A three-string approach to the closest string problem

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

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 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...

Optimal Solutions for the Closest-String Problem via Integer Programming

Integer Programming Cláudio N. Meneses Department of Industrial and Systems Engineering, University of Florida, 303 Weil Hall, Gainesville, Florida, 32611, USA, [email protected] Zhaosong Lu School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0205, USA, [email protected] Carlos A.S. Oliveira, Panos M. Pardalos Department of Industrial and S...

Randomized and Parameterized Algorithms for the Closest String Problem