Literature DB >> 23277602

Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability.

Andreas Raue1, Clemens Kreutz, Fabian Joachim Theis, Jens Timmer.   

Abstract

Increasingly complex applications involve large datasets in combination with nonlinear and high-dimensional mathematical models. In this context, statistical inference is a challenging issue that calls for pragmatic approaches that take advantage of both Bayesian and frequentist methods. The elegance of Bayesian methodology is founded in the propagation of information content provided by experimental data and prior assumptions to the posterior probability distribution of model predictions. However, for complex applications, experimental data and prior assumptions potentially constrain the posterior probability distribution insufficiently. In these situations, Bayesian Markov chain Monte Carlo sampling can be infeasible. From a frequentist point of view, insufficient experimental data and prior assumptions can be interpreted as non-identifiability. The profile-likelihood approach offers to detect and to resolve non-identifiability by experimental design iteratively. Therefore, it allows one to better constrain the posterior probability distribution until Markov chain Monte Carlo sampling can be used securely. Using an application from cell biology, we compare both methods and show that a successive application of the two methods facilitates a realistic assessment of uncertainty in model predictions.

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Year:  2012        PMID: 23277602     DOI: 10.1098/rsta.2011.0544

Source DB:  PubMed          Journal:  Philos Trans A Math Phys Eng Sci        ISSN: 1364-503X            Impact factor:   4.226


  29 in total

1.  Identifiability analysis for stochastic differential equation models in systems biology.

Authors:  Alexander P Browning; David J Warne; Kevin Burrage; Ruth E Baker; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2020-12-16       Impact factor: 4.118

2.  Inference-based assessment of parameter identifiability in nonlinear biological models.

Authors:  Aidan C Daly; David Gavaghan; Jonathan Cooper; Simon Tavener
Journal:  J R Soc Interface       Date:  2018-07       Impact factor: 4.118

3.  Inference for the physical sciences.

Authors:  Nick S Jones; Thomas J Maccarone
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2012-12-31       Impact factor: 4.226

4.  Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering.

Authors:  Benjamin Ballnus; Steffen Schaper; Fabian J Theis; Jan Hasenauer
Journal:  Bioinformatics       Date:  2018-07-01       Impact factor: 6.937

5.  Practical parameter identifiability for spatio-temporal models of cell invasion.

Authors:  Matthew J Simpson; Ruth E Baker; Sean T Vittadello; Oliver J Maclaren
Journal:  J R Soc Interface       Date:  2020-03-04       Impact factor: 4.118

6.  A physiology-based model describing heterogeneity in glucose metabolism: the core of the Eindhoven Diabetes Education Simulator (E-DES).

Authors:  Anne H Maas; Yvonne J W Rozendaal; Carola van Pul; Peter A J Hilbers; Ward J Cottaar; Harm R Haak; Natal A W van Riel
Journal:  J Diabetes Sci Technol       Date:  2014-12-18

7.  In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

Authors:  David J Klinke
Journal:  Biotechnol Prog       Date:  2014-08-26

Review 8.  The best models of metabolism.

Authors:  Eberhard O Voit
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2017-05-19

9.  Nonidentifiability in Model Calibration and Implications for Medical Decision Making.

Authors:  Fernando Alarid-Escudero; Richard F MacLehose; Yadira Peralta; Karen M Kuntz; Eva A Enns
Journal:  Med Decis Making       Date:  2018-10       Impact factor: 2.583

10.  Profile likelihood analysis for a stochastic model of diffusion in heterogeneous media.

Authors:  Matthew J Simpson; Alexander P Browning; Christopher Drovandi; Elliot J Carr; Oliver J Maclaren; Ruth E Baker
Journal:  Proc Math Phys Eng Sci       Date:  2021-06-09       Impact factor: 2.704

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