Permutation editing and matching via embeddings

Graham Cormode, S. Muthukrishnan, Süleyman Cenk Sahinalp

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    If the genetic maps of two species are modelled as permutations of (homologous) genes, the number of chromosomal rearrangements in the form of deletions, block moves, inversions etc. to transform one such permutation to another can be used as a measure of their evolutionary distance. Motivated by such scenarios, we study problems of computing distances between permutations as well as matching permutations in sequences, and finding most similar permutation from a collection (nearest neighbor). We adopt a general approach: embed permutation distances of relevance into well-known vector spaces in an approximately distance-preserving manner, and solve the resulting problems on the well-known spaces. Our results are as follows: We present the first known approximately distance preserving embeddings of these permutation distances into well-known spaces. Using these embeddings, we obtain several results, including the first known ecient solution for approximately solving nearest neighbor problems with permutations and the first known algorithms for finding permutation distances in the data stream model. We consider a novel class of problems called permutation matching problems which are similar to string matching problems, except that the pattern is a permutation (rather than a string) and present linear or near-linear time algorithms for approximately solving permutation matching problems; in contrast, the corresponding string problems take significantly longer.

    Original languageEnglish (US)
    Title of host publicationAutomata, Languages and Programming - 28th International Colloquium, ICALP 2001, Proceedings
    EditorsFernando Orejas, Paul G. Spirakis, Jan van Leeuwen
    PublisherSpringer Verlag
    Pages481-492
    Number of pages12
    ISBN (Print)3540422870, 9783540422877
    DOIs
    StatePublished - 2001
    Event28th International Colloquium on Automata, Languages and Programming, ICALP 2001 - Crete, Greece
    Duration: Jul 8 2001Jul 12 2001

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume2076 LNCS
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other28th International Colloquium on Automata, Languages and Programming, ICALP 2001
    CountryGreece
    CityCrete
    Period7/8/017/12/01

    ASJC Scopus subject areas

    • Theoretical Computer Science
    • Computer Science(all)

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  • Cite this

    Cormode, G., Muthukrishnan, S., & Sahinalp, S. C. (2001). Permutation editing and matching via embeddings. In F. Orejas, P. G. Spirakis, & J. van Leeuwen (Eds.), Automata, Languages and Programming - 28th International Colloquium, ICALP 2001, Proceedings (pp. 481-492). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2076 LNCS). Springer Verlag. https://doi.org/10.1007/3-540-48224-5_40