55,529 research outputs found

    Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks

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    Minimal trap spaces (MTSs) capture subspaces in which the Boolean dynamics is trapped, whatever the update mode. They correspond to the attractors of the most permissive mode. Due to their versatility, the computation of MTSs has recently gained traction, essentially by focusing on their enumeration. In this paper, we address the logical reasoning on universal properties of MTSs in the scope of two problems: the reprogramming of Boolean networks for identifying the permanent freeze of Boolean variables that enforce a given property on all the MTSs, and the synthesis of Boolean networks from universal properties on their MTSs. Both problems reduce to solving the satisfiability of quantified propositional logic formula with 3 levels of quantifiers (\exists\forall\exists). In this paper, we introduce a Counter-Example Guided Refinement Abstraction (CEGAR) to efficiently solve these problems by coupling the resolution of two simpler formulas. We provide a prototype relying on Answer-Set Programming for each formula and show its tractability on a wide range of Boolean models of biological networks.Comment: Accepted at 21st International Conference on Computational Methods in Systems Biology (CMSB 2023

    Message passing for quantified Boolean formulas

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    We introduce two types of message passing algorithms for quantified Boolean formulas (QBF). The first type is a message passing based heuristics that can prove unsatisfiability of the QBF by assigning the universal variables in such a way that the remaining formula is unsatisfiable. In the second type, we use message passing to guide branching heuristics of a Davis-Putnam Logemann-Loveland (DPLL) complete solver. Numerical experiments show that on random QBFs our branching heuristics gives robust exponential efficiency gain with respect to the state-of-art solvers. We also manage to solve some previously unsolved benchmarks from the QBFLIB library. Apart from this our study sheds light on using message passing in small systems and as subroutines in complete solvers.Comment: 14 pages, 7 figure

    On implicational bases of closure systems with unique critical sets

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    We show that every optimum basis of a finite closure system, in D.Maier's sense, is also right-side optimum, which is a parameter of a minimum CNF representation of a Horn Boolean function. New parameters for the size of the binary part are also established. We introduce a K-basis of a general closure system, which is a refinement of the canonical basis of Duquenne and Guigues, and discuss a polynomial algorithm to obtain it. We study closure systems with the unique criticals and some of its subclasses, where the K-basis is unique. A further refinement in the form of the E-basis is possible for closure systems without D-cycles. There is a polynomial algorithm to recognize the D-relation from a K-basis. Thus, closure systems without D-cycles can be effectively recognized. While E-basis achieves an optimum in one of its parts, the optimization of the others is an NP-complete problem.Comment: Presented on International Symposium of Artificial Intelligence and Mathematics (ISAIM-2012), Ft. Lauderdale, FL, USA Results are included into plenary talk on conference Universal Algebra and Lattice Theory, June 2012, Szeged, Hungary 29 pages and 2 figure

    C*-algebras associated to boolean dynamical systems

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    The goal of these notes is to present the C*-algebra C*(B,L,θ) of a Boolean dynamical system (B,L,θ), that generalizes the C*-algebra associated to Labelled graphs introduced by Bates and Pask, and to determine its simplicity, its gauge invariant ideals, as well as compute its K-Theory
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