P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE AND PATTERN ANALYSIS IN BIOLOGICAL INFORMATICS Edited by UJJWAL MAULIK Department of Computer Science and Engineering, Jadavpur University, Kolkata, India SANGHAMITRA BANDYOPADHYAY Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India JASON T. L. WANG Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey A JOHN WILEY & SONS, INC., PUBLICATION www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE AND PATTERN ANALYSIS IN BIOLOGICAL INFORMATICS www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come Wiley Series on Bioinformatics: Computational Techniques and Engineering A complete list of the titles in this series appears at the end of this volume. www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE AND PATTERN ANALYSIS IN BIOLOGICAL INFORMATICS Edited by UJJWAL MAULIK Department of Computer Science and Engineering, Jadavpur University, Kolkata, India SANGHAMITRA BANDYOPADHYAY Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India JASON T. L. WANG Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey A JOHN WILEY & SONS, INC., PUBLICATION www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come Copyright C  2010 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. Published simultaneously in Canada. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. 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Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For more information about Wiley products, visit our web site at www.wiley.com. ISBN 978-0-470-58159-9 Library of Congress Cataloging-in-Publication Data is available. Printed in the United States of America 10987654321 www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come To Utsav, our students and parents —U. Maulik and S. Bandyopadhyay To my wife Lynn and daughter Tiffany —J.T.L.Wang www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come CONTENTS Preface xi Contributors xvii PART 1 INTRODUCTION 1 Computational Intelligence: Foundations, Perspectives, and Recent Trends 3 Swagatam Das, Ajith Abraham, and B. K. Panigrahi 2 Fundamentals of Pattern Analysis: A Brief Overview 39 Basabi Chakraborty 3 Biological Informatics: Data, Tools, and Applications 59 Kevin Byron, Miguel Cervantes-Cervantes, and Jason T. L. Wang PART II SEQUENCE ANALYSIS 4 Promoter Recognition Using Neural Network Approaches 73 T. Sobha Rani, S. Durga Bhavani, and S. Bapi Raju 5 Predicting microRNA Prostate Cancer Target Genes 99 Francesco Masulli, Stefano Rovetta, and Giuseppe Russo vii www.it-ebooks.info P1: TIX/XYZ P2: ABC fm JWBS033-Maulik July 20, 2010 7:44 Printer Name: Yet to Come viii CONTENTS PART III STRUCTURE ANALYSIS 6 Structural Search in RNA Motif Databases 119 Dongrong Wen and Jason T. L. Wang 7 Kernels on Protein Structures 131 Sourangshu Bhattacharya, Chiranjib Bhattacharyya, and Nagasuma R. Chandra 8 Characterization of Conformational Patterns in Active and Inactive Forms of Kinases using Protein Blocks Approach 169 G. Agarwal, D. C. Dinesh, N. Srinivasan, and Alexandre G. de Brevern 9 Kernel Function Applications in Cheminformatics 189 Aaron Smalter and Jun Huan 10 In Silico Drug Design Using a Computational Intelligence Technique 237 Soumi Sengupta and Sanghamitra Bandyopadhyay PART IV MICROARRAY DATA ANALYSIS 11 Integrated Differential Fuzzy Clustering for Analysis of Microarray Data 259 Indrajit Saha and Ujjwal Maulik 12 Identifying Potential Gene Markers Using SVM Classifier Ensemble 277 Anirban Mukhopadhyay, Ujjwal Maulik, and Sanghamitra Bandyopadhyay 13 Gene Microarray Data Analysis Using Parallel Point Symmetry-Based Clustering 293 Ujjwal Maulik and Anasua Sarkar PART V SYSTEMS BIOLOGY 14 Techniques for Prioritization of Candidate Disease Genes 309 Jieun Jeong and Jake Y. Chen www.it-ebooks.info [...]... researchers in biological informatics The chapters dealing with the applications of computational intelligence and pattern analysis techniques in biological informatics provide a representative view of the available methods and their evaluation in real domains The volume will be useful to graduate students and researchers in computer science, bioinformatics, computational and molecular biology, biochemistry,... contains chapters introducing the basic principles and methodologies of computational intelligence techniques along with a description of some of its important components, fundamental concepts in pattern analysis, and different issues in biological informatics, including a description of biological data and their sources Detailed descriptions of the different applications of computational intelligence and. .. of machine intelligence, assessing the arguments against the possibility of creating an intelligent computing machine and suggesting answers to those arguments, proposing the Turing test as an empirical test of intelligence [4] The Turing test, called the imitation game by Turing, measures the performance of a machine against that of a human being The machine and a human (A) are placed in two rooms... reasoning, understanding, learning, and so on Computational intelligence includes neural networks, fuzzy inference systems, global optimization algorithms, probabilistic computing, swarm intelligence, and so on This chapter introduces the fundamental aspects of the key components of modern computational intelligence It presents a comprehensive overview of various tools of computational intelligence (e.g.,... explicitly, using a priori knowledge Another way is to train the neural network by feeding its teaching patterns and letting it change its weights according to some learning rule The learning situations in neural networks may be classified into three distinct types These are supervised, unsupervised, and reinforcement learning In supervised learning, an input vector is presented at the inputs together... Turing proposed the idea of a universal mathematics machine [1,2], a theoretical concept in the mathematical theory of computability Turing and Post independently proved that determining the decidability of mathematical propositions is equivalent to asking what sorts of sequences of a Computational Intelligence and Pattern Analysis in Biological Informatics, Edited by Ujjwal Maulik, Sanghamitra Bandyopadhyay,... Computational intelligence techniques, which combine elements of learning, adaptation, evolution, and logic, are found to be particularly well suited to many of the problems arising in biology as they have flexible information processing capabilities for handling huge volume of reallife data with noise, ambiguity, missing values, and so on Solving problems in biological informatics often involves search... 9:59 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE Computational Intelligence Family Traditional AI Fuzzy and Granular Computing PR Evolutionary Computing BN NeuroComputing Artificial Life, Rough Sets, Chaos Theory, Swarm Intelligence, and others PR= Probabilistic reasoning, BN= Belief networks FIGURE 1.1 The building blocks of CI fuzzy systems, evolutionary computation, swarm intelligence, and. .. intelligence and pattern analysis techniques to biological informatics constitutes the remaining chapters of the book These include tasks related to the analysis of sequences in the second part, structures in the third part, and microarray data in part four Some topics in systems biology form the concluding part of this book In Chapter 1, Das et al present a lucid overview of computational intelligence. .. networks inspired by mammalian neural systems, evolutionary computation inspired by natural selection in biology, simulated annealing inspired by thermodynamics principles and swarm intelligence inspired by collective behavior of insects or micro-organisms, and so on, interacting locally with their environment causing coherent functional global patterns to emerge These techniques have found their way in . practition- ers reporting recent advances in integrating computational intelligence and pattern analysis techniques, either individually or in a hybridized manner, for analyzing bi- ological data in order. 20, 2010 7:44 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE AND PATTERN ANALYSIS IN BIOLOGICAL INFORMATICS Edited by UJJWAL MAULIK Department of Computer Science and Engineering, Jadavpur. 20, 2010 7:44 Printer Name: Yet to Come COMPUTATIONAL INTELLIGENCE AND PATTERN ANALYSIS IN BIOLOGICAL INFORMATICS Edited by UJJWAL MAULIK Department of Computer Science and Engineering, Jadavpur