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Finding a Periodic Attractor of a Boolean Network
Sept.-Oct. 2012 (vol. 9 no. 5)
pp. 1410-1421
Tatsuya Akutsu, Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
Sven Kosub, Dept. of Comput. & Inf. Sci., Univ. of Konstanz, Konstanz, Germany
Avraham A. Melkman, Dept. of Comput. Sci., Ben-Gurion Univ. of the Negev, Beer-Sheva, Israel
Takeyuki Tamura, Inst. for Chem. Res., Kyoto Univ., Kyoto, Japan
In this paper, we study the problem of finding a periodic attractor of a Boolean network (BN), which arises in computational systems biology and is known to be NP-hard. Since a general case is quite hard to solve, we consider special but biologically important subclasses of BNs. For finding an attractor of period 2 of a BN consisting of n OR functions of positive literals, we present a polynomial time algorithm. For finding an attractor of period 2 of a BN consisting of n AND/OR functions of literals, we present an O(1.985n) time algorithm. For finding an attractor of a fixed period of a BN consisting of n nested canalyzing functions and having constant treewidth w, we present an O(n2p(w+1)poly(n)) time algorithm.
Index Terms:
polynomials,biology computing,Boolean functions,genetic algorithms,time algorithm,periodic attractor,Boolean network,computational systems biology,positive literals,polynomial time algorithm,AND-OR functions,nested canalyzing functions,constant treewidth,Boolean functions,Computational systems biology,Polynomials,treewidth.,Boolean network,periodic attractor,SAT,nested canalyzing function
Citation:
Tatsuya Akutsu, Sven Kosub, Avraham A. Melkman, Takeyuki Tamura, "Finding a Periodic Attractor of a Boolean Network," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 5, pp. 1410-1421, Sept.-Oct. 2012, doi:10.1109/TCBB.2012.87
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