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On Boolean Automata Networks (de)Composition

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Języki publikacji
EN
Abstrakty
EN
Boolean automata networks (BANs) are a generalisation of Boolean cellular automata. In such, any theorem describing the way BANs compute information is a strong tool that can be applied to a wide range of models of computation. In this paper we explore a way of working with BANs which involves adding external inputs to the base model (via modules), and more importantly, a way to link networks together using the above mentioned inputs (via wirings). Our aim is to develop a powerful formalism for BAN (de)composition. We formulate three results: the first one shows that our modules/wirings definition is complete; the second one uses modules/wirings to prove simulation results amongst BANs; the final one expresses the complexity of the relation between modularity and the dynamics of modules.
Słowa kluczowe
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Rocznik
Strony
163--188
Opis fizyczny
Bibliogr. 17 poz., rys.
Twórcy
  • Université publique, France
  • Aix-Marseille Université, Université de Toulon, CNRS, LIS, Marseille, France
  • Université publique, France
Bibliografia
  • [1] Perrot K, Perrotin P, Sené S. A framework for (de)composing with Boolean automata networks. In: Proceedings of MCU’18, volume 10881 of LNCS. 2018 pp. 121-136. doi:10.1007/978-3-319-92402-1_7.
  • [2] Demongeot J, Goles E, Morvan M, Noual M, Sené S. Attraction basins as gauges of robustness against boundary conditions in biological complex systems. PLoS One, 2010. 5:e11793. doi:10.1371/journal.pone.0011793.
  • [3] Kauffman SA. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology, 1969. 22(3):437-467. doi:10.1016/0022-5193(69)90015-0.
  • [4] Thomas R. Boolean formalization of genetic control circuits. Journal of Theoretical Biology, 1973. 42(3):563-585. doi: 10.1016/0022-5193(73)90247-6.
  • [5] Alcolei A, Perrot K, Sené S. On the flora of asynchronous locally non-monotonic Boolean automata networks. In: Proceedings of SASB’15, volume 326 of ENTCS. 2016 pp. 3-25. doi: 10.1016/j.entcs.2016.09.016.
  • [6] Noual M. Updating Automata Networks. Ph.D. thesis, École Normale Supérieure de Lyon, 2012.
  • [7] Alon U. Biological networks: the tinkerer as an engineer. Science, 2003. 301:1866-1867. doi: 10.1126/science.1089072.
  • [8] Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. Network motifs: simple building blocks of complex networks. Science, 2002. 298:824-827. doi: 10.1126/science.298.5594.824.
  • [9] Bernot G, Tahi F. Behaviour preservation of a biological regulatory network when embedded into a larger network. Fundamenta Informaticae, 2009. 91(3-4):463-485. doi:10.3233/FI-2009-0052.
  • [10] Delaplace F, Klaudel H, Melliti T, Sené S. Analysis of modular organisation of interaction networks based on asymptotic dynamics. In: Proceedings of CMSB’12, volume 7605 of LNCS. 2012 pp. 148-165. doi: 10.1007/978-3-642-33636-2_10.
  • [11] Siebert H. Dynamical and structural modularity of discrete regulatory networks. In: Proceedings of COMPMOD’09, volume 6 of EPTCS. 2009 pp. 109-124. doi:10.4204/EPTCS.6.8.
  • [12] Feder T. Stable networks and product graphs. Ph.D. thesis, Stanford University, 1990.
  • [13] Cook M. Universality in elementary cellular automata. Complex Systems, 2004. 15:1-40.
  • [14] Aracena J, Gómez L, Salinas L. Limit cycles and update digraphs in Boolean networks. Discrete Applied Mathematics, 2013. 161(1-2):1-12. doi:10.1016/j.dam.2012.07.003.
  • [15] Goles E, Salinas L. Comparison between parallel and serial dynamics of Boolean networks. Theoretical Computer Science, 2008. 396(1-3):247-253. doi:10.1016/j.tcs.2007.09.008.
  • [16] Davidich M, Bornholdt S. Boolean network model predicts cell cycle sequence of fission yeast. PLoS One, 2008. 3:e1672. doi:10.1371/journal.pone.0001672.
  • [17] Dennunzio A, Dorigatti V, Formenti E, Manzoni L, Porreca AE. Polynomial Equations over Finite, Discrete-Time Dynamical Systems. In: Cellular Automata. Springer International Publishing, Cham, 2018 pp. 298-306. doi:10.1007/978-3-319-99813-8_27.
Typ dokumentu
Bibliografia
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