ConvAn: a convergence analyzing tool for optimization of biochemical networks.
Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That causes problems of optimization predictability as most of numerical optimization methods have stochastic properties and the convergence of the objective function to the global optimum is hardly predictable. Determination of suitable optimization method and necessary duration of optimization becomes critical in case of evaluation of high number of combinations of adjustable parameters or in case of large dynamic models. This task is complex due to variety of optimization methods, software tools and nonlinearity features of models in different parameter spaces. A software tool ConvAn is developed to analyze statistical properties of convergence dynamics for optimization runs with particular optimization method, model, software tool, set of optimization method parameters and number of adjustable parameters of the model. The convergence curves can be normalized automatically to enable comparison of different methods and models in the same scale. By the help of the biochemistry adapted graphical user interface of ConvAn it is possible to compare different optimization methods in terms of ability to find the global optima or values close to that as well as the necessary computational time to reach them. It is possible to estimate the optimization performance for different number of adjustable parameters. The functionality of ConvAn enables statistical assessment of necessary optimization time depending on the necessary optimization accuracy. Optimization methods, which are not suitable for a particular optimization task, can be rejected if they have poor repeatability or convergence properties. The software ConvAn is freely available on www.biosystems.lv/convan.
Biosystems Group, Department of Computer Systems, Latvia University of Agriculture, Jelgava, Latvia. andrejs.kostromins@gmail.com
Andrejs
A
Kostromins
Ivars
I
Mozga
Egils
E
Stalidzans
D003198:Computer Simulation; D000431:Ethanol / Q000378:metabolism; D005947:Glucose / Q000378:metabolism; D006019:Glycolysis; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D017711:Nonlinear Dynamics; D012984:Software; D013269:Stochastic Processes; D049490:Systems Biology; D015003:Yeasts / Q000378:metabolism
D000431:Ethanol; D005947:Glucose