zbMATH — the first resource for mathematics

Metabolic pathways as temporal logic programs. (English) Zbl 06658149
Michael, Loizos (ed.) et al., Logics in artificial intelligence. 15th European conference, JELIA 2016, Larnaca, Cyprus, November 9–11, 2016. Proceedings. Cham: Springer (ISBN 978-3-319-48757-1/pbk; 978-3-319-48758-8/ebook). Lecture Notes in Computer Science 10021. Lecture Notes in Artificial Intelligence, 3-17 (2016).
Summary: Metabolic networks, formed by series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell and by a set of interactions that guide and regulate the activity of these reactions. Cancers, for example, can sometimes appear in a cell as a result of some pathology in a metabolic pathway. Most of these pathways are formed by an intricate and complex network of chain reactions, and they can be represented in a human readable form using graphs which describe the cell signaling pathways.
In this paper we present a logic, called molecular equilibrium logic, a nonmonotonic logic which allows representing metabolic pathways. We also show how this logic can be presented in terms of a syntactical subset of temporal equilibrium logic, the temporal extension of equilibrium logic, called splittable temporal logic programs.
For the entire collection see [Zbl 1350.68015].
68T27 Logic in artificial intelligence
Full Text: DOI
[1] Molecular interaction maps site. http://discover.nci.nih.gov/mim/ . Accessed 6 Sept 2016
[2] The systems biology markup language site. http://sbml.org/Documents . Accessed 6 Sept 2016
[3] Aguado, F., Cabalar, P., Diéguez, M., Pérez, G., Vidal, C.: Temporal equilibrium logic: a survey. J. Appl. Non-Classical Logics 23(1–2), 2–24 (2013) · Zbl 1400.68199 · doi:10.1080/11663081.2013.798985
[4] Aguado, F., Cabalar, P., Pérez, G., Vidal, C.: Loop formulas for splitable temporal logic programs. In: Delgrande, J.P., Faber, W. (eds.) LPNMR 2011. LNCS (LNAI), vol. 6645, pp. 80–92. Springer, Heidelberg (2011). doi: 10.1007/978-3-642-20895-9_9 · Zbl 1327.68058 · doi:10.1007/978-3-642-20895-9_9
[5] Alliot, J.M., Demolombe, R., Diéguez, M., Fariñas del Cerro, L., Favre, G., Faye, J.C., Obeid, N., Sordet, O.: Temporal modeling of biological systems. In: Akama, S. (ed.) Towards Paraconsistent Engineering: From Pure Logic to Applied Logic. Springer (2016, to appear) · doi:10.1007/978-3-319-40418-9_11
[6] Alliot, J.M., Demolombe, R., Fariñas del Cerro, L., Diéguez, M., Obeid, N.: Abductive reasoning on molecular interaction maps. In: 7th European Symposium on Computational Intelligence and Mathematics. Springer, Cádiz, Spain (2015)
[7] Balbiani, P., Diéguez, M.: Temporal here and there (2016, unpublished) · Zbl 06658154
[8] Bozzelli, L., Pearce, D.: On the complexity of temporal equilibrium logic. In: LICS 2015, pp. 645–656. IEEE, Kyoto, Japan (2015) · Zbl 1394.68223 · doi:10.1109/LICS.2015.65
[9] Brewka, G., Eiter, T., Truszczyński, M.: Answer set programming at a glance. Commun. ACM 54(12), 92–103 (2011) · doi:10.1145/2043174.2043195
[10] Clark, K.L.: Negation as failure. In: Logic and Databases, pp. 293–322. Plenum Press (1978) · doi:10.1007/978-1-4684-3384-5_11
[11] Demolombe, R., Fariñas del Cerro, L., Obeid, N.: A logical model for molecular interactions maps. In: Fariñas del Cerro, L., Inoue, K. (eds.) Logical Modeling of Biological Systems, pp. 93–123. Wiley, New York (2014)
[12] Doncescu, A., Yamamoto, Y., Inoue, K.: Biological systems analysis using inductive logic programming. In: AINA 2007, pp. 690–695, Niagara Falls, Canada (2007) · doi:10.1109/AINAW.2007.112
[13] Fariñas del Cerro, L., Herzig, A., Su, E.I.: Epistemic equilibrium logic. In: IJCAI 2015, pp. 2964–2970. AAAI Press, Buenos Aires, Argentina (2015)
[14] Ferraris, P., Lee, J., Lifschitz, V.: A generalization of the Lin-Zhao theorem. Ann. Math. Artif. Intell. 47(1–2), 79–101 (2006) · Zbl 1105.68015 · doi:10.1007/s10472-006-9025-2
[15] Gelfond, M., Lifschitz, V.: The stable model semantics for logic programming. In: ICLP 1988, pp. 1070–1080. MIT Press, Cambridge (1988)
[16] Heyting, A.: Die formalen Regeln der intuitionistischen Logik. In: Sitzungsberichte der Preussischen Akademie der Wissenschaften, Physikalisch-mathematische Klasse, pp. 42–56 (1930) · JFM 56.0823.01
[17] Iersel, M.V., Kelder, T., Pico, A., Hanspers, K., Coort, S., Conklin, B., Evelo, C.: Presenting and exploring biological pathways with PathVisio. BMC Bioinform. (2008). doi: 10.1186/1471-2105-9-399 · doi:10.1186/1471-2105-9-399
[18] Jacob, F., Monod, J.: Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961) · doi:10.1016/S0022-2836(61)80072-7
[19] Kennell, D., Riezman, H.: Transcription and translation initiation frequencies of the Escherichia Coli lac operon. J. Mol. Biol. 114(1), 1–21 (1977) · doi:10.1016/0022-2836(77)90279-0
[20] Kohn, K.W., Pommier, Y.: Molecular interaction map of the p53 and Mdm2 logic elements, which control the off-on swith of p53 response to DNA damage. Biochem. Biophys. Res. Commun. 331(3), 816–827 (2005) · doi:10.1016/j.bbrc.2005.03.186
[21] Lin, F., Zhao, Y.: ASSAT: computing answer sets of a logic program by SAT solvers. Artif. Intell. 157(1–2), 112–117 (2002)
[22] Manna, Z., Pnueli, A.: The Temporal Logic of Reactive and Concurrent Systems: Specification. Springer, New York (1991) · Zbl 0753.68003
[23] Mayer, M.C., Pirri, F.: Propositional abduction in modal logic. Logic J. IGPL 3(6), 907–919 (1995) · Zbl 0847.03010 · doi:10.1093/jigpal/3.6.907
[24] McCarthy, J., Hayes, P.: Some philosophical problems from the standpoint of artificial intelligence. Mach. Intell. J. 4, 463–512 (1969) · Zbl 0226.68044
[25] Pearce, D.: A new logical characterisation of stable models and answer sets. In: Dix, J., Pereira, L.M., Przymusinski, T.C. (eds.) NMELP 1996. LNCS, vol. 1216, pp. 57–70. Springer, Heidelberg (1997). doi: 10.1007/BFb0023801 · doi:10.1007/BFb0023801
[26] Pearce, D., Valverde, A.: Abduction in equilibrium logic. In: ASP 2001 Workshop, Stanford, USA (2001)
[27] Reiter, R.: On closed world data bases. In: Logic and Data Bases, pp. 55–76 (1977)
[28] Schaub, T., Thiele, S.: Metabolic network expansion with answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol. 5649, pp. 312–326. Springer, Heidelberg (2009). doi: 10.1007/978-3-642-02846-5_27 · Zbl 05586273 · doi:10.1007/978-3-642-02846-5_27
[29] Tran, N., Baral, C.: Reasoning about non-immediate triggers in biological networks. Ann. Math. Artif. Intell. 51(2–4), 267–293 (2007) · Zbl 1137.68603 · doi:10.1007/s10472-008-9091-8
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. It attempts to reflect the references listed in the original paper as accurately as possible without claiming the completeness or perfect precision of the matching.