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Compressed String Dictionary Search with Edit Distance One

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Abstract

In this paper we present different solutions for the problem of indexing a dictionary of strings in compressed space. Given a pattern \(P\), the index has to report all the strings in the dictionary having edit distance at most one with \(P\). Our first solution is able to solve queries in (almost optimal) \(O(|P|+occ)\) time where \(occ\) is the number of strings in the dictionary having edit distance at most one with \(P\). The space complexity of this solution is bounded in terms of the \(k\)th order entropy of the indexed dictionary. A second solution further improves this space complexity at the cost of increasing the query time. Finally, we propose randomized solutions (Monte Carlo and Las Vegas) which achieve simultaneously the time complexity of the first solution and the space complexity of the second one.

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Notes

  1. However, they can be easily extended to deal with the more general edit distance.

  2. Actually, the paper [11] described only a solution for binary alphabet. However, it is not hard to obtain the claimed space and time complexities also for non-constant alphabet sizes.

  3. Notice that just accessing each symbol of these candidate strings would cost \(O(p + p \cdot occ)\) time in total which is much higher than our claimed complexity.

  4. Recall that we are still assuming that we can check in \(O(1)\) whether a candidate string belongs to \( D \).

  5. Observe that similar considerations hold also for substitutions with the difference that we skip the \(i\)th symbol in factorizations of the form \(P=P[1,i-1] \cdot P[i] \cdot P[i+1, p]\).

  6. Checks for other types of errors are done in a similar way.

  7. We notice that the number of distinct lengths and, thus, compressed permuterm indexes is \(O(\sqrt{n})\).

  8. Notice that this case occurs only when \(P_iP[i]\in D \). In order to properly deal with this case, the value of \(\ell \) is not increased after a successful backward step if it already reached the maximal value \(p+2\).

  9. If we have false positives then the same character may be checked and thus potentially reported twice. To avoid this case, we can use a dynamic hash table at query time which stores all the characters reported so-far. Whenever we find that a character has been already reported, then the query stops and does not report more characters, since a correct query answer can not return the same character twice at the same position.

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Authors and Affiliations

  1. Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland

    Djamal Belazzougui

  2. Department of Computer Science, University of Pisa, Pisa, Italy

    Rossano Venturini

Authors
  1. Djamal Belazzougui
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  2. Rossano Venturini
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Correspondence to Rossano Venturini.

Additional information

The work is an extended version of the paper [8] appeared in Proceedings of 23rd Annual Symposium on Combinatorial Pattern Matching, 2012. This work has been partially supported by Academy of Finland under Grant 250345 (CoECGR), the French ANR-2010-COSI-004 MAPPI project, PRIN ARS Technomedia 2012, the Midas EU Project, Grant Agreement No. 318786, and the eCloud EU Project, Grant Agreement No. 325091.

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Belazzougui, D., Venturini, R. Compressed String Dictionary Search with Edit Distance One. Algorithmica 74, 1099–1122 (2016). https://doi.org/10.1007/s00453-015-9990-0

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