Abstract
Suffix tree construction algorithms based on suffix links are popular because they are simple to implement, can operate online in linear time, and because the suffix links are often convenient for pattern matching. We present an approach using edge-oriented suffix links, which reduces the number of branch lookup operations (known to be a bottleneck in construction time) with some additional techniques to reduce construction cost. We discuss various effects of our approach and compare it to previous techniques. An experimental evaluation shows that we are able to reduce construction time to around half that of the original algorithm, and about two thirds that of previously known branch-reduced construction.
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References
Apostolico, A.: The myriad virtues of subword trees. In: Apostolico, A., Galil, Z. (eds.) Combinatorial Algorithms on Words. NATO ASI Series, vol. F 12, pp. 85–96. Springer (1985)
Arbitman, Y., Naor, M., Segev, G.: Backyard cuckoo hashing: Constant worst-case operations with a succinct representation. In: Proc. 51st Ann. IEEE Symp. Foundations of Comput. Sci., pp. 787–796 (2010)
Cánovas, R., Navarro, G.: Practical compressed suffix trees. In: Festa, P. (ed.) SEA 2010. LNCS, vol. 6049, pp. 94–105. Springer, Heidelberg (2010)
Clark, D.R., Munro, J.I.: Efficient suffix trees on secondary storage. In: Proc. Seventh Ann. ACM–SISM Symp. Discrete Algorithms, pp. 383–391 (1996)
Farach, M.: Optimal suffix tree construction with large alphabets. In: Proc. 38th Ann. IEEE Symp. Foundations of Comput. Sci., pp. 137–143 (October 1997)
Ferragina, P.: Suffix tree construction in hierarchical memory. In: Encyclopedia of Algorithms, pp. 922–925. Springer (2008)
Ferragina, P., Navarro, G.: Pizza & chili corpus (2005), http://pizzachili.dcc.uchile.cl/
Frigo, M., Leiserson, C., Prokop, H., Ramachandran, S.: Cache-oblivious algorithms. In: Proc. 40th Ann. IEEE Symp. Foundations of Comput. Sci., pp. 285–297 (1999)
Giegerich, R., Kurtz, S., Stoye, J.: Efficient implementation of lazy suffix trees. Software – Practice and Experience 33(11), 1035–1049 (2001)
Gusfield, D.: Algorithms on Strings, Trees, and Sequences. Cambridge University Press (1997)
Hagerup, T., Miltersen, P.B., Pagh, R.: Deterministic dictionaries. Journal of Algorithms 41(1), 69–85 (2001)
Kiełbasa, S.M., Wan, R., Sato, K., Horton, P., Frith, M.C.: Adaptive seeds tame genomic sequence comparison. Genome Research 21(3), 487–493 (2011)
Kurtz, S.: Reducing the space requirement of suffix trees. Software – Practice and Experience 29(13), 1149–1171 (1999)
Larsson, N.J.: Extended application of suffix trees to data compression. In: Proc. IEEE Data Compression Conf., pp. 190–199 (March-April 1996)
Manber, U., Myers, G.: Suffix arrays: A new method for on-line string searches. J. Comput. 22(5), 935–948 (1993)
Manzini, G., Ferragina, P.: Lightweight corpus (2004), http://people.unipmn.it/manzini/lightweight/corpus/
McCreight, E.M.: A space-economical suffix tree construction algorithm. J. ACM 23(2), 262–272 (1976)
Perf: Linux profiling with performance counters, https://perf.wiki.kernel.org/
Senft, M., Dvořák, T.: On-line suffix tree construction with reduced branching. Journal of Discrete Algorithms 12(0), 48–60 (2012)
Tian, Y., Tata, S., Hankins, R.A., Patel, J.M.: Practical methods for constructing suffix trees. The VLDB Journal 14(3), 281–289 (2005)
Tsirogiannis, D., Koudas, N.: Suffix tree construction algorithms on modern hardware. In: Proc. 13th International Conference on Extending Database Technology, pp. 263–274 (2010)
Ukkonen, E.: On-line construction of suffix trees. Algorithmica 14(3), 249–260 (1995)
Weiner, P.: Linear pattern matching algorithms. In: Proc. 14th Ann. IEEE Symp. Switching and Automata Theory, pp. 1–11 (1973)
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Larsson, N.J., Fuglsang, K., Karlsson, K. (2014). Efficient Representation for Online Suffix Tree Construction. In: Gudmundsson, J., Katajainen, J. (eds) Experimental Algorithms. SEA 2014. Lecture Notes in Computer Science, vol 8504. Springer, Cham. https://doi.org/10.1007/978-3-319-07959-2_34
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DOI: https://doi.org/10.1007/978-3-319-07959-2_34
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