Iterative probabilistic tree search for the minimum common string partition problem

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 8457 LNCS, Issue , 2014, Pages 145-154

  Blum, Christian ^a,b   Lozano, José A ^a   Pinacho Davidson, Pedro ^a,c  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^b BASQUE FOUNDATION FOR SCIENCE   (Spain)

^c UNIVERSIDAD SANTO TOMÁS   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION ALGORITHMS; BIOINFORMATICS; COMBINATORIAL OPTIMIZATION; HEURISTIC ALGORITHMS; OPTIMIZATION;

COMBINATORIAL OPTIMIZATION PROBLEMS; COMPUTATIONAL BIOLOGY; EXPERIMENTAL EVALUATION; GREEDY ALGORITHMS; METAHEURISTIC; MINIMUM COMMON STRING PARTITION; NP-HARD; PROBABILISTIC TREE SEARCHES;

ITERATIVE METHODS;

EID: 84903639393     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-319-07644-7_11     Document Type: Conference Paper

References (21)

1. Blum, C., Puchinger, J., Raidl, G., Roli, A.: Hybrid metaheuristics in combinatorial optimization: A survey. Applied Soft Computing 11(6), 4135-4151 (2011)
2. Chen, X., Zheng, J., Fu, Z., Nan, P., Zhong, Y., Lonardi, S., Jiang, T.: Computing the assignment of orthologous genes via genome rearrangement. In: Proceedings of the Asia Pacific Bioinformatics Conference 2005, pp. 363-378 (2005)
3. Chrobak, M., Kolman, P., Sgall, J.: The greedy algorithm for the minimum common string partition problem. In: Jansen, K., Khanna, S., Rolim, J.D.P., Ron, D. (eds.) RANDOM 2004 and APPROX 2004. LNCS, vol. 3122, pp. 84-95. Springer, Heidelberg (2004)
4. Cormode, G., Muthukrishnan, S.: The string edit distance matching problem with moves. ACM Transactions on Algorithms 3(2), 1-19 (2007)
5. Damaschke, P.: Minimum common string partition parameterized. In: Crandall, K.A., Lagergren, J. (eds.) WABI 2008. LNCS (LNBI), vol. 5251, pp. 87-98. Springer, Heidelberg (2008)
6. Ferdous, S.M., Rahman, M.S.: Solving the minimum common string partition problem with the help of ants. In: Tan, Y., Shi, Y., Mo, H. (eds.) ICSI 2013, Part I. LNCS, vol. 7928, pp. 306-313. Springer, Heidelberg (2013)
7. Festa, P., Resende, M.: GRASP: An annotated bibliography. In: Ribeiro, C., Hansen, P. (eds.) Essays and Surveys on Metaheuristics, pp. 325-367. Kluwer Academic Publishers (2002)
8. Fu, B., Jiang, H., Yang, B., Zhu, B.: Exponential and polynomial time algorithms for the minimum common string partition problem. In: Wang, W., Zhu, X., Du, D.-Z. (eds.) COCOA 2011. LNCS, vol. 6831, pp. 299-310. Springer, Heidelberg (2011)
9. Goldstein, A., Kolman, P., Zheng, J.: Minimum common string partition problem: Hardness and approximations. In: Fleischer, R., Trippen, G. (eds.) ISAAC 2004. LNCS, vol. 3341, pp. 484-495. Springer, Heidelberg (2004)
10. Goldstein, I., Lewenstein, M.: Quick greedy computation for minimum common string partitions. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 273-284. Springer, Heidelberg (2011)
11. Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Computer Science and Computational Biology. Cambridge University Press, Cambridge (1997)
12. He, D.: A novel greedy algorithm for the minimum common string partition problem. In: Mandoiu, I.I., Zelikovsky, A. (eds.) ISBRA 2007. LNCS (LNBI), vol. 4463, pp. 441-452. Springer, Heidelberg (2007)
13. Hsu, W.J., Du, M.W.: Computing a longest common subsequence for a set of strings. BIT Numerical Mathematics 24(1), 45-59 (1984)
14. Jiang, H., Zhu, B., Zhu, D., Zhu, H.: Minimum common string partition revisited. Journal of Combinatorial Optimization 23(4), 519-527 (2012)
15. Kaplan, H., Shafrir, N.: The greedy algorithm for edit distance with moves. Information Processing Letters 97(1), 23-27 (2006)
16. Kolman, P.: Approximating reversal distance for strings with bounded number of duplicates. In: Jedrzejowicz, J., Szepietowski, A. (eds.) MFCS 2005. LNCS, vol. 3618, pp. 580-590. Springer, Heidelberg (2005)
17. Kolman, P., Wale'n, T.: Reversal distance for strings with duplicates: Linear time approximation using hitting set. In: Erlebach, T., Kaklamanis, C. (eds.) WAOA 2006. LNCS, vol. 4368, pp. 279-289. Springer, Heidelberg (2007)
18. Meneses, C., Oliveira, C., Pardalos, P.: Optimization techniques for string selection and comparison problems in genomics. IEEE Engineering in Medicine and Biology Magazine 24(3), 81-87 (2005)
19. Mousavi, S., Babaie, M., Montazerian, M.: An improved heuristic for the far from most strings problem. Journal of Heuristics 18, 239-262 (2012)
20. Shapira, D., Storer, J.A.: Edit distance with move operations. In: Apostolico, A., Takeda, M. (eds.) CPM 2002. LNCS, vol. 2373, pp. 85-98. Springer, Heidelberg (2002)
21. Smith, T., Waterman, M.: Identification of common molecular subsequences. Journal of Molecular Biology 147(1), 195-197 (1981)