The Inverse Aspect of Metaheuristics for the Parameter Identification of S-systems

作者: Shinq-Jen Wu , Cheng-Tao Wu , Jyh-Yeong Chang

DOI:

关键词: Estimation theoryComputationMathematical optimizationMathematicsNonlinear systemMetaheuristicGenetic algorithmMeta-optimizationDifferential (infinitesimal)Attractor

摘要: The genetic regulatory network, which is constructed from the time‐courses data sets, always described as highly nonlinear differential equations. Mathematical and computational modeling technologies focus on efficiently identifying parameters of dynamic biological system. Various derivative‐free derivative‐ based optimization have been proposed recently to infer S‐type networks (S‐systems). S‐system coupled power‐law functions. As involved genes and/or proteins increase, identification becomes increasingly difficult; multiple attractors exist in How develop an algorithm reduce computation time while keeping accuracy necessary. In this study, a gradient‐based metaheuristics proposed. method starts with hill‐climbing optimization, solves stagnation phenomenon by using climbing operation migration synchronous evolution. This was tested four systems. To show performance solution quality time, we let learning be implemented wide search space ([0, 100] for rate constants [‐100, kinetic orders) initialized all at bad point (the neighbourhood 80).

参考文章(24)
H. Wang, E. Dougherty, L. Qian, Inference of gene regulatory networks using S-system: a unified approach Iet Systems Biology. ,vol. 4, pp. 145- 156 ,(2010) , 10.1049/IET-SYB.2008.0175
SIMEONE MARINO, EBERHARD O. VOIT, An automated procedure for the extraction of metabolic network information from time series data. Journal of Bioinformatics and Computational Biology. ,vol. 4, pp. 665- 691 ,(2006) , 10.1142/S0219720006002259
Chung-Ming Chen, Chih Lee, Cheng-Long Chuang, Chia-Chang Wang, Grace S Shieh, Inferring genetic interactions via a nonlinear model and an optimization algorithm BMC Systems Biology. ,vol. 4, pp. 16- 16 ,(2010) , 10.1186/1752-0509-4-16
Rui Xu, D.C. Wunsch, R.L. Frank, Inference of Genetic Regulatory Networks with Recurrent Neural Network Models Using Particle Swarm Optimization IEEE/ACM Transactions on Computational Biology and Bioinformatics. ,vol. 4, pp. 681- 692 ,(2007) , 10.1109/TCBB.2007.1057
William S. Hlavacek, Michael A. Savageau, Rules for coupled expression of regulator and effector genes in inducible circuits. Journal of Molecular Biology. ,vol. 255, pp. 121- 139 ,(1996) , 10.1006/JMBI.1996.0011
Kansuporn Sriyudthsak, Fumihide Shiraishi, Masami Yokota Hirai, Identification of a metabolic reaction network from time-series data of metabolite concentrations. PLOS ONE. ,vol. 8, ,(2013) , 10.1371/JOURNAL.PONE.0051212