CVC: A Cooperating Validity Checker
CAV '02 Proceedings of the 14th International Conference on Computer Aided Verification
A satisfiability procedure for quantified boolean formulae
Discrete Applied Mathematics - The renesse issue on satisfiability
Stability analysis of biological systems with real solution classification
Proceedings of the 2005 international symposium on Symbolic and algebraic computation
IJCAI'05 Proceedings of the 19th international joint conference on Artificial intelligence
Automated symbolic reachability analysis: with application to delta-notch signaling automata
HSCC'03 Proceedings of the 6th international conference on Hybrid systems: computation and control
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
A fast linear-arithmetic solver for DPLL(T)
CAV'06 Proceedings of the 18th international conference on Computer Aided Verification
Algorithmic algebraic model checking i: challenges from systems biology
CAV'05 Proceedings of the 17th international conference on Computer Aided Verification
PHAVer: algorithmic verification of hybrid systems past hytech
HSCC'05 Proceedings of the 8th international conference on Hybrid Systems: computation and control
From propositional satisfiability to satisfiability modulo theories
SAT'06 Proceedings of the 9th international conference on Theory and Applications of Satisfiability Testing
Finding Lean Induced Cycles in Binary Hypercubes
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Periodic orbits and equilibria in glass models for gene regulatory networks
IEEE Transactions on Information Theory - Special issue on information theory in molecular biology and neuroscience
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Glass piecewise linear ODE models are frequently used for simulation of neural and gene regulatory networks. Efficient computational tools for automatic synthesis of such models are highly desirable. However, the existing algorithms for the identification of desired models are limited to four-dimensional networks, and rely on numerical solutions of eigenvalue problems. We suggest a novel algebraic criterion to detect the type of the phase flow along network cyclic attractors that is based on a corollary of the Perron-Frobenius theorem. We show an application of the criterion to the analysis of bifurcations in the networks. We propose to encode the identification of models with periodic orbits along cyclic attractors as a propositional formula, and solving it using state-of-the-art SAT-based tools for real linear arithmetic. New lower bounds for the number of equivalence classes are calculated for cyclic attractors in six-dimensional networks. Experimental results indicate that the run-time of our algorithm increases slower than the size of the search space of the problem.