Intelligent Engineering Systems through Artificial Neural Networks, Volume 16
43 Comparison of Simulated Annealing and Genetic Algorithm Approaches in Optimizing the Output of Biological Pathways
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Biological processes are random in nature and studying them through laboratory experiments alone is costly and time-consuming. Applying mathematical modeling provides a more efficient method for understanding and modifying them. Recently we proposed an algorithm Box to assist in modeling and controlling any biological pathway. In the Box algorithm, the output (protein concentration) control and optimization is carried out by applying simulated annealing to selective high-sensitivity reactions. Here we apply an alternative approach, a genetic algorithm, in place of simulated annealing, in the Box algorithm. The improved Box algorithm compares outputs derived by simulated annealing with outputs derived by the genetic algorithm and chooses the better set of values. We thus provide a tool to guide the modification of biological pathways that is both accurate and easy to apply. We illustrate our technique using the TNFα-mediated NF-κB pathway.