Year

2018

Season

Summer

Paper Type

Master's Thesis

College

College of Computing, Engineering & Construction

Degree Name

Master of Science in Computer and Information Sciences (MS)

Department

Computing

NACO controlled Corporate Body

University of North Florida. School of Computing

First Advisor

Dr. Swapnoneel Roy

Second Advisor

Dr. Asai Asaithambi

Rights Statement

http://rightsstatements.org/vocab/InC/1.0/

Third Advisor

Dr. William F. Klostermeyer

Department Chair

Dr. Sherif Elfayoumy

College Dean

Dr. Mark A. Tumeo

Abstract

An implementation framework has been developed in this thesis for a well-known APX-hard combinatorial optimization problem known as Block Sorting. The motivation for the study of this problem comes from applications such as computational biology and optical character recognition. While existing Block Sorting research has been theoretically focused on the development and analysis of several approximation algorithms for Block Sorting, little or no work has been carried out thus far on the implementation of the proposed approximation algorithms. The conceptualization of an implementation framework and illustrating its use by experimenting with the existing approximation algorithms will provide means for discovering newer approaches to handling this important problem. As the main contribution, the research in this thesis provides a new greedy algorithm for Block Sorting in which each block move either reduces the number of blocks by two or three blocks, or reduces by one the number of reversals or inversions in the orig- inal permutation. Experimental results for all algorithms are also provided along with a comparison of their performance using the number of block moves and approximation ratios as performance metrics when sorting permutations of a given order, and as the order of permutations is varied. Preliminary results from the experimentation were shared at the 2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) [1]. To the best of our knowledge, this is the first work that has been focused on the implementation and experimental performance analysis of any algorithm for Block Sorting. We believe the results presented in this thesis will be useful for researchers and practitioners working in this area.

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