×

Optimal designs for nonlinear mixed-effects models using competitive swarm optimizer with mutated agents. (English) Zbl 07914852

Summary: Nature-inspired meta-heuristic algorithms are increasingly used in many disciplines to tackle challenging optimization problems. Our focus is to apply a newly proposed nature-inspired meta-heuristics algorithm called CSO-MA to solve challenging design problems in biosciences and demonstrate its flexibility to find various types of optimal approximate or exact designs for nonlinear mixed models with one or several interacting factors and with or without random effects. We show that CSO-MA is efficient and can frequently outperform other algorithms either in terms of speed or accuracy. The algorithm, like other meta-heuristic algorithms, is free of technical assumptions and flexible in that it can incorporate cost structure or multiple user-specified constraints, such as, a fixed number of measurements per subject in a longitudinal study. When possible, we confirm some of the CSO-MA generated designs are optimal with theory by developing theory-based innovative plots. Our applications include searching optimal designs to estimate (i) parameters in mixed nonlinear models with correlated random effects, (ii) a function of parameters for a count model in a dose combination study, and (iii) parameters in a HIV dynamic model. In each case, we show the advantages of using a meta-heuristic approach to solve the optimization problem, and the added benefits of the generated designs.

MSC:

62-08 Computational methods for problems pertaining to statistics

Software:

PSPSO; PFIM; scGTM; PySwarms
Full Text: DOI

References:

[1] Berger, MPF; Wong, WK, An introduction to optimal designs for social and biomedical research, 2009, Amsterdam: Wiley, Amsterdam · Zbl 1182.62154 · doi:10.1002/9780470746912
[2] Blum, C.; Raidl, GR, Hybrid metaheuristics: powerful tools for optimization, 2016, New York: Springer, New York
[3] Blum, C.; Puchinger, J.; Raidl, GR; Roli, A., Hybrid metaheuristics in combinatorial optimization: a survey, Appl. Soft Comput., 11, 4135-4151, 2011 · doi:10.1016/j.asoc.2011.02.032
[4] Breslow, NE; Clayton, DG, Approximate inference in generalized linear mixed models, J. Am. Stat. Assoc., 88, 421, 9-25, 1993 · Zbl 0775.62195 · doi:10.1080/01621459.1993.10594284
[5] Chen, P-Y; Chen, R-B; Tung, H-C; Wong, WK, Standardized maximim D-optimal designs for enzyme kinetic inhibition models, Chemom. Intell. Lab. Syst., 169, 79-86, 2017 · doi:10.1016/j.chemolab.2017.08.009
[6] Cheng, R.; Jin, Y., A competitive swarm optimizer for large scale optimization, IEEE Trans. Cybern., 45, 2, 191-204, 2015 · doi:10.1109/TCYB.2014.2322602
[7] Cui, EH; Song, D.; Wong, WK; Li, JJ, Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime, Bioinformatics, 38, 3927, 2022 · doi:10.1093/bioinformatics/btac423
[8] Dobson, AJ; Barnett, AG, An introduction to generalized linear models, 2018, London: Chapman & Hall, London · Zbl 1412.62001
[9] Du, Y., Optimal allocation in regression models with cost consideration, J. Phys. Conf. Ser., 1592, 012033, 2020 · doi:10.1088/1742-6596/1592/1/012033
[10] Dumont, C.; Lestini, G.; Nagard, HL; Mentré, F.; Comets, E.; Nguyen, TT, PFIM 4.0, an extended R program for design evaluation and optimization in nonlinear mixed-effect models, Comput. Methods Programs Biomed., 156, 217-229, 2018 · doi:10.1016/j.cmpb.2018.01.008
[11] Ezugwu, AE; Shukla, AK; Nath, R., Metaheuristics: a comprehensive overview and classification along with bibliometric analysis, Artif. Intell. Rev., 54, 4237-4316, 2021 · doi:10.1007/s10462-020-09952-0
[12] Fu, L.; Ma, F.; Yu, Z.; Zhu, Z., Multiplication algorithms for approximate optimal distributions with cost constraints, Mathematics, 11, 8, 1963, 2023 · doi:10.3390/math11081963
[13] Grossi, E., Do artificial neural networks love sex? How the combination of artificial neural networks with evolutionary algorithms may help to identify gender influences in rheumatic diseases, Clin. Exp. Rheumatol., 41, 1-5, 2023
[14] Gu, S.; Cheng, R.; Jin, Y., Feature selection for high-dimensional classification using a competitive swarm optimizer, Soft Comput., 22, 3, 811-822, 2018 · doi:10.1007/s00500-016-2385-6
[15] Gupta, AK; Nagar, DK, Matrix variate distributions, 2018, London: Chapman and Hall/CRC, London · doi:10.1201/9780203749289
[16] Haidar, A., Field, M., Sykes, J., Carolan, M., Holloway, L.: PSPSO: a package for parameters selection using particle swarm optimization. SoftwareX 15, 100706 (2021)
[17] Han, C.; Chaloner, K., Bayesian experimental design for nonlinear mixed-effects models with application to HIV dynamics, Biometrics, 60, 1, 25-33, 2004 · Zbl 1130.62316 · doi:10.1111/j.0006-341X.2004.00148.x
[18] Han, C.; Chaloner, K.; Perelson, AS, Bayesian analysis of a population HIV dynamic model, 223-237, 2002, New York: Springer, New York
[19] Hassan, SA; Agrawal, P.; Ganesh, T.; Mohamed, AW, Optimum scheduling of the disinfection process for COVID-19 in public places with a case study from Egypt, a novel discrete binary gaining-sharing knowledge-based metaheuristic algorithm, Artificial Intelligence for COVID-19, 215-228, 2021, New York: Springer, New York · doi:10.1007/978-3-030-69744-0_13
[20] Healy, BC; Ikle, D.; Macklin, EA; Cutter, G., Optimal design and analysis of phase I/II clinical trials in multiple sclerosis with gadolinium-enhanced lesions as the endpoint, Mult. Scler. J., 16, 840-847, 2010 · doi:10.1177/1352458510371409
[21] Heaton, J., Artificial intelligence for humans volume 2: Nature-inspired algorithms, 2019, Chesterfield: Heaton Researcher Inc, Chesterfield
[22] Hesami, M.; Maxwell, A.; Jones, P., Application of artificial intelligence models and optimization algorithms in plant cell and tissue culture, Appl. Microbiol. Biotechnol., 104, 9449-9485, 2020 · doi:10.1007/s00253-020-10888-2
[23] Jang, W.; Lim, J., A numerical study of PQL estimation biases in generalized linear mixed models under heterogeneity of random effects, Commun. Stat. Simul. Comput., 38, 4, 692-702, 2009 · Zbl 1290.62053 · doi:10.1080/03610910802627055
[24] Jiang, H-Y; Yue, R-X, Pseudo-Bayesian D-optimal designs for longitudinal Poisson mixed models with correlated errors, Comput. Stat., 34, 1, 71-87, 2019 · Zbl 1417.62220 · doi:10.1007/s00180-018-0834-7
[25] Kashif, H.; Mohd, S.; Shi, C.; Yuhui, S., Metaheuristic research: a comprehensive survey, Artif. Intell. Rev., 52, 52, 2191-2233, 2019
[26] Khan, AZ; Khalid, A.; Javaid, N.; Haseeb, A.; Saba, T.; Shafiq, M., Exploiting nature-inspired-based artificial intelligence techniques for coordinated day-ahead scheduling to efficiently manage energy in smart grid, IEEE Access, 18, Article ID 425853, 140102-140125, 2019 · doi:10.1109/ACCESS.2019.2942813
[27] Kiefer, J., General equivalence theory for optimum design (approximate theory), Ann. Stat., 2, 849-879, 1974 · Zbl 0291.62093 · doi:10.1214/aos/1176342810
[28] Korani, W., Mouhoub, M.: Review on nature-inspired algorithms. Oper. Res. Forum (2021). doi:10.1007/s43069-021-00068-x · Zbl 1476.90357
[29] Kumar, S.; Nayyar, A.; Paul, A., Swarm intelligence and evolutionary algorithms in healthcare and drug development, 2020, London: Chapman & Hall, London
[30] Lawless, JF, Negative binomial and mixed Poisson regression, Can. J. Stat., 15, 209-225, 1987 · Zbl 0632.62060 · doi:10.2307/3314912
[31] Li, Y.; Wei, Y.; Chu, Y., Research on solving systems of nonlinear equations based on improved PSO, Math. Probl. Eng., 2015, 1-10, 2015
[32] Long, J.; Ryoo, J., Using fractional polynomials to model non-linear trends in longitudinal data, Br. J. Math. Stat. Psychol., 63, 1, 177-203, 2010 · doi:10.1348/000711009X431509
[33] Lukemire, J.; Mandal, A.; Wong, WK, d-QPSO: a quantum-behaved particle swarm technique for finding D-optimal designs with discrete and continuous factors and a binary response, Technometrics, 61, 1, 71-87, 2018
[34] Mendes, J.M., Oliveira, P.M., Santos, F.M., Santos, R.M.: Nature-inspired metaheuristics and their applications to agriculture: a short review. In: Oliveira, P.M. Novais, P. and Reis, l.P. (eds) EPIA conference on artificial intelligence: Epia 2019 Progress in artificial intelligence, pp. 167-179 (2019)
[35] Miranda, LJ, Pyswarms: a research toolkit for particle swarm optimization in python, J. Open Sour. Softw., 3, 21, 433, 2018 · doi:10.21105/joss.00433
[36] Mohapatra, P.; Das, KN; Roy, S., A modified competitive swarm optimizer for large scale optimization problems, Appl. Soft Comput., 59, 340-362, 2017 · doi:10.1016/j.asoc.2017.05.060
[37] Nowak, M.; May, RM, Virus dynamics: mathematical principles of immunology and virology: mathematical principles of immunology and virology, 2000, Oxford: Oxford University Press, Oxford · Zbl 1101.92028 · doi:10.1093/oso/9780198504184.001.0001
[38] Pázman, A., Foundations of optimum experimental design, 1986, New York: Springer, New York · Zbl 0588.62117
[39] Pazman, A.; Pronzato, L., Optimum design accounting for the global nonlinear behavior of the model, Ann. Stat., 42, 4, 1426-1451, 2014 · Zbl 1302.62174 · doi:10.1214/14-AOS1232
[40] Piotrowski, AP; Piotrowska, AE, Differential evolution and particle swarm optimization against covid-19, Artif. Intell. Rev., 55, 2149-2219, 2022 · doi:10.1007/s10462-021-10052-w
[41] Retout, S.; Comets, E.; Samson, A.; Mentré, F., Design in nonlinear mixed effects models: optimization using the Fedorov-Wynn algorithm and power of the Wald test for binary covariates, Stat. Med., 26, 28, 5162-5179, 2007 · doi:10.1002/sim.2910
[42] Riaz, M.; Bashir, M.; Younas, I., Metaheuristics based covid-19 detection using medical images: a review, Comput. Biol. Med., 144, 105344, 2022 · doi:10.1016/j.compbiomed.2022.105344
[43] Rodríguez-Torreblanca, C.; Rodríguez-Díaz, J., Locally D-and C-optimal designs for Poisson and negative binomial regression models, Metrika, 66, 2, 161-172, 2007 · Zbl 1433.62218 · doi:10.1007/s00184-006-0103-6
[44] Royston, P.; Altman, DG, Regression using fractional polynomials of continuous covariates: parsimonious parametric modelling, J. R. Stat. Soc. Ser. C Appl. Stat., 43, 3, 429-453, 1994
[45] Schmelter, T.; Benda, N.; Schwabe, R., Some curiosities in optimal designs for random slopes, 189-195, 2007, New York: Springer, New York
[46] Sharma, M.; Kaur, P., A comprehensive analysis of nature-inspired meta-heuristic techniques for feature selection problem, Arch. Comput. Methods Eng., 28, 1103-1127, 2021 · doi:10.1007/s11831-020-09412-6
[47] Shi, Y.; Zhang, Z.; Wong, WK, Particle swarm based algorithms for finding locally and Bayesian D-optimal designs, J. Stat. Distrib. Appl., 6, 1, 1-17, 2019 · Zbl 1478.62221 · doi:10.1186/s40488-019-0092-4
[48] Shi, Y.; Wong, WK; Goldin, J.; Brown, MS; Kim, HJ, Prediction of progression in idiopathic pulmonary fibrosis using quantum particle swarm optimization hybridized random forest, Artif. Intell. Med., 100, 2019 · doi:10.1016/j.artmed.2019.101709
[49] Silvey, SD, Optimal design: an introduction to the theory for parameter estimation, 1980, London: Chapman & Hall, London · Zbl 0468.62070 · doi:10.1007/978-94-009-5912-5
[50] Sun, X., Xu, Y., Du, Y.: Convergence of optimal allocation sequence in regression models with cost consideration. In: IEEE Xplore: International conference on frontiers of artificial intelligence and machin learning, pp. 39-41 (2022) doi:10.1109/FAIML570028.2022.00017
[51] Sun, C.; Ding, J.; Zeng, J.; Jin, Y., A fitness approximation assisted competitive swarm optimizer for large scale expensive optimization problems, Memet. Comput., 10, 1-12, 2016
[52] Tekle, FB; Tan, FES; Berger, MPF, D-optimal cohort designs for linear mixed-effects models, Stat. Med., 27, 14, 2586-2600, 2008 · doi:10.1002/sim.3045
[53] Whitacre, JM, Recent trends indicate rapid growth of nature-inspired optimization in academia and industry, Computing, 93, 121-133, 2011 · Zbl 1293.90086 · doi:10.1007/s00607-011-0154-z
[54] Whitacre, JM, Survival of the flexible: explaining the recent dominance of nature-inspired optimization within a rapidly evolving World, Computing, 93, 135-146, 2011 · Zbl 1293.90087 · doi:10.1007/s00607-011-0156-x
[55] Xiong, G.; Shi, D., Orthogonal learning competitive swarm optimizer for economic dispatch problems, Appl. Soft Comput., 66, 134, 2018 · doi:10.1016/j.asoc.2018.02.019
[56] Xu, W.; Wong, WK; Tan, KC; Xu, JX, Finding high-dimensional \(D\)-optimal designs for logistic models via differential evolution, IEEE Access, 7, 1, 7133-7146, 2019 · doi:10.1109/ACCESS.2018.2890593
[57] Yang, XS, Engineering optimization: an introduction with metaheuristic applications, 2010, Amsterdam: Wiley, Amsterdam · doi:10.1002/9780470640425
[58] Zhang, W.X., Chen, W.N., Zhang, J.: A dynamic competitive swarm optimizer based-on entropy for large scale optimization. In: 2016 8th International conference on advanced computational intelligence (ICACI), pp. 365-371 (2016). IEEE
[59] Zhang, Q., Cheng, H., Ye, Z., Wang, Z.: A competitive swarm optimizer integrated with Cauchy and Gaussian mutation for large scale optimization. In: 2017 36th Chinese control conference (CCC), pp. 9829-9834 (2017). IEEE
[60] Zhang, Z., Wong, W.K., Tan, K.C.: Competitive swarm optimizer with mutated agents for finding optimal designs for nonlinear regression models with multiple interacting factors. Memet. Comput. 12, 219-233 (2020)
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.