2018/04/20 by Xinwei Chai, Chai, Xinwei, Morgan Magnin +3
Biochemistry, Genetics and Molecular Biology · Computer Science · #Formal Methods in Verification #Gene Regulatory Network Analysis #Microbial Metabolic Engineering and Bioproduction #cs.FL
paper · pdf · doi:10.48550/arxiv.1804.07543
10 pages including appendix and references
arxiv created 2018/04/20 · arxiv updated 2018/04/23
On demand of efficient reachability analysis due to the inevitable complexity of large-scale biological models, this paper is dedicated to a novel approach: PermReach, for reachability problem of our new framework, Asynchronous Binary Automata Networks (ABAN). ABAN is an expressive modeling framework which contains all the dynamics behaviors performed by Asynchronous Boolean Networks. Compared to Boolean Networks (BN), ABAN has a finer description of state transitions (from a local state to another, instead of symmetric Boolean functions). To analyze the reachability properties on large-scale models (like the ones from systems biology), previous works exhibited an efficient abstraction technique called Local Causality Graph (LCG). However, this technique may be not conclusive. Our contribution here is to extend these results by tackling those complex intractable cases via a heuristic technique. To validate our method, tests were conducted in large biological networks, showing that our method is more conclusive than existing ones.