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Appears in Collections:Computing Science and Mathematics Journal Articles
Peer Review Status: Refereed
Title: A hyper-heuristic approach to sequencing by hybridization of DNA sequences
Author(s): Blazewicz, Jacek
Burke, Edmund
Kendall, Graham
Mruczkiewicz, Wojciech
Oguz, Ceyda
Swiercz, Aleksandra
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Keywords: Hyper-heuristics
Simulated annealing
Tabu search
Choice function
Sequencing by hybridization
Issue Date: Aug-2013
Date Deposited: 3-Jul-2013
Citation: Blazewicz J, Burke E, Kendall G, Mruczkiewicz W, Oguz C & Swiercz A (2013) A hyper-heuristic approach to sequencing by hybridization of DNA sequences. Annals of Operations Research, 207 (1), pp. 27-41.
Abstract: In this paper we investigate the use of hyper-heuristic methodologies for predicting DNA sequences. In particular, we utilize Sequencing by Hybridization. We believe that this is the first time that hyper-heuristics have been investigated in this domain. A hyper-heuristic is provided with a set of low-level heuristics and the aim is to decide which heuristic to call at each decision point. We investigate three types of hyper-heuristics. Two of these (simulated annealing and tabu search) draw their inspiration from meta-heuristics. The choice function hyper-heuristic draws its inspiration from reinforcement learning. We utilize two independent sets of low-level heuristics. The first set is based on a previous tabu search method, with the second set being a significant extension to this basic set, including utilizing a different representation and introducing the definition of clusters. The datasets we use comprises two randomly generated datasets and also a publicly available biological dataset. In total, we carried out experiments using 70 different combinations of heuristics, using the three datasets mentioned above and investigating six different hyper-heuristic algorithms. Our results demonstrate the effectiveness of a hyper-heuristic approach to this problem domain. It is necessary to provide a good set of low-level heuristics, which are able to both intensify and diversify the search but this approach has demonstrated very encouraging results on this extremely difficult and important problem domain.
DOI Link: 10.1007/s10479-011-0927-y
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