Bayesian robustness in the control of gene regulatory networks

IEEE Transactions on Signal Processing

Volumn 57, Issue 9, 2009, Pages 3667-3678

  Pal, Ranadip ^a   Datta, Aniruddha ^b   Dougherty, Edward R ^b,c  

^a Texas Tech University   (United States)

^b Department of Electrical and Computer Engineering   (United States)

^c TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

Bayesian robustness; Gene regulatory networks; Intervention; Parameter estimation; Robust control

Indexed keywords

BAYESIAN APPROACHES; BAYESIAN DESIGN; BAYESIAN ROBUSTNESS; DATA EXTRACTION; GENE REGULATORY NETWORKS; GENE SELECTION; INFERENCE PROCESS; INTERVENTION; INTERVENTION STRATEGY; MINIMAX; MINIMAX CONTROL; MODELING ERRORS; NETWORK INFERENCE; TRANSITION PROBABILITIES; WORST CASE;

ERRORS; PARAMETER ESTIMATION; ROBUST CONTROL; ROBUSTNESS (CONTROL SYSTEMS);

BAYESIAN NETWORKS;

EID: 69349084710     PISSN: 1053587X     EISSN: None     Source Type: Journal    
DOI: 10.1109/TSP.2009.2022872     Document Type: Article

References (28)

1. A. Datta and E. R. Dougherty, Introduction to Genomic Signal Processing With Control. Boca Raton, FL: CRC Press, 2007.
2. A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External control in Markovian genetic regulatory networks," Mach. Learn., vol. 52, pp. 169-191, 2003.
3. R. Pal, A. Datta, and E. R. Dougherty, "Optimal infinite horizon control for probabilistic boolean networks," IEEE Trans. Signal Process., vol. 54, no. 6, pp. 2375-2387, Jun. 2006.
4. S. A. Kauffman, The Origins of Order: Self-Organization and Selection in Evolution. New York: Oxford Univ. Press, 1993.
5. I. Shmulevich, E. R. Dougherty, and W. Zhang, "From boolean to probabilistic Boolean networks as models of genetic regulatory networks," Proc. IEEE, vol. 90, pp. 1778-1792, 2002.
6. N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Bayesian networks to analyze expression data," in Proc. 4th Annu. Int. Conf. Computational Molecular Biology, 2000, pp. 127-135.
7. I. Shmulevich, E. R. Dougherty, and W. Zhang, "Gene perturbation and intervention in probabilistic boolean networks," Bioinformatics, vol. 18, pp. 1319-1331, 2002.
8. W.-K. Ching, S.-Q. Zhang, Y. Jiao, T. Akutsu, and A. S. Wong, "Optimal finite-horizon control for probabilistic boolean networks with hard constraints," in Int. Symp. Optimization Systems Biology, 2007, pp. 21-28.
9. P. C. Y. Chen and J. W. Chen, "A Markovian approach to the control of genetic regulatory networks," BIOSYSTEMS, vol. 90, pp. 535-545, 2007.
10. R. Pal, A. Datta, and E. R. Dougherty, "Robust intervention in probabilistic boolean networks," IEEE Trans. Signal Process., vol. 56, no. 3, pp. 1280-1294, Mar. 2008.
11. A. Nilim and L. El Ghaoui, "Robust Markov decision processes with uncertain transition matrices," EECS Dept., Univ. of California, Berkeley, CA, Tech. Rep. UCB/ERL M04/28, 2004.
12. G. Lyengar, "Robust dynamic programming," Math. Oper. Res., vol. 30, pp. 1-21, 2005.
13. V. P. Kuznetsov, "Stable detection when the signal and spectrum of normal noise are inaccurately known," Telecommun. Radio Eng., vol. 30-31, pp. 58-64, 1976.
14. S. A. Kassam and T. I. Lim, "Robust wiener filters," Franklin Inst. vol. 304, pp. 171-185, 1977.
15. H. V. Poor, "On robust wiener filtering," IEEE Trans. Autom. Control, vol. 26, pp. 531-536, 1980.
16. K. S. Vastola and H. V. Poor, "Robust Wiener-Kolmogorov theory," IEEE Trans. Inf. Theory, vol. 28, pp. 316-327, 1983.
17. A. M. Grygorian and E. R. Dougherty, "Design and analysis of robust optimal binary filters in the context of a prior distribution for the states of nature," Math. Imag. Vis., vol. 11, pp. 239-254, 2001.
18. A. M. Grygorian and E. R. Dougherty, "Bayesian robust optimal linear filters," Signal Process., vol. 81, pp. 2503-2521, 2001.
19. E. R. Dougherty, J. Hua, Z. Xiong, and Y. Chen, "Optimal robust classifiers," Pattern Recogn., vol. 38, pp. 1520-1532, 2005.
20. Y. Chen, E. R. Dougherty, and M. L. Bittner, "Ratio-based decisions and the quantitative analysis of CDNA microarray images," J. Biomed. Opt., vol. 2, pp. 364-374, 1997.
21. D. Longo and J. Hasty, "Dynamics of single-cell gene expression," Molecul. Syst. Biol., vol. 2, pp. 4100-4110, 2006.
22. I. Shmulevich and S. A. Kauffman, "Activities and sensitivities in boolean network models," Phys. Rev. Lett., vol. 93, pp. 048701-4, 2004.
23. R. Pal, A. Datta, M. L. Bittner, and E. R. Dougherty, "Intervention in context-sensitive probabilistic boolean networks," Bioinformatics vol. 21, pp. 1211-1218, 2005.
24. D. P. Bertsekas, Dynamic Programming and Optimal Control, 2nd ed. Singapore: Athena Scientific, 2001.
25. M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, A. Ben-Dor, N. Sampas, E. Dougherty, E. Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, J. Carpten, E. Gillanders, D. Leja, K. Dietrich, C. Beaudry, M. Berens, D. Alberts, and V. Sondak, "Molecular classification of cutaneous malignant melanoma by gene expression profiling," Nature, vol. 406, pp. 536-540, 2000.
26. A. T. Weeraratna, Y. Jiang, G. Hostetter, K. Rosenblatt, P. Duray, M. Bittner, and J. M. Trent, "Wnt5a signalling directly affects cell motility and invasion of metastatic melanoma," Cancer Cell, vol. 1, pp. 279-288, 2002.
27. A. Datta, A. Choudhary, M. L. Bittner, and E. R. Dougherty, "External control in Markovian genetic regulatory networks: The imperfect information case," Bioinformatics, vol. 20, pp. 924-930, 2004.
28. R. Pal, I. Ivanov, A. Datta, M. L. Bittner, and E. R. Dougherty, "Generating boolean networks with a prescribed attractor structure," Bioinformatics, vol. 21, pp. 4021-4025, 2005.