Optimal Reconstruction of Probabilistic Boolean Networks

In gene regulatory networks (GRNs), it is important to model gene regulation based on a priori information and experimental data. As a useful mathematical model, probabilistic Boolean networks (PBNs) have been widely applied in GRNs. This article addresses the optimal reconstruction problem of PBNs based on several priori Boolean functions and sampled data. When all candidate Boolean functions are known in advance, the optimal reconstruction problem is reformulated into an optimization problem. This problem can be well solved by a recurrent neural network approach which decreases the computational cost. When parts of candidate Boolean functions are known in advance, necessary and sufficient conditions are provided for the reconstruction of PBNs. In this case, two types of reconstruction problems are further proposed: one is aimed at minimizing the number of reconstructed Boolean functions, and the other one is aimed at maximizing the selection probability of the main dynamics under noises. At last, examples in GRNs are elaborated to demonstrate the effectiveness of the main results.