A hyper‐heuristic approach to sequencing by hybridization of DNA sequences

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.