Skip to main content
Fachgebiete
Automobil + Motoren Bauwesen + Immobilien Business IT + Informatik Elektrotechnik + Elektronik Energie + Nachhaltigkeit Finance + Banking Management + Führung Marketing + Vertrieb Maschinenbau + Werkstoffe Versicherung + Risiko
DE
EN
Themenseiten
Organisationspsychologie Projektmanagement Marketing Smart Manufacturing
Bücher
Zeitschriften
Weitere Formate
Podcasts Webinare Technik Webinare Wirtschaft Kongresse Veranstaltungskalender Awards
Jetzt Einzelzugang starten
Zugang für Unternehmen
Referenzkunden
MTZ-Fachkongress

Antriebe und Energiesysteme von morgen


Austausch von Automobil- und Energiewirtschaft

Am 14./15. Mai geht es in Chemnitz um die Mobilitätswende durch Elektro- und Wasserstofffahrzeuge.
Erweiterte Suche
Anmelden
nach oben
Erschienen in:
Buchtitelbild

2016 | OriginalPaper | Buchkapitel

Metabolic Pathways as Temporal Logic Programs

verfasst von : Jean-Marc Alliot, Martín Diéguez, Luis Fariñas del Cerro

Erschienen in: Logics in Artificial Intelligence

Verlag: Springer International Publishing

Einloggen

Aktivieren Sie unsere intelligente Suche, um passende Fachinhalte oder Patente zu finden.

search-config
loading …

Abstract

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.

Sie haben noch keine Lizenz? Dann Informieren Sie sich jetzt über unsere Produkte:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

Jetzt informieren

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

Jetzt informieren
Nächstes Kapitel On Decidability of a Logic of Gossips
Fußnoten
1
Regarding non-monotonic approaches to model biological systems, there are several contributions in the area of Answer Set Programming [9, 28], action languages [29] or Inductive Logic Programming [12]. In these contributions the temporal behaviour is considered in [29] but both representation and query languages are different.
 
2
The Nobel prize was awarded to Monod, Jacob and Lwoff in 1965 partly for the discovery of the lac operon by Monod and Jacob [18], which was the first genetic regulatory mechanism to be understood clearly, and is now a “standard” introductory example in molecular biology classes.
 
3
A less formal explanation can be found in https://​en.​wikipedia.​org/​wiki/​Lac_​operon.
 
4
It is important here to notice that lactose can be either considered as a weak endogenous variable, or as an exogenous variable if we consider that the environment is always providing “enough” lactose. It is a simple example which shows that variables in a graph can be interpreted differently according to what is going to be observed.
 
5
Notice that only the pathway formula associated with the production of Galactosidase has an associated context, defined in (1), while the rest of pathway formulas have an empty context.
 
6
Here and There [16] is an intermediate logic which severs as a monotonic basis for the Equilibrium Models [25], a logical characterisation of the Stable Model semantics [15].
 
7
Modal extensions of Equilibrium Logic and the logic of Here and There can be considered as promising lines of research which lead to several remarkable results, among others, [7, 13].
 
8
We refer the reader to [4] for details about the computation of such loop formulas.
 
9
We omitted the completion at time step 0 since the formula at the initial state depends on the extensional database, which is not considered here.
 
Literatur
1.
2.
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)MathSciNetCrossRef
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 CrossRef
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)
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)
8.
Bozzelli, L., Pearce, D.: On the complexity of temporal equilibrium logic. In: LICS 2015, pp. 645–656. IEEE, Kyoto, Japan (2015)
9.
Brewka, G., Eiter, T., Truszczyński, M.: Answer set programming at a glance. Commun. ACM 54(12), 92–103 (2011)CrossRef
10.
Clark, K.L.: Negation as failure. In: Logic and Databases, pp. 293–322. Plenum Press (1978)
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)
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)MathSciNetCrossRefMATH
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)
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
18.
Jacob, F., Monod, J.: Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318–356 (1961)CrossRef
19.
Kennell, D., Riezman, H.: Transcription and translation initiation frequencies of the Escherichia Coli lac operon. J. Mol. Biol. 114(1), 1–21 (1977)CrossRef
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)CrossRef
21.
Lin, F., Zhao, Y.: ASSAT: computing answer sets of a logic program by SAT solvers. Artif. Intell. 157(1–2), 112–117 (2002)MathSciNet
22.
Manna, Z., Pnueli, A.: The Temporal Logic of Reactive and Concurrent Systems: Specification. Springer, New York (1991)MATH
23.
24.
McCarthy, J., Hayes, P.: Some philosophical problems from the standpoint of artificial intelligence. Mach. Intell. J. 4, 463–512 (1969)MATH
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 CrossRef
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.
29.
Tran, N., Baral, C.: Reasoning about non-immediate triggers in biological networks. Ann. Math. Artif. Intell. 51(2–4), 267–293 (2007)MathSciNetCrossRefMATH
Metadaten
Titel
Metabolic Pathways as Temporal Logic Programs
verfasst von
Jean-Marc Alliot
Martín Diéguez
Luis Fariñas del Cerro
Copyright-Jahr
2016
Buch
Logics in Artificial Intelligence

Print ISBN: 978-3-319-48757-1

Electronic ISBN: 978-3-319-48758-8

Copyright-Jahr: 2016

DOI
https://doi.org/10.1007/978-3-319-48758-8_1

Premium Partner

    Bildnachweise