Faster phylogenetic inference with MXG

Authors:
David G. Mitchell;Faraz Hach;Raheleh Mohebali
Affiliations:
Computational Logic Laboratory, Simon Fraser University, Burnaby, BC, Canada;Computational Logic Laboratory, Simon Fraser University, Burnaby, BC, Canada;Computational Logic Laboratory, Simon Fraser University, Burnaby, BC, Canada
Venue:
LPAR'07 Proceedings of the 14th international conference on Logic for programming, artificial intelligence and reasoning
Year:
2007

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Abstract

We apply the logic-based declarative programming approach of Model Expansion (MX) to a phylogenetic inference task. We axiomatize the task in multi-sorted first-order logic with cardinality constraints. Using the model expansion solver MXG and SAT+cardinality solver MXC, we compare the performance of several MX axiomatizations on a challenging set of test instances. Our methods perform orders of magnitude faster than previously reported declarative solutions. Our best solution involves polynomial-time pre-processing, redundant axioms, and symmetry-breaking axioms. We also discuss our method of test instance generation, and the role of pre-processing in declarative programming.