A Pseudo-Boolean Solution to the Maximum Quartet Consistency Problem

TL;DR

This paper introduces a pseudo-Boolean encoding for the Maximum Quartet Consistency problem, offering an efficient alternative to existing methods like ASP for reconstructing evolutionary histories from biological data.

Contribution

It presents a novel pseudo-Boolean formulation of the MQC problem, enabling the use of PB solvers and exploring different modeling approaches.

Findings

PB encoding is promising for solving MQC efficiently

PB approach offers flexibility in modeling MQC

Initial results show competitive performance

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.