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 approaching 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.
WCB08 - Workshop on Constraint Based Methods for Bioinformatics, Paris, France.
Record type:
Conference or Workshop Item
(Paper)
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 approaching 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.
Text
jpms-wcb08a.pdf
- Other
More information
Published date: May 2008
Additional Information:
Event Dates: May 22
Venue - Dates:
WCB08 - Workshop on Constraint Based Methods for Bioinformatics, Paris, France, 2008-05-22
Organisations:
Electronics & Computer Science
Identifiers
Local EPrints ID: 265436
URI: http://eprints.soton.ac.uk/id/eprint/265436
PURE UUID: 507413e2-d597-4fcf-9c3c-7295ceb52af9
Catalogue record
Date deposited: 15 Apr 2008 21:02
Last modified: 14 Mar 2024 08:09
Export record
Contributors
Author:
Antonio Jose Morgado
Author:
Joao Marques-Silva
Download statistics
Downloads from ePrints over the past year. Other digital versions may also be available to download e.g. from the publisher's website.
View more statistics