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Analysis of Practical Identifiability of a Viral Infection Model

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  • Van Kinh Nguyen
  • Frank Klawonn
  • Rafael Mikolajczyk
  • Esteban A Hernandez-Vargas

Abstract

Mathematical modelling approaches have granted a significant contribution to life sciences and beyond to understand experimental results. However, incomplete and inadequate assessments in parameter estimation practices hamper the parameter reliability, and consequently the insights that ultimately could arise from a mathematical model. To keep the diligent works in modelling biological systems from being mistrusted, potential sources of error must be acknowledged. Employing a popular mathematical model in viral infection research, existing means and practices in parameter estimation are exemplified. Numerical results show that poor experimental data is a main source that can lead to erroneous parameter estimates despite the use of innovative parameter estimation algorithms. Arbitrary choices of initial conditions as well as data asynchrony distort the parameter estimates but are often overlooked in modelling studies. This work stresses the existence of several sources of error buried in reports of modelling biological systems, voicing the need for assessing the sources of error, consolidating efforts in solving the immediate difficulties, and possibly reconsidering the use of mathematical modelling to quantify experimental data.

Suggested Citation

  • Van Kinh Nguyen & Frank Klawonn & Rafael Mikolajczyk & Esteban A Hernandez-Vargas, 2016. "Analysis of Practical Identifiability of a Viral Infection Model," PLOS ONE, Public Library of Science, vol. 11(12), pages 1-16, December.
    • Handle: RePEc:plo:pone00:0167568
    DOI: 10.1371/journal.pone.0167568
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    References listed on IDEAS

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    1. Hana M Dobrovolny & Micaela B Reddy & Mohamed A Kamal & Craig R Rayner & Catherine A A Beauchemin, 2013. "Assessing Mathematical Models of Influenza Infections Using Features of the Immune Response," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-20, February.
    2. Mullen, Katharine M. & Ardia, David & Gil, David L. & Windover, Donald & Cline, James, 2011. "DEoptim: An R Package for Global Optimization by Differential Evolution," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 40(i06).
    3. Amber M Smith & Frederick R Adler & Julie L McAuley & Ryan N Gutenkunst & Ruy M Ribeiro & Jonathan A McCullers & Alan S Perelson, 2011. "Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics," PLOS Computational Biology, Public Library of Science, vol. 7(2), pages 1-12, February.
    4. Ma, Shuangge & Kosorok, Michael R., 2005. "Robust semiparametric M-estimation and the weighted bootstrap," Journal of Multivariate Analysis, Elsevier, vol. 96(1), pages 190-217, September.
    5. Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna, 2007. "Universally Sloppy Parameter Sensitivities in Systems Biology Models," PLOS Computational Biology, Public Library of Science, vol. 3(10), pages 1-8, October.
    6. Mark Girolami & Ben Calderhead, 2011. "Riemann manifold Langevin and Hamiltonian Monte Carlo methods," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 73(2), pages 123-214, March.
    7. Simon N. Wood, 2011. "Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 73(1), pages 3-36, January.
    8. Benjamin P Holder & Philippe Simon & Laura E Liao & Yacine Abed & Xavier Bouhy & Catherine A A Beauchemin & Guy Boivin, 2011. "Assessing the In Vitro Fitness of an Oseltamivir-Resistant Seasonal A/H1N1 Influenza Strain Using a Mathematical Model," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-11, March.
    9. Liang, Hua & Wu, Hulin, 2008. "Parameter Estimation for Differential Equation Models Using a Framework of Measurement Error in Regression Models," Journal of the American Statistical Association, American Statistical Association, vol. 103(484), pages 1570-1583.
    10. J. O. Ramsay & G. Hooker & D. Campbell & J. Cao, 2007. "Parameter estimation for differential equations: a generalized smoothing approach," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 69(5), pages 741-796, November.
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