A Multiobjective Evolutionary-Simplex Hybrid Approach for the Optimization of Differential Equation Models of Gene Networks

• Published in: IEEE transactions on evolutionary computation 2008-10, Vol.12 (5), p.572-590
• Main Authors: Koduru, P., Zhanshan Dong, Das, S., Welch, S.M., Roe, J.L., Charbit, E.
• Format: Article
• Language: English
• Subjects: Applied sciences; Arabidopsis; Bioinformatics; Biological system modeling; Biology computing; Combinatorics; Combinatorics. Ordered structures; Computer networks; Computer science; control theory; systems; Data mining; Data processing. List processing. Character string processing; Differential equations; Exact sciences and technology; Flows in networks. Combinatorial problems; Fuzzy; fuzzy dominance; Genes; Genetic algorithms; genetic algorithms (GAs); Genomics; Graph theory; hybrid algorithms; Information retrieval. Graph; Mathematical models; Mathematics; Memory organisation. Data processing; multiobjective optimization; Networks; Operational research and scientific management; Operational research. Management science; Optimization; Organisms; Oryza sativa; Parameter estimation; Sciences and techniques of general use; Searching; simplex; Software; Studies; Theoretical computing
• ISSN: 1089-778X; 1941-0026
• DOI: 10.1109/TEVC.2008.917202

This paper describes genetic and hybrid approaches for multiobjective optimization using a numerical measure called fuzzy dominance. Fuzzy dominance is used when implementing tournament selection within the genetic algorithm (GA). In the hybrid version, it is also used to carry out a Nelder-Mead simplex-based local search. The proposed GA is shown to perform better than NSGA-II and SPEA-2 on standard benchmarks, as well as for the optimization of a genetic model for flowering time control in rice. Adding the local search achieves faster convergence, an important feature in computationally intensive optimization of gene networks. The hybrid version also compares well with ParEGO on a few other benchmarks. The proposed hybrid algorithm is then applied to estimate the parameters of an elaborate gene network model of flowering time control in Arabidopsis. Overall solution quality is quite good by biological standards. Tradeoffs are discussed between accuracy in gene activity levels versus in the plant traits that they influence. These tradeoffs suggest that data mining the Pareto front may be useful in bioinformatics.