메뉴 건너뛰기




Volumn 247, Issue 2, 2015, Pages 349-358

Modeling nonlinear dynamic biological systems with human-readable fuzzy rules optimized by convergent heterogeneous particle swarm

Author keywords

Computational biology; Dynamical system; Global optimization; Particle swarm optimization (PSO); Takagi Sugeno (T S) fuzzy model

Indexed keywords

BIOINFORMATICS; BIOLOGICAL SYSTEMS; DYNAMICAL SYSTEMS; ELECTRIC NETWORK TOPOLOGY; FUZZY INFERENCE; FUZZY RULES; GLOBAL OPTIMIZATION; PARAMETER ESTIMATION; TOPOLOGY;

EID: 84938749469     PISSN: 03772217     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejor.2015.03.047     Document Type: Article
Times cited : (10)

References (46)
  • 2
    • 4344592548 scopus 로고    scopus 로고
    • Neural-network-based parameter estimation in S-system models of biological networks
    • Almeida J.S., and Voit E.O. Neural-network-based parameter estimation in S-system models of biological networks Genome Informatics 14 2003 114 123
    • (2003) Genome Informatics , vol.14 , pp. 114-123
    • Almeida, J.S.1    Voit, E.O.2
  • 4
    • 31944448941 scopus 로고    scopus 로고
    • A study of particle swarm optimization particle trajectories
    • van den Bergh F., and Engelbrecht A. A study of particle swarm optimization particle trajectories Information Sciences 176 8 2006 937 971
    • (2006) Information Sciences , vol.176 , Issue.8 , pp. 937-971
    • Van Den Bergh, F.1    Engelbrecht, A.2
  • 6
    • 0031163944 scopus 로고    scopus 로고
    • Analysis and design for a class of complex control systems Part I: Fuzzy modelling and identification
    • Cao S., Rees N., and Feng G. Analysis and design for a class of complex control systems Part I: Fuzzy modelling and identification Automatica 33 6 1997 1017 1028
    • (1997) Automatica , vol.33 , Issue.6 , pp. 1017-1028
    • Cao, S.1    Rees, N.2    Feng, G.3
  • 7
    • 20744452513 scopus 로고    scopus 로고
    • A new measure of the robustness of biochemical networks
    • Chen B.-S., Wang Y.-C., Wu W.-S., and Li W.-H. A new measure of the robustness of biochemical networks Bioinformatics 21 11 2005 2698 2705
    • (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2698-2705
    • Chen, B.-S.1    Wang, Y.-C.2    Wu, W.-S.3    Li, W.-H.4
  • 8
    • 84863518282 scopus 로고    scopus 로고
    • On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: Systematic approach
    • Chen B.-S., and Wu C.-C. On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach Bioinformatics 28 12 2012 1604 1611
    • (2012) Bioinformatics , vol.28 , Issue.12 , pp. 1604-1611
    • Chen, B.-S.1    Wu, C.-C.2
  • 9
    • 77949372252 scopus 로고    scopus 로고
    • Inferring genetic interactions via a nonlinear model and an optimization algorithm
    • Chen C.-M., Lee C., Chuang C.-L., Wang C.-C., and Shieh G. Inferring genetic interactions via a nonlinear model and an optimization algorithm BMC Systems Biology 4 1 2010 1 11
    • (2010) BMC Systems Biology , vol.4 , Issue.1 , pp. 1-11
    • Chen, C.-M.1    Lee, C.2    Chuang, C.-L.3    Wang, C.-C.4    Shieh, G.5
  • 10
    • 84905561952 scopus 로고    scopus 로고
    • OptiFel: A convergent heterogeneous particle swarm optimization algorithm for Takagi-Sugeno fuzzy modeling
    • Cheung N.J., Ding X.-M., and Shen H.-B. OptiFel: A convergent heterogeneous particle swarm optimization algorithm for Takagi-Sugeno fuzzy modeling IEEE Transactions on Fuzzy Systems 22 4 2014 919 933
    • (2014) IEEE Transactions on Fuzzy Systems , vol.22 , Issue.4 , pp. 919-933
    • Cheung, N.J.1    Ding, X.-M.2    Shen, H.-B.3
  • 11
    • 84863525026 scopus 로고    scopus 로고
    • Estimation of dynamic flux profiles from metabolic time series data
    • Chou I.-C., and Voit E.O. Estimation of dynamic flux profiles from metabolic time series data BMC Systems Biology 6 84 2012 1 17
    • (2012) BMC Systems Biology , vol.6 , Issue.84 , pp. 1-17
    • Chou, I.-C.1    Voit, E.O.2
  • 13
    • 33947685522 scopus 로고    scopus 로고
    • Modeling gene regulatory networks with piecewise linear differential equations
    • Gebert J., Radde N., and Weber G.-W. Modeling gene regulatory networks with piecewise linear differential equations European Journal of Operational Research 181 3 2007 1148 1165
    • (2007) European Journal of Operational Research , vol.181 , Issue.3 , pp. 1148-1165
    • Gebert, J.1    Radde, N.2    Weber, G.-W.3
  • 14
    • 62549093118 scopus 로고    scopus 로고
    • Benchmarks for identification of ordinary differential equations from time series data
    • Gennemark P., and Wedelin D. Benchmarks for identification of ordinary differential equations from time series data BMC Systems Biology 25 6 2009 780 786
    • (2009) BMC Systems Biology , vol.25 , Issue.6 , pp. 780-786
    • Gennemark, P.1    Wedelin, D.2
  • 15
    • 33847314052 scopus 로고    scopus 로고
    • Parameter estimation using simulated annealing for S-system models of biochemical networks
    • Gonzalez O.R., Kuper C., Jung K., Prospero J., Naval C., and Mendoza E. Parameter estimation using simulated annealing for S-system models of biochemical networks Bioinformatics 23 4 2007 480 486
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 480-486
    • Gonzalez, O.R.1    Kuper, C.2    Jung, K.3    Prospero, J.4    Naval, C.5    Mendoza, E.6
  • 16
    • 0037903772 scopus 로고    scopus 로고
    • Fuzzy sets and operations research: Perspectives
    • Herrera F., and Verdegay J. Fuzzy sets and operations research: Perspectives Fuzzy Sets and Systems 90 2 1997 207 218
    • (1997) Fuzzy Sets and Systems , vol.90 , Issue.2 , pp. 207-218
    • Herrera, F.1    Verdegay, J.2
  • 17
    • 2942676743 scopus 로고    scopus 로고
    • Metabolomics and systems biology: Making sense of the soup
    • Kell D.B. Metabolomics and systems biology: making sense of the soup Current Opinion in Microbiology 7 3 2004 296 307
    • (2004) Current Opinion in Microbiology , vol.7 , Issue.3 , pp. 296-307
    • Kell, D.B.1
  • 18
    • 33644959172 scopus 로고    scopus 로고
    • Metabolomics, modelling and machine learning in systems biology-Towards an understanding of the languages of cells
    • Kell D.B. Metabolomics, modelling and machine learning in systems biology-Towards an understanding of the languages of cells FEBS Journal 273 5 2006 873 894
    • (2006) FEBS Journal , vol.273 , Issue.5 , pp. 873-894
    • Kell, D.B.1
  • 20
    • 0037461033 scopus 로고    scopus 로고
    • Dynamic modeling of genetic networks using genetic algorithm and S-system
    • Kikuchi S., Tominaga D., Arita M., Takahashi K., and Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system Bioinformatics 19 5 2003 643 650
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 643-650
    • Kikuchi, S.1    Tominaga, D.2    Arita, M.3    Takahashi, K.4    Tomita, M.5
  • 21
    • 84857915067 scopus 로고    scopus 로고
    • A stochastic control formalism for dynamic biologically conformal radiation therapy
    • Feature Clusters
    • Kim M., Ghate A., and Phillips M.H. A stochastic control formalism for dynamic biologically conformal radiation therapy European Journal of Operational Research 219 3 2012 541 556. Feature Clusters
    • (2012) European Journal of Operational Research , vol.219 , Issue.3 , pp. 541-556
    • Kim, M.1    Ghate, A.2    Phillips, M.H.3
  • 22
    • 0000469445 scopus 로고    scopus 로고
    • Identification of functional fuzzy models using multidimensional reference fuzzy sets
    • Kroll A. Identification of functional fuzzy models using multidimensional reference fuzzy sets Fuzzy Sets and Systems 80 2 1996 149 158
    • (1996) Fuzzy Sets and Systems , vol.80 , Issue.2 , pp. 149-158
    • Kroll, A.1
  • 23
    • 84863431143 scopus 로고    scopus 로고
    • Grey particle swarm optimization
    • Leu M.-S., and Yeh M.-F. Grey particle swarm optimization Applied Soft Computing 12 9 2012 2985 2996
    • (2012) Applied Soft Computing , vol.12 , Issue.9 , pp. 2985-2996
    • Leu, M.-S.1    Yeh, M.-F.2
  • 25
    • 33744730797 scopus 로고    scopus 로고
    • Comprehensive learning particle swarm optimizer for global optimization of multimodal functions
    • Liang J.J., Qin A.K., Suganthan P.N., and Baskar S. Comprehensive learning particle swarm optimizer for global optimization of multimodal functions IEEE Transactions on Evolutionary Computation 10 3 2006 281 295
    • (2006) IEEE Transactions on Evolutionary Computation , vol.10 , Issue.3 , pp. 281-295
    • Liang, J.J.1    Qin, A.K.2    Suganthan, P.N.3    Baskar, S.4
  • 26
    • 41949109225 scopus 로고    scopus 로고
    • Inference of biochemical network models in S-system using multiobjective optimization approach
    • Liu P.-K., and Wang F.-S. Inference of biochemical network models in S-system using multiobjective optimization approach BMC Systems Biology 24 8 2008 1085 1092
    • (2008) BMC Systems Biology , vol.24 , Issue.8 , pp. 1085-1092
    • Liu, P.-K.1    Wang, F.-S.2
  • 27
    • 84863341615 scopus 로고
    • The general problem of the stability of motion
    • Lyapunov A.M. The general problem of the stability of motion International Journal of Control 55 3 1992 531 534
    • (1992) International Journal of Control , vol.55 , Issue.3 , pp. 531-534
    • Lyapunov, A.M.1
  • 28
    • 84889096436 scopus 로고    scopus 로고
    • RMARS: Robustification of multivariate adaptive regression spline under polyhedral uncertainty
    • Özmen A., and Weber G.W. RMARS: Robustification of multivariate adaptive regression spline under polyhedral uncertainty Journal of Computational and Applied Mathematics 259 Part B 2014 914 924
    • (2014) Journal of Computational and Applied Mathematics , vol.259 , pp. 914-924
    • Özmen, A.1    Weber, G.W.2
  • 29
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S., Fell D.A., and Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nature Biotechnology 18 2000 326 332
    • (2000) Nature Biotechnology , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 32
    • 0027544110 scopus 로고
    • A fuzzy-logic-based approach to qualitative modeling
    • Sugeno M., and Yasukawa T. A fuzzy-logic-based approach to qualitative modeling IEEE Transactions on Fuzzy Systems 1 1 1993 7 31
    • (1993) IEEE Transactions on Fuzzy Systems , vol.1 , Issue.1 , pp. 7-31
    • Sugeno, M.1    Yasukawa, T.2
  • 34
    • 0021892282 scopus 로고
    • Fuzzy identification of systems and its applications to modeling and control
    • Takagi T., and Sugeno M. Fuzzy identification of systems and its applications to modeling and control IEEE Transaction on System, Man, and Cybernetics 15 1 1985 116 132
    • (1985) IEEE Transaction on System, Man, and Cybernetics , vol.15 , Issue.1 , pp. 116-132
    • Takagi, T.1    Sugeno, M.2
  • 35
    • 16344385431 scopus 로고    scopus 로고
    • Evolutionary optimization with data collocation for reverse engineering of biological networks
    • Tsai K.-Y., and Wang F.-S. Evolutionary optimization with data collocation for reverse engineering of biological networks Bioinformatics 21 7 2005 1180 1188
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1180-1188
    • Tsai, K.-Y.1    Wang, F.-S.2
  • 37
    • 4444351989 scopus 로고    scopus 로고
    • Decoupling dynamical systems for pathway identification from metabolic profiles
    • Voit E.O., and Almeida J. Decoupling dynamical systems for pathway identification from metabolic profiles Bioinformatics 20 11 2004 1670 1681
    • (2004) Bioinformatics , vol.20 , Issue.11 , pp. 1670-1681
    • Voit, E.O.1    Almeida, J.2
  • 38
    • 84860334238 scopus 로고    scopus 로고
    • CMARS: A new contribution to nonparametric regression with multivariate adaptive regression splines supported by continuous optimization
    • Weber G.-W., Batmaz I., Köksal G., Taylan P., and Yerlikaya-Özkurt F. CMARS: A new contribution to nonparametric regression with multivariate adaptive regression splines supported by continuous optimization Inverse Problems in Science and Engineering 20 3 2012 371 400
    • (2012) Inverse Problems in Science and Engineering , vol.20 , Issue.3 , pp. 371-400
    • Weber, G.-W.1    Batmaz, I.2    Köksal, G.3    Taylan, P.4    Yerlikaya-Özkurt, F.5
  • 40
    • 84875378548 scopus 로고    scopus 로고
    • Adaptive neural-based fuzzy modeling for biological systems
    • Wu S.-J., Wu C.-T., and Chang J.-Y. Adaptive neural-based fuzzy modeling for biological systems Mathematical Biosciences 242 2 2013 153 160
    • (2013) Mathematical Biosciences , vol.242 , Issue.2 , pp. 153-160
    • Wu, S.-J.1    Wu, C.-T.2    Chang, J.-Y.3
  • 41
    • 84868485168 scopus 로고    scopus 로고
    • Steady-state optimization of biochemical systems through geometric programming
    • Xu G. Steady-state optimization of biochemical systems through geometric programming European Journal of Operational Research 225 1 2013 12 20
    • (2013) European Journal of Operational Research , vol.225 , Issue.1 , pp. 12-20
    • Xu, G.1
  • 42
    • 36248944068 scopus 로고    scopus 로고
    • Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization
    • Xu R., Wunsch D. II, and Frank R. Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization IEEE/ACM Transactions on Computational Biology and Bioinformatics 4 4 2007 681 692
    • (2007) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.4 , Issue.4 , pp. 681-692
    • Xu, R.1    Wunsch, I.I.D.2    Frank, R.3
  • 43
    • 80052269746 scopus 로고    scopus 로고
    • Generalized Markov models of infectious disease spread: A novel framework for developing dynamic health policies
    • Yaesoubi R., and Cohen T. Generalized Markov models of infectious disease spread: A novel framework for developing dynamic health policies European Journal of Operational Research 215 3 2011 679 687
    • (2011) European Journal of Operational Research , vol.215 , Issue.3 , pp. 679-687
    • Yaesoubi, R.1    Cohen, T.2
  • 44
  • 45
    • 78751647229 scopus 로고    scopus 로고
    • Parameter estimation in systems biology models using spline approximation
    • Zhan C., and Yeung L.F. Parameter estimation in systems biology models using spline approximation BMC Systems Biology 5 14 2011 1 12
    • (2011) BMC Systems Biology , vol.5 , Issue.14 , pp. 1-12
    • Zhan, C.1    Yeung, L.F.2
  • 46
    • 84899436101 scopus 로고    scopus 로고
    • Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits
    • Zomorrodi A.R., and Maranas C.D. Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits European Journal of Operational Research 237 2 2014 665 676
    • (2014) European Journal of Operational Research , vol.237 , Issue.2 , pp. 665-676
    • Zomorrodi, A.R.1    Maranas, C.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.