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Estimating Parameters of 3D Cell Model Using a Bayesian Recursive Global Optimizer (BaRGO)

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Computational Science – ICCS 2023 (ICCS 2023)

Abstract

In the field of Evolutionary Strategy, parameter estimation for functions with multiple minima is a difficult task when interdependencies between parameters have to be investigated. Most of the current routines that are used to estimate such parameters leverage state-of-the-art machine learning approaches to identify the global minimum, ignoring the relevance of the potential local minima. In this paper, we present a novel Evolutionary Strategy routine that uses sampling tools deriving from the Bayesian field to find the best parameters according to a certain loss function. The Bayesian Recursive Global Optimizer (BaRGO) presented in this work explores the parameter space identifying both local and global minima. Applications of BaRGO to 2D minimization problems and to parameter estimation of Red Blood Cell model are reported.

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References

  1. Balogh, P., Gounley, J., Roychowdhury, S., Randles, A.: A data-driven approach to modeling cancer cell mechanics during microcirculatory transport. Sci. Rep. 11(1), 15232 (2021)

    Article  Google Scholar 

  2. Benhamou, E., Saltiel, D., Vérel, S., Teytaud, F.: BCMA-ES: a Bayesian approach to CMA-ES. CoRR abs/1904.01401 (2019)

    Google Scholar 

  3. Dao, M., Lim, C.T., Suresh, S.: Mechanics of the human red blood cell deformed by optical tweezers. J. Mech. Phys. Solids 51(11–12), 2259–2280 (2003)

    Article  Google Scholar 

  4. Dempster, A.P., Laird, N.M., Rubin, D.B.: Maximum likelihood from incomplete data via the EM algorithm. J. R. Stat. Soc. Ser. B (Methodol.) 39(1), 1–38 (1977). http://www.jstor.org/stable/2984875

  5. Economides, A., et al.: Hierarchical Bayesian uncertainty quantification for a model of the red blood cell. Phys. Rev. Appl. 15, 034062 (2021)

    Article  Google Scholar 

  6. Goldberg, D.E.: Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley Longman Publishing Co., Inc., USA (1989)

    Google Scholar 

  7. Hansen, N.: The CMA evolution strategy: a tutorial. arXiv preprint arXiv:1604.00772 (2016)

  8. Hansen, N., Müller, S.D., Koumoutsakos, P.: Reducing the time complexity of the derandomized evolution strategy with covariance matrix adaptation (CMA-ES). Evol. Comput. 11(1), 1–18 (2003)

    Article  Google Scholar 

  9. Hoff, P.: A First Course in Bayesian Statistical Methods. Springer Texts in Statistics, Springer, New York (2009). https://doi.org/10.1007/978-0-387-92407-6

  10. Kullback, S., Leibler, R.A.: On information and sufficiency. Ann. Math. Stat. 22, 79–86 (1951)

    Article  MathSciNet  Google Scholar 

  11. Sigüenza, J., Mendez, S., Nicoud, F.: How should the optical tweezers experiment be used to characterize the red blood cell membrane mechanics? Biomech. Model. Mechanobiol. 16(5), 1645–1657 (2017). https://doi.org/10.1007/s10237-017-0910-x

    Article  Google Scholar 

  12. LAMMPS: Lammps (2015). http://lammps.sandia.gov/bench.html

  13. Lim, C., Zhou, E., Quek, S.: Mechanical models for living cells - a review. J. Biomech. 39(2), 195–216 (2006)

    Article  Google Scholar 

  14. Mills, J.P., Qie, L., Dao, M., Lim, C.T., Suresh, S.: Nonlinear elastic and viscoelastic deformation of the human red blood cell with optical tweezers. Mech. Chem. Biosyst. 1(3), 169–80 (2004)

    Google Scholar 

  15. Pedregosa, F., et al.: Scikit-learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011)

    MathSciNet  Google Scholar 

  16. Pivkin, I.V., Karniadakis, G.E.: Accurate coarse-grained modeling of red blood cells. Phys. Rev. Lett. 101(11), 118105 (2008)

    Article  Google Scholar 

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Acknowledgements

The authors acknowledge support from the Swiss National Science Foundation grants 200021L_204817 and 192549. Simulations were carried out at the Swiss National Supercomputer Center under project u4.

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Correspondence to Pietro Miotti .

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Miotti, P., Filippi-Mazzola, E., Wit, E.C., Pivkin, I.V. (2023). Estimating Parameters of 3D Cell Model Using a Bayesian Recursive Global Optimizer (BaRGO). In: Mikyška, J., de Mulatier, C., Paszynski, M., Krzhizhanovskaya, V.V., Dongarra, J.J., Sloot, P.M. (eds) Computational Science – ICCS 2023. ICCS 2023. Lecture Notes in Computer Science, vol 10475. Springer, Cham. https://doi.org/10.1007/978-3-031-36024-4_27

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  • DOI: https://doi.org/10.1007/978-3-031-36024-4_27

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-36023-7

  • Online ISBN: 978-3-031-36024-4

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