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Nuha Saud Fahad BinTayyash - نهى سعود الطياش

Assistant Professor

Department of Information Technology

علوم الحاسب والمعلومات
Building 6 3rd Floor Office 101
publication
Journal Article
2017

BeamGA Median: A Hybrid Heuristic Search Approach

Badr, Ghada . 2017

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation that minimizes the sum of distances between itself and a set of three signed permutations. Genomes with equal number of genes but different order can be represented as permutations. In this paper, an algorithm, namely BeamGA median, is proposed that combines a heuristic search approach (local beam) as an initialization step to generate a number of solutions, and then a Genetic Algorithm (GA) is applied in order to refine the solutions, aiming to achieve a better median with the smallest possible reversal distance from the three original permutations. In this approach, any genome rearrangement distance can be applied. In this paper, we use the reversal distance. To the best of our knowledge, the proposed approach was not applied before for solving the median problem. Our approach considers true biological evolution scenario by applying the concept of common intervals during the GA optimization process. This allows us to imitate a true biological behavior and enhance genetic approach time convergence. We were able to handle permutations with a large number of genes, within an acceptable time performance and with same or better accuracy as compared to existing algorithms

Volume Number
11
Issue Number
6
Magazine \ Newspaper
World Academy of Science, Engineering and Technology International Journal of Bioengineering and Life Sciences Vol:11, No:6, 2017
Pages
6
more of publication
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publications

The median problem is significantly applied to derive the most reasonable rearrangement phylogenetic tree for many species. More specifically, the problem is concerned with finding a permutation…

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publications

BeamGA is a general hybrid heuristic framework that can be used to solve the median problem in comparative genomics, where any distance function can be used. It starts with a heuristic search…

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