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Practical identifiability of parametrised models: a review of benefits and limitations of various approaches. (English) Zbl 1540.65008

Summary: This systematic review of practical identifiability (PI) explores the challenging issue of how parameter identification of models is affected by both experimental considerations and model structure. Structural identifiability (SI) analyses that yield binary assessment of parameter uniqueness have been historically dominant in the field. However, recent developments in the less explored PI domain have facilitated more nuanced estimates of identified model parameter trade-off and variance. As PI acknowledges variation in parameter estimates due to real-world limitations in data quality and quantity, it can both explore how parameters may trade-off, and guide more informative experimental design.
In this review, PI analysis methodologies used across various fields of study are compared, and their role in aiding experimental design is discussed. The methods presented show that the choice of PI approach requires careful consideration based on the modelling context and desired research outcomes. Illustrative examples are included for common methodologies, and some ongoing research is briefly reviewed. Overall, the concept of PI brings value to model-based analyses across a broad range of disciplines.

MSC:

65C05 Monte Carlo methods
62F15 Bayesian inference
92C37 Cell biology
Full Text: DOI

References:

[1] Connected papers (2021), [Online] Available: http://www.connectedpapers.com. (Accessed 17 May 2021)
[2] Anstett-Collin, F.; Denis-Vidal, L.; Millérioux, G., A priori identifiability: An overview on definitions and approaches, Ann. Rev. Control, 50, 139-149 (2020)
[3] Baker, S. M.; Poskar, C. H.; Schreiber, F.; Junker, B. H., A unified framework for estimating parameters of kinetic biological models, BMC Bioinform., 16, 1-21 (2015)
[4] Balsa-Canto, E.; Alonso, A. A.; Banga, J. R., Computational procedures for optimal experimental design in biological systems, IET Syst. Biol., 2, 163-172 (2008)
[5] Bellman, R.; Åström, K. J., On structural identifiability, Math. Biosci., 7, 329-339 (1970)
[6] Brastein, O. M.; Lie, B.; Sharma, R.; Skeie, N. O., Parameter estimation for externally simulated thermal network models, Energy Build., 191, 200-210 (2019)
[7] Brooks, S., Handbook for Markov Chain Monte Carlo (2011), Taylor & Francis: Taylor & Francis Boca Raton · Zbl 1218.65001
[8] Buja, A.; Eyuboglu, N., Remarks on parallel analysis, Multivariate Behav. Res., 27, 509-540 (1992)
[9] Chaloner, K.; Verdinelli, I., BayesIan experimental design: A review, Stat. Sci., 10, 273-304 (1995), 232 · Zbl 0955.62617
[10] Chis, O.-T.; Villaverde, A. F.; Banga, J. R.; Balsa-Canto, E., On the relationship between sloppiness and identifiability, Math. biosci., 282, 147-161 (2016) · Zbl 1352.92059
[11] Chowell, G., Fitting dynamic models to epidemic outbreaks with quantified uncertainty: A primer for parameter uncertainty, identifiability, and forecasts, Infect. Dis. Model., 2, 379-398 (2017)
[12] Cobelli, C.; DiStefano, J. J., Parameter and structural identifiability concepts and ambiguities: a critical review and analysis, Am. J. Physiol., 239, R7 (1980)
[13] David, I.; Ricard, A., A unified model for inclusive inheritance in livestock species, Genetics, 212, 1075-1099 (2019)
[14] Davidson, S.; Docherty, P. D.; Murray, R., The dimensional reduction method for identification of parameters that trade-off due to similar model roles, Math. Biosci., 285, 119-127 (2017) · Zbl 1361.92004
[15] Docherty, P. D.; Chase, J. G.; David, T., Characterisation of the iterative integral parameter identification method, Med. Biol. Eng. Comput., 50, 127-134 (2012)
[16] Docherty, P.; Chase, J. G.; Lotz, T.; Desaive, T., A graphical method for practical and informative identifiability analyses of physiological models: A case study of insulin kinetics and sensitivity, Biomed. Eng. Online, 10 (2011)
[17] Docherty, P. D.; Schranz, C.; Chase, J. G.; Chiew, Y. S.; Möller, K., Utility of a novel error-stepping method to improve gradient-based parameter identification by increasing the smoothness of the local objective surface: A case-study of pulmonary mechanics, Comput. Methods Programs Biomed., 114, e70-e78 (2014)
[18] Eberly, L. E.; Carlin, B. P., Identifiability and convergence issues for Markov chain Monte Carlo fitting of spatial models, Stat. med., 19, 2279-2294 (2000)
[19] Eisenberg, M. C.; Hayashi, M. A.L., Determining identifiable parameter combinations using subset profiling, Math. biosci., 256, 116-126 (2014) · Zbl 1330.92009
[20] Fröhlich, F.; Theis, F. J.; Hasenauer, J., Uncertainty Analysis for Non-Identifiable Dynamical Systems: Profile Likelihoods, Bootstrapping and more, 61-72 (2014), Springer International Publishing: Springer International Publishing Cham
[21] Gábor, A.; Villaverde, A. F.; Banga, J. R., Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems, BMC Syst. Biol., 11, 1-16 (2017)
[22] Geyer, C. J., Introduction to markov chain monte carlo, (Handbook of Markov Chain Monte Carlo. Vol. 20116022 (2011)), 45 · Zbl 1229.65014
[23] Gibiansky, L.; Gibiansky, E., Target-mediated drug disposition model: approximations, identifiability of model parameters and applications to the population pharmacokinetic-pharmacodynamic modeling of biologics, Expert Opin. Drug Metab Toxicol, 5, 803-812 (2009)
[24] Gottu Mukkula, A. R.; Paulen, R., Model-based design of optimal experiments for nonlinear systems in the context of guaranteed parameter estimation, Comput. Chem. Eng., 99, 198-213 (2017)
[25] Hann, C.; Chase, J.; Lin, J.; Lotz, T.; Doran, C.; Shaw, G., Integral-based parameter identification for long-term dynamic verification of a glucose-insulin system model, Comput. Methods Programs Biomed., 77, 259-270 (2005)
[26] Hastings, W. K., Monte Carlo sampling methods using Markov chains and their applications (1970) · Zbl 0219.65008
[27] Hines, K. E.; Middendorf, T. R.; Aldrich, R. W., Determination of parameter identifiability in nonlinear biophysical models: A Bayesian approach, J. Gen. Physiol., 143, 401-416 (2014)
[28] Holmberg, A., On the practical identifiability of microbial growth models incorporating Michaelis-Menten type nonlinearities, Math. biosci., 62, 23-43 (1982) · Zbl 0489.92021
[29] Huan, X.; Marzouk, Y. M., Simulation-based optimal Bayesian experimental design for nonlinear systems, J. Comput. Phys., 232, 288-317 (2013)
[30] Hug, S.; Raue, A.; Hasenauer, J.; Bachmann, J.; Klingmüller, U.; Timmer, J.; Theis, F. J., High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling, Math. biosci., 246, 293-304 (2013) · Zbl 1284.62174
[31] Janzén, D. L.I.; Bergenholm, L.; Jirstrand, M.; Parkinson, J.; Yates, J.; Evans, N. D.; Chappell, M. J., Parameter identifiability of fundamental pharmacodynamic models, Front. physiol., 7, 590 (2016)
[32] Joshi, M.; Seidel-Morgenstern, A.; Kremling, A., Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems, Metab. Eng., 8, 447-455 (2006)
[33] Joubert, D.; Stigter, J.; Molenaar, J., Determining minimal output sets that ensure structural identifiability, PloS One, 13, Article e0207334 pp. (2018)
[34] Kesavan, P.; Law, V. J., Practical identifiability of parameters in monod kinetics and statistical analysis of residuals, Biochem. Eng. J., 24, 95-104 (2005)
[35] Krausch, N.; Barz, T.; Sawatzki, A.; Gruber, M.; Kamel, S.; Neubauer, P.; Cruz Bournazou, M. N., Monte Carlo simulations for the analysis of non-linear parameter confidence intervals in optimal experimental design, Front. Bioeng. Biotechnol., 7 (2019)
[36] Kreutz, C., An easy and efficient approach for testing identifiability, Bioinformatics, 34, 1913-1921 (2018)
[37] Lizarralde-Bejarano, D. P.; Rojas-Díaz, D.; Arboleda-Sánchez, S.; Puerta-Yepes, M. E., Sensitivity, uncertainty and identifiability analyses to define a dengue transmission model with real data of an endemic municipality of Colombia, PloS One, 15, Article e0229668 pp. (2020)
[38] Ljung, L.; Glad, T., On global identifiability for arbitrary model parametrizations, Automatica (Oxford), 30, 265-276 (1994) · Zbl 0795.93026
[39] López C, D. C.; Barz, T.; Körkel, S.; Wozny, G., Nonlinear ill-posed problem analysis in model-based parameter estimation and experimental design, Comput. Chem. Eng., 77, 24-42 (2015)
[40] Meshkat, N.; Sullivant, S.; Eisenberg, M., Identifiability results for several classes of linear compartment models, Bull. Math. Biol., 77, 1620-1651 (2015) · Zbl 1336.92004
[41] Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E., Equation of state calculations by fast computing machines, J. Chem. Phys., 21, 1087-1092 (1953) · Zbl 1431.65006
[42] Metropolis, N.; Ulam, S., The Monte Carlo method, J. Am. Stat. Assoc., 44, 335-341 (1949) · Zbl 0033.28807
[43] Miao, H.; Xia, X.; Perelson, A. S.; Wu, H., On identifiability of nonlinear ODE models and applications in viral dynamics, SIAM Rev., 53, 3-39 (2011) · Zbl 1215.34015
[44] Muñoz-Tamayo, R.; Puillet, L.; Daniel, J.-B.; Sauvant, D.; Martin, O.; Taghipoor, M.; Blavy, P., To be or not to be an identifiable model. Is this a relevant question in animal science modelling?, Animal, 12, 701-712 (2018)
[45] Neale, M. C.; Miller, M. B., The use of likelihood-based confidence intervals in genetic models, Behav. Genet., 27, 113-120 (1997)
[46] Nihtilä, M.; Virkkunen, J., Practical identifiability of growth and substrate consumption models, Biotechnol. Bioeng., 19, 1831-1850 (1977)
[47] Pillonetto, G.; Sparacino, G.; Cobelli, C., Numerical non-identifiability regions of the minimal model of glucose kinetics: superiority of Bayesian estimation, Math. biosci., 184, 53-67 (2003) · Zbl 1016.62126
[48] Pironet, A.; Docherty, P. D.; Dauby, P. C.; Chase, J. G.; Desaive, T., Practical identifiability analysis of a minimal cardiovascular system model, Comput. Methods Programs Biomed., 171, 53-65 (2019)
[49] Poole, M.; Murray, R.; Davidson, S. M.; Docherty, P. D., The quadratic dimensional reduction method for parameter identification, Commun. Nonlinear Sci. Numer. Simul., 73, 425-436 (2019) · Zbl 1464.65285
[50] Pronzato, L., Optimal experimental design and some related control problems, Automatica, 44, 303-325 (2008) · Zbl 1283.93154
[51] Raman, D. V.; Anderson, J.; Papachristodoulou, A., Delineating parameter unidentifiabilities in complex models, Phys. Rev. E, 95, Article 032314 pp. (2017)
[52] Rao, C. R., (Information and the Accuracy Attainable in the Estimation of Statistical Parameters. Information and the Accuracy Attainable in the Estimation of Statistical Parameters, Breakthroughs in statistics (1992), Springer), 235-247
[53] Raue, A.; Becker, V.; Klingmüller, U.; Timmer, J., Identifiability and observability analysis for experimental design in nonlinear dynamical models, Chaos Interdiscipl. J. Nonlinear Sci., 20, Article 045105 pp. (2010) · Zbl 1311.92066
[54] Raue, A.; Kreutz, C.; Maiwald, T.; Bachmann, J.; Schilling, M.; Klingmüller, U.; Timmer, J., Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood, Bioinformatics, 25, 1923-1929 (2009)
[55] Raue, A.; Kreutz, C.; Theis, F. J.; Timmer, J., Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability, Philos. Trans. R. Soc. Lond. Ser. A Math. Phys. Eng. Sci., 371, Article 20110544 pp. (2013) · Zbl 1353.62013
[56] Roda, W. C.; Varughese, M. B.; Han, D.; Li, M. Y., Why is it difficult to accurately predict the COVID-19 epidemic?, Infect. Dis. Model., 5, 271-281 (2020)
[57] Saccomani, M. P., Structural vs practical identifiability in system biology, (Rojasa, I.; Guzman, F. M.O., IWBBIO (2013), Copicentro Editorial: Copicentro Editorial Granada), 305-313
[58] Saccomani, M. P.; Thomaseth, K., The union between structural and practical identifiability makes strength in reducing oncological model complexity: a case study, Complexity, 2018 (2018) · Zbl 1398.93040
[59] Saltelli, A.; Ratto, M.; Andres, T.; Campolongo, F.; Cariboni, J.; Gatelli, D.; Saisana, M.; Tarantola, S., Global sensitivity analysis, (The Primer (2008), John Wiley & Sons) · Zbl 1161.00304
[60] Simpson, M. J.; Baker, R. E.; Vittadello, S. T.; Maclaren, O. J., Practical parameter identifiability for spatio-temporal models of cell invasion, J. R. Soc. Interface, 17, Article 20200055 pp. (2020)
[61] Sin, G.; Meyer, A. S.; Gernaey, K. V., Assessing reliability of cellulose hydrolysis models to support biofuel process design—Identifiability and uncertainty analysis, Comput. Chem. Eng., 34, 1385-1392 (2010)
[62] Smith, A. E.; Coit, D. W., Penalty functions, (Handbook of Evolutionary Computation. Vol. 97 (1997)), C5
[63] Tönsing, C.; Timmer, J.; Kreutz, C., Profile likelihood-based analyses of infectious disease models, Stat. Methods Med. Res., 27, 1979-1998 (2018)
[64] Van de Schoot, R.; Kaplan, D.; Denissen, J.; Asendorpf, J. B.; Neyer, F. J.; Van Aken, M. A., A gentle introduction to Bayesian analysis: Applications to developmental research, Child Dev., 85, 842-860 (2014)
[65] Venzon, D. J.; Moolgavkar, S. H., A method for computing profile-likelihood-based confidence intervals, J. R. Stat. Soc. Ser. C (Appl. Stat.), 37, 87-94 (1988)
[66] Villaverde, A. F.; Banga, J. R., Reverse engineering and identification in systems biology: strategies, perspectives and challenges, J. R. Soc. Interface, 11, Article 20130505 pp. (2014)
[67] Villaverde, A. F.; Evans, N. D.; Chappell, M. J.; Banga, J. R., Input-dependent structural identifiability of nonlinear systems, IEEE Control Syst. Lett., 3, 272-277 (2019)
[68] Walter, E.; Pronzato, L., Identification of Parametric Models: From Experimental Data (1997), Springer Verlag · Zbl 0864.93014
[69] White, A.; Tolman, M.; Thames, H. D.; Withers, H. R.; Mason, K. A.; Transtrum, M. K., The limitations of model-based experimental design and parameter estimation in sloppy systems, PLoS Comput. Biol., 12, Article e1005227 pp. (2016)
[70] Wieland, F.-G.; Hauber, A. L.; Rosenblatt, M.; Tönsing, C.; Timmer, J., On structural and practical identifiability (2021), arXiv:2102.05100
[71] Zhou, W.; Huang, R.; Liu, K.; Zhang, W., A novel interval-based approach for quantifying practical parameter identifiability of a lithium-ion battery model, Int. J. Energy Res., 44, 3558-3573 (2020)
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