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Published in: Journal of Combinatorial Optimization 1/2016

01-01-2016

Efficient algorithms for cluster editing

Authors: Lucas Bastos, Luiz Satoru Ochi, Fábio Protti, Anand Subramanian, Ivan César Martins, Rian Gabriel S. Pinheiro

Published in: Journal of Combinatorial Optimization | Issue 1/2016

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Abstract

The cluster editing problem consists of transforming an input graph \(G\) into a cluster graph (a disjoint union of complete graphs) by performing a minimum number of edge editing operations. Each edge editing operation consists of either adding a new edge or removing an existing edge. In this paper we propose new theoretical results on data reduction and instance generation for the cluster editing problem, as well as two algorithms based on coupling an exact method to, respectively, a GRASP or ILS heuristic. Experimental results show that the proposed algorithms are able to find high-quality solutions in practical runtime.

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Literature
go back to reference Aiex RM, Binato S, Resende MGC (2003) Parallel grasp with path-relinking for job shop scheduling. Parallel Comput 29:393–430MathSciNetCrossRef Aiex RM, Binato S, Resende MGC (2003) Parallel grasp with path-relinking for job shop scheduling. Parallel Comput 29:393–430MathSciNetCrossRef
go back to reference Bastos LO (2012) Novos algoritmos e resultados teóricos para o problema de particionamento de grafos por edição de arestas. PhD thesis, Universidade Federal Fluminense (in Portuguese) Bastos LO (2012) Novos algoritmos e resultados teóricos para o problema de particionamento de grafos por edição de arestas. PhD thesis, Universidade Federal Fluminense (in Portuguese)
go back to reference Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3/4):281–297CrossRef Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3/4):281–297CrossRef
go back to reference Böcker S, Briesemeister B, A QB, Truss A (2008) Going weighted: parameterized algorithms for cluster editing. Comb Optim Appl 5165:1–12MATH Böcker S, Briesemeister B, A QB, Truss A (2008) Going weighted: parameterized algorithms for cluster editing. Comb Optim Appl 5165:1–12MATH
go back to reference Böcker S, Briesemeister S, Klau G (2009) Exact algorithms for cluster editing: evaluation and experiments. Algorithmica. 1–19 Böcker S, Briesemeister S, Klau G (2009) Exact algorithms for cluster editing: evaluation and experiments. Algorithmica. 1–19
go back to reference Dehne F, Langston MA, Luo X, Pitre S, Shaw P, Zhang Y (2006) The cluster editing problem: implementations and experiments. LNCS 4169:13–24MathSciNetMATH Dehne F, Langston MA, Luo X, Pitre S, Shaw P, Zhang Y (2006) The cluster editing problem: implementations and experiments. LNCS 4169:13–24MathSciNetMATH
go back to reference Gramm J, Guo J, Hüffner F, Niedermeier R (2005) Graph-modeled data clustering: exact algorithms for clique generation. Theor Comput Sys 38:373–392CrossRefMATH Gramm J, Guo J, Hüffner F, Niedermeier R (2005) Graph-modeled data clustering: exact algorithms for clique generation. Theor Comput Sys 38:373–392CrossRefMATH
go back to reference Hansen P, Mladenovic N (2003) Variable neighborhood search. In: Glover F, Kochenberger G (eds) Handbook of metaheuristics, Chap 6, Kluwer Academic Publishers, Philip Drive Norwell, MA, pp 145–183 Hansen P, Mladenovic N (2003) Variable neighborhood search. In: Glover F, Kochenberger G (eds) Handbook of metaheuristics, Chap 6, Kluwer Academic Publishers, Philip Drive Norwell, MA, pp 145–183
go back to reference Hartuv E, Schmitt AO, Lange J, Meier-Ewert S, Lehrach H, Shamir R (2000) An algorithm for clustering cdna fingerprints. Genomics 66(3):249–256CrossRef Hartuv E, Schmitt AO, Lange J, Meier-Ewert S, Lehrach H, Shamir R (2000) An algorithm for clustering cdna fingerprints. Genomics 66(3):249–256CrossRef
go back to reference Jain AK, Murty MN, Flynn PJ (1999) Data clustering: a review. ACM Comput Surv 31(3):264–323CrossRef Jain AK, Murty MN, Flynn PJ (1999) Data clustering: a review. ACM Comput Surv 31(3):264–323CrossRef
go back to reference Lourenço HR, Martin OC, Stützle T (2003) Iterated local search. In: Glover F, Kochenberger G (eds) Handbook of metaheuristics, Chap 11, Kluwer Academic Publishers, Philip Drive Norwell, MA, pp 321–353 Lourenço HR, Martin OC, Stützle T (2003) Iterated local search. In: Glover F, Kochenberger G (eds) Handbook of metaheuristics, Chap 11, Kluwer Academic Publishers, Philip Drive Norwell, MA, pp 321–353
go back to reference Milosavljevic A, Strezoska Z, Zeremski M, Grujic D, Paunesku T, Crkvenjakov R (1995) Clone clustering by hybridization. Genomics 27(1):83–89CrossRef Milosavljevic A, Strezoska Z, Zeremski M, Grujic D, Paunesku T, Crkvenjakov R (1995) Clone clustering by hybridization. Genomics 27(1):83–89CrossRef
go back to reference Penna PHV, Subramanian A, Ochi LS (2013) An iterated local search heuristic for the heterogeneous fleet vehiclerouting problem. J Heuristics 19(2):201–232CrossRef Penna PHV, Subramanian A, Ochi LS (2013) An iterated local search heuristic for the heterogeneous fleet vehiclerouting problem. J Heuristics 19(2):201–232CrossRef
go back to reference Protti F, Silva MD, Szwarcfiter J (2009) Applying modular decomposition to parameterized cluster editing problems. Theory Comput Sys 44:91–104CrossRefMathSciNetMATH Protti F, Silva MD, Szwarcfiter J (2009) Applying modular decomposition to parameterized cluster editing problems. Theory Comput Sys 44:91–104CrossRefMathSciNetMATH
go back to reference Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Böcker S (2007) Exact and heuristic algorithms for weighted cluster editing. In: Markstein P, Xu Y (eds) Comput Sys Bioinforma: CSB 2007 Conference Proceedings of the, Imp. Coll. Press, Covent Garden, London WC2H 9HE, vol 6, pp 391–400. Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Böcker S (2007) Exact and heuristic algorithms for weighted cluster editing. In: Markstein P, Xu Y (eds) Comput Sys Bioinforma: CSB 2007 Conference Proceedings of the, Imp. Coll. Press, Covent Garden, London WC2H 9HE, vol 6, pp 391–400.
go back to reference Resende M, Ribeiro C (2003) Greedy randomized adaptive search procedures, Chap 8, Kluwer Academic Publishers, Philip Drive Norwell MA, pp 219–249 Resende M, Ribeiro C (2003) Greedy randomized adaptive search procedures, Chap 8, Kluwer Academic Publishers, Philip Drive Norwell MA, pp 219–249
go back to reference Sen Gupta A, Palit A (1979) On clique generation using boolean equations. In: Proceedings of the IEEE. The IEEE Inc, New York. NY 10017 67:T178–180 Sen Gupta A, Palit A (1979) On clique generation using boolean equations. In: Proceedings of the IEEE. The IEEE Inc, New York. NY 10017 67:T178–180
go back to reference Sharan R, Maron-Katz A, Shamir R (2003) Click and expander: a system for clustering and visualizing gene expression data. Bioinforma 19(14):1787–1799CrossRef Sharan R, Maron-Katz A, Shamir R (2003) Click and expander: a system for clustering and visualizing gene expression data. Bioinforma 19(14):1787–1799CrossRef
go back to reference Souza MJF, Mine MT, de Silva MSA, Ochi LS, Subramanian A (2011) A hybrid heuristic, based on iterated local search and genius, for the vehicle routing problem with simultaneous pickup and delivery. Int J Logist Sys Manag 10(2):142–157CrossRef Souza MJF, Mine MT, de Silva MSA, Ochi LS, Subramanian A (2011) A hybrid heuristic, based on iterated local search and genius, for the vehicle routing problem with simultaneous pickup and delivery. Int J Logist Sys Manag 10(2):142–157CrossRef
go back to reference Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, Rao BS, Smirnov S, Sverdlov A, Vasudevan S, Wolf Y, Yin J, Natale D (2003) The cog database: an updated version includes eukaryotes. BMC Bioinforma 4(1):41CrossRef Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, Rao BS, Smirnov S, Sverdlov A, Vasudevan S, Wolf Y, Yin J, Natale D (2003) The cog database: an updated version includes eukaryotes. BMC Bioinforma 4(1):41CrossRef
go back to reference Wittkop T, Baumbach J, Lobo FP, Rahmann S (2007) Large scale clustering of protein sequences with FORCE: a layout based heuristic for weighted cluster editing. BMC Bioinforma 8:396CrossRef Wittkop T, Baumbach J, Lobo FP, Rahmann S (2007) Large scale clustering of protein sequences with FORCE: a layout based heuristic for weighted cluster editing. BMC Bioinforma 8:396CrossRef
go back to reference Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010) Partitioning biological data with transitivity clustering. Nature Methods 7(6):419–420CrossRef Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Böcker S, Stoye J, Baumbach J (2010) Partitioning biological data with transitivity clustering. Nature Methods 7(6):419–420CrossRef
Metadata
Title
Efficient algorithms for cluster editing
Authors
Lucas Bastos
Luiz Satoru Ochi
Fábio Protti
Anand Subramanian
Ivan César Martins
Rian Gabriel S. Pinheiro
Publication date
01-01-2016
Publisher
Springer US
Published in
Journal of Combinatorial Optimization / Issue 1/2016
Print ISSN: 1382-6905
Electronic ISSN: 1573-2886
DOI
https://doi.org/10.1007/s10878-014-9756-7

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