Evolutionary Computation in Gene Regulatory Network Research

Author: Hitoshi Iba
Publisher: John Wiley & Sons
ISBN: 9781119079774
Release Date: 2016-01-20
Genre: Computers

Introducing a handbook for gene regulatory network research using evolutionary computation, with applications for computer scientists, computational and system biologists This book is a step-by-step guideline for research in gene regulatory networks (GRN) using evolutionary computation (EC). The book is organized into four parts that deliver materials in a way equally attractive for a reader with training in computation or biology. Each of these sections, authored by well-known researchers and experienced practitioners, provides the relevant materials for the interested readers. The first part of this book contains an introductory background to the field. The second part presents the EC approaches for analysis and reconstruction of GRN from gene expression data. The third part of this book covers the contemporary advancements in the automatic construction of gene regulatory and reaction networks and gives direction and guidelines for future research. Finally, the last part of this book focuses on applications of GRNs with EC in other fields, such as design, engineering and robotics. • Provides a reference for current and future research in gene regulatory networks (GRN) using evolutionary computation (EC) • Covers sub-domains of GRN research using EC, such as expression profile analysis, reverse engineering, GRN evolution, applications • Contains useful contents for courses in gene regulatory networks, systems biology, computational biology, and synthetic biology • Delivers state-of-the-art research in genetic algorithms, genetic programming, and swarm intelligence Evolutionary Computation in Gene Regulatory Network Research is a reference for researchers and professionals in computer science, systems biology, and bioinformatics, as well as upper undergraduate, graduate, and postgraduate students. Hitoshi Iba is a Professor in the Department of Information and Communication Engineering, Graduate School of Information Science and Technology, at the University of Tokyo, Toyko, Japan. He is an Associate Editor of the IEEE Transactions on Evolutionary Computation and the journal of Genetic Programming and Evolvable Machines. Nasimul Noman is a lecturer in the School of Electrical Engineering and Computer Science at the University of Newcastle, NSW, Australia. From 2002 to 2012 he was a faculty member at the University of Dhaka, Bangladesh. Noman is an Editor of the BioMed Research International journal. His research interests include computational biology, synthetic biology, and bioinformatics.

Evolutionary Approach to Machine Learning and Deep Neural Networks

Author: Hitoshi Iba
Publisher: Springer
ISBN: 9789811302008
Release Date: 2018-06-15
Genre: Computers

This book provides theoretical and practical knowledge about a methodology for evolutionary algorithm-based search strategy with the integration of several machine learning and deep learning techniques. These include convolutional neural networks, Gröbner bases, relevance vector machines, transfer learning, bagging and boosting methods, clustering techniques (affinity propagation), and belief networks, among others. The development of such tools contributes to better optimizing methodologies. Beginning with the essentials of evolutionary algorithms and covering interdisciplinary research topics, the contents of this book are valuable for different classes of readers: novice, intermediate, and also expert readers from related fields. Following the chapters on introduction and basic methods, Chapter 3 details a new research direction, i.e., neuro-evolution, an evolutionary method for the generation of deep neural networks, and also describes how evolutionary methods are extended in combination with machine learning techniques. Chapter 4 includes novel methods such as particle swarm optimization based on affinity propagation (PSOAP), and transfer learning for differential evolution (TRADE), another machine learning approach for extending differential evolution. The last chapter is dedicated to the state of the art in gene regulatory network (GRN) research as one of the most interesting and active research fields. The author describes an evolving reaction network, which expands the neuro-evolution methodology to produce a type of genetic network suitable for biochemical systems and has succeeded in designing genetic circuits in synthetic biology. The author also presents real-world GRN application to several artificial intelligent tasks, proposing a framework of motion generation by GRNs (MONGERN), which evolves GRNs to operate a real humanoid robot.

Encyclopedia of Information Science and Technology Fourth Edition

Author: Khosrow-Pour, D.B.A., Mehdi
Publisher: IGI Global
ISBN: 9781522522560
Release Date: 2017-06-20
Genre: Computers

In recent years, our world has experienced a profound shift and progression in available computing and knowledge sharing innovations. These emerging advancements have developed at a rapid pace, disseminating into and affecting numerous aspects of contemporary society. This has created a pivotal need for an innovative compendium encompassing the latest trends, concepts, and issues surrounding this relevant discipline area. During the past 15 years, the Encyclopedia of Information Science and Technology has become recognized as one of the landmark sources of the latest knowledge and discoveries in this discipline. The Encyclopedia of Information Science and Technology, Fourth Edition is a 10-volume set which includes 705 original and previously unpublished research articles covering a full range of perspectives, applications, and techniques contributed by thousands of experts and researchers from around the globe. This authoritative encyclopedia is an all-encompassing, well-established reference source that is ideally designed to disseminate the most forward-thinking and diverse research findings. With critical perspectives on the impact of information science management and new technologies in modern settings, including but not limited to computer science, education, healthcare, government, engineering, business, and natural and physical sciences, it is a pivotal and relevant source of knowledge that will benefit every professional within the field of information science and technology and is an invaluable addition to every academic and corporate library.

Advanced Methodologies and Technologies in Artificial Intelligence Computer Simulation and Human Computer Interaction

Author: Khosrow-Pour, D.B.A., Mehdi
Publisher: IGI Global
ISBN: 9781522573692
Release Date: 2018-09-28
Genre: Computers

As modern technologies continue to develop and evolve, the ability of users to adapt with new systems becomes a paramount concern. Research into new ways for humans to make use of advanced computers and other such technologies through artificial intelligence and computer simulation is necessary to fully realize the potential of tools in the 21st century. Advanced Methodologies and Technologies in Artificial Intelligence, Computer Simulation, and Human-Computer Interaction provides emerging research in advanced trends in robotics, AI, simulation, and human-computer interaction. Readers will learn about the positive applications of artificial intelligence and human-computer interaction in various disciples such as business and medicine. This book is a valuable resource for IT professionals, researchers, computer scientists, and researchers invested in assistive technologies, artificial intelligence, robotics, and computer simulation.

Analysis of Biological Networks

Author: Björn H. Junker
Publisher: John Wiley & Sons
ISBN: 9781118209912
Release Date: 2011-09-20
Genre: Computers

An introduction to biological networks and methods for theiranalysis Analysis of Biological Networks is the first book of itskind to provide readers with a comprehensive introduction to thestructural analysis of biological networks at the interface ofbiology and computer science. The book begins with a brief overviewof biological networks and graph theory/graph algorithms and goeson to explore: global network properties, network centralities,network motifs, network clustering, Petri nets, signal transductionand gene regulation networks, protein interaction networks,metabolic networks, phylogenetic networks, ecological networks, andcorrelation networks. Analysis of Biological Networks is a self-containedintroduction to this important research topic, assumes no expertknowledge in computer science or biology, and is accessible toprofessionals and students alike. Each chapter concludes with asummary of main points and with exercises for readers to test theirunderstanding of the material presented. Additionally, an FTP sitewith links to author-provided data for the book is available fordeeper study. This book is suitable as a resource for researchers in computerscience, biology, bioinformatics, advanced biochemistry, and thelife sciences, and also serves as an ideal reference text forgraduate-level courses in bioinformatics and biologicalresearch.

Bioinformatics Algorithms

Author: Ion Mandoiu
Publisher: John Wiley & Sons
ISBN: 0470253428
Release Date: 2008-02-15
Genre: Computers

Presents algorithmic techniques for solving problems in bioinformatics, including applications that shed new light on molecular biology This book introduces algorithmic techniques in bioinformatics, emphasizing their application to solving novel problems in post-genomic molecular biology. Beginning with a thought-provoking discussion on the role of algorithms in twenty-first-century bioinformatics education, Bioinformatics Algorithms covers: General algorithmic techniques, including dynamic programming, graph-theoretical methods, hidden Markov models, the fast Fourier transform, seeding, and approximation algorithms Algorithms and tools for genome and sequence analysis, including formal and approximate models for gene clusters, advanced algorithms for non-overlapping local alignments and genome tilings, multiplex PCR primer set selection, and sequence/network motif finding Microarray design and analysis, including algorithms for microarray physical design, missing value imputation, and meta-analysis of gene expression data Algorithmic issues arising in the analysis of genetic variation across human population, including computational inference of haplotypes from genotype data and disease association search in case/control epidemiologic studies Algorithmic approaches in structural and systems biology, including topological and structural classification in biochemistry, and prediction of protein-protein and domain-domain interactions Each chapter begins with a self-contained introduction to a computational problem; continues with a brief review of the existing literature on the subject and an in-depth description of recent algorithmic and methodological developments; and concludes with a brief experimental study and a discussion of open research challenges. This clear and approachable presentation makes the book appropriate for researchers, practitioners, and graduate students alike.

Proceedings of the 4th Asia Pacific Bioinformatics Conference

Author: Tao Jiang
Publisher:
ISBN: 1860946232
Release Date: 2006
Genre: Computers

High-throughput sequencing and functional genomics technologies have given us a draft human genome sequence and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, and gene expression profiles of normal and diseased tissues in different clinical states are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences, in the understanding of the interplay between genes and proteins, in the analysis of the genetic variability of species, and so on. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 4th Asia-Pacific Bioinformatics Conference held in Taipei in February 2006.

Recent developments in biologically inspired computing

Author: Leandro N. De Castro
Publisher: IGI Global
ISBN: UOM:39015060104885
Release Date: 2005
Genre: Computers

Recent Developments in Biologically Inspired Computing is necessary reading for undergraduate and graduate students, and researchers interested in knowing the most recent advances in problem solving techniques inspired by nature. This book covers the most relevant areas in computational intelligence, including evolutionary algorithms, artificial neural networks, artificial immune systems and swarm systems. It also brings together novel and philosophical trends in the exciting fields of artificial life and robotics. This book has the advantage of covering a large number of computational approaches, presenting the state-of-the-art before entering into the details of specific extensions and new developments. Pseudocodes, flow charts and examples of applications are provided so as to help newcomers and mature researchers to get the point of the new approaches presented.

Encyclopedia of Artificial Intelligence

Author:
Publisher: IGI Global
ISBN: 9781599048499
Release Date: 2009-01-01
Genre: Computers

"This book is a comprehensive and in-depth reference to the most recent developments in the field covering theoretical developments, techniques, technologies, among others"--Provided by publisher.