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2015 | OriginalPaper | Buchkapitel

Parallelized Parameter Estimation of Biological Pathway Models

verfasst von : R. Ramanathan, Yan Zhang, Jun Zhou, Benjamin M. Gyori, Weng-Fai Wong, P. S. Thiagarajan

Erschienen in: Hybrid Systems Biology

Verlag: Springer International Publishing

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Abstract

We develop a GPU based technique to analyze bio-pathway models consisting of systems of ordinary differential equations (ODEs). A key component in our technique is an online procedure for verifying whether a numerically generated trajectory of a model satisfies a property expressed in bounded linear temporal logic. Using this procedure, we construct a statistical model checking algorithm which exploits the massive parallelism offered by GPUs while respecting the severe constraints imposed by their memory hierarchy and the hardware execution model. To demonstrate the computational power of our method, we use it to solve the parameter estimation problem for bio-pathway models. With three realistic benchmarks, we show that the proposed technique is computationally efficient and scales well with the number of GPU units deployed. Since both the verification framework and the computational platform are generic, our scheme can be used to solve a variety of analysis problems for models consisting of large systems of ODEs.

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Vorheriges Kapitel Comparative Statistical Analysis of Qualitative Parametrization Sets

Nächstes Kapitel High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems

Source code available at https://www.comp.nus.edu.sg/~rpsysbio/smcgpu/.

Barnat, J., Brim, L., Cerná, I., Drazan, S., Fabriková, J., Láník, J., Safránek, D., Ma, H.: Biodivine: A framework for parallel analysis of biological models. In: Proceedings Second International Workshop on Computational Models for Cell Processes, COMPMOD 2009, Eindhoven, The Netherlands, 3 November 2009, pp. 31–45 (2009)

Barnat, J., Brim, L., Ceska, M., Lamr, T.: Cuda accelerated LTL model checking. In: 2009 15th International Conference on Parallel and Distributed Systems (ICPADS), pp. 34–41. IEEE (2009)

Barre, B., Klein, M., Soucy-Boivin, M., Ollivier, P.-A., Hallé, S.: MapReduce for parallel trace validation of LTL properties. In: Qadeer, S., Tasiran, S. (eds.) RV 2012. LNCS, vol. 7687, pp. 184–198. Springer, Heidelberg (2013)CrossRef

Biere, A., Cimatti, A., Clarke, E., Zhu, Y.: Symbolic model checking without BDDs. In: Cleaveland, W.R. (ed.) TACAS 1999. LNCS, vol. 1579, p. 193. Springer, Heidelberg (1999)CrossRef

Bortolussi, L., Sanguinetti, G.: Learning and designing stochastic processes from logical constraints. In: Joshi, K., Siegle, M., Stoelinga, M., D’Argenio, P.R. (eds.) QEST 2013. LNCS, vol. 8054, pp. 89–105. Springer, Heidelberg (2013)CrossRef

Brown, K.S., Hill, C.C., Calero, G.A., Myers, C.R., Lee, K.H., Sethna, J.P., Cerione, R.A.: The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys. Biol. 1(3), 184 (2004)CrossRef

Bulychev, P., David, A., Larsen, K.G., Mikučionis, M., Poulsen, D.B., Legay, A., Wang, Z.: Uppaal-smc: Statistical model checking for priced timed automata. arXiv preprint arXiv:1207.1272 (2012)

Clarke, E.M., Faeder, J.R., Langmead, C.J., Harris, L.A., Jha, S.K., Legay, A.: Statistical model checking in BioLab: applications to the automated analysis of T-cell receptor signaling pathway. In: Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. LNCS (LNBI), vol. 5307, pp. 231–250. Springer, Heidelberg (2008)CrossRef

David, A., Du, D., Guldstrand Larsen, K., Legay, A., Mikučionis, M.: Optimizing control strategy using statistical model checking. In: Brat, G., Rungta, N., Venet, A. (eds.) NFM 2013. LNCS, vol. 7871, pp. 352–367. Springer, Heidelberg (2013)CrossRef

10.

Dean, J., Ghemawat, S.: MapReduce: simplified data processing on large clusters. Commun. ACM 51(1), 107–113 (2008)CrossRef

11.

Goldbeter, A., Pourquié, O.: Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J. Theoret. Biol. 252(3), 574–585 (2008)MathSciNetCrossRef

12.

Gyori, B.M., Liu, B., Paul, S., Ramanathan, R., Thiagarajan, P.: Approximate probabilistic verification of hybrid systems. In: Abate, A., Sǎfránek, D. (eds.) HSB 2015. LNCS (LNBI), vol. 9271, pp. 96–116. Springer, Heidelberg (2015)

13.

Hagiescu, A., Liu, B., Ramanathan, R., Palaniappan, S.K., Cui, Z., Chattopadhyay, B., Thiagarajan, P., Wong, W.F.: GPU code generation for ode-based applications with phased shared-data access patterns. ACM Trans. Archit. Code Optim. (TACO) 10(4), 55 (2013)

14.

Hindmarsh, A., Brown, P., Grant, K., Lee, S., Serban, R., Shumaker, D., Woodward, C.: SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers. ACM T. Math. Softw. 31(3), 363–396 (2005)MathSciNetCrossRefMATH

15.

Hirsch, M., Smale, S., Devaney, R.: Differential equations, dynamical systems, and an introduction to chaos. Academic Press, New York (2012)MATH

16.

Jha, S.K., Langmead, C.J.: Synthesis and infeasibility analysis for stochastic models of biochemical systems using statistical model checking and abstraction refinement. Theoret. Comput. Sci. 412(21), 2162–2187 (2011)MathSciNetCrossRefMATH

17.

Klipp, E., Herwig, R., Kowald, A., Wierling, C., Lehrach, H.: Systems Biology in Practice: Concepts, Implementation and Application. Wiley-VCH, Weinheim (2005)CrossRef

18.

Kuhtz, L., Finkbeiner, B.: Efficient parallel path checking for linear-time temporal logic with past and bounds. arXiv preprint arXiv:1210.0574 (2012)

19.

Lambert, J.D.: Numerical Methods for Ordinary Differential Systems: The Initial Value Problem. Wiley, Chichester (1991)MATH

20.

Le Novere, N., Bornstein, B., Broicher, A., Courtot, M., Donizelli, M., Dharuri, H., Li, L., Sauro, H., Schilstra, M., Shapiro, B., Snoep, J., Hucka, M.: BioModels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689–D691 (2006)CrossRef

21.

Legay, A., Delahaye, B., Bensalem, S.: Statistical model checking: an overview. In: Barringer, H., et al. (eds.) RV 2010. LNCS, vol. 6418, pp. 122–135. Springer, Heidelberg (2010)CrossRef

22.

Lindholm, E., Nickolls, J., Oberman, S., Montrym, J.: Nvidia tesla: a unified graphics and computing architecture. IEEE Micro 28(2), 39–55 (2008)CrossRef

23.

Liu, B., Hagiescu, A., Palaniappan, S.K., Chattopadhyay, B., Cui, Z., Wong, W.F., Thiagarajan, P.: Approximate probabilistic analysis of biopathway dynamics. Bioinformatics 28(11), 1508–1516 (2012)CrossRef

24.

Maeda, A., Ozaki, Y.I., Sivakumaran, S., Akiyama, T., Urakubo, H., Usami, A., Sato, M., Kaibuchi, K., Kuroda, S.: Ca2+-independent phospholipase A2-dependent sustained Rho-kinase activation exhibits all-or-none response. Genes to Cells 11(9), 1071–1083 (2006)CrossRef

25.

Maedo, A., Ozaki, Y., Sivakumaran, S., Akiyama, T., Urakubo, H., Usami, A., Sato, M., Kaibuchi, K., Kuroda, S.: Ca\(^{2+}\)-independent phospholipase A2-dependent sustained Rho-kinase activation exhibits all-or-none response. Genes Cells 11, 1071–1083 (2006)CrossRef

26.

Moles, C.G., Mendes, P., Banga, J.R.: Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res. 13(11), 2467–2474 (2003)CrossRef

27.

Murray, L.: GPU acceleration of Runge-Kutta integrators. IEEE Trans. Parallel Distrib. Syst. 23(1), 94–101 (2012)CrossRef

28.

Oshima, K., Matsumoto, T., Fujita, M.: Hardware implementation of BLTL property checkers for acceleration of statistical model checking. In: Proceedings of the International Conference on Computer-Aided Design, pp. 670–676. IEEE Press (2013)

29.

Palaniappan, S.K., Gyori, B.M., Liu, B., Hsu, D., Thiagarajan, P.S.: Statistical model checking based calibration and analysis of bio-pathway models. In: Gupta, A., Henzinger, T.A. (eds.) CMSB 2013. LNCS, vol. 8130, pp. 120–134. Springer, Heidelberg (2013)CrossRef

30.

Runarsson, T.P., Yao, X.: Stochastic ranking for constrained evolutionary optimization. IEEE Trans. Evol. Comput. 4(3), 284–294 (2000)CrossRef

31.

Sen, K., Viswanathan, M., Agha, G.: On statistical model checking of stochastic systems. In: Etessami, K., Rajamani, S.K. (eds.) CAV 2005. LNCS, vol. 3576, pp. 266–280. Springer, Heidelberg (2005)CrossRef

32.

Wald, A.: Sequential tests of statistical hypotheses. Ann. Math. Stat. 16, 117–186 (1945)MathSciNetCrossRefMATH

33.

Younes, H.L., Kwiatkowska, M., Norman, G., Parker, D.: Numerical vs. statistical probabilistic model checking. Int. J. Softw. Tools Technol. Transfer 8(3), 216–228 (2006)CrossRefMATH

34.

Younes, H.L., Simmons, R.G.: Statistical probabilistic model checking with a focus on time-bounded properties. Inf. Comput. 204(9), 1368–1409 (2006)MathSciNetCrossRefMATH

35.

Zhou, Y., Liepe, J., Sheng, X., Stumpf, M.P., Barnes, C.: GPU accelerated biochemical network simulation. Bioinformatics 27(6), 874–876 (2011)CrossRef

Titel: Parallelized Parameter Estimation of Biological Pathway Models
verfasst von: R. Ramanathan
Yan Zhang
Jun Zhou
Benjamin M. Gyori
Weng-Fai Wong
P. S. Thiagarajan
Verlag: Springer International Publishing
Buch: Hybrid Systems Biology
Print ISBN: 978-3-319-26915-3

Electronic ISBN: 978-3-319-26916-0

Copyright-Jahr: 2015
DOI: https://doi.org/10.1007/978-3-319-26916-0_3

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