Cited By
View all- Sun JGaribaldi JHodgman C(2012)Parameter Estimation Using Metaheuristics in Systems BiologyIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2011.639:1(185-202)Online publication date: 1-Jan-2012
Nonuniform sampling for global optimization of kinetic rate constants in biological pathways
Authors: 
Steven H. Kleinstein, Dean Bottino, Anna Georgieva, Ramesh Sarangapani, G. Scott LettAuthors Info & Claims
Steven H. Kleinstein, Dean Bottino, Anna Georgieva, Ramesh Sarangapani, G. Scott LettAuthors Info & ClaimsPages 1611 - 1616
Abstract
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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- Nonuniform sampling for global optimization of kinetic rate constants in biological pathways
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Published In
December 2006
2429 pages
ISBN:1424405017
- Editors:
- L. Felipe Perrone,
- Barry G. Lawson,
- Jason Liu,
- Frederick P. Wieland,
- General Chair:
- David Nicol,
- Program Chair:
- Richard Fujimoto
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- IIE: Institute of Industrial Engineers
- ASA: American Statistical Association
- IEICE ESS: Institute of Electronics, Information and Communication Engineers, Engineering Sciences Society
- IEEE-CS\DATC: The IEEE Computer Society
- SIGSIM: ACM Special Interest Group on Simulation and Modeling
- NIST: National Institute of Standards and Technology
- (SCS): The Society for Modeling and Simulation International
- INFORMS-CS: Institute for Operations Research and the Management Sciences-College on Simulation
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Winter Simulation Conference
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Published: 03 December 2006
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- IEICE ESS
- IEEE-CS\DATC
- SIGSIM
- NIST
- (SCS)
- INFORMS-CS
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WSC '06 Paper Acceptance Rate 177 of 252 submissions, 70%;
Overall Acceptance Rate 3,413 of 5,075 submissions, 67%
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View all- Sun JGaribaldi JHodgman C(2012)Parameter Estimation Using Metaheuristics in Systems BiologyIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2011.639:1(185-202)Online publication date: 1-Jan-2012
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