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A hyper-heuristic for the Longest Common Subsequence problem

Paper ID Volume ID Publish Year Pages File Format Full-Text
15208 1391 2012 13 PDF Available
Title
A hyper-heuristic for the Longest Common Subsequence problem
Abstract

The Longest Common Subsequence Problem is the problem of finding a longest string that is a subsequence of every member of a given set of strings. It has applications in FPGA circuit minimization, data compression, and bioinformatics, among others. The problem is NP-hard in its general form, which implies that no exact polynomial-time algorithm currently exists for the problem. Consequently, inexact algorithms have been proposed to obtain good, but not necessarily optimal, solutions in an affordable time. In this paper, a hyper-heuristic algorithm incorporated within a constructive beam search is proposed for the problem. The proposed hyper-heuristic is based on two basic heuristic functions, one of which is new in this paper, and determines dynamically which one to use for a given problem instance. The proposed algorithm is compared with state-of-the-art algorithms on simulated and real biological sequences. Extensive experimental reveals that the proposed hyper-heuristic is superior to the state-of-the-art methods with respect to the solution quality and the running-time.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► The Longest Common Subsequence (LCS) problem is used in molecular biology to compare DNA or RNA sequences. ► LCS is used to determine homology in macromolecules. ► More similar sequences imply more similarity in structures and functions of bimolecular sequences. ► HH-LCS achieves longer common subsequences than the other algorithms. ► HH-LCS is also remarkably fast.

Keywords
Hyper-heuristic algorithms; Longest Common Subsequence; Tree search; Heuristic functions; Sequence analysis
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A hyper-heuristic for the Longest Common Subsequence problem
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 36, February 2012, Pages 42–54
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us