Scalable detection of frequent substrings by grammar-based compression

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

Volumn 6926 LNAI, Issue , 2011, Pages 236-246

  Nakahara, Masaya ^a   Maruyama, Shirou ^b   Kuboyama, Tetsuji ^c   Sakamoto, Hiroshi ^a,d  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^b KYUSHU UNIVERSITY   (Japan)

^c GAKUSHUIN UNIVERSITY   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EDIT DISTANCE; FREQUENT PATTERNS; GRAMMAR-BASED COMPRESSION; LINEAR-TIME ALGORITHMS; LOWER BOUNDS; OPTIMIZATION PROBLEMS; PATTERN DISCOVERY; PRACTICAL ALGORITHMS; SUB-STRINGS;

DATA COMPRESSION; DNA SEQUENCES;

APPROXIMATION ALGORITHMS;

EID: 80053976591     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-24477-3_20     Document Type: Conference Paper

References (17)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403-410 (1990)
2. Charikar, M., Lehman, E., Liu, D., Panigrahy, R., Prabhakaran, M., Sahai, A., Shelat, A.: The smallest grammar problem. IEEE Transactions on Information Theory 51(7), 2554-2576 (2005)
3. Cilibrasi, R., Vitanyi, P.M.B.: Clustering by compression. IEEE Transactions on Information Theory 51(4), 1523-1545 (2005)
4. Cormode, G., Muthukrishnan, S.: The string edit distance matching problem with moves. ACM Trans. Algor. 3(1), Article 2 (2007)
5. Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Cambridge (1997)
6. Karp, R.M., Miller, R.E., Rosenberg, A.L.: Rapid identification of repeated patterns in strings, trees and arrays. In: STOC 1972, pp. 125-136 (1972)
7. Kieffer, J.C., Yang, E.-H.: Grammar-based codes: A new class of universal lossless source codes. IEEE Transactions on Information Theory 46(3), 737-754 (2000)
8. Lehman, E., Shelat, A.: Approximation algorithms for grammar-based compression. In: SODA 2002, pp. 205-212 (2002)
9. Li, M., Chen, X., Li, X., Ma, B., Vitanyi, P.M.B.: The similarity metric. IEEE Transactions on Information Theory 50(12), 3250-3264 (2004)
10. Pearson, W.R.: Flexible sequence similarity searching with the fasta3 program package methods. Mol. Biol. 132, 185-219 (2000)
11. Rytter, W.: Application of Lempel-Ziv factorization to the approximation of grammar-based compression. Theor. Comput. Sci. 302(1-3), 211-222 (2003)
12. Sadakane, K.: Compressed text databases with efficient query algorithms based on the compressed suffix array. In: Lee, D.T., Teng, S.-H. (eds.) ISAAC 2000. LNCS, vol. 1969, pp. 410-421. Springer, Heidelberg (2000)
13. Sakamoto, H.: A fully linear-time approximation algorithm for grammar-based compression. J. Discrete Algorithms 3(2-4), 416-430 (2005)
14. Sakamoto, H., Maruyama, S., Kida, T., Shimozono, S.: A space-saving approximation algorithm for grammar-based compression. IEICE Trans. on Information and Systems E92-D(2), 158-165 (2009)
15. Shapira, D., Storer, J.A.: Edit distance with move operations. J. Discrete Algorithms 5(2), 380-392 (2007)
16. Uno, T.: An efficient algorithm for finding similar short substrings from large scale string data. In: Washio, T., Suzuki, E., Ting, K.M., Inokuchi, A. (eds.) PAKDD 2008. LNCS (LNAI), vol. 5012, pp. 345-356. Springer, Heidelberg (2008)
17. Välimäki, N., Mäkinen, V., Gerlach, W., Dixit, K.: Engineering a compressed suffix tree implementation. ACM Journal of Experimental Algorithmics 14 (2009)