Computational Intelligence in Bioinformatics

A breakthrough guide employing knowledge that unites cheminformatics and bioinformatics as innovation for the future Bridging the gap between cheminformatics and bioinformatics for the first time, Computational Approaches in Cheminformatics and Bioinformatics provides insight on how to blend these two sciences for progressive research benefits. It describes the development and evolution of these fields, how chemical information may be used for biological relations and vice versa, the implications of these new connections, and foreseeable developments in the future. Using algorithms and domains as workflow tools, this revolutionary text drives bioinformaticians to consider chemical structure, and similarly, encourages cheminformaticians to consider large biological systems such as protein targets and networks. Computational Approaches in Cheminformatics and Bioinformatics covers: Data sources available for modelling and prediction purposes Developments of conventional Quantitative Structure-Activity Relationships (QSAR) Computational tools for manipulating chemical and biological data Novel ways of probing the interactions between small molecules and proteins Also including insight from public (NIH), academic, and industrial sources (Novartis, Pfizer), this book offers expert knowledge to aid scientists through industry and academic study. The invaluable applications for drug discovery, cellular and molecular biology, enzymology, and metabolism make Computational Approaches in Cheminformatics and Bioinformatics the essential guidebook for evolving drug discovery research and alleviating the issue of chemical control and manipulation of various systems.

Computational Intelligence: Synergies of Fuzzy Logic, Neural Networks and Evolutionary Computing presents an introduction to some of the cutting edge technological paradigms under the umbrella of computational intelligence. Computational intelligence schemes are investigated with the development of a suitable framework for fuzzy logic, neural networks and evolutionary computing, neuro-fuzzy systems, evolutionary-fuzzy systems and evolutionary neural systems. Applications to linear and non-linear systems are discussed with examples. Key features: Covers all the aspects of fuzzy, neural and evolutionary approaches with worked out examples, MATLAB® exercises and applications in each chapter Presents the synergies of technologies of computational intelligence such as evolutionary fuzzy neural fuzzy and evolutionary neural systems Considers real world problems in the domain of systems modelling, control and optimization Contains a foreword written by Lotfi Zadeh Computational Intelligence: Synergies of Fuzzy Logic, Neural Networks and Evolutionary Computing is an ideal text for final year undergraduate, postgraduate and research students in electrical, control, computer, industrial and manufacturing engineering.

Computational Intelligence: An Introduction, Second Edition offers an in-depth exploration into the adaptive mechanisms that enable intelligent behaviour in complex and changing environments. The main focus of this text is centred on the computational modelling of biological and natural intelligent systems, encompassing swarm intelligence, fuzzy systems, artificial neutral networks, artificial immune systems and evolutionary computation. Engelbrecht provides readers with a wide knowledge of Computational Intelligence (CI) paradigms and algorithms; inviting readers to implement and problem solve real-world, complex problems within the CI development framework. This implementation framework will enable readers to tackle new problems without any difficulty through a single Java class as part of the CI library. Key features of this second edition include: A tutorial, hands-on based presentation of the material. State-of-the-art coverage of the most recent developments in computational intelligence with more elaborate discussions on intelligence and artificial intelligence (AI). New discussion of Darwinian evolution versus Lamarckian evolution, also including swarm robotics, hybrid systems and artificial immune systems. A section on how to perform empirical studies; topics including statistical analysis of stochastic algorithms, and an open source library of CI algorithms. Tables, illustrations, graphs, examples, assignments, Java code implementing the algorithms, and a complete CI implementation and experimental framework. Computational Intelligence: An Introduction, Second Edition is essential reading for third and fourth year undergraduate and postgraduate students studying CI. The first edition has been prescribed by a number of overseas universities and is thus a valuable teaching tool. In addition, it will also be a useful resource for researchers in Computational Intelligence and Artificial Intelligence, as well as engineers, statisticians, operational researchers, and bioinformaticians with an interest in applying AI or CI to solve problems in their domains. Check out http://www.ci.cs.up.ac.za for examples, assignments and Java code implementing the algorithms.

An invaluable tool in Bioinformatics, this unique volume provides both theoretical and experimental results, and describes basic principles of computational intelligence and pattern analysis while deepening the reader's understanding of the ways in which these principles can be used for analyzing biological data in an efficient manner. This book synthesizes current research in the integration of computational intelligence and pattern analysis techniques, either individually or in a hybridized manner. The purpose is to analyze biological data and enable extraction of more meaningful information and insight from it. Biological data for analysis include sequence data, secondary and tertiary structure data, and microarray data. These data types are complex and advanced methods are required, including the use of domain-specific knowledge for reducing search space, dealing with uncertainty, partial truth and imprecision, efficient linear and/or sub-linear scalability, incremental approaches to knowledge discovery, and increased level and intelligence of interactivity with human experts and decision makers Chapters authored by leading researchers in CI in biology informatics. Covers highly relevant topics: rational drug design; analysis of microRNAs and their involvement in human diseases. Supplementary material included: program code and relevant data sets correspond to chapters.

Provides an in-depth and even treatment of the three pillars of computational intelligence and how they relate to one another This book covers the three fundamental topics that form the basis of computational intelligence: neural networks, fuzzy systems, and evolutionary computation. The text focuses on inspiration, design, theory, and practical aspects of implementing procedures to solve real-world problems. While other books in the three fields that comprise computational intelligence are written by specialists in one discipline, this book is co-written by current former Editor-in-Chief of IEEE Transactions on Neural Networks and Learning Systems, a former Editor-in-Chief of IEEE Transactions on Fuzzy Systems, and the founding Editor-in-Chief of IEEE Transactions on Evolutionary Computation. The coverage across the three topics is both uniform and consistent in style and notation. Discusses single-layer and multilayer neural networks, radial-basis function networks, and recurrent neural networks Covers fuzzy set theory, fuzzy relations, fuzzy logic interference, fuzzy clustering and classification, fuzzy measures and fuzzy integrals Examines evolutionary optimization, evolutionary learning and problem solving, and collective intelligence Includes end-of-chapter practice problems that will help readers apply methods and techniques to real-world problems Fundamentals of Computational intelligence is written for advanced undergraduates, graduate students, and practitioners in electrical and computer engineering, computer science, and other engineering disciplines.

The rough and fuzzy set approaches presented here open up many new frontiers for continued research and development Computational Intelligence and Feature Selection provides readers with the background and fundamental ideas behind Feature Selection (FS), with an emphasis on techniques based on rough and fuzzy sets. For readers who are less familiar with the subject, the book begins with an introduction to fuzzy set theory and fuzzy-rough set theory. Building on this foundation, the book provides: A critical review of FS methods, with particular emphasis on their current limitations Program files implementing major algorithms, together with the necessary instructions and datasets, available on a related Web site Coverage of the background and fundamental ideas behind FS A systematic presentation of the leading methods reviewed in a consistent algorithmic framework Real-world applications with worked examples that illustrate the power and efficacy of the FS approaches covered An investigation of the associated areas of FS, including rule induction and clustering methods using hybridizations of fuzzy and rough set theories Computational Intelligence and Feature Selection is an ideal resource for advanced undergraduates, postgraduates, researchers, and professional engineers. However, its straightforward presentation of the underlying concepts makes the book meaningful to specialists and nonspecialists alike.

ALGORITHMS IN BIOINFORMATICS Explore a comprehensive and insightful treatment of the practical application of bioinformatic algorithms in a variety of fields Algorithms in Bioinformatics: Theory and Implementation delivers a fulsome treatment of some of the main algorithms used to explain biological functions and relationships. It introduces readers to the art of algorithms in a practical manner which is linked with biological theory and interpretation. The book covers many key areas of bioinformatics, including global and local sequence alignment, forced alignment , detection of motifs, Sequence logos, Markov chains or information entropy. Other novel approaches are also described, such as Self-Sequence alignment, Objective Digital Stains (ODSs) or Spectral Forecast and the Discrete Probability Detector (DPD) algorithm. The text incorporates graphical illustrations to highlight and emphasize the technical details of computational algorithms found within, to further the reader’s understanding and retention of the material. Throughout, the book is written in an accessible and practical manner, showing how algorithms can be implemented and used in JavaScript on Internet Browsers. The author has included more than 120 open-source implementations of the material, as well as 33 ready-to-use presentations. The book contains original material that has been class-tested by the author and numerous cases are examined in a biological and medical context. Readers will also benefit from the inclusion of: A thorough introduction to biological evolution, including the emergence of life, classifications and some known theories and molecular mechanismsA detailed presentation of new methods, such as Self-sequence alignment, Objective Digital Stains and Spectral Forecast A treatment of sequence alignment, including local sequence alignment, global sequence alignment and forced sequence alignment with full implementationsDiscussions of position-specific weight matrices, including the count, weight, relative frequencies, and log-likelihoods matricesA detailed presentation of the methods related to Markov Chains as well as a description of their implementation in Bioinformatics and adjacent fieldsAn examination of information and entropy, including sequence logos and explanations related to their meaningAn exploration of the current state of bioinformatics, including what is known and what issues are usually avoided in the fieldA chapter on philosophical transactions that allows the reader a broader view of the prediction processNative computer implementations in the context of the field of BioinformaticsExtensive worked examples with detailed case studies that point out the meaning of different results Perfect for professionals and researchers in biology, medicine, engineering, and information technology, as well as upper level undergraduate students in these fields, Algorithms in Bioinformatics: Theory and Implementation will also earn a place in the libraries of software engineers who wish to understand how to implement bioinformatic algorithms in their products.

An in-depth look at the latest research, methods, and applications in the field of protein bioinformatics This book presents the latest developments in protein bioinformatics, introducing for the first time cutting-edge research results alongside novel algorithmic and AI methods for the analysis of protein data. In one complete, self-contained volume, Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics addresses key challenges facing both computer scientists and biologists, arming readers with tools and techniques for analyzing and interpreting protein data and solving a variety of biological problems. Featuring a collection of authoritative articles by leaders in the field, this work focuses on the analysis of protein sequences, structures, and interaction networks using both traditional algorithms and AI methods. It also examines, in great detail, data preparation, simulation, experiments, evaluation methods, and applications. Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics: Highlights protein analysis applications such as protein-related drug activity comparison Incorporates salient case studies illustrating how to apply the methods outlined in the book Tackles the complex relationship between proteins from a systems biology point of view Relates the topic to other emerging technologies such as data mining and visualization Includes many tables and illustrations demonstrating concepts and performance figures Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics is an essential reference for bioinformatics specialists in research and industry, and for anyone wishing to better understand the rich field of protein bioinformatics.

An introduction to machine learning methods and their applications to problems in bioinformatics Machine learning techniques are increasingly being used to address problems in computational biology and bioinformatics. Novel computational techniques to analyze high throughput data in the form of sequences, gene and protein expressions, pathways, and images are becoming vital for understanding diseases and future drug discovery. Machine learning techniques such as Markov models, support vector machines, neural networks, and graphical models have been successful in analyzing life science data because of their capabilities in handling randomness and uncertainty of data noise and in generalization. From an internationally recognized panel of prominent researchers in the field, Machine Learning in Bioinformatics compiles recent approaches in machine learning methods and their applications in addressing contemporary problems in bioinformatics. Coverage includes: feature selection for genomic and proteomic data mining; comparing variable selection methods in gene selection and classification of microarray data; fuzzy gene mining; sequence-based prediction of residue-level properties in proteins; probabilistic methods for long-range features in biosequences; and much more. Machine Learning in Bioinformatics is an indispensable resource for computer scientists, engineers, biologists, mathematicians, researchers, clinicians, physicians, and medical informaticists. It is also a valuable reference text for computer science, engineering, and biology courses at the upper undergraduate and graduate levels.

The purpose of this edited book is to bring together the ideas and findings of data mining researchers and bioinformaticians by discussing cutting-edge research topics such as, gene expressions, protein/RNA structure prediction, phylogenetics, sequence and structural motifs, genomics and proteomics, gene findings, drug design, RNAi and microRNA analysis, text mining in bioinformatics, modelling of biochemical pathways, biomedical ontologies, system biology and pathways, and biological database management.