Dynamic Model Inference of Gene Regulatory Network based on Hybrid Parallel Genetic Algorithm and Threshold Qualification Method

Abstract

Gene regulation is the process by which various substances in cells regulate the behaviour of gene expression, thereby controlling almost all cellular activities. Therefore, studying gene regulation not only helps to uncover the internal laws governing life processes but also plays a crucial role in predicting, diagnosing, treating, and designing drugs for genetic diseases. By utilizing multi-source biological information such as gene expression profiles, transcription factor information, and protein interaction data, a network model can be developed to depict the regulatory relationships between genes, facilitating further research. To address the limitations of traditional gene regulatory network construction methods, a novel dynamic model has been created by combining hybrid genetics and threshold restriction. This model comprises two parts: solution space reduction and parameter fitting. During solution space reduction, singular value decomposition is employed to define a mathematically feasible gene regulatory network, reducing unnecessary calculations. Subsequently, the control genes of each gene are constrained within a certain range using threshold limitation, enhancing computational efficiency while adhering to bioinformatics principles. In the parameter fitting phase, parallel genetic algorithms are utilized to expediently optimize the entire solution space. The mountain climbing method is then applied to solve problems meticulously within a limited scope, improving calculation accuracy. In this study, this approach was applied to establish genetic regulatory systems for complex skin melanoma and type 2 diabetes. Through comparison with actual networks, the validity of the method was confirmed. Compared to traditional genetic and particle swarm optimization methods, the effectiveness of the proposed method was verified. This paper models the intricate mechanism of gene regulation and elucidates the regulatory process involving genes, proteins, and small biological molecules in greater detail than other models, aligning more closely with intracellular dynamics laws.