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

European Journal of Operational Research

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

  Cheung, Ngaam J ^a,b,c   Xu, Zhen Kai ^b   Ding, Xue Ming ^b   Shen, Hong Bin ^a  

^a Key Laboratory of Marine Intelligent Equipment and System of Ministry of Education   (China)

^b UNIVERSITY OF SHANGHAI FOR SCIENCE AND TECHNOLOGY   (China)

^c UNIVERSITY OF CHICAGO   (United States)

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;

COMPUTATIONAL BIOLOGY; EXPLORATION AND EXPLOITATION; FUZZY RULE-BASED MODELS; HETEROGENEOUS PARTICLES; OPTIMIZATION FRAMEWORK; PARAMETERS ESTIMATION; TAKAGI SUGENO FUZZY MODELS; TIME-COURSE RESPONSE;

PARTICLE SWARM OPTIMIZATION (PSO);

EID: 84938749469     PISSN: 03772217     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ejor.2015.03.047     Document Type: Article

References (46)

1. Acharya L., Judeh T., Duan Z., Rabbat M., and Zhu D. Signal transduction cascades regulating fungal development and virulence Microbiology and Molecular Biology Reviews 64 4 2000 746 785
2. 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
3. Ascher U.M., and Petzold L.R. Computer methods for ordinary differential equations and differential-algebraic equations 1st ed. 1998 Society for Industrial and Applied Mathematics Philadelphia, PA, USA
4. van den Bergh F., and Engelbrecht A. A study of particle swarm optimization particle trajectories Information Sciences 176 8 2006 937 971
5. Bratton D., and Kennedy J. Defining a standard for particle swarm optimization Proceedings of the IEEE conference on swarm intelligence symposium 2007 120 127
6. 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
7. 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
8. 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
9. 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
10. 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
11. 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
12. Engelbrecht A.P. Scalability of a heterogeneous particle swarm optimizer IEEE symposium on swarm intelligence (SIS) 2011 1 8
13. 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
14. Gennemark P., and Wedelin D. Benchmarks for identification of ordinary differential equations from time series data BMC Systems Biology 25 6 2009 780 786
15. 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
16. Herrera F., and Verdegay J. Fuzzy sets and operations research: Perspectives Fuzzy Sets and Systems 90 2 1997 207 218
17. Kell D.B. Metabolomics and systems biology: making sense of the soup Current Opinion in Microbiology 7 3 2004 296 307
18. 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
19. Kennedy J., and Eberhart R.C. Particle swarm optimization Proceedings of the IEEE conference, IEEE service center, Perth, Australia 1995 1942 1948
20. 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
21. 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
22. Kroll A. Identification of functional fuzzy models using multidimensional reference fuzzy sets Fuzzy Sets and Systems 80 2 1996 149 158
23. Leu M.-S., and Yeh M.-F. Grey particle swarm optimization Applied Soft Computing 12 9 2012 2985 2996
24. Liang J., and Suganthan P. Dynamic multi-swarm particle swarm optimizer Proceedings of the IEEE conference on swarm intelligence symposium 2005 124 129
25. 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
26. 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
27. Lyapunov A.M. The general problem of the stability of motion International Journal of Control 55 3 1992 531 534
28. 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
29. 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
30. Shi Y., Eberhart R., and Chen Y. Implementation of evolutionary fuzzy systems IEEE Transactions on Fuzzy Systems 7 2 1999 109 119
31. Shirai H., Prades C., Vita R., Marcatili P., Popovic B., Xu J., and et al. Antibody informatics for drug discovery Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1844 11 2014 2002 2015
32. Sugeno M., and Yasukawa T. A fuzzy-logic-based approach to qualitative modeling IEEE Transactions on Fuzzy Systems 1 1 1993 7 31
33. Sun J., Garibaldi J.M., and Hodgman C. Parameter estimation using metaheuristics in systems biology: A comprehensive review IEEE/ACM Transactions on Computational Biology and Bioinformatics 9 01 2012 185 202
34. 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
35. Tsai K.-Y., and Wang F.-S. Evolutionary optimization with data collocation for reverse engineering of biological networks Bioinformatics 21 7 2005 1180 1188
36. Voit E.O. Computational analysis of biochemical systems: A practical guide for biochemists and molecular biologists 2000 Cambridge University Press
37. Voit E.O., and Almeida J. Decoupling dynamical systems for pathway identification from metabolic profiles Bioinformatics 20 11 2004 1670 1681
38. 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
39. Weber G.-W., Defterli O., Gökc S.Z.A., and Kropat E. Modeling, inference and optimization of regulatory networks based on time series data European Journal of Operational Research 211 1 2011 1 14
40. 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
41. Xu G. Steady-state optimization of biochemical systems through geometric programming European Journal of Operational Research 225 1 2013 12 20
42. 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
43. 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
44. Zazopoulos E., Huang K., Staffa A., Liu W., Bachmann B.O., Nonaka K., and et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways Nature Biotechnology 21 2003 187 190
45. Zhan C., and Yeung L.F. Parameter estimation in systems biology models using spline approximation BMC Systems Biology 5 14 2011 1 12
46. 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