Literature DB >> 30815837

Using Experimental Data and Information Criteria to Guide Model Selection for Reaction-Diffusion Problems in Mathematical Biology.

David J Warne1, Ruth E Baker2, Matthew J Simpson3.   

Abstract

Reaction-diffusion models describing the movement, reproduction and death of individuals within a population are key mathematical modelling tools with widespread applications in mathematical biology. A diverse range of such continuum models have been applied in various biological contexts by choosing different flux and source terms in the reaction-diffusion framework. For example, to describe the collective spreading of cell populations, the flux term may be chosen to reflect various movement mechanisms, such as random motion (diffusion), adhesion, haptotaxis, chemokinesis and chemotaxis. The choice of flux terms in specific applications, such as wound healing, is usually made heuristically, and rarely it is tested quantitatively against detailed cell density data. More generally, in mathematical biology, the questions of model validation and model selection have not received the same attention as the questions of model development and model analysis. Many studies do not consider model validation or model selection, and those that do often base the selection of the model on residual error criteria after model calibration is performed using nonlinear regression techniques. In this work, we present a model selection case study, in the context of cell invasion, with a very detailed experimental data set. Using Bayesian analysis and information criteria, we demonstrate that model selection and model validation should account for both residual errors and model complexity. These considerations are often overlooked in the mathematical biology literature. The results we present here provide a straightforward methodology that can be used to guide model selection across a range of applications. Furthermore, the case study we present provides a clear example where neglecting the role of model complexity can give rise to misleading outcomes.

Entities:  

Keywords:  Bayesian inference; Collective cell spreading; Continuum models; Information criteria; Model selection

Mesh:

Year:  2019        PMID: 30815837     DOI: 10.1007/s11538-019-00589-x

Source DB:  PubMed          Journal:  Bull Math Biol        ISSN: 0092-8240            Impact factor:   1.758


  13 in total

1.  Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art.

Authors:  David J Warne; Ruth E Baker; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2019-02-28       Impact factor: 4.118

2.  Revisiting the Fisher-Kolmogorov-Petrovsky-Piskunov equation to interpret the spreading-extinction dichotomy.

Authors:  Maud El-Hachem; Scott W McCue; Wang Jin; Yihong Du; Matthew J Simpson
Journal:  Proc Math Phys Eng Sci       Date:  2019-09-04       Impact factor: 2.704

3.  Identifying density-dependent interactions in collective cell behaviour.

Authors:  Alexander P Browning; Wang Jin; Michael J Plank; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2020-04-29       Impact factor: 4.118

4.  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

5.  Comparative assessment of immune evasion mechanisms in human whole-blood infection assays by a systems biology approach.

Authors:  Teresa Lehnert; Maria T E Prauße; Kerstin Hünniger; Jan-Philipp Praetorius; Oliver Kurzai; Marc Thilo Figge
Journal:  PLoS One       Date:  2021-04-01       Impact factor: 3.240

Review 6.  Parameter estimation and uncertainty quantification using information geometry.

Authors:  Jesse A Sharp; Alexander P Browning; Kevin Burrage; Matthew J Simpson
Journal:  J R Soc Interface       Date:  2022-04-27       Impact factor: 4.293

7.  Topological Approximate Bayesian Computation for Parameter Inference of an Angiogenesis Model.

Authors:  Thomas Thorne; Paul D W Kirk; Heather A Harrington
Journal:  Bioinformatics       Date:  2022-02-22       Impact factor: 6.931

8.  WEAK SINDY FOR PARTIAL DIFFERENTIAL EQUATIONS.

Authors:  Daniel A Messenger; David M Bortz
Journal:  J Comput Phys       Date:  2021-06-23       Impact factor: 4.645

9.  Modelling collective cell migration: neural crest as a model paradigm.

Authors:  Rasa Giniūnaitė; Ruth E Baker; Paul M Kulesa; Philip K Maini
Journal:  J Math Biol       Date:  2019-10-05       Impact factor: 2.259

10.  Population Dynamics with Threshold Effects Give Rise to a Diverse Family of Allee Effects.

Authors:  Nabil T Fadai; Matthew J Simpson
Journal:  Bull Math Biol       Date:  2020-06-12       Impact factor: 1.758

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.