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SCIENCE CHINA Information Sciences, Volume 59, Issue 8: 080101(2016) https://doi.org/10.1007/s11432-016-5594-9

Improving BDD-based attractor detection for synchronous Boolean networks

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  • ReceivedApr 25, 2016
  • AcceptedMay 18, 2016
  • PublishedJul 18, 2016

Abstract

Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years. An~important challenge in Boolean networks is to exhaustively find attractors, which represent steady states of a~biological network. In this paper, we propose a~new approach to improve the efficiency of BDD-based attractor detection. Our approach includes a~monolithic algorithm for small networks, an~enumerative strategy to deal with large networks, a~method to accelerate attractor detection based on an~analysis of the network structure, and two heuristics on ordering BDD variables. We demonstrate the performance of our approach on a~number of examples and on a~realistic model of apoptosis in hepatocytes. We compare it with one existing technique in the literature.


Funded by

EPSRC project EP/J011894/2 and Royal Society Project IE141180. Qixia YUAN was supported by National Research Fund Luxembourg(7814267)


Acknowledgment

Acknowledgments

Honyang QU was supported by EPSRC project EP/J011894/2 and Royal Society Project IE141180. Qixia YUAN was supported by National Research Fund, Luxembourg (Grant No. 7814267).


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