An improved Bayesian network method for reconstructing gene regulatory network based on candidate auto selection

Abstract

Background: The reconstruction of gene regulatory network (GRN) from gene expression data can discover regulatory relationships among genes and gain deep insights into the complicated regulation mechanism of life. However, it is still a great challenge in systems biology and bioinformatics. During the past years, numerous computational approaches have been developed for this goal, and Bayesian network (BN) methods draw most of attention among these methods because of its inherent probability characteristics. However, Bayesian network methods are time consuming and cannot handle large-scale networks due to their high computational complexity, while the mutual information-based methods are highly effective but directionless and have a high false-positive rate. Results: To solve these problems, we propose a Candidate Auto Selection algorithm (CAS) based on mutual information and breakpoint detection to restrict the search space in order to accelerate the learning process of Bayesian network. First, the proposed CAS algorithm automatically selects the neighbor candidates of each node before searching the best structure of GRN. Then based on CAS algorithm, we propose a globally optimal greedy search method (CAS + G), which focuses on finding the highest rated network structure, and a local learning method (CAS + L), which focuses on faster learning the structure with little loss of quality. Conclusion: Results show that the proposed CAS algorithm can effectively reduce the search space of Bayesian networks through identifying the neighbor candidates of each node. In our experiments, the CAS + G method outperforms the state-of-the-art method on simulation data for inferring GRNs, and the CAS + L method is significantly faster than the state-of-the-art method with little loss of accuracy. Hence, the CAS based methods effectively decrease the computational complexity of Bayesian network and are more suitable for GRN inference.