Back to Journals » Advances and Applications in Bioinformatics and Chemistry » Volume 3

Efficient algorithms for multidimensional global optimization in genetic mapping of complex traits

Authors Ljungberg K, Mishchenko K, Holmgren S

Published 28 October 2010 Volume 2010:3 Pages 75—88

DOI https://doi.org/10.2147/AABC.S9240

Review by Single anonymous peer review

Peer reviewer comments 3



Kajsa Ljungberg1, Kateryna Mishchenko2, Sverker Holmgren1
1Division of Scientific Computing, Department of Information Technology, Uppsala University, Uppsala, Sweden; 2Department of Mathematics and Physics, Mälardalen University College, Västerås, Sweden

Abstract: We present a two-phase strategy for optimizing a multidimensional, nonconvex function arising during genetic mapping of quantitative traits. Such traits are believed to be affected by multiple so called QTL, and searching for d QTL results in a d-dimensional optimization problem with a large number of local optima. We combine the global algorithm DIRECT with a number of local optimization methods that accelerate the final convergence, and adapt the algorithms to problem-specific features. We also improve the evaluation of the QTL mapping objective function to enable exploitation of the smoothness properties of the optimization landscape. Our best two-phase method is demonstrated to be accurate in at least six dimensions and up to ten times faster than currently used QTL mapping algorithms.

Keywords: global optimization, QTL mapping, DIRECT

 

Creative Commons License © 2010 The Author(s). This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution - Non Commercial (unported, v3.0) License. By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms.