Consensus optimizing both distance sum and radius

Amihood Amir; Gad M. Landau; Joong Chae Na; Heejin Park; Kunsoo Park; Jeong Seop Sim

doi:10.1007/978-3-642-03784-9_23

Consensus optimizing both distance sum and radius

Amihood Amir, Gad M. Landau, Joong Chae Na, Heejin Park, Kunsoo Park, Jeong Seop Sim

Department of Computer Science

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

Abstract

The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.

Original language	English
Title of host publication	String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings
Pages	234-242
Number of pages	9
DOIs	https://doi.org/10.1007/978-3-642-03784-9_23
State	Published - 2009
Event	16th International Symposium on String Processing and Information Retrieval, SPIRE 2009 - Saariselka, Finland Duration: 25 Aug 2009 → 27 Aug 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5721 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	16th International Symposium on String Processing and Information Retrieval, SPIRE 2009
Country/Territory	Finland
City	Saariselka
Period	25/08/09 → 27/08/09

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-03784-9_23

Cite this

Amir, A., Landau, G. M., Na, J. C., Park, H., Park, K., & Sim, J. S. (2009). Consensus optimizing both distance sum and radius. In String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings (pp. 234-242). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5721 LNCS). https://doi.org/10.1007/978-3-642-03784-9_23

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title = "Consensus optimizing both distance sum and radius",

abstract = "The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.",

author = "Amihood Amir and Landau, {Gad M.} and Na, {Joong Chae} and Heejin Park and Kunsoo Park and Sim, {Jeong Seop}",

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pages = "234--242",

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Amir, A, Landau, GM, Na, JC, Park, H, Park, K & Sim, JS 2009, Consensus optimizing both distance sum and radius. in String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5721 LNCS, pp. 234-242, 16th International Symposium on String Processing and Information Retrieval, SPIRE 2009, Saariselka, Finland, 25/08/09. https://doi.org/10.1007/978-3-642-03784-9_23

Consensus optimizing both distance sum and radius. / Amir, Amihood; Landau, Gad M.; Na, Joong Chae et al.
String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings. 2009. p. 234-242 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5721 LNCS).

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

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T1 - Consensus optimizing both distance sum and radius

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AU - Landau, Gad M.

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AU - Sim, Jeong Seop

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AB - The consensus string problem is finding a representative string (consensus) of a given set of strings. In this paper we deal with the consensus string problems optimizing both distance sum and radius, where the distance sum is the sum of (Hamming) distances from the strings in to the consensus and the radius is the longest (Hamming) distance from the strings in to the consensus. Although there have been results considering either distance sum or radius, there have been no results considering both as far as we know. We present two algorithms to solve the consensus string problems optimizing both distance sum and radius for three strings. The first algorithm finds the optimal consensus string that minimizes both distance sum and radius, and the second algorithm finds the bounded consensus string such that, given constants s and r, the distance sum is at most s and the radius is at most r. Both algorithms take linear time.

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Amir A, Landau GM, Na JC, Park H, Park K, Sim JS. Consensus optimizing both distance sum and radius. In String Processing and Information Retrieval - 16th International Symposium, SPIRE 2009, Proceedings. 2009. p. 234-242. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-03784-9_23

Consensus optimizing both distance sum and radius

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