Large neighborhood search for the most strings with few bad columns problem

Large neighborhood search for the most strings with few bad columns problem In this work, we consider the following NP-hard combinatorial optimization problem from computational biology. Given a set of input strings of equal length, the goal is to identify a maximum cardinality subset of strings that differ maximally in a pre-defined number of positions. First of all, we introduce an integer linear programming model for this problem. Second, two variants of a rather simple greedy strategy are proposed. Finally, a large neighborhood search algorithm is presented. A comprehensive experimental comparison among the proposed techniques shows, first, that larger neighborhood search generally outperforms both greedy strategies. Second, while large neighborhood search shows to be competitive with the stand-alone application of CPLEX for small- and medium-sized problem instances, it outperforms CPLEX in the context of larger instances. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Soft Computing Springer Journals

Large neighborhood search for the most strings with few bad columns problem

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Publisher
Springer Berlin Heidelberg
Copyright
Copyright © 2016 by Springer-Verlag Berlin Heidelberg
Subject
Engineering; Computational Intelligence; Artificial Intelligence (incl. Robotics); Mathematical Logic and Foundations; Control, Robotics, Mechatronics
ISSN
1432-7643
eISSN
1433-7479
D.O.I.
10.1007/s00500-016-2379-4
Publisher site
See Article on Publisher Site

Abstract

In this work, we consider the following NP-hard combinatorial optimization problem from computational biology. Given a set of input strings of equal length, the goal is to identify a maximum cardinality subset of strings that differ maximally in a pre-defined number of positions. First of all, we introduce an integer linear programming model for this problem. Second, two variants of a rather simple greedy strategy are proposed. Finally, a large neighborhood search algorithm is presented. A comprehensive experimental comparison among the proposed techniques shows, first, that larger neighborhood search generally outperforms both greedy strategies. Second, while large neighborhood search shows to be competitive with the stand-alone application of CPLEX for small- and medium-sized problem instances, it outperforms CPLEX in the context of larger instances.

Journal

Soft ComputingSpringer Journals

Published: Oct 6, 2016

References

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