메뉴 건너뛰기




Volumn 13, Issue 11, 2003, Pages 2467-2474

Parameter estimation in biochemical pathways: A comparison of global optimization methods

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ANALYTICAL PARAMETERS; BIOCHEMISTRY; CONTROLLED STUDY; INTERMETHOD COMPARISON; MATHEMATICAL MODEL; NONLINEAR SYSTEM; PRIORITY JOURNAL; PROBLEM SOLVING; PROCESS OPTIMIZATION; REVIEW; STOCHASTIC MODEL;

EID: 0242574982     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.1262503     Document Type: Review
Times cited : (716)

References (53)
  • 1
    • 0031316575 scopus 로고    scopus 로고
    • Application of stochastic global optimization algorithms to practical problems
    • Ali, M.M., Storey, C., and Törn, A. 1997. Application of stochastic global optimization algorithms to practical problems. J. Optim. Theory Appl. 95: 545-563.
    • (1997) J. Optim. Theory Appl. , vol.95 , pp. 545-563
    • Ali, M.M.1    Storey, C.2    Törn, A.3
  • 2
    • 0003519344 scopus 로고    scopus 로고
    • Optimization toolbox user's guide
    • Anonymous The Math Works Inc., Natick, MA
    • Anonymous. 2000. Optimization toolbox user's guide. The Math Works Inc., Natick, MA.
    • (2000)
  • 3
    • 0002803449 scopus 로고    scopus 로고
    • Evolution strategies: An alternative evolutionary algorithm
    • (eds. J.M. Alliott et al.) Springer, Berlin
    • Bäck, T. 1996. Evolution strategies: An alternative evolutionary algorithm. In Artificial evolution (eds. J.M. Alliott et al.), pp. 3-20. Springer, Berlin.
    • (1996) Artificial Evolution , pp. 3-20
    • Bäck, T.1
  • 4
    • 0038511525 scopus 로고    scopus 로고
    • Dynamic optimization of bioprocesses: Deterministic and stochastic strategies
    • Proceedings of ACoFop IV (Automatic Control of Food and Biological Processes), (eds. C. Skjoldebremd and G. Trystrom), Göteborg, Sweden
    • Balsa-Canto, E., Alonso, A.A., and Banga, J.R. 1998. Dynamic optimization of bioprocesses: Deterministic and stochastic strategies. In Proceedings of ACoFop IV (Automatic Control of Food and Biological Processes), (eds. C. Skjoldebremd and G. Trystrom), pp. 2-23. Göteborg, Sweden.
    • (1998) , pp. 2-23
    • Balsa-Canto, E.1    Alonso, A.A.2    Banga, J.R.3
  • 5
    • 0000319471 scopus 로고
    • ICRS: Application to a wastewater treatment plant model
    • IChemE Symposium Series No. 100, Pergamon Press, Oxford, UK
    • Banga, J.R. and Casares, J.J. 1987. ICRS: Application to a wastewater treatment plant model. In IChemE Symposium Series No. 100, pp.183-192. Pergamon Press, Oxford, UK.
    • (1987) , pp. 183-192
    • Banga, J.R.1    Casares, J.J.2
  • 6
    • 0002271401 scopus 로고    scopus 로고
    • Global optimization of chemical processes using stochastic algorithms
    • (eds. C.A. Floudas and P.M. Pardalos), Kluwer Academic Publishers, Dordrecht, The Netherlands
    • Banga, J.R. and Seider, W.D. 1996. Global optimization of chemical processes using stochastic algorithms. In State of the art in global optimization (eds. C.A. Floudas and P.M. Pardalos), pp. 563-583. Kluwer Academic Publishers, Dordrecht, The Netherlands.
    • (1996) State of the Art in Global Optimization , pp. 563-583
    • Banga, J.R.1    Seider, W.D.2
  • 7
    • 0030917521 scopus 로고    scopus 로고
    • Stochastic dynamic optimization of batch and semicontinuous bioprocesses
    • Banga, J.R., Alonso, A.A., and Singh, R.P. 1997. Stochastic dynamic optimization of batch and semicontinuous bioprocesses. Biotechnology Prog. 13: 326-335.
    • (1997) Biotechnology Prog. , vol.13 , pp. 326-335
    • Banga, J.R.1    Alonso, A.A.2    Singh, R.P.3
  • 8
    • 25744454776 scopus 로고    scopus 로고
    • Efficient and robust numerical strategies for the optimal control of non-linear bio-processes
    • Proceedings of the Mediterranean Conference on Control and Automation (MED2002), (eds. J.S. Sentievio and M. Attrans), CD-ROM. IEEE CSS, Lisbon, Portugal
    • Banga, J.R., Alonso, A.A., Moles, C.G., and Balsa-Canto, E. 2002. Efficient and robust numerical strategies for the optimal control of non-linear bio-processes. In Proceedings of the Mediterranean Conference on Control and Automation (MED2002), (eds. J.S. Sentievio and M. Attrans), CD-ROM. IEEE CSS, Lisbon, Portugal.
    • (2002)
    • Banga, J.R.1    Alonso, A.A.2    Moles, C.G.3    Balsa-Canto, E.4
  • 9
    • 0037592480 scopus 로고    scopus 로고
    • Evolution strategies - A comprehensive introduction
    • Beyer, H.G. and Schwefel, H.P. 2002. Evolution strategies - A comprehensive introduction. Natural Computing 1: 3-52.
    • (2002) Natural Computing , vol.1 , pp. 3-52
    • Beyer, H.G.1    Schwefel, H.P.2
  • 10
    • 0001614474 scopus 로고
    • A discussion of random methods for seeking maxima
    • Brooks, S.H. 1958. A discussion of random methods for seeking maxima. Op. Res. 6: 244-251.
    • (1958) Op. Res. , vol.6 , pp. 244-251
    • Brooks, S.H.1
  • 11
    • 84958662607 scopus 로고    scopus 로고
    • Mathematical modelling of the influence of RKIP on the ERK signalling pathway
    • (ed. C. Priami), Lecture Notes in Computer Science (LNCS) 2602. Springer Verlag, New York
    • Cho, K.H., Shin, S.Y., Kim, H.W., Wolkenhauer, O., McFerran, B., and Kolch, W. 2003. Mathematical modelling of the influence of RKIP on the ERK signalling pathway. In Computational methods in systems biology (ed. C. Priami), pp. 127-141. Lecture Notes in Computer Science (LNCS) 2602. Springer Verlag, New York.
    • (2003) Computational Methods in Systems Biology , pp. 127-141
    • Cho, K.H.1    Shin, S.Y.2    Kim, H.W.3    Wolkenhauer, O.4    McFerran, B.5    Kolch, W.6
  • 12
    • 0004033139 scopus 로고    scopus 로고
    • New ideas in optimization
    • McGraw-Hill, New York
    • Corne, D., Dorigo, M., and Glover, F. 1999. New ideas in optimization. McGraw-Hill, New York.
    • (1999)
    • Corne, D.1    Dorigo, M.2    Glover, F.3
  • 13
    • 0035868814 scopus 로고    scopus 로고
    • Evolutionary algorithms approach to the solution of mixed integer non-linear programming problems
    • Costa, L. and Oliveira, P. 2001. Evolutionary algorithms approach to the solution of mixed integer non-linear programming problems. Comput. Chem. Eng. 25: 257-266.
    • (2001) Comput. Chem. Eng. , vol.25 , pp. 257-266
    • Costa, L.1    Oliveira, P.2
  • 14
    • 0003668973 scopus 로고
    • On the origin of species by means of natural selection
    • J. Murray, London
    • Darwin, C.R. 1859. On the origin of species by means of natural selection. J. Murray, London.
    • (1859)
    • Darwin, C.R.1
  • 15
    • 0034102942 scopus 로고    scopus 로고
    • Global optimization for the parameter estimation of differential-algebraic systems
    • Esposito, W.R. and Floudas, C.A. 2000. Global optimization for the parameter estimation of differential-algebraic systems. Indust. Eng. Chem. Res. 39: 1291-1310.
    • (2000) Indust. Eng. Chem. Res. , vol.39 , pp. 1291-1310
    • Esposito, W.R.1    Floudas, C.A.2
  • 16
    • 0003929250 scopus 로고    scopus 로고
    • Evolutionary computation: Toward a new philosophy of machine intelligence
    • IEEE Press, New York
    • Fogel, D.B. 2000. Evolutionary computation: Toward a new philosophy of machine intelligence. IEEE Press, New York.
    • (2000)
    • Fogel, D.B.1
  • 17
    • 0003806013 scopus 로고
    • Artificial intelligence through simulated evolution
    • Wiley, New York
    • Fogel, L.J., Owens, A.J., and Walsh, M.J. 1966. Artificial intelligence through simulated evolution. Wiley, New York.
    • (1966)
    • Fogel, L.J.1    Owens, A.J.2    Walsh, M.J.3
  • 18
    • 0003722376 scopus 로고
    • Genetic algorithms in search, optimization and machine learning
    • Addison Wesley Longman, London
    • Goldberg, D.E. 1989. Genetic algorithms in search, optimization and machine learning. Addison Wesley Longman, London.
    • (1989)
    • Goldberg, D.E.1
  • 19
    • 0017914867 scopus 로고
    • The solution of steady-state chemical engineering optimisation problems using a random-search algorithm
    • Goulcher, R. and Casares, J.J. 1978. The solution of steady-state chemical engineering optimisation problems using a random-search algorithm. Comput. Chem. Eng. 2: 33-36.
    • (1978) Comput. Chem. Eng. , vol.2 , pp. 33-36
    • Goulcher, R.1    Casares, J.J.2
  • 21
    • 0002017426 scopus 로고
    • Stochastic methods
    • (eds. R. Horst and P.M. Pardalos), Kluwer Academic Publishers, Dordrecht, The Netherlands
    • Guus, C., Boender, E., and Romeijn, H.E. 199S. Stochastic methods. In Handbook of global optimization (eds. R. Horst and P.M. Pardalos), pp.829-869. Kluwer Academic Publishers, Dordrecht, The Netherlands.
    • (1995) Handbook of Global Optimization , pp. 829-869
    • Guus, C.1    Boender, E.2    Romeijn, H.E.3
  • 22
    • 0002640882 scopus 로고    scopus 로고
    • Convergence properties of evolution strategies with the derandomized covariance matrix adaptation: The (μ/μI, λ )-CMA-ES
    • Verlag Maing, Auchen, Germany
    • Hansen, N. and Ostermeier, A. 1997. Convergence properties of evolution strategies with the derandomized covariance matrix adaptation: the (μ/μI, λ)-CMA-ES. In Proceedings of the 5th European Congress on Intelligent Techniques and Soft Computing, EUFIT '97 pp.650-654. Verlag Maing, Auchen, Germany.
    • (1997) Proceedings of the 5th European Congress on Intelligent Techniques and Soft Computing, EUFIT '97 , pp. 650-654
    • Hansen, N.1    Ostermeier, A.2
  • 23
    • 0001811061 scopus 로고
    • ODEPACK, a systematized collection of ODE solvers
    • (ed. R.S. Stepleman) North-Holland, Amsterdam
    • Hindmarsh, A.C. 1983. ODEPACK, a systematized collection of ODE solvers. In Scientific computing (ed. R.S. Stepleman), pp. 55-64. North-Holland, Amsterdam.
    • (1983) Scientific Computing , pp. 55-64
    • Hindmarsh, A.C.1
  • 24
    • 84904687670 scopus 로고
    • Genetic algorithms and evolution strategies: Similarities and differences
    • Proceedings of Parallel Problem Solving from Nature - 1st Workshop, PPSN 1 (eds. H.-P. Schwefel and R. Männer), Lecture Notes in Computer Science, Springer-Verlag, Berlin
    • Hoffmeister, F. and Bäck, T. 1991. Genetic algorithms and evolution strategies: Similarities and differences. In Proceedings of Parallel Problem Solving from Nature - 1st Workshop, PPSN 1 (eds. H.-P. Schwefel and R. Männer), pp. 455-469. Lecture Notes in Computer Science, Vol. 496. Springer-Verlag, Berlin.
    • (1991) , vol.496 , pp. 455-469
    • Hoffmeister, F.1    Bäck, T.2
  • 25
    • 0003463297 scopus 로고
    • Adaptation in natural and artificial systems: An introductory analysis with applications to biology, control, and artificial intelligence
    • MIT Press, Cambridge, MA
    • Holland, J.H. 1992. Adaptation in natural and artificial systems: An introductory analysis with applications to biology, control, and artificial intelligence. MIT Press, Cambridge, MA.
    • (1992)
    • Holland, J.H.1
  • 26
    • 0002370361 scopus 로고    scopus 로고
    • The TOMLAB optimization environment in Matlab
    • Holmström, K. 1999. The TOMLAB optimization environment in Matlab. Adv. Model. Optim. 1: 47-69.
    • (1999) Adv. Model. Optim. , vol.1 , pp. 47-69
    • Holmström, K.1
  • 27
    • 25744472713 scopus 로고    scopus 로고
    • Practical optimization with the TOMLAB environment in Matlab
    • Telemark University College, Porsgrunn, Norway
    • Holmström, K. 2001. Practical optimization with the TOMLAB environment in Matlab. In Proceedings of the 42nd SIMS Conference, pp. 89-108, Telemark University College, Porsgrunn, Norway.
    • (2001) Proceedings of the 42nd SIMS Conference , pp. 89-108
    • Holmström, K.1
  • 28
    • 0004070444 scopus 로고
    • Global optimization: Deterministic approaches
    • Springer-Verlag, Berlin
    • Horst, R. and Tuy, H. 1990. Global optimization: Deterministic approaches. Springer-Verlag, Berlin.
    • (1990)
    • Horst, R.1    Tuy, H.2
  • 29
    • 0000951235 scopus 로고    scopus 로고
    • A global optimization by multilevel coordinate search
    • Huyer, W. and Neumaier, A. 1999. A global optimization by multilevel coordinate search. J. Global Optim. 14: 331-355.
    • (1999) J. Global Optim. , vol.14 , pp. 331-355
    • Huyer, W.1    Neumaier, A.2
  • 30
    • 0000518270 scopus 로고    scopus 로고
    • DIRECT global optimization algorithm
    • (eds. C.A. Floudas and P.M. Pardalos), Kluwer Academic Publishers, Dordrecht, The Netherlands
    • Jones, D.R. 2001. DIRECT global optimization algorithm. In Encyclopedia of optimization (eds. C.A. Floudas and P.M. Pardalos), pp. 431-440. Kluwer Academic Publishers, Dordrecht, The Netherlands.
    • (2001) Encyclopedia of Optimization , pp. 431-440
    • Jones, D.R.1
  • 32
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., Gellatt, C.D., and Vecchi, M.P. 1983. Optimization by simulated annealing. Science 220: 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gellatt, C.D.2    Vecchi, M.P.3
  • 33
  • 34
    • 0027370376 scopus 로고
    • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes, P. 1993. GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9: 563-571.
    • (1993) Comput. Appl. Biosci. , vol.9 , pp. 563-571
    • Mendes, P.1
  • 35
    • 0000718866 scopus 로고    scopus 로고
    • Modeling large biological systems from functional genomic data: Parameter estimation
    • (ed. H. Kitano), MIT Press, Cambridge, MA
    • Mendes, P. 2001. Modeling large biological systems from functional genomic data: Parameter estimation. In Foundations of systems biology (ed. H. Kitano), pp. 163-186. MIT Press, Cambridge, MA.
    • (2001) Foundations of Systems Biology , pp. 163-186
    • Mendes, P.1
  • 36
    • 0032406131 scopus 로고    scopus 로고
    • Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
    • Mendes, P. and Kell, D.B. 1998. Non-linear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883.
    • (1998) Bioinformatics , vol.14 , pp. 869-883
    • Mendes, P.1    Kell, D.B.2
  • 37
    • 0242566781 scopus 로고    scopus 로고
    • Genetic algorithms + data structures = evolution programs. Springer-Verlag, Berlin, New York
    • Michalewicz, Z. 1996. Genetic algorithms + data structures = evolution programs. Springer-Verlag, Berlin, New York.
    • (1996)
    • Michalewicz, Z.1
  • 38
    • 84947474756 scopus 로고    scopus 로고
    • Integrated process design and control via global optimization: A wastewater treatment plant case study
    • Proceedings of the European Control Conference (ECC) 2001, 4-7 September (ed. J.L. Martins), CD-ROM, EUCA, Porto, Portugal
    • Moles, C.G., Gutierrez, G., Alonso, A.A., and Banga, J.R. 2001. Integrated process design and control via global optimization: A wastewater treatment plant case study. In Proceedings of the European Control Conference (ECC) 2001, 4-7 September (ed. J.L. Martins), CD-ROM, EUCA, Porto, Portugal.
    • (2001)
    • Moles, C.G.1    Gutierrez, G.2    Alonso, A.A.3    Banga, J.R.4
  • 39
    • 31244435059 scopus 로고    scopus 로고
    • A rigorous global optimization algorithm for problems with ordinary differential equations
    • Papamichail, I. and Adjiman, C.S. 2002. A rigorous global optimization algorithm for problems with ordinary differential equations. J. Global Optim. 24: 1-33.
    • (2002) J. Global Optim. , vol.24 , pp. 1-33
    • Papamichail, I.1    Adjiman, C.S.2
  • 40
    • 0003736179 scopus 로고    scopus 로고
    • Global optimization in action. Continuous and Lipschitz optimization: Algorithms, implementations and applications
    • Kluwer Academics Publishers, Dordrecht, The Netherlands
    • Pinter, J. 1996. Global optimization in action. Continuous and Lipschitz optimization: Algorithms, implementations and applications. Kluwer Academics Publishers, Dordrecht, The Netherlands.
    • (1996)
    • Pinter, J.1
  • 41
    • 0037592469 scopus 로고
    • The comparison of random search and stochastic approximation while solving the problem of optimization
    • Rastrigin, L.A. and Rubinstein, Y. 1969. The comparison of random search and stochastic approximation while solving the problem of optimization. Automat. Control 2: 23-29.
    • (1969) Automat. Control , vol.2 , pp. 23-29
    • Rastrigin, L.A.1    Rubinstein, Y.2
  • 42
    • 0033738766 scopus 로고    scopus 로고
    • Case studies in evolutionary experimentation and computation
    • Rechenberg, I. 2000. Case studies in evolutionary experimentation and computation. Computer Meth. Appl. Mech. Eng. 186: 125-140.
    • (2000) Computer Meth. Appl. Mech. Eng. , vol.186 , pp. 125-140
    • Rechenberg, I.1
  • 43
    • 0023420912 scopus 로고
    • Stochastic global optimization methods. Part I: Clustering methods
    • Rinnooy-Kan, A.H.G. and Timmer, G.T. 1987. Stochastic global optimization methods. Part I: Clustering methods. Math. Prog. 39: 27-56.
    • (1987) Math. Prog. , vol.39 , pp. 27-56
    • Rinnooy-Kan, A.H.G.1    Timmer, G.T.2
  • 44
    • 0034266683 scopus 로고    scopus 로고
    • Stochastic ranking for constrained evolutionary optimization
    • Runarsson, T.P. and Yao, X, 2000. Stochastic ranking for constrained evolutionary optimization. IEEE Trans. Evol. Comput. 4: 284-294.
    • (2000) IEEE Trans. Evol. Comput. , vol.4 , pp. 284-294
    • Runarsson, T.P.1    Yao, X.2
  • 45
    • 0028970936 scopus 로고
    • A comparison of methods for self-adaptation in evolutionary algorithms
    • Saravanan, N., Fogel, D.B., and Nelson, K.M. 1995. A comparison of methods for self-adaptation in evolutionary algorithms. Biosystems 36: 157-166.
    • (1995) Biosystems , vol.36 , pp. 157-166
    • Saravanan, N.1    Fogel, D.B.2    Nelson, K.M.3
  • 46
    • 0003636650 scopus 로고
    • Evolution and optimum seeking
    • Wiley, New York
    • Schwefel, H.P. 1995. Evolution and optimum seeking. Wiley, New York.
    • (1995)
    • Schwefel, H.P.1
  • 47
    • 0038267718 scopus 로고    scopus 로고
    • Convex underestimators for variational and optimal control problems
    • Singer, A.B., Bok, J.K., and Barton, P.I. 2001. Convex underestimators for variational and optimal control problems. Comput. Aided Chem. Eng. 9: 767-772.
    • (2001) Comput. Aided Chem. Eng. , vol.9 , pp. 767-772
    • Singer, A.B.1    Bok, J.K.2    Barton, P.I.3
  • 48
    • 0142000477 scopus 로고    scopus 로고
    • Differential Evolution - A simple and efficient heuristic for global optimization over continuous spaces
    • Storn, R. and Price, K. 1997. Differential Evolution - A simple and efficient heuristic for global optimization over continuous spaces. J. Global Optim. 11: 341-359.
    • (1997) J. Global Optim. , vol.11 , pp. 341-359
    • Storn, R.1    Price, K.2
  • 49
    • 0037417886 scopus 로고    scopus 로고
    • Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling
    • Swameye, I., Muller, T.G., Timmer, J., Sandra, O., and Klingmuller, U. 2003. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc. Natl. Acad. Sci. 100: 1028-1033.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 1028-1033
    • Swameye, I.1    Muller, T.G.2    Timmer, J.3    Sandra, O.4    Klingmuller, U.5
  • 50
    • 0003457959 scopus 로고
    • Global optimization as a combination of global and local search
    • Proceedings of computer simulation versus analytical solutions for business and economic models, Gothenburg, Sweden
    • Törn, A.A. 1973. Global optimization as a combination of global and local search. Proceedings of computer simulation versus analytical solutions for business and economic models, pp. 191-206. Gothenburg, Sweden.
    • (1973) , pp. 191-206
    • Törn, A.A.1
  • 51
    • 0001591529 scopus 로고    scopus 로고
    • Stochastic global optimization: Problem classes and solution techniques
    • Törn, A., Ali, M., and Viitanen, S. 1999. Stochastic global optimization: Problem classes and solution techniques. J. Global Opt. 14: 437-447.
    • (1999) J. Global Opt. , vol.14 , pp. 437-447
    • Törn, A.1    Ali, M.2    Viitanen, S.3
  • 52
    • 0003533473 scopus 로고
    • Simulated annealing: Theory and applications
    • Reidel, Dordrecht, The Netherlands
    • van Laarhoven, P.J.M. and Aarts, E.H.L. 1987. Simulated annealing: Theory and applications. Reidel, Dordrecht, The Netherlands.
    • (1987)
    • van Laarhoven, P.J.M.1    Aarts, E.H.L.2
  • 53
    • 0027110125 scopus 로고
    • Pure adaptive search in global optimization
    • Zabinsky, Z.B. and Smith, R.L. 1992. Pure adaptive search in global optimization. Math. Prog. 53: 323-338.
    • (1992) Math. Prog. , vol.53 , pp. 323-338
    • Zabinsky, Z.B.1    Smith, R.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.