A Pseudo-Boolean Solution to the Maximum Quartet Consistency Problem
A Pseudo-Boolean Solution to the Maximum Quartet Consistency Problem
Determining the evolutionary history of a given biological data is an important task in biological sciences. Given a set of quartet topologies over a set of taxa, the Maximum Quartet Consistency (MQC) problem consists of computing a global phylogeny that satisfies the maximum number of quartets. A number of solutions have been proposed for the MQC problem, including Dynamic Programming, Constraint Programming, and more recently Answer Set Programming (ASP). ASP is currently the most efficient approach for optimally solving the MQC problem. This paper proposes encoding the MQC problem with pseudo-Boolean (PB) constraints. The use of PB allows solving the MQC problem with efficient PB solvers, and also allows considering different modeling approaches for the MQC problem. Initial results are promising, and suggest that PB can be an effective alternative for solving the MQC problem.
Morgado, Antonio Jose
17d9afef-09da-47c7-9f64-5ae06ee40229
Marques-Silva, Joao
f992f61f-cedd-4897-9f73-1a3ac7ebb35c
May 2008
Morgado, Antonio Jose
17d9afef-09da-47c7-9f64-5ae06ee40229
Marques-Silva, Joao
f992f61f-cedd-4897-9f73-1a3ac7ebb35c
Morgado, Antonio Jose and Marques-Silva, Joao
(2008)
A Pseudo-Boolean Solution to the Maximum Quartet Consistency Problem
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Abstract
Determining the evolutionary history of a given biological data is an important task in biological sciences. Given a set of quartet topologies over a set of taxa, the Maximum Quartet Consistency (MQC) problem consists of computing a global phylogeny that satisfies the maximum number of quartets. A number of solutions have been proposed for the MQC problem, including Dynamic Programming, Constraint Programming, and more recently Answer Set Programming (ASP). ASP is currently the most efficient approach for optimally solving the MQC problem. This paper proposes encoding the MQC problem with pseudo-Boolean (PB) constraints. The use of PB allows solving the MQC problem with efficient PB solvers, and also allows considering different modeling approaches for the MQC problem. Initial results are promising, and suggest that PB can be an effective alternative for solving the MQC problem.
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jpms-corr08b.pdf
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Published date: May 2008
Additional Information:
ArXiv Report arXiv:0805.0202
Organisations:
Electronics & Computer Science
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Local EPrints ID: 265826
URI: http://eprints.soton.ac.uk/id/eprint/265826
PURE UUID: 1b938652-b743-49d8-8993-013bf803c5cf
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Date deposited: 29 May 2008 13:38
Last modified: 14 Mar 2024 08:15
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Author:
Antonio Jose Morgado
Author:
Joao Marques-Silva
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