Logic programming for boolean networks

IJCAI International Joint Conference on Artificial Intelligence

Volumn , Issue , 2011, Pages 924-930

  Inoue, Katsumi ^a  

^a NATIONAL INSTITUTE OF INFORMATICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BOOLEAN NETWORKS; LOGIC PROGRAMS; LOGICAL INFERENCE; REGULATORY SYSTEMS; STABLE STATE;

ARTIFICIAL INTELLIGENCE; DYNAMICAL SYSTEMS; LOGIC PROGRAMMING; MATHEMATICAL MODELS;

BOOLEAN ALGEBRA;

EID: 84864260450     PISSN: 10450823     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.5591/978-1-57735-516-8/IJCAI11-160     Document Type: Conference Paper

References (27)

1. Akutsu, T., Hayashida, M., Ching, W-K. and Ng, M. K., Control of Boolean networks: Hardness results and algorithms for tree structured networks, Journal of Theoretical Biology, 244:670-679, 2007. (Pubitemid 46148979)
2. Apt, K. R., Blair, H.A. andWalker, A., Towards a theory of declarative knowledge, in: J. Minker (ed.), Foundations of Deductive Databases and Logic Programming, Morgan Kaufmann, pp.89-148, 1988.
3. Baral, C. and Subrahmanian, V. S., Stable and extension class theory for logic programs and default logics, Journal of Automated Reasoning, 8:345-366, 1992.
4. Blair, H. A., Dushin, F. and Humenn, P.R., Simulations between programs as cellular automata, Proceedings of LPNMR '97, LNAI 1265, pp.115-131, 1997.
5. Dubrova, E. and Teslenko, M., A SAT-based algorithm for finding attractors in synchronous Boolean networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010.
6. Fayruzov, T., De Cock, M., Cornelis, C. and Vermeir, D., Modeling protein interaction networks with answer set programming, Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, pp.99-104, 2009.
7. Garg, A., Di Cara, A., Xenarios, I., Mendoza, L. and De Micheli, G., Synchronous versus asynchronous modeling of gene regulatory networks, Bioinformatics, 24(17):1917-1925, 2008.
8. Gebser, M., Schaub, T., Thiele, S., Usadel, B. and Veber, P., Detecting inconsistencies in large biological networks with answer set programming, Proceedings of ICLP '08, LNCS 5366, pp.130-144, 2008.
9. Gelfond, M. and Lifschitz, V., The stable model semantics for logic programming, Proceedings of ICLP '88, pp.1070-1080, MIT Press, 1988.
10. Gershenson, C., Classification of random Boolean networks, in: Artificial Life VIII, pp.1-8, MIT Press, 2002.
11. Harvey, I. and Bossomaier, T., Time out of joint: Attractors in asynchronous random Boolean networks, in: Proceedings of the 4th European Conference on Artificial Life, pp.67-75, MIT Press, 1997.
12. Irons, D. J., Improving the efficiency of attractor cycle identification in Boolean networks, Physica D, 217:7-21, 2006. (Pubitemid 44287871)
13. Kauffman, S. A., Metabolic stability and epigenesis in randomly constructed genetic nets, Journal of Theoretical Biology, 22(3):437-467, 1969.
14. Kauffman, S.A., The Origins of Order: Self-Organization and Selection in Evolution, Oxford University Press, 1993.
15. Lin, F. and Zhao, Y., ASSAT: computing answer sets of a logic program by SAT solvers, Artificial Intelligence, 157:115-137, 2004.
16. Marek, V.W., Niemelä, I. and Truszczyński, M., Logic programs with monotone abstract constraint atoms, Theory and Practice of Logic Programming, 8(2):167-199, 2007.
17. Marek, W. and Subrahmanian, V. S., The relationship between stable, supported, default and autoepistemic semantics for general logic programs, Theor. Comp. Sci., 103(2):365-386, 1992.
18. Marek, W. and Truszczyński, M., Computing intersection of autoepistemic expansions, Proceedings of LPNMR '91, pp.37-50, 1991.
19. n) time, Information Processing Letters, 110(14-15):565-569, 2010.
20. Milano, M. and Roli, A., Solving the satisfiability problem through Boolean networks, Proceedings of AI*IA '99, pp.72-83, LNAI 1792, 1999.
21. Ray, O., Soh, T. and Inoue, K., Analyzing pathways using ASP-based approaches, in: Proceedings of the International Conference on Algebraic and Numeric Biology 2010, LNCS, to appear, Springer, 2011.
22. Remy, E. and Ruet, P., From elementary signed circuits to the dynamics of Boolean regulatory networks, Bioinformatics, 24:220-226, 2008.
23. Shmulevich, I., Dougherty, E.R. and Zhang, W., From Boolean to probabilistic Boolean networks as models of genetic regulatory networks, Proceedings of the IEEE, 90(11):1778-1792, 2002.
24. Simons, P., Niemelä, I. and Soininen, T., Extending and implementing the stable model semantics, Artificial Intelligence, 138(1-2):181-234, 2002.
25. Tamura, T. and Akutsu, T., Detecting a singleton attractor in a Boolean network utilizing SAT algorithms, IEICE Trans., 92-A(s):493-501, 2009.
26. Truszczyński, M. and Woltran, S., Hyperequivalence of logic programs with respect to supported models, Annals of Mathematics and Artificial Intelligence, 53:331-365, 2008.
27. You, J. H. and Yuan, L., A three-valued semantics for deductive database and logic programs, J. Comput. Syst. Sci., 49:334-361, 1994.