ASSA-PBN: An Approximate Steady-State Analyser of Probabilistic Boolean Networks

Abstract

Abstract. We present ASSA-PBN, a tool for approximate steady-state analysis of large probabilistic Boolean networks (PBNs). ASSA-PBN contains a constructor, a simulator, and an analyser which can approximately compute the steadystate probabilities of PBNs. For large PBNs, such approximate analysis is the only viable way to study their long-run behaviours. Experiments show that ASSA-PBN can handle large PBNs with a few thousands of nodes.

Improving BDD-based attractor detection for synchronous Boolean networks

“…The BNs we use for the experiments are randomly generated with ASSA-PBN [19], which can generate random BNs complying with specified parameters, e.g., the number of nodes in the BN and the maximal number of variables of the predictor functions.…”

ASSA-PBN 2.0: A Software Tool for Probabilistic Boolean Networks

“…The PBN modeller can either load a PBN from a specification file or generate a random PBN (e.g., for benchmarking and testing purposes) complying with a given parametrisation [4]. In ASSA-PBN 2.0, a high-level PBN definition format is provided and visualisation of a PBN is supported in the GUI.…”

“…The steady-state distributions can be computed either in an exact way or in a statistical way. Two iterative methods, i.e., the Jacobi method and the Gauss-Seidel method are implemented for exact computation; while three statistical methods, i.e., the perfect simulation, the two-state Markov chain approach, and the Skart method are implemented for the approximate computation [4]. Due to their large memory and time costs, the two iterative methods and the perfect simulation method are only suitable for analysing small-size PBNs [4].…”

“…As shown in [4], the first version of ASSA-PBN has shown a significant advantage in terms of speed compared to the Matlab tool optPBN [2]. We proceed to compare the performance of ASSA-PBN 2.0 with its previous version.…”

“…ASSA-PBN in its previous version [4] has overcome the above mentioned network size limitation with the implementation of an efficient simulator and state-of-the-art techniques for steady-state analysis, e.g., the two-state Markov chain approach. The newly released version of ASSA-PBN contributes mainly in three aspects.…”