Fast simulation of probabilistic Boolean networks
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Publication:1706589
DOI10.1007/978-3-319-45177-0_14zbMATH Open1382.92146arXiv1605.00854OpenAlexW2516917634MaRDI QIDQ1706589FDOQ1706589
Authors: Andrzej Mizera, Jun Pang, Qixia Yuan 
Publication date: 22 March 2018
Abstract: Probabilistic Boolean networks (PBNs) is an important mathematical framework widely used for modelling and analysing biological systems. PBNs are suited for modelling large biological systems, which more and more often arise in systems biology. However, the large system size poses a~significant challenge to the analysis of PBNs, in particular, to the crucial analysis of their steady-state behaviour. Numerical methods for performing steady-state analyses suffer from the state-space explosion problem, which makes the utilisation of statistical methods the only viable approach. However, such methods require long simulations of PBNs, rendering the simulation speed a crucial efficiency factor. For large PBNs and high estimation precision requirements, a slow simulation speed becomes an obstacle. In this paper, we propose a structure-based method for fast simulation of PBNs. This method first performs a network reduction operation and then divides nodes into groups for parallel simulation. Experimental results show that our method can lead to an approximately 10 times speedup for computing steady-state probabilities of a real-life biological network.
Full work available at URL: https://arxiv.org/abs/1605.00854
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- A look-ahead simulation algorithm for DBN models of biochemical pathways
- Generating probabilistic Boolean networks from a prescribed stationary distribution
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