Compressing and indexing labeled trees, with applications

Journal of the ACM

Volumn 57, Issue 1, 2009, Pages

  Ferragina, Paolo ^a   Luccio, Fabrizio ^a   Manzini, Giovanni ^b   Muthukrishnan, S ^c  

^a UNIVERSITY OF PISA   (Italy)

^b UNIVERSITY OF EASTERN PIEDMONT   (Italy)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

Burrows Wheeler transform; Labeled tree compression; Labeled tree indexing; Path searching; Tree navigation; XML compression; XML indexing

Indexed keywords

BURROWS WHEELER TRANSFORM; LABELED TREES; TREE NAVIGATION; XML COMPRESSION; XML INDEXING;

COMPRESSION RATIO (MACHINERY); CONTROL THEORY; INDEXING (OF INFORMATION); INFORMATION THEORY; LABELS; MARKUP LANGUAGES; NAVIGATION; XML;

DATA COMPRESSION;

COMPRESSION; INDEXING; LABELS; TREES;

EID: 71449088969     PISSN: 00045411     EISSN: 1557735X     Source Type: Journal    
DOI: 10.1145/1613676.1613680     Document Type: Article

References (56)

1. ADIEGO, J., DE LA FUENTE, P., AND NAVARRO, G. 2004. Merging prediction by partial matching with structural contexts model. In Proceedings of the IEEE Data Compression Conference (DCC). IEEE Computer Society Press, Los Alamitos, CA, 522.
2. ARION, A.,BONIFATI, A.,COSTA, G., D'AGUANNO, S.,MANOLESCU, I., AND PUGLIESE,A. 2003. XQueC: pushing queries to compressed XML data. In Proceedings of the 29th International Conference on Very Large Data Bases (VLDB). 1065-1068.
3. ARROYUELO, D., NAVARRO, G., AND SADAKANE, K. 2006. Reducing the space requirement of LZindex. In Proceedings of the 17th Combinatorial Pattern Matching conference (CPM). Lecture Notes in Computer Science vol. 4009. Springer-Verlag, New York, 318-329.
4. BARBAY, J., GOLYNSKI, A., MUNRO, J. I., AND RAO, S. 2007. Adaptive searching in succinctly encoded binary relations and tree-structured documents. Theoret. Comput. Sci. 387, 3, 284-297.
5. BARBAY, J., HE, M., MUNRO, J., AND RAO, S. 2008. Succinct indexes for string, bynary relations and multi-labeled trees. Submitted to Journal (Preliminary version appeared in Proceedings of the 18th ACMSIAM Symposium on Discrete Algorithms (SODA 07)).
6. BENOIT, D., DEMAINE, E.,MUNRO, J. I.,RAMAN, R., RAMAN, V., AND RAO, S. 2005. Representing trees of higher degree. Algorithmica 43, 275-292.
7. BURROWS, M., AND WHEELER, D. 1994. A block-sorting lossless data compression algorithm. Tech. Rep. 124, Digital Equipment Corporation.
8. BUSATTO, G., LOHREY, M., AND MANETH, S. 2008. Efficient memory representation of XML document trees. Inf. Syst. 33, 4-5, 456-474.
9. CATANIA, B., MADDALENA, A., AND VAKALI, A. 2005. XML document indexes: A classification. IEEE Internet Computing, 1, 5, 64-71.
10. CHENEY, J. 2001. Compressing XML with multiplexed hierarchical PPM models. In Proceedings of the IEEE Data Compression Conference (DCC). IEEE Computer Society Press, Los Alamitos, CA, 163-172.
11. CHENG, J., AND NG,W. 2004. XQzip: Querying compressedXMLusing structural indexing. In Proceedings of the 9th International Conference on Extending Database Technology. Lecture Notes in Computer Science, vol.2992. Springer-Verlag, Berlin, Germany, 219-236.
12. FARZAN, A., AND MUNRO, I. 2008. Succinct representations of arbitrary graphs. In Proceedings of the 16th European Symposium on Algorithms (ESA). Lecture Notes in Computer Science vol. 4009. Springer-Verlag, Berlin Germany.
13. FERNANDEZ, M. F., SIMEON, J., CHOI, B., MARIAN, A., AND SUR, G. 2003. Implementing Xquery 1.0: the Galax experience. In Proceedings of the 29th International Conference on Very Large Data Bases (VLDB). 1077-1080.
14. FERRAGINA, P., GIANCARLO, R., AND MANZINI, G. 2006a. The engineering of a compression boosting library: Theory vs practice in BWT compression. In Proceedings of the 14th European Symposium on Algorithms (ESA). Lecture Notes in Computer Science, vol.4168. Springer-Verlag, Berlin, Germany, 756-767.
15. FERRAGINA, P., GIANCARLO, R., AND MANZINI, G. 2009. The myriad virtues of wavelet trees. Inf. Comput. 207, 849-866.
16. FERRAGINA, P., GIANCARLO, R.,MANZINI, G., AND SCIORTINO,M. 2005a. Boosting textual compression in optimal linear time. J. ACM 52, 688-713.
17. FERRAGINA, P., GONŹALEZ, R., NAVARRO, G., AND VENTURINI, R. 2008. Compressed text indexes: From theory to practice. ACM J. Exper. Algor. 13.
18. FERRAGINA, P., LUCCIO, F., MANZINI, G., AND MUTHUKRISHNAN, S. 2005b. Structuring labeled trees for optimal succinctness, and beyond. In Proceedings of the 46th IEEE Symposium on Foundations of Computer Science (FOCS). IEEE Computer Society Press, Los Alamitos, CA, 184-193.
19. FERRAGINA, P., LUCCIO, F.,MANZINI, G., AND MUTHUKRISHNAN, S. 2006b. Compressing and searching XML data via two zips. In Proceedings of the 15th International World Wide Web Conference (WWW). 751-760.
20. FERRAGINA, P., AND MANZINI, G. 2001. An experimental study of a compressed index. Information Sciences: special issue on "Dictionary Based Compression" 135, 13-28.
21. FERRAGINA, P., AND MANZINI, G. 2005. Indexing compressed text. J. ACM 52, 4, 552-581.
22. FERRAGINA, P., MANZINI, G., MAKINEN, V., AND NAVARRO, G. 2007. Compressed representations of sequences and full-text indexes. ACM Trans. Algor. 3, 2.
23. FERRAGINA, P., AND NAVARRO, G. 2007. The Pizza & Chili corpus home page. http://pizzachili.dcc.uchile.cl/or http://pizzachili.di.unipi.it/.
24. FERRAGINA, P., AND RAO, S. 2008. Tree compression and indexing. In Encyclopedia of Algorithms, Springer. 964-967.
25. FERRAGINA, P., AND VENTURINI, R. 2007. Asimple storage scheme for strings achieving entropy bounds. Theoret. Comput. Sci. 372, 1, 115-121.
26. GEARY, R., RAMAN, R., AND RAMAN, V. 2006. Succinct ordinal trees with level-ancestor queries. ACM Trans. Algor. 2, 4, 510-534.
27. GOLDMAN, R., AND WIDOM, J. 1997. Dataguides: Enabling query formulation and optimization in semistructured databases. In Proceedings of the 23rd International Conference on Very Large Data Bases (VLDB). 436-445.
28. GOLYNSKI, A., MUNRO, J. I., AND RAO, S. 2006. Rank/select operations on large alphabets: A tool for text indexing. In Proceedings of the 17th ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 368-373.
29. GUPTA, A., HON,W., SHAH, R., AND VITTER, J. 2007. A framework for dynamizing succinct data structures. In Proceedings of the 34th International Colloquium on Automata, Languages and Programming (ICALP). Lecture Notes in Computer Science, vol.4596. Springer-Verlag, Berlin, Germany, 521-532.
30. JACOBSON, G. 1989. Space-efficient static trees and graphs. In Proceedings of the 30th IEEE Symposium on Foundations of Computer Science (FOCS). IEEE Computer Society Press, Los Alamitos, CA, 549-554.
31. JANSSON, J., SADAKANE, K., AND SUNG, W. 2007. Ultra-succinct representation of ordered trees. In Proceedings of the 18th ACM-SIAM Symposium on Discrete Algorithms (SODA). ACM, New York, 575-584.
32. K̈ARKK̈AINEN, J., SANDERS, P., AND BURKHARDT, S. 2006. Linear work suffix array construction. J. ACM 53, 6, 918-936. (Pubitemid 46276961)
33. KARP, R., MILLER, R., AND ROSENBERG, A. 1972. Rapid identification of repeated patterns in strings, arrays and trees. In Proceedings of the ACM Symposium on Theory of Computation. ACM, New York, 125-136.
34. KAUSHIK, R., KRISHNAMURTHY, R., NAUGHTON, J., AND RAMAKRISHNAN, R. 2004. On the integration of structure indexes and inverted lists. In Proceedings of the ACM SIGMOD International Conference on Management of Data. ACM, New York, 779-790.
35. KOSARAJU, S. R. 1989. Efficient tree pattern matching. In Proceedings of the 20th IEEE Foundations of Computer Science (FOCS). 178-183.
36. KURTZ, S. 1999. Reducing the space requirement of suffix trees. Software-Practice and Experience 29, 13, 1149-1171.
37. LIEFKE, H., AND SUCIU, D. 2000. XMill: An efficient compressor for xml data. In Proceedings of the ACM SIGMOD International Conference on Management of Data. 153-164.
38. M̈AKINEN, V., AND NAVARRO,G. 2006. Position-restricted substring searching. In Proceedings of the 7th Latin American Symposium on Theoretical Informatics (LATIN). Lecture Notes in Computer Science, vol.3887. Springer-Verlag, Berlin, Germany, 703-714.
39. MANZINI, G. 2001. An analysis of the Burrows-Wheeler transform. J. ACM 48, 3, 407-430.
40. MILO, T., AND SUCIU, D. 1999. Index structures for path expressions. In Proceedings of the 3rd International Conference on Database Theory. 277-295.
41. MIN, J., PARK,M., AND CHUNG,C. 2003. Xpress:Aqueriable compression forXMLdata. In Proceedings of the ACM SIGMOD International Conference on Management of Data. ACM, New York, 122-133.
42. MOURA, E., NAVARRO, G., ZIVIANI, N., AND BAEZA-YATES, R. 2000. Fast and flexible word searching on compressed text. ACM Trans. Inform. Syst. 18, 2, 113-139.
43. MUNRO, J. I. 1996. Tables. In Proceeding of the 16th Conference on Foundations of Software Technology and Theoretical Computer Science. Lecture Notes in Computer Science, vol.1180. Springer-Verlag, Berlin, Germany, 37-42.
44. MUNRO, J. I., RAMAN, R., RAMAN, V., AND RAO, S. 2003. Succinct representations of permutations. In Proceedings of the 30th International Colloquium on Automata, Languages and Programming (ICALP). Lecture Notes in Computer Science, vol.2719. Springer-Verlag, Berlin, Germany, 345-356.
45. MUNRO, J. I., AND RAMAN, V. 1997. Succinct representation of balanced parentheses, static trees and planar graphs. In Proceedings of the 38th IEEE Symposium on Foundations of Computer Science (FOCS). IEEE Computer Society Press, Los Alamitos, CA, 118-126.
46. MUNRO, J. I., AND RAMAN, V. 2001. Succinct representation of balanced parentheses and static trees. SIAM J. Comput. 31, 762-776.
47. MUNRO, J. I., AND RAO, S. 2004. Succinct representations of functions. In Proceedings of the 31st International Colloquium on Automata, Languages and Programming (ICALP). Lecture Notes in Computer Science, vol.3142. Springer-Verlag, Germany, 1006-1015.
48. NAVARRO, G., AND M̈AKINEN, V. 2007. Compressed full-text indexes. ACM Comput. Surv. 39, 1.
49. NG, W., LAM, W., WOOD, P., AND LEVENE, M. 2006. XCQ: A queriable XML compression system. Know. Inform. Syst. 10, 4, 421-452.
50. RAMAN,R.,RAMAN,V., ANDRAO, S. 2007. Succinct indexable dictionaries with applications to encoding k-ary trees, prefix sums and multisets. ACM Trans. Algor. 3, 4.
51. RAW, P., AND MOON, B. 2004. PRIX: Indexing and querying XML using Prüfer sequences. In Proceedings of the 20th International Conference on Data Engineering (ICDE). 288-300.
52. TOLANI, P. M., AND HARITSA, J. R. 2002. XGRIND: A query-friendly XML compressor. In Proceedings of the 18th International Conference on Data Engineering (ICDE). 225-234.
53. WANG, H., PARK, S., FAN, W., AND YU, P. S. 2003. ViST: A dynamic index methd for querying XML data by tree structures. In Proceedings of the ACM SIGMOD International Conference on Management of Data. ACM, New York, 110-121.
54. WANG, W., WANG, H., LU, H., JANG, H., LIN, X., AND LI, J. 2005. Efficient processing of XML path queries using the disk-based F & B index. In Proceedings of the 31st International Conference on Very Large Data Bases (VLDB). 145-156.
55. WITTEN, I. H., MOFFAT, A., AND BELL, T. C. 1999. Managing Gigabytes: Compressing and Indexing Documents and Images, Second ed. Morgan Kaufmann, Los Altos, CA.
56. YE, Z., AND BERGER, T. 1998. Information measures for discrete random fields. Science Press.