharmaceuticals. An essential part is the characterization of equipment for which Computational Fluid Dynamics (CFD) is an important tool. While the steady, Reynolds-averaged Navier–Stokes (RANS) k − ε approach has been extensively reviewed in the literature and may be used for fast equipment characterization in terms of power number determination, transient schemes have to be further investigated and validated to gain more detailed insights into flow patterns because they are the method of choice for mixing time simulations. Due to the availability of commercial solvers, such as M-Star CFD, Lattice Boltzmann simulations have recently become popular in the industry, as they are easy to set up and require relatively low computing power. However, extensive validation studies for transient Lattice Boltzmann Large Eddy Simulations (LB LES) are still missing. In this study, transient LB LES were applied to simulate a 3 L bioreactor system. The results were compared to novel 4D particle tracking (4D PTV) experiments, which resolve the motion of thousands of passive tracer particles on their journey through the bioreactor. Steady simulations for the determination of the power number followed a structured workflow, including grid studies and rotating reference frame volume studies, resulting in high prediction accuracy with less than 11% deviation, compared to experimental data. Likewise, deviations for the transient simulations were less than 10% after computational demand was reduced as a result of prior grid studies. The time averaged flow fields from LB LES were in good accordance with the novel 4D PTV data. Moreover, 4D PTV data enabled the validation of transient flow structures by analyzing Lagrangian particle trajectories. This enables a more detailed determination of mixing times and mass transfer as well as local exposure times of local velocity and shear stress peaks. For the purpose of standardization of common industry CFD models, steady RANS simulations for the 3 L vessel were included in this study as well. Full article
(This article belongs to the Special Issue Model Validation Procedures)
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15 pages, 4709 KiB  
Article
Hybrid Approach for Mixing Time Characterization and Scale-Up in Geometrical Nonsimilar Stirred Vessels Equipped with Eccentric Multi-Impeller Systems—An Industrial Perspective
by Michael C. Martinetz, Florian Kaiser, Martin Kellner, Dominik Schlosser, Andreas Lange, Michaela Brueckner-Pichler, Cécile Brocard and Miroslav Šoóš
Processes 2021, 9(5), 880; https://doi.org/10.3390/pr9050880 - 17 May 2021
Cited by 7 | Viewed by 3772
Abstract
Multipurpose stirring and blending vessels equipped with various impeller systems are indispensable in the pharmaceutical industry because of the high flexibility necessary during multiproduct manufacturing. On the other hand, process scale-up and scale-down during process development and transfer from bench or pilot to [...] Read more.
Multipurpose stirring and blending vessels equipped with various impeller systems are indispensable in the pharmaceutical industry because of the high flexibility necessary during multiproduct manufacturing. On the other hand, process scale-up and scale-down during process development and transfer from bench or pilot to manufacturing scale, or the design of so-called scale-down models (SDMs), is a difficult task due to the geometrical differences of used vessels. The present work comprises a hybrid approach to predict mixing times from pilot to manufacturing scale for geometrical nonsimilar vessels equipped with single top, bottom or multiple eccentrically located impellers. The developed hybrid approach is based on the experimental characterization of mixing time in the dedicated equipment and evaluation of the vessel-averaged energy dissipation rate employing computational fluid dynamics (CFD) using single-phase steady-state simulations. Obtained data are consequently used to develop a correlation of mixing time as a function of vessel filling volume and vessel-averaged energy dissipation rate, which enables the prediction of mixing times in specific vessels based on the process parameters. Predicted mixing times are in good agreement with those simulated using time-dependent CFD simulations for tested operating conditions. Full article
(This article belongs to the Special Issue Model Validation Procedures)
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18 pages, 4525 KiB  
Article
Monitoring E. coli Cell Integrity by ATR-FTIR Spectroscopy and Chemometrics: Opportunities and Caveats
by Jens Kastenhofer, Julian Libiseller-Egger, Vignesh Rajamanickam and Oliver Spadiut
Processes 2021, 9(3), 422; https://doi.org/10.3390/pr9030422 - 26 Feb 2021
Cited by 7 | Viewed by 2603
Abstract
During recombinant protein production with E. coli, the integrity of the inner and outer membrane changes, which leads to product leakage (loss of outer membrane integrity) or lysis (loss of inner membrane integrity). Motivated by current Quality by Design guidelines, there is [...] Read more.
During recombinant protein production with E. coli, the integrity of the inner and outer membrane changes, which leads to product leakage (loss of outer membrane integrity) or lysis (loss of inner membrane integrity). Motivated by current Quality by Design guidelines, there is a need for monitoring tools to determine leakiness and lysis in real-time. In this work, we assessed a novel approach to monitoring E. coli cell integrity by attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Various preprocessing strategies were tested in combination with regression (partial least squares, random forest) or classification models (partial least squares discriminant analysis, linear discriminant analysis, random forest, artificial neural network). Models were validated using standard procedures, and well-performing methods were additionally scrutinized by removing putatively important features and assessing the decrease in performance. Whereas the prediction of target compound concentration via regression was unsuccessful, possibly due to a lack of samples and low sensitivity, random forest classifiers achieved prediction accuracies of over 90% within the datasets tested in this study. However, strong correlations with untargeted spectral regions were revealed by feature selection, thereby demonstrating the need to rigorously validate chemometric models for bioprocesses, including the evaluation of feature importance. Full article
(This article belongs to the Special Issue Model Validation Procedures)
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Review

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16 pages, 601 KiB  
Review
About Model Validation in Bioprocessing
by Vignesh Rajamanickam, Heiko Babel, Liliana Montano-Herrera, Alireza Ehsani, Fabian Stiefel, Stefan Haider, Beate Presser and Bettina Knapp
Processes 2021, 9(6), 961; https://doi.org/10.3390/pr9060961 - 28 May 2021
Cited by 20 | Viewed by 5147
Abstract
In bioprocess engineering the Qualtiy by Design (QbD) initiative encourages the use of models to define design spaces. However, clear guidelines on how models for QbD are validated are still missing. In this review we provide a comprehensive overview of the validation methods, [...] Read more.
In bioprocess engineering the Qualtiy by Design (QbD) initiative encourages the use of models to define design spaces. However, clear guidelines on how models for QbD are validated are still missing. In this review we provide a comprehensive overview of the validation methods, mathematical approaches, and metrics currently applied in bioprocess modeling. The methods cover analytics for data used for modeling, model training and selection, measures for predictiveness, and model uncertainties. We point out the general issues in model validation and calibration for different types of models and put this into the context of existing health authority recommendations. This review provides a starting point for developing a guide for model validation approaches. There is no one-fits-all approach, but this review should help to identify the best fitting validation method, or combination of methods, for the specific task and the type of bioprocess model that is being developed. Full article
(This article belongs to the Special Issue Model Validation Procedures)
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