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Genetic operators for combinatorial optimization in TSP and microarray gene ordering

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Abstract

This paper deals with some new operators of genetic algorithms and demonstrates their effectiveness to the traveling salesman problem (TSP) and microarray gene ordering. The new operators developed are nearest fragment operator based on the concept of nearest neighbor heuristic, and a modified version of order crossover operator. While these result in faster convergence of Genetic Algorithm (GAs) in finding the optimal order of genes in microarray and cities in TSP, the nearest fragment operator can augment the search space quickly and thus obtain much better results compared to other heuristics. Appropriate number of fragments for the nearest fragment operator and appropriate substring length in terms of the number of cities/genes for the modified order crossover operator are determined systematically. Gene order provided by the proposed method is seen to be superior to other related methods based on GAs, neural networks and clustering in terms of biological scores computed using categorization of the genes.

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Authors and Affiliations

  1. Center for Soft Computing Research: A National Facility, Indian Statistical Institute, Kolkata, 700108, India

    Shubhra Sankar Ray & Sankar K. Pal

  2. Machine Intelligence Unit, Indian Statistical Institute, Kolkata, 700108, India

    Sanghamitra Bandyopadhyay

Authors
  1. Shubhra Sankar Ray
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  2. Sanghamitra Bandyopadhyay
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  3. Sankar K. Pal
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Correspondence to Shubhra Sankar Ray.

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Shubhra Sankar Ray is a Visiting Research Fellow at the Center for Soft Computing Research: A National Facility, Indian Statistical Institute, Kolkata, India. He received the M.Sc. in Electronic Science and M.Tech in Radiophysics & Electronics from University of Calcutta, Kolkata, India, in 2000 and 2002, respectively. Till March 2006, he had been a Senior Research Fellow of the Council of Scientific and Industrial Research (CSIR), New Delhi, India, working at Machine Intelligence Unit, Indian Statistical Institute, India. His research interests include bioinformatics, evolutionary computation, neural networks, and data mining.

Sanghamitra Bandyopadhyay is an Associate Professor at Indian Statistical Institute, Calcutta, India. She did her Bachelors in Physics and Computer Science in 1988 and 1992 respectively. Subsequently, she did her Masters in Computer Science from Indian Institute of Technology (IIT), Kharagpur in 1994 and Ph.D in Computer Science from Indian Statistical Institute, Calcutta in 1998.

She has worked in Los Alamos National Laboratory, Los Alamos, USA, in 1997, as a graduate research assistant, in the University of New South Wales, Sydney, Australia, in 1999, as a post doctoral fellow, in the Department of Computer Science and Engineering, University of Texas at Arlington, USA, in 2001 as a faculty and researcher, and in the Department of Computer Science and Engineering, University of Maryland Baltimore County, USA, in 2004 as a visiting research faculty.

Dr. Bandyopadhyay is the first recipient of Dr. Shanker Dayal Sharma Gold Medal and Institute Silver Medal for being adjudged the best all round post graduate performer in IIT, Kharagpur in 1994. She has received the Indian National Science Academy (INSA) and the Indian Science Congress Association (ISCA) Young Scientist Awards in 2000, as well as the Indian National Academy of Engineering (INAE) Young Engineers' Award in 2002. She has published over ninety articles in international journals, conference and workshop proceedings, edited books and journal special issues and served as the Program Co-Chair of the 1st International Conference on Pattern Recognition and Machine Intelligence, 2005, Kolkata, India, and as the Tutorial Co-Chair, World Congress on Lateral Computing, 2004, Bangalore, India. She is on the editorial board of the International Journal on Computational Intelligence. Her research interests include Evolutionary and Soft Computation, Pattern Recognition, Data Mining, Bioinformatics, Parallel & Distributed Systems and VLSI.

Sankar K. Pal (www.isical.ac.in/∼sankar) is the Director and Distinguished Scientist of the Indian Statistical Institute. He has founded the Machine Intelligence Unit, and the Center for Soft Computing Research: A National Facility in the Institute in Calcutta. He received a Ph.D. in Radio Physics and Electronics from the University of Calcutta in 1979, and another Ph.D. in Electrical Engineering along with DIC from Imperial College, University of London in 1982.

He worked at the University of California, Berkeley and the University of Maryland, College Park in 1986-87; the NASA Johnson Space Center, Houston, Texas in 1990-92 & 1994; and in US Naval Research Laboratory, Washington DC in 2004. Since 1997 he has been serving as a Distinguished Visitor of IEEE Computer Society (USA) for the Asia-Pacific Region, and held seve ral visiting positions in Hong Kong and Australian universities. Prof. Pal is a Fellow of the IEEE, USA, Third World Academy of Sciences, Italy, International Association for Pattern recognition, USA, and all the four National Academies for Science/Engineering in India. He is a co-author of thirteen books and about three hundred research publications in the areas of Pattern Recognition and Machine Learning, Image Processing, Data Mining and Web Intelligence, Soft Computing, Neural Nets, Genetic Algorithms, Fuzzy Sets, Rough Sets, and Bioinformatics.

He has received the 1990 S.S. Bhatnagar Prize (which is the most coveted award for a scientist in India), and many prestigious awards in India and abroad including the 1999 G.D. Birla Award, 1998 Om Bhasin Award, 1993 Jawaharlal Nehru Fellowship, 2000 Khwarizmi International Award from the Islamic Republic of Iran, 2000–2001 FICCI Award, 1993 Vikram Sarabhai Research Award, 1993 NASA Tech Brief Award (USA), 1994 IEEE Trans. Neural Networks Outstanding Paper Award (USA), 1995 NASA Patent Application Award (USA), 1997 IETE-R.L. Wadhwa Gold Medal, the 2001 INSA-S.H. Zaheer Medal, and 2005-06 P.C. Mahalanobis Birth Centenary Award (Gold Medal) for Lifetime Achievement .

Prof. Pal is an Associate Editor of IEEE Trans. Pattern Analysis and Machine Intelligence, IEEE Trans. Neural Networks [1994–98, 2003–06], Pattern Recognition Letters, Neurocomputing (1995–2005), Applied Intelligence, Information Sciences, Fuzzy Sets and Systems, Fundamenta Informaticae, Int. J. Computational Intelligence and Applications, and Proc. INSA-A; a Member, Executive Advisory Editorial Board, IEEE Trans. Fuzzy Systems, Int. Journal on Image and Graphics, and Int. Journal of Approximate Reasoning; and a Guest Editor of IEEE Computer.

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Ray, S.S., Bandyopadhyay, S. & Pal, S.K. Genetic operators for combinatorial optimization in TSP and microarray gene ordering. Appl Intell 26, 183–195 (2007). https://doi.org/10.1007/s10489-006-0018-y

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