A heuristic algorithm based on Lagrangian relaxation for the closest string problem

Abstract

The closest string problem that arises in both computational biology and coding theory is to find a string minimizing the maximum Hamming distance from a given set of strings. This study proposes an efficient heuristic algorithm for this NP-hard problem. The key idea is to apply the Lagrangian relaxation technique to the problem formulated as a mixed-integer programming problem. This enables us to decompose the problem into trivial subproblems corresponding to each position of the strings. Furthermore, a feasible solution can be easily obtained from a solution of the relaxation. Based on this, a heuristic algorithm is constructed by combining a Lagrangian multiplier adjustment procedure and a tabu search. Computational experiments will show that the proposed algorithm can find good approximate solutions very fast.