Parameterized complexity analysis for the Closest String with Wildcards problem

Randomized and Parameterized Algorithms for the Closest String Problem

Iterative Rounding for the Closest String Problem

The closest string problem is an NP-hard problem, which arises in computational molecular biology and coding theory. Its task is to find a string that minimizes maximum Hamming distance to a given set of strings. This problem can be reduced to an integer program (IP). However, to date, there exists no known polynomial-time algorithm for integer programs. In 2004, Meneses et al. introduced a bra...

The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity

Given a set S of n strings, each of length `, and a nonnegative value d, we define a center string as a string of length ` that has Hamming distance at most d from each string in S. The Closest String problem aims to determine whether there exists a center string for a given set of strings S and input parameters n, `, and d. When n is relatively large with respect to ` then the basic majority a...

A Three-String Approach to the Closest String Problem

Article history: Received 18 May 2010 Received in revised form 11 January 2011 Accepted 21 January 2011 Available online 28 January 2011

The Exact Closest String Problem as a Constraint Satisfaction Problem

We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that provide several orders of magnitude speedup at and above the optimal distance. We also report (to our knowledge) the first analysis and evaluation – using any tec...