title: An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters.
abstract: The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.
authors.affiliation: Artificial Intelligence and Bioinformatics Group, Faculty of Computing, Universiti Teknologi Malaysia, Johor, Malaysia. afnizanfaizal@utm.my
authors.forename: Afnizanfaizal
authors.initials: A
authors.lastname: Abdullah
authors.forename: Safaai
authors.initials: S
authors.lastname: Deris
authors.forename: Sohail
authors.initials: S
authors.lastname: Anwar
authors.forename: Satya N V
authors.initials: SN
authors.lastname: Arjunan
mesh_terms: D000465:Algorithms; D000818:Animals; D001120:Arginine / Q000378:metabolism; D005075:Biological Evolution; D025461:Feedback, Physiological; D048888:Fireflies / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D017711:Nonlinear Dynamics; D015203:Reproducibility of Results; D015398:Signal Transduction; D016159:Tumor Suppressor Protein p53 / Q000235:genetics / Q000378:metabolism
chemical_list: D016159:Tumor Suppressor Protein p53; D001120:Arginine