TY - GEN

T1 - NAPX

T2 - 8th International Workshop on Algorithms in Bioinformatics, WABI 2008

AU - Hickey, Glenn

AU - Carmi, Paz

AU - Maheshwari, Anil

AU - Zeh, Norbert

PY - 2008/11/28

Y1 - 2008/11/28

N2 - 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.

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.

KW - Approximation algorithm

KW - Noah's ark problem

KW - Phylogenetic diversity

UR - http://www.scopus.com/inward/record.url?scp=56649102088&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-87361-7_7

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

M3 - Conference contribution

AN - SCOPUS:56649102088

SN - 3540873600

SN - 9783540873600

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 76

EP - 86

BT - Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings

Y2 - 15 September 2008 through 19 September 2008

ER -