Abstract
In this work we present an efficient method to tackle the problem of parameter inference for stochastic biological models. We develop a variant of the Particle Swarm Optimization algorithm by including Probabilistic Dependency statistical models to detect the parameter dependencies. This results in a more efficient parameter inference of the biological model.We test the Probabilistic Dependency- PSO on a well-known benchmark problem: the thermal isomerization of α-pinene
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Balsa-Canto, E., Peifer, M., Banga, J.R., Timmer, J., Fleck, C.: Hybrid optimization method with general switching strategy for parameter estimation. BMC Systems Biology 2(1), 26 (2008)
Boys, R.J., Wilkinson, D.J., Kirkwood, T.B.L.: Bayesian inference for a discretely observed stochastic kinetic model. Statistics and Computing 18(2), 125–135 (2008)
Box, G.E.P., Hunter, W.G., MacGregor, J.F., Erjavec, J.: Some problems associated with the analysis of multiresponse data. Technometrics 15(1), 33–51 (1973)
Darwiche, A.: Modeling and reasoning with Bayesian networks. Ebooks Corporation (2009)
Dematté, L., Priami, C., Romanel, A.: Modelling and simulation of biological processes in BlenX. ACM SIGMETRICS Performance Evaluation Review 35(4), 32–39 (2008)
Dolan, E.D., Moré, J.J., Munson, T.S.: Benchmarking optimization software with COPS 3.0. Argonne National Laboratory Research Report (2004)
Forlin, M.: Knowledge discovery for stochastic models of biological systems. University of Trento, PhD Thesis (2010)
Geiger, D., Heckerman, D.: Learning gaussian networks (1994)
Hunt, H.G., Hawkins, J.E.: The rate of thermal isomerization of α-pinene and βpinene in the liquid phase. Journal of the American Chemical Society 72, 5618–5620 (1950)
Kennedy, J., Eberhart, R.C.: Particle swarm optimization. In: Proceedings of IEEE International Conference on Neural Networks, vol. 4, pp. 1942–1948 (2005)
Koller, D., Friedman, N.: Probabilistic graphical models: Principles and techniques. MIT Press (2009)
Liu, B., Wang, L., Jin, Y.H., Tang, F., Huang, D.X.: Improved particle swarm optimization combined with chaos. Chaos, Solitons & Fractals 25(5), 1261–1271 (2005)
Neapolitan, R.E.: Learning bayesian networks. Pearson Prentice Hall, Upper Saddle River (2004)
Reinker, S., Altman, R.M., Timmer, J.: Parameter estimation in stochastic biochemical reactions. IEE Proc. -Syst. Biol. 153(4), 168 (2006)
Rodriguez-Fernandez, M., Egea, J.A., Banga, J.R.: Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics 7(1), 483 (2006)
Tsamardinos, I., Brown, L.E., Aliferis, C.F.: The max-min hill-climbing Bayesian network structure learning algorithm. Machine learning 65(1), 31–78 (2006)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag GmbH Berlin Heidelberg
About this paper
Cite this paper
Forlin, M., Slanzi, D., Poli, I. (2012). Combining Probabilistic Dependency Models and Particle Swarm Optimization for Parameter Inference in Stochastic Biological Systems. In: Gaol, F., Nguyen, Q. (eds) Proceedings of the 2011 2nd International Congress on Computer Applications and Computational Science. Advances in Intelligent and Soft Computing, vol 145. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28308-6_60
Download citation
DOI: https://doi.org/10.1007/978-3-642-28308-6_60
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28307-9
Online ISBN: 978-3-642-28308-6
eBook Packages: EngineeringEngineering (R0)