Dynamic model inference of gene regulatory network based on hybrid
parallel genetic algorithm and threshold qualification method
Abstract
Gene regulation is the regulation of gene expression behavior by various
related substances in cells, which controls almost all cell activities.
Therefore, the study of gene regulation can not only explore the
internal law of life activities, but also play a great role in the
prediction, diagnosis, treatment and drug design of gene-related
diseases. Using multi-source biological information such as gene
expression profile data, transcription factor information and protein
interaction information, a network model can be established to describe
the regulatory relationship between genes, so as to facilitate the above
studies. In order to solve the problem of low accuracy of traditional
gene regulatory network construction methods, a new dynamic model of
gene regulatory network was established by combining hybrid genetics and
threshold restriction. The model is divided into two parts: solution
space reduction and parameter fitting. In the phase of solution space
reduction, singular value decomposition method is used to define the
mathematically feasible gene regulatory network to reduce unnecessary
calculation, and then the control gene of each gene is limited to a
certain scale by threshold limitation method, which improves the
computational efficiency and accords with the bioinformatics rules. In
the parameter fitting part, the parallel genetic algorithm is used to
optimize the whole solution space quickly, and then the mountain
climbing method is used to solve the problem carefully in a small range
to improve the calculation accuracy. In this study, we applied this
method to the establishment of genetic regulatory systems for complex
skin melanoma and type 2 diabetes. By comparing with the real network,
the correctness of the method is proved. Compared with traditional
genetic and PSO methods, the effectiveness of the proposed method was
verified. In this paper, the deep mechanism of gene regulation is
modeled, and the regulation process involving genes, proteins and small
biological molecules is described in more detail, so as to be more
detailed than other models and more consistent with the intracellular
dynamics law.