An O(1.787n)-Time Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes

The Boolean network (BN) is a mathematical model of genetic networks. It is known that detecting a singleton attractor, which is also called a fixed point, is NP-hard even for AND/OR BNs (i.e., BNs consisting of AND/OR nodes), where singleton attractors correspond to steady states. Though a naive algorithm can detect a singleton attractor for an AND/OR BN in O(n2n) time, no O((2 - e)n) (e > 0) time algorithm was known even for an AND/OR BN with non-restricted indegree, where n is the number of nodes in a BN. In this paper, we present an O(1.787n) time algorithm for detecting a singleton attractor of a given AND/OR BN, along with related results.

[1]  Kazuo Iwama,et al.  Improved upper bounds for 3-SAT , 2004, SODA '04.

[2]  Andrea Roli,et al.  Solving the Satisfiability Problem through Boolean Networks , 1999, AI*IA.

[3]  Satoru Miyano,et al.  Inferring qualitative relations in genetic networks and metabolic pathways , 2000, Bioinform..

[4]  L. Glass,et al.  The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.

[5]  Carsten Peterson,et al.  Random Boolean network models and the yeast transcriptional network , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Michael K. Ng,et al.  Algorithms for Finding Small Attractors in Boolean Networks , 2007, EURASIP J. Bioinform. Syst. Biol..

[7]  S. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets. , 1969, Journal of theoretical biology.

[8]  Edward A. Hirsch,et al.  New Worst-Case Upper Bounds for SAT , 2000, Journal of Automated Reasoning.

[9]  Albert,et al.  Dynamics of complex systems: scaling laws for the period of boolean networks , 2000, Physical review letters.

[10]  A. Mochizuki An analytical study of the number of steady states in gene regulatory networks. , 2005, Journal of theoretical biology.

[11]  Sui Huang Gene expression profiling, genetic networks, and cellular states: an integrating concept for tumorigenesis and drug discovery , 1999, Journal of Molecular Medicine.

[12]  Giorgio Parisi,et al.  Finite size corrections to random Boolean networks , 2006 .

[13]  Yamamoto Masaki An Improved (1.234m)-Time Deterministic Algorithm for SAT , 2005 .

[14]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[15]  Masaki Yamamoto,et al.  An Improved O(1.234m)-Time Deterministic Algorithm for SAT , 2005, ISAAC.

[16]  B. Drossel,et al.  Number and length of attractors in a critical Kauffman model with connectivity one. , 2004, Physical review letters.

[17]  S. Kauffman,et al.  Activities and sensitivities in boolean network models. , 2004, Physical review letters.

[18]  Roland Somogyi,et al.  Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation , 1996, Complex..

[19]  B. Samuelsson,et al.  Superpolynomial growth in the number of attractors in Kauffman networks. , 2003, Physical review letters.

[20]  Akutsu,et al.  A System for Identifying Genetic Networks from Gene Expression Patterns Produced by Gene Disruptions and Overexpressions. , 1998, Genome informatics. Workshop on Genome Informatics.