The Cluster Editing Problem: Implementations and Experiments
In this paper, we study the cluster editing problem which is fixed parameter tractable. We present the first practical implementation of a FPT based method for cluster editing, using the approach in [6,7], and compare our implementation with the straightforward greedy method and a solution based on linear programming . Our experiments show that the best results are obtained by using the refined branching method in  together with interleaving (re-kernelization). We also observe an interesting lack of monotonicity in the running times for “yes” instances with increasing values of k.
KeywordsBinary Search Vertex Cover Edit Distance Common Neighbor Greedy Method
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- 1.Abu-Khzam, F.N., Collins, R.L., Fellows, M.R., Langston, M.A., Suters, W.H., Symons, C.T.: Kernelization algorithms for the vertex cover problem: Theory and experiments. In: Proceedings, Workshop on Algorithm Engineering and Experiments, New Orleans, Louisiana (2004)Google Scholar
- 2.Abu-Khzam, F.N., Langston, M.A., Shanbhag, P., Symons, C.T.: Scalable parallel algorithms for FPT problems. Algorithmica (2006) (accepted for publication)Google Scholar
- 7.Guo, J.: Algorithm design techniques for parameterized graph modification problems. PhD thesis, Univ. Jena (2005)Google Scholar
- 9.Knuth, D.E.: The Art of Computer Programming, Seminumerical algorithms, 3rd edn., vol. 2. Addison-Wesley, Reading (1997)Google Scholar
- 10.Zhang, Y., Abu-Khzam, F.N., Baldwin, N.E., Chesler, E.J., Langston, M.A., Samatova, N.F.: Genome-scale computational approaches to memory-intensive applications in systems biology. In: Proceedings, Supercomputing, Seattle, Washington (2005)Google Scholar