A parallel attractor-finding algorithm based on Boolean satisfiability for genetic regulatory networks.
In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network. The interactions of activation and inhibition in the genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory network. A difficult problem for state transition analysis is the finding of attractors. In this paper, we modeled the genetic regulatory network as a Boolean network and proposed a solving algorithm to tackle the attractor finding problem. In the proposed algorithm, we partitioned the Boolean network into several blocks consisting of the strongly connected components according to their gradients, and defined the connection between blocks as decision node. Based on the solutions calculated on the decision nodes and using a satisfiability solving algorithm, we identified the attractors in the state transition graph of each block. The proposed algorithm is benchmarked on a variety of genetic regulatory networks. Compared with existing algorithms, it achieved similar performance on small test cases, and outperformed it on larger and more complex ones, which happens to be the trend of the modern genetic regulatory network. Furthermore, while the existing satisfiability-based algorithms cannot be parallelized due to their inherent algorithm design, the proposed algorithm exhibits a good scalability on parallel computing architectures.
School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China; Electrical Engineering Department, University of California Los Angeles, Los Angeles, California, United States of America.
Wensheng
W
Guo
School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
Guowu
G
Yang
Electrical Engineering Department, University of California Los Angeles, Los Angeles, California, United States of America.
Wei
W
Wu
Electrical Engineering Department, University of California Los Angeles, Los Angeles, California, United States of America.
Lei
L
He
Institute of Liver Diseases, ShuGuang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Mingyu
M
Sun
D000465:Algorithms; D019295:Computational Biology; D003198:Computer Simulation; D005240:Feasibility Studies; D053263:Gene Regulatory Networks; D008957:Models, Genetic