An Integer Programming Formulation of the Minimum Common String Partition problem

TL;DR

This paper introduces an integer programming approach to solve the NP-hard minimum common string partition problem, demonstrating promising experimental results compared to existing algorithms.

Contribution

It develops and implements a novel integer programming formulation for the MCSP problem, advancing solution methods for genome comparison applications.

Findings

The IP formulation effectively solves MCSP instances.

Experimental results outperform previous algorithms.

The approach shows promise for practical genome analysis.

Abstract

We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP) formulation for the problem and implement it. The experimental results are compared with the previous state-of-the-art algorithms and are found to be promising.