Dynamic entropy-compressed sequences and full-text indexes

ACM Transactions on Algorithms

Volumn 4, Issue 3, 2008, Pages

  Mäkinen, Veli ^a   Navarro, Gonzalo ^b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF CHILE   (Chile)

Author keywords

Compressed dynamic data structures; Compressed text databases; Entropy; Partial sums; Sequences

Indexed keywords

BIT NUMBERS; LOWER BOUNDS; NEW SOLUTIONS; PARTIAL SUMS; TIME COMPLEXITIES; ZERO-ORDER ENTROPY;

CONTROL THEORY; MILITARY DATA PROCESSING;

VIBRATIONS (MECHANICAL);

EID: 47249098580     PISSN: 15496325     EISSN: 15496333     Source Type: Journal    
DOI: 10.1145/1367064.1367072     Document Type: Conference Paper

References (40)

1. APOSTOLICO, A. 1985. The myriad virtues of subword trees. In Combinatorial Algorithms on Words. NATO ISI Series. Springer-Verlag, New York, 85-96.
2. ARROYUELO, D., AND NAVARRO, G. 2005. Space-efficient construction of LZ-index. In Proceedings of ISAAC'05. Lecture Notes in Computer Science, vol. 3827. Springer-Verlag, New York, 1143-1152.
3. BELL, T., CLEARY, J., AND WITTEN, I. 1990. Text Compression. Prentice Hall, Englewood Cliffs, NJ.
4. BLANDFORD, D., AND BLELLOCH, G. 2004. Compact representations of ordered sets. In Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 11-19.
5. BURROWS, M., AND WHEELER, D. 1994. A block sorting lossless data compression algorithm. Tech. Rep. 124, Digital Equipment Corporation.
6. CHAN, H.-L., HON, W.-K., AND LAM, T.-W. 2004. Compressed index for a dynamic collection of texts. In Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM). Lecture Notes in Computer Science, vol. 3109. Springer-Verlag, New York, 445-456.
7. CHAN, H.-L., HON, W.-K., LAM, T.-W., AND SADAKANE, K. 2007. Compressed indexes for dynamic text collections. ACM Trans. Algor. 3, 2, article 21.
8. CRAUSER, A., AND FERRAGINA, P. 2002. A theoretical and experimental study on the construction of suffix arrays in external memory. Algorithmica 32, 1, 1-35.
9. DIETZ, P. 1989. Optimal algorithms for list indexing and subset rank. In Proceedings of WADS'89. 39-46.
10. ELIAS, P. 1975. Universal codeword sets and representation of the integers. IEEE Trans. Inf. Theory 21, 2, 194-203.
11. FERRAGINA, P., GIANCARLO, R., AND MANZINI, G. 2006. The myriad virtues of wavelet trees. In Proceedings of the 33rd International Colloquium on Automata, Languages and Programming (ICALP). 560-571.
12. FERRAGINA, P., AND MANZINI, G. 2000. Opportunistic data structures with applications. In Proceedings of the Symposium on Foundations of Computer Science (FOCS'00). IEEE Computer Society Press, Los Alamitos, CA, 390-398.
13. FERRAGINA, P., AND MANZINI, G. 2004. Compression boosting in optimal linear time using the Burrows-Wheeler transform. In Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 655-663.
14. FERRAGINA, P., AND MANZINI, G. 2005. Indexing compressed texts. J. ACM 52, 4, 552-581.
15. FERRAGINA, P., MANZINI, G., MÄKINEN, V., AND NAVARRO, G. 2007. Compressed representation of sequences and full-text indexes. ACM Trans. Algor. 3, 2, article 20.
16. FERRAGINA, P., AND VENTURINI, R. 2007. A simple storage scheme for strings achieving entropy bounds. Theoret. Comput. Sci. 372, 1, 115-121.
17. GOLYNSKI, A., MUNRO, I., AND RAO, S. 2006. Rank/select operations on large alphabets: a tool for text indexing. In Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 368-373.
18. GONNET, G., BAEZA-YATES, R., AND SNIDER, T. 1992. Information Retrieval: Data Structures and Algorithms. Prentice-Hall, Chapter 3: New indices for text: Pat trees and Pat arrays, 66-82.
19. GONZÁLEZ, R., AND NAVARRO, G. 2006. Statistical encoding of succinct data structures. In Proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching (CPM 2006). Lecture Notes in Computer Science, vol. 4009. Springer-Verlag, New York, 295-306.
20. GONZÁLEZ, R., AND NAVARRO, G. 2008. Improved dynamic rank-select entropy-bound structures. In Proceedings of the 8th Latin American Symposium on Theoretical Informatics (LATIN). Lecture Notes in Computer Science , vol. 4957, Springer-Verlag, 374-386.
21. GROSSI, R., GUPTA, A., AND VITTER, J. 2003. High-order entropy-compressed text indexes. In Proceedings of the 14th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 841-850.
22. GROSSI, R., GUPTA, A., AND VITTER, J. 2004. When indexing equals compression: Experiments with compressing suffix arrays and applications. In Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 636-645.
23. GROSSI, R., AND VITTER, J. 2006. Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM J. Comput. 35, 2, 378-407.
24. GUPTA, A., HON, W.-K., SHAH, R., AND VITTER, J. 2006a. Compressed data structures: dictionaries and data-aware measures. In Proceedings of the 5th International Workshop on Experimental Algorithms (WEA). 158-169.
25. GUPTA, A., HON, W.-K., SHAH, R., AND VITTER, J. 2006b. Dynamic rank/select dictionaries with applications to XML indexing. Tech. Rep. CSD TR #06-014, Purdue Univ. July.
26. HON, W.-K., LAM, T.-W., SADAKANE, K., AND SUNG, W.-K. 2003a. Constructing compressed suffix arrays with large alphabets. In Proceedings of the 14th Annual International Symposium on Algorithms and Computation (ISAAC). 240-249.
27. HON, W.-K., SADAKANE, K., AND SUNG, W.-K. 2003b. Breaking a time-and-space barrier in constructing full-text indexes. In Proceedings of the Symposium on Foundations of Computer Science (FOCS'03). IEEE Computer Society Press, Los Alamitos, CA, 251-260.
28. HON, W.-K., SADAKANE, K., AND SUNG, W.-K. 2003c. Succinct data structures for searchable partial sums. In Proceedings of the International Symposium on Algorithms and Computation (ISAAC'03). Lecture Notes in Computer Science, vol. 2906. Springer-Verlag, New York, 505-516.
29. KÄRKKÄINEN, J. 2004. Fast BWT in small space by blockwise suffix sorting. In Proceedings of DIMACS Working Group on the Burrows-Wheeler Transform: Ten Years Later.
30. LEE, S., AND PARK, K. 2007. Static and dynamic rank-select dictionaries for run-length encoded texts. In Proceedings of the 18th Annual Symposium on Combinatorial Pattern Matching (CPM). Lecture Notes in Computer Science, vol. 4580. Springer-Verlag, New York.
31. MÄKINEN, V. AND NAVARRO, G. 2005. Succinct suffix arrays based on run-length encoding. Nord. J. Comput. 12, 1, 40-66.
32. MÄKINEN, V., AND NAVARRO, G. 2007. Rank and select revisited and extended. Theoret. Comput. Sci 387, 3, 332-347.
33. MANBER, U., AND MYERS, G. 1993. Suffix arrays: a new method for on-line string searches. SIAM J. Comput. 22, 5, 935-948.
34. MANZINI, G. 2001. An analysis of the Burrows-Wheeler transform. J. ACM 48, 3, 407-430.
35. NAVARRO, G., AND MÄKINEN, V. 2007. Compressed full-text indexes. ACM Comput. Surv. 39, 1, article 2.
36. PAGH, R. 1999. Low redundancy in dictionaries with O(1) worst case lookup time. In Proceedings of the 26th International Colloquium on Automata, Languages and Programming (ICALP). 595-604.
37. PATRASCU, M., AND DEMAINE, E. 2004. Tight bounds for the partial-sums problem. In Proceedings of the 15th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 20-29.
38. RAMAN, R., RAMAN, V., AND RAO, S. S. 2001. Succinct dynamic data structures. In Proceedings of WADS'01. 426-437.
39. RAMAN, R., RAMAN, V., AND RAO, S. S. 2002. Succinct indexable dictionaries with applications to encoding k-ary trees and multisets. In Proceedings of the ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 233-242.
40. SADAKANE, K., AND GROSSI, R. 2006. Squeezing succinct data structures into entropy bounds. In Proceedings of the 17th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 1230-1239.