Nonuniform Sampling for Global Optimization of Kinetic Rate Constants in Biological Pathways
Kleinstein, S.H.; Bottino, D.; Georgieva, A.; Sarangapani, R.; Scott Lett, G.
Simulation Conference, 2006. WSC 06. Proceedings of the Winter
Volume , Issue , 3-6 Dec. 2006 Page(s):1611 - 1616
Digital Object Identifier   10.1109/WSC.2006.322934
Summary:Global optimization has proven to be a powerful tool for solving parameter estimation problems in biological applications, such as the estimation of kinetic rate constants in pathway models. These optimization algorithms sometimes suffer from slow convergence, stagnation or misconvergence to a non-optimal local minimum. Here we show that a nonuniform sampling method (implemented by running the optimization in a transformed space) can improve convergence and robustness for evolutionary-type algorithms, specifically differential evolution and evolutionary strategies. Results are shown from two case studies exemplifying the common problems of stagnation and misconvergence

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