IJMS, Vol. 19, Pages 3178: HSCVFNT: Inference of Time-Delayed Gene Regulatory Network Based on Complex-Valued Flexible Neural Tree Model (International Journal of Molecular Sciences)

Gene regulatory network (GRN) inference can understand the growth and development of animals and plants, and reveal the mystery of biology. Many computational approaches have been proposed to infer GRN. However, these inference approaches have hardly met the need of modeling, and the reducing redundancy methods based on individual information theory method have bad universality and stability. To overcome the limitations and shortcomings, this thesis proposes a novel algorithm, named HSCVFNT, to infer gene regulatory network with time-delayed regulations by utilizing a hybrid scoring method and complex-valued flexible neural network (CVFNT). The regulations of each target gene can be obtained by iteratively performing HSCVFNT. For each target gene, the HSCVFNT algorithm utilizes a novel scoring method based on time-delayed mutual information (TDMI), time-delayed maximum information coefficient (TDMIC) and time-delayed correlation coefficient (TDCC), to reduce the redundancy of regulatory relationships and obtain the candidate regulatory factor set. Then, the TDCC method is utilized to create time-delayed gene expression time-series matrix. Finally, a complex-valued flexible neural tree model is proposed to infer the time-delayed regulations of each target gene with the time-delayed time-series matrix. Three real time-series expression datasets from (Save Our Soul) SOS DNA repair system in E. coli and Saccharomyces cerevisiae are utilized to evaluate the performance of the HSCVFNT algorithm. As a result, HSCVFNT obtains outstanding F-scores of 0.923, 0.8 and 0.625 for SOS network and (In vivo Reverse-Engineering and Modeling Assessment) IRMA network inference, respectively, which are 5.5%, 14.3% and 72.2% higher than the best performance of other state-of-the-art GRN inference methods and time-delayed methods.