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11 - Texts

Published online by Cambridge University Press:  05 September 2016

Gonzalo Navarro
Affiliation:
Universidad de Chile
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Compact Data Structures
A Practical Approach
, pp. 395 - 449
Publisher: Cambridge University Press
Print publication year: 2016

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References

Abeliuk, A., Cánovas, R., and Navarro, G. (2013). Practical compressed suffix trees. Algorithms, 6(2), 319–351.Google Scholar
Adjeroh, D., Bell, T., and Mukherjee, A. (2008). The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching. Springer.
Apostolico, A. (1985). The myriad virtues of subword trees. In Combinatorial Algorithms on Words, NATO ISI Series, pages 85–96. Springer-Verlag.
Arroyuelo, D., Claude, F., Maneth, S., Mäkinen, V., Navarro, G., Nguy∼ˆen, K., Sirén, J., and Välimäki, N. (2015). Fast in-memory XPath search using compressed indexes. Software Practice and Experience, 45(3), 399–434.Google Scholar
Barbay, J., Claude, F., Gagie, T., Navarro, G., and Nekrich, Y. (2014). Efficient fully-compressed sequence representations. Algorithmica, 69(1), 232–268.Google Scholar
Belazzougui, D. (2014). Linear time construction of compressed text indices in compact space. In Proc. 46th ACM Symposium on Theory of Computing (STOC), pages 148–193.Google Scholar
Belazzougui, D. (2015). Linear time construction of compressed text indices in compact space. CoRR, abs/1401.0936. http://arxiv.org/abs/1401.0936v2.
Belazzougui, D. and Navarro, G. (2014). Alphabet-independent compressed text indexing. ACM Transactions on Algorithms, 10(4), article 23.Google Scholar
Beller, T., Gog, S., Ohlebusch, E., and Schnattinger, T. (2013). Computing the longest common prefix array based on the Burrows-Wheeler transform. Journal of Discrete Algorithms, 18, 22–31.Google Scholar
Bingmann, T., Fischer, J., and Osipov, V. (2013). Inducing suffix and lcp arrays in external memory. In Proc. 15th Workshop on Algorithm Engineering and Experiments (ALENEX), pages 88–102.Google Scholar
Burrows, M. and Wheeler, D. (1994). A block sorting lossless data compression algorithm. Technical Report 124, Digital Equipment Corporation.
Chien, Y.-F., Hon, W.-K., Shah, R., Thankachan, S. V., and Vitter, J. S. (2015). Geometric BWT: compressed text indexing via sparse suffixes and range searching. Algorithmica, 71(2), 258–278.Google Scholar
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.Google Scholar
Crochemore, M. and Rytter, W. (2002). Jewels of Stringology. World Scientific.
Dementiev, R., Kärkkäinen, J., Mehnert, J., and Sanders, P. (2008). Better external memory suffix array construction. ACM Journal of Experimental Algorithmics, 12, article 3.4.Google Scholar
Farach-Colton, M., Ferragina, P., and Muthukrishnan, S. (2000). On the sorting-complexity of suffix tree construction. Journal of the ACM, 47(6), 987–1011.Google Scholar
Ferragina, P., and Manzini, G., (2005). Indexing compressed texts. Journal of the ACM, 52(4), 552–581.Google Scholar
Ferragina, P., Giancarlo, R., Manzini, G., and Sciortino, M. (2005). Boosting textual compression in optimal linear time. Journal of the ACM, 52(4), 688–713.Google Scholar
Ferragina, P., Manzini, G., Mäkinen, V., and Navarro, G. (2007). Compressed representations of sequences and full-text indexes. ACM Transactions on Algorithms, 3(2), article 20.Google Scholar
Ferragina, P., González, R., Navarro, G., and Venturini, R. (2009a). Compressed text indexes: From theory to practice. ACM Journal of Experimental Algorithmics, 13, article 12.Google Scholar
Ferragina, P., Luccio, F., Manzini, G., and Muthukrishnan, S. (2009b). Compressing and indexing labeled trees, with applications. Journal of the ACM, 57(1), article 4.Google Scholar
Ferragina, P., Gagie, T., and Manzini, G., (2012). Lightweight data indexing and compression in external memory. Algorithmica, 63(3), 707–730.Google Scholar
Fischer, J. (2010). Wee LCP. Information Processing Letters, 110, 317–320.Google Scholar
Fischer, J., Mäkinen, V., and Navarro, G., (2009). Faster entropy-bounded compressed suffix trees. Theoretical Computer Science, 410(51), 5354–5364.Google Scholar
Foschini, L., Grossi, R., Gupta, A., and Vitter, J. S. (2006). When indexing equals compression: Experiments with compressing suffix arrays and applications. ACM Transactions on Algorithms, 2(4), 611–639.Google Scholar
Gog, S. (2011). Compressed Suffix Trees: Design, Construction, and Applications. Ph.D. thesis, Ulm University, Germany.
Gog, S. and Ohlebusch, E. (2013). Compressed suffix trees: Efficient computation and storage of lcp-values. ACM Journal of Experimental Algorithmics, 18, article 2.1.Google Scholar
Gog, S., Navarro, G., and Petri, M. (2015). Improved and extended locating functionality on compressed suffix arrays. Journal of Discrete Algorithms, 32, 53–63.Google Scholar
Gog, S., Kärkkäinen, J., Kempa, D., Petri, M., and Puglisi, S. J. (2016). Faster, minuter. In Proc. 26th Data Compression Conference (DCC), pages 53–62.Google Scholar
Gonnet, G., Baeza-Yates, R., and Snider, T. (1992). Information Retrieval: Data Structures and Algorithms, chapter 3: New indices for text: Pat trees and Pat arrays, pages 66–82. Prentice-Hall.
González, R., Navarro, G., and Ferrada, H. (2014). Locally compressed suffix arrays. ACM Journal of Experimental Algorithmics, 19(1), article 1.Google Scholar
Grossi, R. (2011). A quick tour on suffix arrays and compressed suffix arrays. Theoretical Computer Science, 412(27), 2964–2973.Google Scholar
Grossi, R. and Vitter, J. S. (2006). Compressed suffix arrays and suffix trees with applications to text indexing and string matching. SIAM Journal on Computing, 35(2), 378–407.Google Scholar
Grossi, R., Gupta, A., and Vitter, J. S. (2003). High-order entropy-compressed text indexes. In Proc. 14th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 841–850.Google Scholar
Gusfield, D. (1997). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press.
Hon, W.-K., Lam, T.-W., Sadakane, K., Sung, W.-K., and Yiu, S.-M. (2007). Aspace and time efficient algorithm for constructing compressed suffix arrays. Algorithmica, 48(1), 23–36.Google Scholar
Hon, W.-K., Sadakane, K., and Sung, W.-K. (2009). Breaking a time-and-space barrier in constructing full-text indices. SIAM Journal on Computing, 38(6), 2162–2178.Google Scholar
Huo, H., Chen, L., Vitter, J. S., and Nekrich, Y. (2014). A practical implementation of compressed suffix arrays with applications to self-indexing. In Proc. 24th Data Compression Conference (DCC), pages 292–301.Google Scholar
Huo, H., Chen, L., Zhao, H., Vitter, J. S., Nekrich, Y., and Yu, Q. (2015). A data-aware FM-index. In Proc. 17th Workshop on Algorithm Engineering and Experiments (ALENEX), pages 10–23.Google Scholar
Itoh, H. and Tanaka, H. (1999). An efficient method for in memory construction of suffix arrays. In Proc. 6th International Symposium on String Processing and Information Retrieval (SPIRE), pages 81–88.Google Scholar
Kärkkäinen, J. (2007). Fast BWT in small space by blockwise suffix sorting. Theoretical Computer Science, 387(3), 249–257.Google Scholar
Kärkkäinen, J. and Kempa, D. (2014). LCP array construction in external memory. In Proc. 13th International Symposium on Experimental Algorithms (SEA), LNCS 8504, pages 412–423.Google Scholar
Kärkkäinen, J. and Puglisi, S. J. (2011). Fixed block compression boosting in FM-indexes. In Proc. 18th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 7024, pages 174–184.Google Scholar
Kärkkäinen, J., Sanders, P., and Burkhardt, S. (2006). Linear work suffix array construction. Journal of the ACM, 53(6), 918–936.Google Scholar
Kärkkäinen, J., Manzini, G., and Puglisi, S. J. (2009). Permuted longest-common-prefix array. In Proc. 20th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS 5577, pages 181–192.Google Scholar
Kärkkäinen, J., Kempa, D., and Puglisi, S. J. (2014). Hybrid compression of bitvectors for the FMindex. In Proc. 24th Data Compression Conference (DCC), pages 302–311.Google Scholar
Kärkkäinen, J., Kempa, D., and Puglisi, S. J. (2015). Parallel external memory suffix sorting. In Proc. 26th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS 9133, pages 329–342.Google Scholar
Kasai, T., Lee, G., Arimura, H., Arikawa, S., and Park, K. (2001). Linear-time longest-common-prefix computation in suffix arrays and its applications. In Proc. 12th Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS 2089, pages 181–192.Google Scholar
Kempa, D. (2015). Efficient Construction of Fundamental Data Structures in Large-Scale Text Indexing. Ph.D. thesis, University of Helsinki, Finland.
Kim, D. K., Sim, J. S., Park, K., and Park, K. (2005). Constructing suffix arrays in linear time. Journal of Discrete Algorithms, 3(2–4), 126–142.Google Scholar
Ko, P. and Aluru, S. (2005). Space efficient linear time construction of suffix arrays. Journal of Discrete Algorithms, 3(2–4), 143–156.Google Scholar
Mäkinen, V. and Navarro, G., (2008). Dynamic entropy-compressed sequences and full-text indexes. ACM Transactions on Algorithms, 4(3), article 32.Google Scholar
Manber, U. and Myers, G. (1993). Suffix arrays: a new method for on-line string searches. SIAM. Journal on Computing, 22(5), 935–948.Google Scholar
McCreight, E. (1976). A space-economical suffix tree construction algorithm. Journal of the ACM, 23(2), 262–272.Google Scholar
Munro, J. I., Raman, V., and Rao, S. S. (2001). Space efficient suffix trees. Journal of Algorithms, 39(2), 205–222.Google Scholar
Muthukrishnan, S. (2002). Efficient algorithms for document retrieval problems. In Proc. 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 657–666.Google Scholar
Navarro, G., (2014). Spaces, trees and colors: The algorithmic landscape of document retrieval on sequences. ACM Computing Surveys, 46(4), article 52.Google Scholar
Navarro, G., and Mäkinen, V. (2007). Compressed full-text indexes. ACM Computing Surveys, 39(1), article 2.Google Scholar
Navarro, G., and Raffinot, M. (2002). Flexible Pattern Matching in Strings. Cambridge University Press.
Navarro, G., and Russo, L. M. S. (2014). Fast fully-compressed suffix trees. In Proc. 24th Data Compression Conference (DCC), pages 283–291.Google Scholar
Nong, G., Zhang, S., and Chan, W. H. (2011). Two efficient algorithms for linear time suffix array construction. IEEE Transactions on Computers, 60(10), 1471–1484.Google Scholar
Ocker, C. (2015). Engineering Fully-Compressed Suffix Trees. MSc thesis, Karlsruhe Institute of Technology, Germany.
Ohlebusch, E. and Gog, S. (2009). A compressed enhanced suffix array supporting fast string matching. In Proc. 16th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 5721, pages 51–62.Google Scholar
Okanohara, D. and Sadakane, K. (2009). A linear-time Burrows-Wheeler transform using induced sorting. In Proc. 16th International Symposium on String Processing and Information Retrieval (SPIRE), LNCS 5721, pages 90–101.Google Scholar
Puglisi, S. J., Smyth, W. F., and Turpin, A. (2007). Ataxonomy of suffix array construction algorithms. ACM Computing Surveys, 39(2), article 4.Google Scholar
Rao, S. S. (2002). Time-space trade-offs for compressed suffix arrays. Information Processing Letters, 82(6), 307–311.Google Scholar
Russo, L. M. S., Navarro, G., and Oliveira, A. (2011). Fully-compressed suffix trees. ACM Transactions on Algorithms, 7(4), article 53.Google Scholar
Sadakane, K. (2002). Succinct representations o. lcp information and improvements in the compressed suffix arrays. In Proc. 13th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 225–232.Google Scholar
Sadakane, K. (2003). New text indexing functionalities of the compressed suffix arrays. Journal of Algorithms, 48(2), 294–313.Google Scholar
Sadakane, K. (2007a). Compressed suffix trees with full functionality. Theory of Computing Systems, 41(4), 589–607.Google Scholar
Sadakane, K. (2007b). Succinct data structures for flexible text retrieval systems. Journal of Discrete Algorithms, 5, 12–22.Google Scholar
Sedgewick, R. and Wayne, K. (2011). Algorithms. Addison-Wesley, 4th edition.
Sirén, J. (2010). Sampled longest common prefix array. In Proc. 21st Annual Symposium on Combinatorial Pattern Matching (CPM), LNCS 6129, pages 227–237.Google Scholar
Szpankowski, W. (1993). A generalized suffix tree and its (un)expected asymptotic behaviors. SIAM. Journal on Computiing, 22(6), 1176–1198.Google Scholar
Ukkonen, E. (1995). On-line construction of suffix trees. Algorithmica, 14(3), 249–260.Google Scholar
Weiner, P. (1973). Linear pattern matching algorithm. In Proc. 14th Annual IEEE Symposium on Switching and Automata Theory, pages 1–11.Google Scholar

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  • Texts
  • Gonzalo Navarro, Universidad de Chile
  • Book: Compact Data Structures
  • Online publication: 05 September 2016
  • Chapter DOI: https://doi.org/10.1017/CBO9781316588284.012
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  • Texts
  • Gonzalo Navarro, Universidad de Chile
  • Book: Compact Data Structures
  • Online publication: 05 September 2016
  • Chapter DOI: https://doi.org/10.1017/CBO9781316588284.012
Available formats
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Save book to Google Drive

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  • Texts
  • Gonzalo Navarro, Universidad de Chile
  • Book: Compact Data Structures
  • Online publication: 05 September 2016
  • Chapter DOI: https://doi.org/10.1017/CBO9781316588284.012
Available formats
×