Exact algorithms for cluster editing: Evaluation and experiments

Algorithmica (New York)

Volumn 60, Issue 2, 2011, Pages 316-334

  Böcker, Sebastian ^a,b   Briesemeister, Sebastian ^c   Klau, Gunnar W ^d  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b Jena Centre for Bioinformatics   (Germany)

^c UNIVERSITY OF TÜBINGEN   (Germany)

^d CWI   (Netherlands)

Author keywords

Algorithm engineering; Branch and cut algorithm; Cluster editing; Computer experiments; Fixed parameter tractability; FPT; ILP; Integer linear programming; NP complete problem

Indexed keywords

ALGORITHM ENGINEERING; BRANCH-AND-CUT ALGORITHMS; CLUSTER EDITING; COMPUTER EXPERIMENTS; FIXED-PARAMETER TRACTABILITY; FPT; ILP; INTEGER LINEAR PROGRAMMING; NP COMPLETE PROBLEMS;

COMPUTATIONAL COMPLEXITY; COMPUTER PROGRAMMING; DATA REDUCTION; EXPERIMENTS; GRAPH THEORY; INTEGER PROGRAMMING; LINEAR PROGRAMMING; OPERATIONS RESEARCH; PARAMETER ESTIMATION; STATISTICS;

CLUSTERING ALGORITHMS;

EID: 79953212248     PISSN: 01784617     EISSN: 14320541     Source Type: Journal    
DOI: 10.1007/s00453-009-9339-7     Document Type: Article

References (20)

1. A. Ben-Dor R. Shamir Z. Yakhini 1999 Clustering gene expression patterns J. Comput. Biol. 6 3-4 281 297 10.1089/106652799318274
2. Böcker, S., Briesemeister, S., Bui, Q.B.A., Tru, A.: A fixed-parameter approach for weighted cluster editing. In: Proc. of Asia-Pacific Bioinformatics Conference (APBC 2008). Series on Advances in Bioinformatics and Computational Biology, vol. 5, pp. 211-220. Imperial College Press, London (2008)
3. Böcker, S., Briesemeister, S., Bui, Q.B.A., Tru, A.: Going weighted: Parameterized algorithms for cluster editing. In: Proc. of Conference on Combinatorial Optimization and Applications (COCOA 2008). Lect. Notes Comput. Sc., vol. 5165, pp. 1-12. Springer, Berlin (2008)
4. M. Charikar V. Guruswami A. Wirth 2005 Clustering with qualitative information J. Comput. Syst. Sci. 71 3 360 383 10.1016/j.jcss.2004.10.012 2168358 (Pubitemid 41278185)
5. Dehne, F., Langston, M.A., Luo, X., Pitre, S., Shaw, P., Zhang, Y.: The cluster editing problem: Implementations and experiments. In: Proc. of International Workshop on Parameterized and Exact Computation (IWPEC 2006). Lect. Notes Comput. Sc., vol. 4169, pp. 13-24. Springer, Berlin (2006) (Pubitemid 44609908)
6. J. Gramm J. Guo F. Hüffner R. Niedermeier 2004 Automated generation of search tree algorithms for hard graph modification problems Algorithmica 39 4 321 347 10.1007/s00453-004-1090-5 2057269 (Pubitemid 40871661)
7. J. Gramm J. Guo F. Hüffner R. Niedermeier 2005 Graph-modeled data clustering: Fixed-parameter algorithms for clique generation Theor. Comput. Syst. 38 4 373 392 10.1007/s00224-004-1178-y (Pubitemid 40997666)
8. M. Grötschel Y. Wakabayashi 1989 A cutting plane algorithm for a clustering problem Math. Program. 45 52 96 10.1007/BF01589097
9. J. Guo 2009 A more effective linear kernelization for cluster editing Theor. Comput. Sci. 410 8-10 718 726 10.1016/j.tcs.2008.10.021
10. G.A. Kochenberger F. Glover B. Alidaee H. Wang 2005 Clustering of microarray data via clique partitioning J. Comb. Optim. 10 1 77 92 10.1007/s10878-005-1861-1 2160790 (Pubitemid 41205698)
11. M. Křivánek J. Morávek 1986 NP-hard problems in hierarchical-tree clustering Acta Inform. 23 3 311 323 10.1007/BF00289116 853580
12. R. Müller 1996 On the partial order polytope of a digraph Math. Program. 73 31 49 10.1007/BF02592097 (Pubitemid 126373496)
13. Niedermeier, R.: Invitation to Fixed-Parameter Algorithms. Oxford University Press, London (2006)
14. Rahmann, S., Wittkop, T., Baumbach, J., Martin, M., Tru, A., Böcker, S.: Exact and heuristic algorithms for weighted cluster editing. In: Proc. of Computational Systems Bioinformatics (CSB 2007), vol. 6, pp. 391-401 (2007)
15. R. Shamir R. Sharan D. Tsur 2004 Cluster graph modification problems Discrete Appl. Math. 144 1-2 173 182 10.1016/j.dam.2004.01.007 2095392
16. R. Sharan A. Maron-Katz R. Shamir 2003 CLICK and EXPANDER: a system for clustering and visualizing gene expression data Bioinformatics 19 14 1787 1799 10.1093/bioinformatics/btg232 (Pubitemid 37220471)
17. M. Stoer F. Wagner 1997 A simple min-cut algorithm J. ACM 4 585 591 10.1145/263867.263872 1481316 (Pubitemid 127617705)
18. R.L. Tatusov N.D. Fedorova J.D. Jackson A.R. Jacobs B. Kiryutin E.V. Koonin D.M. Krylov R. Mazumder S.L. Mekhedov A.N. Nikolskaya B.S. Rao S. Smirnov A.V. Sverdlov S. Vasudevan Y.I. Wolf J.J. Yin D.A. Natale 2003 The COG database: an updated version includes eukaryotes BMC Bioinformatics 4 41 10.1186/1471-2105-4-41 (Pubitemid 38751229)
19. van Zuylen, A., Williamson, D.P.: Deterministic algorithms for rank aggregation and other ranking and clustering problems. In: Proc. of Workshop on Approximation and Online Algorithms (WAOA 2007). Lect. Notes Comput. Sc., vol. 4927, pp. 260-273. Springer, Berlin (2008)
20. T. Wittkop J. Baumbach F. Lobo S. Rahmann 2007 Large scale clustering of protein sequences with FORCE-a layout based heuristic for weighted cluster editing BMC Bioinformatics 8 1 396 10.1186/1471-2105-8-396 (Pubitemid 350278739)