Home // BIOTECHNO 2014, The Sixth International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies // View article
Authors:
Susanne Rosenthal
Markus Borschbach
Keywords: multi-objective biochemical optimization; population size; average cuboid volume; open source Java tools.
Abstract:
The key part in the area of peptide design is the prediction of the peptides’ molecular features. The performance of the drug design process depends on the identification of peptides that optimize several molecular properties at the same time. The synthesis of peptides for laboratory characterization is very cost-intensive. Therefore, drug development is a wide field of activity for multi-objective Genetic Algorithms (moGAs). A customized NSGA-II has been especially evolved for biochemical optimization with the focus on producing a great number of very different high quality peptides within a very low number of generations (under 20), termed early convergence. The main task of this paper is to verify empirically the effect of early convergence for this customized NSGA-II within a limited range of population size. Furthermore, an insight into the impact of the interdependence between the population size and the selection procedure is examined with the objective of giving a configuration rule for the selection parameter and the population size exemplary determined for a three-dimensional biochemical minimization problem. Although, this optimization problem is as generic as possible. The performance is assessed on the basis of a convergence indicator especially evolved for our preference of comparing the convergence behavior of populations with different sizes. Moreover, we propose a summarization of open source Java tools that are discussed regarding the potential of an easy implementation of the customized NSGA-II for biochemical optimization.
Pages: 1 to 7
Copyright: Copyright (c) IARIA, 2014
Publication date: April 20, 2014
Published in: conference
ISSN: 2308-4383
ISBN: 978-1-61208-335-3
Location: Chamonix, France
Dates: from April 20, 2014 to April 24, 2014