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Implementation of sequence BDDs in Erlang

Published: 23 September 2011 Publication History

Abstract

In this paper, we present an implementation of Erlang of an efficient index structure, called Sequence Binary Decision Diagrams (SeqBDDs), for knowledge discovery in large sequence data. Recently, Loekito, Bailey, and Pei (KAIS, 2009) proposed SeqBDD. SeqBDDs are a compact indices for efficiently representing the set of sequences. Furthermore, SeqBDDs provide a rich collection of operations for sets of sequences, which are useful for implementing sequence mining algorithms. We propose SeqBDDs as powerful framework for string processing and Erlang is appropriate language for SeqBDD. SeqBDD system heavily uses hash tables to avoid redundant memory and computation. We implemented SeqBDD package with ETS for hash tables.

References

[1]
Blumer, A., Blumer, J., Ehrenfeucht, A., Haussler, D., McConnell, R.: Linear size finite automata for the set of all subwords of a word: an outline of results, Bull. Europ. Assoc. Theoret. Comput. Sci., 21, pp.12--20 (1983)
[2]
Gusfield, D.: Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge (1997)
[3]
Loekito, E., Bailey, J., Pei, J.: A Binary decision diagram based approach for mining frequent subsequences, Knowl. Inf. Syst., (2009)
[4]
Ukkonen, E.: On-line construction of suffix trees, Algorithmica, vol.14, no.3, pp.249--260 (1995)

Cited By

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  • (2016)Sequence binary decision diagramDiscrete Applied Mathematics10.1016/j.dam.2014.11.022212:C(61-80)Online publication date: 30-Oct-2016
  • (2012)Compact Representation of Biological Sequences Using Set Decision Diagrams6th International Conference on Practical Applications of Computational Biology & Bioinformatics10.1007/978-3-642-28839-5_27(231-239)Online publication date: 2012

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cover image ACM Conferences
Erlang '11: Proceedings of the 10th ACM SIGPLAN workshop on Erlang
September 2011
108 pages
ISBN:9781450308595
DOI:10.1145/2034654
Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 23 September 2011

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Author Tags

  1. SeqBDD
  2. erlang term storage table
  3. recursive structure
  4. sequence binary decision diagram
  5. sequence mining

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Erlang '11 Paper Acceptance Rate 10 of 14 submissions, 71%;
Overall Acceptance Rate 51 of 68 submissions, 75%

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Cited By

View all
  • (2016)Sequence binary decision diagramDiscrete Applied Mathematics10.1016/j.dam.2014.11.022212:C(61-80)Online publication date: 30-Oct-2016
  • (2012)Compact Representation of Biological Sequences Using Set Decision Diagrams6th International Conference on Practical Applications of Computational Biology & Bioinformatics10.1007/978-3-642-28839-5_27(231-239)Online publication date: 2012

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