NAPX: A0 polynomial time approximation scheme for the Noah's ark problem

Glenn Hickey; Paz Carmi; Anil Maheshwari; Norbert Zeh

doi:10.1007/978-3-540-87361-7_7

NAPX: A0 polynomial time approximation scheme for the Noah's ark problem

Glenn Hickey
, Paz Carmi
, Anil Maheshwari
, Norbert Zeh

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

3 Scopus citations

Abstract

The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated with a cost of conservation and a probability of extinction. NAP has received renewed interest with the rise in availability of genetic sequence data, allowing PD to be used as a practical measure of biodiversity. However, only simplified instances of the problem, where one or more parameters are fixed as constants, have as of yet been addressed in the literature. We present NAPX, the first algorithm for the general version of NAP that returns a 1∈-∈ε approximation of the optimal solution. It runs in time where n is the number of species, and B is the total budget and h is the height of the input tree. We also provide improved bounds for its expected running time.

Original language	English
Title of host publication	Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings
Pages	76-86
Number of pages	11
DOIs	https://doi.org/10.1007/978-3-540-87361-7_7
State	Published - 28 Nov 2008
Externally published	Yes
Event	8th International Workshop on Algorithms in Bioinformatics, WABI 2008 - Karlsruhe, Germany Duration: 15 Sep 2008 → 19 Sep 2008

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5251 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	8th International Workshop on Algorithms in Bioinformatics, WABI 2008
Country/Territory	Germany
City	Karlsruhe
Period	15/09/08 → 19/09/08

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 15 Life on Land

Keywords

Approximation algorithm
Noah's ark problem
Phylogenetic diversity

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-540-87361-7_7

Cite this

Hickey, G., Carmi, P., Maheshwari, A., & Zeh, N. (2008). NAPX: A0 polynomial time approximation scheme for the Noah's ark problem. In Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings (pp. 76-86). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5251 LNBI). https://doi.org/10.1007/978-3-540-87361-7_7

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title = "NAPX: A0 polynomial time approximation scheme for the Noah's ark problem",

abstract = "The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated with a cost of conservation and a probability of extinction. NAP has received renewed interest with the rise in availability of genetic sequence data, allowing PD to be used as a practical measure of biodiversity. However, only simplified instances of the problem, where one or more parameters are fixed as constants, have as of yet been addressed in the literature. We present NAPX, the first algorithm for the general version of NAP that returns a 1∈-∈ε approximation of the optimal solution. It runs in time where n is the number of species, and B is the total budget and h is the height of the input tree. We also provide improved bounds for its expected running time.",

keywords = "Approximation algorithm, Noah's ark problem, Phylogenetic diversity",

author = "Glenn Hickey and Paz Carmi and Anil Maheshwari and Norbert Zeh",

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Hickey, G, Carmi, P, Maheshwari, A & Zeh, N 2008, NAPX: A0 polynomial time approximation scheme for the Noah's ark problem. in Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5251 LNBI, pp. 76-86, 8th International Workshop on Algorithms in Bioinformatics, WABI 2008, Karlsruhe, Germany, 15/09/08. https://doi.org/10.1007/978-3-540-87361-7_7

NAPX: A0 polynomial time approximation scheme for the Noah's ark problem. / Hickey, Glenn; Carmi, Paz; Maheshwari, Anil et al.
Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. 2008. p. 76-86 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5251 LNBI).

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

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PY - 2008/11/28

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AB - The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated with a cost of conservation and a probability of extinction. NAP has received renewed interest with the rise in availability of genetic sequence data, allowing PD to be used as a practical measure of biodiversity. However, only simplified instances of the problem, where one or more parameters are fixed as constants, have as of yet been addressed in the literature. We present NAPX, the first algorithm for the general version of NAP that returns a 1∈-∈ε approximation of the optimal solution. It runs in time where n is the number of species, and B is the total budget and h is the height of the input tree. We also provide improved bounds for its expected running time.

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Hickey G, Carmi P, Maheshwari A, Zeh N. NAPX: A0 polynomial time approximation scheme for the Noah's ark problem. In Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. 2008. p. 76-86. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-87361-7_7

NAPX: A0 polynomial time approximation scheme for the Noah's ark problem

Abstract

Publication series

Conference

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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