55,529 research outputs found
Tackling Universal Properties of Minimal Trap Spaces of Boolean Networks
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
(). 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
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
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
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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