Intelligent mutation based evolutionary optimization algorithm for genomics and precision medicine

• Published in: Functional & integrative genomics 2024-08, Vol.24 (4), p.128, Article 128
• Main Authors: Singh, Shailendra Pratap, Yadav, Dileep Kumar, Chamran, Mohammad Kazem, Perera, Darshika G.
• Format: Article
• Language: English
• Subjects: Algorithms; Animal Genetics and Genomics; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cell Biology; Correspondence; Evolution; Evolution, Molecular; Genomes; Genomics; Genomics - methods; Genotypes; Humans; Information processing; Life Sciences; Microbial Genetics and Genomics; Mutation; Next-generation sequencing; Optimization algorithms; Phenotypes; Plant Genetics and Genomics; Precision medicine; Precision Medicine - methods; Reproductive fitness
• ISSN: 1438-793X; 1438-7948; 1438-7948
• DOI: 10.1007/s10142-024-01401-3

In this paper, genomics and precision medicine have witnessed remarkable progress with the advent of high-throughput sequencing technologies and advances in data analytics. However, because of the data’s great dimensionality and complexity, the processing and interpretation of large-scale genomic data present major challenges. In order to overcome these difficulties, this research suggests a novel Intelligent Mutation-Based Evolutionary Optimization Algorithm (IMBOA) created particularly for applications in genomics and precision medicine. In the proposed IMBOA, the mutation operator is guided by genome-based information, allowing for the introduction of variants in candidate solutions that are consistent with known biological processes. The algorithm’s combination of Differential Evolution with this intelligent mutation mechanism enables effective exploration and exploitation of the solution space. Applying a domain-specific fitness function, the system evaluates potential solutions for each generation based on genomic correctness and fitness. The fitness function directs the search toward ideal solutions that achieve the problem’s objectives, while the genome accuracy measure assures that the solutions have physiologically relevant genomic properties. This work demonstrates extensive tests on diverse genomics datasets, including genotype-phenotype association studies and predictive modeling tasks in precision medicine, to verify the accuracy of the proposed approach. The results demonstrate that, in terms of precision, convergence rate, mean error, standard deviation, prediction, and fitness cost of physiologically important genomic biomarkers, the IMBOA consistently outperforms other cutting-edge optimization methods.