Data-driven Bayesian estimation of Monod kinetics
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arXiv
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| Format: | Preprint |
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2024
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| _version_ | 1866911772804382720 |
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| author | Colin, Kévin Hjalmarsson, Håkan Chotteau, Véronique |
| author_facet | Colin, Kévin Hjalmarsson, Håkan Chotteau, Véronique |
| contents | In this paper, we consider the well known problem of non-linear identification of the rates of the reactions involved in cells with Monod functions. In bioprocesses, generating data is very expensive and long and so it is important to incorporate prior knowledge on the Monod kinetic parameters. Bayesian estimation is an elegant estimation technique which deals with parameter estimation with prior knowledge modeled as probability density functions. However, we might not have an accurate knowledge of the kinetic parameters such as interval bounds, especially for newly developed cell lines. Hence, we consider the case when there is no accurate prior information on the kinetic parameters except qualitative knowledge such that their non-negativity. A log-Gaussian prior distribution is considered for the parameters and the mean and variances of these distribution are tuned using the Expectation Maximization algorithm. The algorithm requires to use Metropolis Hastings within Gibbs sampling which can be computationally expensive. We develop a novel variant of the Metropolis-Hastings within Gibbs sampling sampling scheme in order to accelerate and improve on the hyperparameter tuning. We show that it can give better modeling performances on a relatively large-scale simulation example compared to available methods in the literature. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2402_04727 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Data-driven Bayesian estimation of Monod kinetics Colin, Kévin Hjalmarsson, Håkan Chotteau, Véronique Methodology Systems and Control In this paper, we consider the well known problem of non-linear identification of the rates of the reactions involved in cells with Monod functions. In bioprocesses, generating data is very expensive and long and so it is important to incorporate prior knowledge on the Monod kinetic parameters. Bayesian estimation is an elegant estimation technique which deals with parameter estimation with prior knowledge modeled as probability density functions. However, we might not have an accurate knowledge of the kinetic parameters such as interval bounds, especially for newly developed cell lines. Hence, we consider the case when there is no accurate prior information on the kinetic parameters except qualitative knowledge such that their non-negativity. A log-Gaussian prior distribution is considered for the parameters and the mean and variances of these distribution are tuned using the Expectation Maximization algorithm. The algorithm requires to use Metropolis Hastings within Gibbs sampling which can be computationally expensive. We develop a novel variant of the Metropolis-Hastings within Gibbs sampling sampling scheme in order to accelerate and improve on the hyperparameter tuning. We show that it can give better modeling performances on a relatively large-scale simulation example compared to available methods in the literature. |
| title | Data-driven Bayesian estimation of Monod kinetics |
| topic | Methodology Systems and Control |
| url | https://arxiv.org/abs/2402.04727 |