SOME EXPERIENCES WITH SOLVING SEMIDEFINITE PROGRAMMING RELAXATIONS OF BINARY QUADRATIC OPTIMIZATION MODELS IN COMPUTATIONAL BIOLOGY

Alexander Engau ()
Additional contact information
Alexander Engau: Department of Mathematical and Statistical Sciences, University of Colorado Denver, Auraria Campus, Campus Box 170, PO Box 173364, Denver, CO 80217-3364, USA;

Asia-Pacific Journal of Operational Research (APJOR), 2014, vol. 31, issue 04, 1-18

Abstract: We present two recent integer programming models in molecular biology and study practical reformulations to compute solutions to some of these problems. In extension of previously tested linearization techniques, we formulate corresponding semidefinite relaxations and discuss practical rounding strategies to find good feasible approximate solutions. Our computational results highlight the possible advantages and remaining challenges of this approach especially on large-scale problems.

Keywords: Combinatorial optimization; integer programming; binary quadratic programming; semidefinite programming; doubly non-negative relaxation; computational biology; protein folding; protein similarity; rotamer assignment; contact map overlap (search for similar items in EconPapers)
Date: 2014
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://www.worldscientific.com/doi/abs/10.1142/S0217595914500225
Access to full text is restricted to subscribers

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:wsi:apjorx:v:31:y:2014:i:04:n:s0217595914500225

Ordering information: This journal article can be ordered from

DOI: 10.1142/S0217595914500225

Access Statistics for this article

Asia-Pacific Journal of Operational Research (APJOR) is currently edited by Gongyun Zhao

More articles in Asia-Pacific Journal of Operational Research (APJOR) from World Scientific Publishing Co. Pte. Ltd.
Bibliographic data for series maintained by Tai Tone Lim ().