Noise strategies for improving local search
AAAI '94 Proceedings of the twelfth national conference on Artificial intelligence (vol. 1)
Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
Journal of the ACM (JACM)
Tabu Search
PPSN VII Proceedings of the 7th International Conference on Parallel Problem Solving from Nature
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
INFORMS Journal on Computing
Using median sets for inferring phylogenetic trees
Bioinformatics
Reversal and transposition medians
Theoretical Computer Science
Multi-break rearrangements and chromosomal evolution
Theoretical Computer Science
Improving inversion median computation using commuting reversals and cycle information
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
A unifying view of genome rearrangements
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Multichromosomal Genome Median and Halving Problems
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Decompositions of Multiple Breakpoint Graphs and Rapid Exact Solutions to the Median Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
A Fast and Exact Algorithm for the Median of Three Problem--A Graph Decomposition Approach
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
RECOMB-CG '09 Proceedings of the International Workshop on Comparative Genomics
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The genomic median problem is an optimization problem inspired by a biological issue: it aims to find the chromosome organization of the common ancestor to multiple living species. It is formulated as the search for a genome that minimizes a rearrangement distance measure among given genomes. Several attempts have been reported for solving this NP-hard problem. These range from simple heuristic methods to a stochastic local search algorithm inspired by WalkSAT, a well-known local search algorithm for the satisfiability problem in propositional logic. The main objective of this research is to develop improved algorithmic techniques for tackling the genomic median problem and to provide new state-of-the-art solutions. In particular, we have developed an algorithm that is based on tabu search and iterated local search and that shows high performance. To alleviate the dependence of the algorithm performance on a single fixed parameter setting, we have included a reactive scheme that automatically adapts the tabu list length of the tabu search part and the perturbation strength of the iterated local search part. In fact, computational results show that we have developed a new very high-performing stochastic local search algorithm for the genomic median problem and we also have found a new best solution for a realworld case.