A simple algorithm for approximating the text-to-pattern hamming distance

Tsvi Kopelowitz; Ely Porat

doi:10.4230/OASIcs.SOSA.2018.10

A simple algorithm for approximating the text-to-pattern hamming distance

Tsvi Kopelowitz, Ely Porat

Department of Computer Science

Bar-Ilan University

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

The algorithmic task of computing the Hamming distance between a given pattern of length m and each location in a text of length n, both over a general alphabet Σ, is one of the most fundamental algorithmic tasks in string algorithms. The fastest known runtime for exact computation is Õ(n √m). We recently introduced a complicated randomized algorithm for obtaining a 1 ± ∈ approximation for each location in the text in O(n/∈ log 1/∈ log n log m log |Σ|) total time, breaking a barrier that stood for 22 years. In this paper, we introduce an elementary and simple randomized algorithm that takes O(n/∈ log n log m) time.

Original language	English
Title of host publication	1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018
Editors	Raimund Seidel
Publisher	Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)	9783959770644
DOIs	https://doi.org/10.4230/OASIcs.SOSA.2018.10
State	Published - 1 Jan 2018
Event	1st Symposium on Simplicity in Algorithms, SOSA 2018 - New Orleans, United States Duration: 7 Jan 2018 → 10 Jan 2018

Publication series

Name	OpenAccess Series in Informatics
Volume	61

Conference

Conference	1st Symposium on Simplicity in Algorithms, SOSA 2018
Country/Territory	United States
City	New Orleans
Period	7/01/18 → 10/01/18

Keywords

Approximation algorithms
Hamming distance
Pattern matching

All Science Journal Classification (ASJC) codes

Geography, Planning and Development
Modelling and Simulation

Access to Document

10.4230/OASIcs.SOSA.2018.10

Cite this

Kopelowitz, T., & Porat, E. (2018). A simple algorithm for approximating the text-to-pattern hamming distance. In R. Seidel (Ed.), 1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018 Article 10 (OpenAccess Series in Informatics; Vol. 61). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/OASIcs.SOSA.2018.10

Kopelowitz, Tsvi ; Porat, Ely. / A simple algorithm for approximating the text-to-pattern hamming distance. 1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018. editor / Raimund Seidel. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. (OpenAccess Series in Informatics).

@inproceedings{a58183f8ad6d492898b0150a2d3969bf,

title = "A simple algorithm for approximating the text-to-pattern hamming distance",

abstract = "The algorithmic task of computing the Hamming distance between a given pattern of length m and each location in a text of length n, both over a general alphabet Σ, is one of the most fundamental algorithmic tasks in string algorithms. The fastest known runtime for exact computation is {\~O}(n √m). We recently introduced a complicated randomized algorithm for obtaining a 1 ± ∈ approximation for each location in the text in O(n/∈ log 1/∈ log n log m log |Σ|) total time, breaking a barrier that stood for 22 years. In this paper, we introduce an elementary and simple randomized algorithm that takes O(n/∈ log n log m) time.",

keywords = "Approximation algorithms, Hamming distance, Pattern matching",

author = "Tsvi Kopelowitz and Ely Porat",

note = "Publisher Copyright: {\textcopyright} Tsvi Kopelowitz and Ely Porat.; 1st Symposium on Simplicity in Algorithms, SOSA 2018 ; Conference date: 07-01-2018 Through 10-01-2018",

year = "2018",

month = jan,

day = "1",

doi = "10.4230/OASIcs.SOSA.2018.10",

language = "الإنجليزيّة",

series = "OpenAccess Series in Informatics",

publisher = "Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing",

editor = "Raimund Seidel",

booktitle = "1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018",

address = "ألمانيا",

}

Kopelowitz, T & Porat, E 2018, A simple algorithm for approximating the text-to-pattern hamming distance. in R Seidel (ed.), 1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018., 10, OpenAccess Series in Informatics, vol. 61, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 1st Symposium on Simplicity in Algorithms, SOSA 2018, New Orleans, United States, 7/01/18. https://doi.org/10.4230/OASIcs.SOSA.2018.10

A simple algorithm for approximating the text-to-pattern hamming distance. / Kopelowitz, Tsvi ; Porat, Ely.
1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018. ed. / Raimund Seidel. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2018. 10 (OpenAccess Series in Informatics; Vol. 61).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - A simple algorithm for approximating the text-to-pattern hamming distance

AU - Kopelowitz, Tsvi

AU - Porat, Ely

PY - 2018/1/1

Y1 - 2018/1/1

N2 - The algorithmic task of computing the Hamming distance between a given pattern of length m and each location in a text of length n, both over a general alphabet Σ, is one of the most fundamental algorithmic tasks in string algorithms. The fastest known runtime for exact computation is Õ(n √m). We recently introduced a complicated randomized algorithm for obtaining a 1 ± ∈ approximation for each location in the text in O(n/∈ log 1/∈ log n log m log |Σ|) total time, breaking a barrier that stood for 22 years. In this paper, we introduce an elementary and simple randomized algorithm that takes O(n/∈ log n log m) time.

AB - The algorithmic task of computing the Hamming distance between a given pattern of length m and each location in a text of length n, both over a general alphabet Σ, is one of the most fundamental algorithmic tasks in string algorithms. The fastest known runtime for exact computation is Õ(n √m). We recently introduced a complicated randomized algorithm for obtaining a 1 ± ∈ approximation for each location in the text in O(n/∈ log 1/∈ log n log m log |Σ|) total time, breaking a barrier that stood for 22 years. In this paper, we introduce an elementary and simple randomized algorithm that takes O(n/∈ log n log m) time.

KW - Approximation algorithms

KW - Hamming distance

KW - Pattern matching

UR - http://www.scopus.com/inward/record.url?scp=85040659907&partnerID=8YFLogxK

U2 - 10.4230/OASIcs.SOSA.2018.10

DO - 10.4230/OASIcs.SOSA.2018.10

M3 - منشور من مؤتمر

T3 - OpenAccess Series in Informatics

BT - 1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018

A2 - Seidel, Raimund

PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing

T2 - 1st Symposium on Simplicity in Algorithms, SOSA 2018

Y2 - 7 January 2018 through 10 January 2018

ER -

Kopelowitz T , Porat E. A simple algorithm for approximating the text-to-pattern hamming distance. In Seidel R, editor, 1st Symposium on Simplicity in Algorithms, SOSA 2018 - Co-located with the 29th ACM-SIAM Symposium on Discrete Algorithms, SODA 2018. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. 2018. 10. (OpenAccess Series in Informatics). doi: 10.4230/OASIcs.SOSA.2018.10

A simple algorithm for approximating the text-to-pattern hamming distance

Abstract

Publication series

Conference

Keywords

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this