SIAM Journal on Numerical Analysis
Genetic programming: an introduction: on the automatic evolution of computer programs and its applications
`` Direct Search'' Solution of Numerical and Statistical Problems
Journal of the ACM (JACM)
An Adaptive Nonlinear Least-Squares Algorithm
ACM Transactions on Mathematical Software (TOMS)
Swarm intelligence
SNOPT: An SQP Algorithm for Large-Scale Constrained Optimization
SIAM Journal on Optimization
Journal of Global Optimization
Evolutionary modeling and inference of gene network
Information Sciences—Informatics and Computer Science: An International Journal - Bioinformatics-selected papers from 4th CBGI & 6th JCIS Proceedings
Theoretical Analysis of Simplex Crossover for Real-Coded Genetic Algorithms
PPSN VI Proceedings of the 6th International Conference on Parallel Problem Solving from Nature
A Trigonometric Mutation Operation to Differential Evolution
Journal of Global Optimization
Advances in evolutionary computing
An analysis of the behavior of a class of genetic adaptive systems.
An analysis of the behavior of a class of genetic adaptive systems.
Interior algorithms for linear, quadratic, and linearly constrained convex programming
Interior algorithms for linear, quadratic, and linearly constrained convex programming
Computational Optimization and Applications
Generalized pattern searches with derivative information
Mathematical Programming: Series A and B
Inference of gene regulatory networks using s-system and differential evolution
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Evolving petri nets to represent metabolic pathways
GECCO '05 Proceedings of the 7th annual conference on Genetic and evolutionary computation
Comparing evolutionary algorithms on the problem of network inference
Proceedings of the 8th annual conference on Genetic and evolutionary computation
Inference of S-system Models for Large-Scale Genetic Networks
ICDEW '05 Proceedings of the 21st International Conference on Data Engineering Workshops
COPASI---a COmplex PAthway SImulator
Bioinformatics
Evolutionary Computation in Dynamic and Uncertain Environments (Studies in Computational Intelligence)
Scatter search for chemical and bio-process optimization
Journal of Global Optimization
Nonuniform sampling for global optimization of kinetic rate constants in biological pathways
Proceedings of the 38th conference on Winter simulation
Proceedings of the 38th conference on Winter simulation
Metabolic Flux Estimation-A Self-Adaptive Evolutionary Algorithm with Singular Value Decomposition
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Covariance Matrix Adaptation for Multi-objective Optimization
Evolutionary Computation
Preventing Over-Fitting during Model Selection via Bayesian Regularisation of the Hyper-Parameters
The Journal of Machine Learning Research
Multiobjective Optimization in Bioinformatics and Computational Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Inferring gene regulatory networks from temporal expression profiles under time-delay and noise
Computational Biology and Chemistry
Optimum experimental designs for dynamic systems in the presence of correlated errors
Computational Statistics & Data Analysis
Inferring biomolecular interaction networks based on convex optimization
Computational Biology and Chemistry
Inferring Gene Regulatory Networks using Differential Evolution with Local Search Heuristics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Analysis of Biological Networks (Wiley Series in Bioinformatics)
Analysis of Biological Networks (Wiley Series in Bioinformatics)
Bioinformatics
Hybrid Evolutionary Algorithms
Hybrid Evolutionary Algorithms
Proceedings of the 11th Annual conference on Genetic and evolutionary computation
Fuzzy Systems in Bioinformatics and Computational Biology
Fuzzy Systems in Bioinformatics and Computational Biology
Parameter estimation in modulated, unbranched reaction chains within biochemical systems
Computational Biology and Chemistry
Computational approaches to parameter estimation and model selection in immunology
Journal of Computational and Applied Mathematics - Special issue: Mathematics applied to immunology
Grammatical evolution for the discovery of Petri net models of complex genetic systems
GECCO'03 Proceedings of the 2003 international conference on Genetic and evolutionary computation: PartII
Towards evolutionary network reconstruction tools for systems biology
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Bio-mimetic evolutionary reverse engineering of genetic regulatory networks
EvoBIO'07 Proceedings of the 5th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Multi-stage evolutionary algorithms for efficient identification of gene regulatory networks
EuroGP'06 Proceedings of the 2006 international conference on Applications of Evolutionary Computing
Differential evolution and its application to metabolic flux analysis
EC'05 Proceedings of the 3rd European conference on Applications of Evolutionary Computing
Accelerating evolutionary algorithms with Gaussian process fitness function models
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
Combining Global and Local Surrogate Models to Accelerate Evolutionary Optimization
IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews
No free lunch theorems for optimization
IEEE Transactions on Evolutionary Computation
Stochastic ranking for constrained evolutionary optimization
IEEE Transactions on Evolutionary Computation
IEEE Transactions on Evolutionary Computation
Analog Genetic Encoding for the Evolution of Circuits and Networks
IEEE Transactions on Evolutionary Computation
Cellular automata with fuzzy parameters in microscopic study of positive HIV individuals
Mathematical and Computer Modelling: An International Journal
A hybrid approach to piecewise modelling of biochemical systems
PPSN'12 Proceedings of the 12th international conference on Parallel Problem Solving from Nature - Volume Part I
SEAL'12 Proceedings of the 9th international conference on Simulated Evolution and Learning
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This paper gives a comprehensive review of the application of metaheuristics to optimization problems in systems biology, mainly focusing on the parameter estimation problem (also called the inverse problem or model calibration). It is intended for either the system biologist who wishes to learn more about the various optimization techniques available and/or the metaheuristic optimizer who is interested in applying such techniques to problems in systems biology. First, the parameter estimation problems emerging from different areas of systems biology are described from the point of view of machine learning. Brief descriptions of various metaheuristics developed for these problems follow, along with outlines of their advantages and disadvantages. Several important issues in applying metaheuristics to the systems biology modeling problem are addressed, including the reliability and identifiability of model parameters, optimal design of experiments, and so on. Finally, we highlight some possible future research directions in this field.