Parameter Estimation by Using an Improved Bee Memory Differential Evolution Algorithm (IBMDE) to Simulate Biochemical Pathways

Abstract

Assessing and estimating essential parameters for a metabolic pathway by using a mathematical model is a significant step in Systems Biology. However, estimating process often faces numerous obstacles, for example when the number of unknown parameters escalates or data has noise, gets trapped in local minima and or having repeated exploration of poor solution during search process. Thus, this study proposes an improved Bee Memory Differential Evolution algorithm (IBMDE), which is a combination of the Differential Evolution algorithm (DE), the Kalman Filter (KF), the Artificial Bee Colony algorithm (ABC), and a memory feature to solve the aforementioned problems. The implemented metabolic pathways for this improved estimation algorithm were glycerol and pyruvate synthesis pathways. IBMDE was successful in generating the estimated optimal kinetic parameter values with noticeable reduction in errors (81.36% and 99.46% respectively) and faster convergence times (6.19% and 15.72% respectively) compared to DE, the Genetic Algorithm (GA), the Nelder Mead (NM), and the Simulated Annealing (SA). The results indicated that, most importantly, the kinetic parameters produced by IBMDE had enhanced the production of desired metabolites than the other estimation algorithms. Besides that, the results also demonstrated the reliability of IBMDE as an estimation algorithm in terms of lower error.