Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 73, Issue 2, 2006, Pages

  McKinney, B A ^a   Crowe, J E ^a   Voss, H U ^b   Crooke, P S ^a   Barney, N ^c   Moore, J H ^c  

^a VANDERBILT UNIVERSITY   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MODEL ARCHITECTURES; MODEL PARAMETERS; SMALLPOX VACCINES;

COMPUTER ARCHITECTURE; CONTEXT FREE GRAMMARS; GENETIC ALGORITHMS; IDENTIFICATION (CONTROL SYSTEMS); KALMAN FILTERING; MATHEMATICAL MODELS; TIME SERIES ANALYSIS;

NONLINEAR SYSTEMS;

TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; METABOLISM; NONLINEAR SYSTEM; PHYSIOLOGY; PROCEDURES; SIGNAL TRANSDUCTION; TIME;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS; PATTERN RECOGNITION, AUTOMATED; SIGNAL TRANSDUCTION; TIME FACTORS; TRANSCRIPTION FACTORS;

EID: 33644555826     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.73.021912     Document Type: Article

References (37)

1. M. Schena, D. Shalon, R. Davis, and P. Brown, Science SCIEAS 0036-8075 270, 467 (1995).
2. D. Lockhart, H. Dong, M. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Norton, and E. L. Brown, Nat. Biotechnol. NABIF9 1087-0156 10.1038/nbt1296-1675 14, 1675 (1996).
3. S. P. Gygi and R. Aebersold, Curr. Opin. Chem. Biol. COCBF4 1367-5931 4, 489 (2000).
4. L. Raamsdonk, Nat. Biotechnol. NABIF9 1087-0156 19, 45 (2001).
5. R. Cho, Mol. Cell MOCEFL 1097-2765 2, 65 (1998).
6. X. Wen, S. Fuhrman, G. Michaels, D. Carr, S. Smith, J. Barker, and R. Somogyi, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.95.1.334 95, 334 (1998).
7. S. E. Baranznin, PLoS Biol. PBLIBG 1545-7885 3, 166 (2005).
8. C. Nedellec, C. Rouveirol, H. Ade, F. Bergadano, and B. Tausend, in Advances in Inductive Logic Programming, edited by, L. D. Raedt, (IOS Press, Amsterdam, 1996), Vol. 32, pp. 82-103.
9. V. Vapnik and Y. Chervonekis, Theor. Probab. Appl. TPRBAU 0040-585X 26, 532 (1981).
10. P. Moscato, Memetic Algorithms: A Short Introduction (McGraw-Hill, London, 1999), pp. 219-234.
11. R. Dawkins, The Selfish Gene (Oxford University Press, New York, 1976).
12. S. Julier, J. Uhlmann, and H. F. Durrant-Whyte, IEEE Trans. Autom. Control IETAA9 0018-9286 10.1109/9.847726 45, 477 (2000).
13. A. Sitz, U. Schwarz, J. Kurths, and H. U. Voss, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.66.016210 66, 016210 (2002).
14. M. O'Neill and C. Ryan, IEEE Trans. Evol. Comput. ITEVF5 1089-778X 5, 349 (2001).
15. X. Yao, Int. J. Intell. Syst. IJISED 0884-8173 8, 539 (1993).
16. C. W. Chau, S. Kwong, C. K. Diu, and W. R. Fahrner, in IEEE International Conference on Acoustics, Speech, and Signal Processing, Vol. 3 (IEEE, New Jersey, 1997), pp. 1727-1730.
17. M. Marcotty and H. Ledgard, The World of Programming Languages (Springer-Verlag, New York, 1986).
18. I. Dempsey, M. O'Neill, and A. Brabazon, in GECCO'98: Proceedings of the Genetic and Evolutionary Computation Conference, edited by, W. Banzhaf, (Morgan Kaufman, San Francisco, 2004), pp. 447-458.
19. M. Evett and T. Fernandez, in Genetic Programming 1998: Proceedings of the Third Annual Conference, edited by, J. R. Koza, (Morgan Kaufman, San Francisco, 1998), pp. 66.
20. A. Gelb, Applied Optimal Estimation (The MIT Press, Cambridge, MA, 1974).
21. R. E. Kalman, J. Basic Eng. JBAEAI 0021-9223 82, Series D, 35 (1960).
22. H. U. Voss, J. Timmer, and J. Kurths, Int. J. Bifurcation Chaos Appl. Sci. Eng. IJBEE4 0218-1274 10.1142/S0218127404010345 14, 1905 (2004).
23. F. Jacob and J. Monod, Cold Spring Harbor Symp. Quant. Biol. CSHSAZ 0091-7451 26, 193 (1961).
24. J. Tyson and H. Othmer, Prog. Theor. Biol. PTHBAW 0079-6859 5, 2 (1978).
25. P. Smolen, D. A. Baxter, and J. Byrne, Bull. Math. Biol. BMTBAP 0092-8240 10.1006/bulm.1999.0155 62, 247 (2000).
26. H. de Jong, J. Comput. Biol. JCOBEM 1066-5277 10.1089/10665270252833208 9, 67 (2002).
27. M. Wall, GALIB, http://lancet.mit.edu/ga/ (1995).
28. W. Gropp, E. Lush, and A. Skjellum, Using MPI: Portable Parallel Programming with the Message-Passing Interface, 2nd ed. (MIT Press, Cambridge, MA, 1999).
29. M. O'Neill and C. Ryan, in Grammatical Evolution: Evolutionary Automatic Programming in an Arbitrary Language (Genetic Programming Series) Vol. 4, (Kluwer Academic, 2003).
30. M. Mitchell, J. Crutchfield, and P. Hraber, Physica D PDNPDT 0167-2789 10.1016/0167-2789(94)90293-3 75, 361 (1994).
31. M. T. Rock, S. M. Toder, T. F. Talbot, K. M. Edwards, and J. E. C. Jr., J. Infect. Dis. 0022-1899 189, 1401 (2004).
32. J. Tegnér, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0933416100 100, 5944 (2003).
33. M. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, and S. Miyano, in Proceedings of the Pacific Symposium on Biocomputing, edited by, R. B. Altman, (World Scientific, New Jersey, 2003), pp. 17.
34. A. Shin and H. Iba, Genome Informatics 14, 94 (2003).
35. M. Wahde and J. Hertz, BioSystems BSYMBO 0303-2647 10.1016/S0303-2647(99) 00090-8 55, 129 (2000).
36. J. Koza, Genetic Programming: On the Programming of Computers by Means of Natural Selection (MIT Press, Cambridge, MA, 1992).
37. M. Koern, T. C. Elston, W. J. Blake, and J. J. Collins, Nat. Rev. Genet. NRGAAM 1471-0056 10.1038/nrg1615 6, 451 (2005).