Evolutionary Computation In Gene Regulatory Network Research

Author : Hitoshi Iba,Nasimul Noman
Publisher : John Wiley & Sons
Page : 464 pages
File Size : 43,6 Mb
Release : 2016-01-21
Category : Computers
ISBN : 9781119079781

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Evolutionary Computation in Gene Regulatory Network Research by Hitoshi Iba,Nasimul Noman Pdf

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.

Author : Andy Goodwin
Publisher : Createspace Independent Publishing Platform
Page : 428 pages
File Size : 50,5 Mb
Release : 2017-05-23
Category : Electronic
ISBN : 1975978102

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Evolutionary Computation in Gene Regulatory Network Research by Andy Goodwin Pdf

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.

Author : Hitoshi Iba
Publisher : Springer
Page : 245 pages
File Size : 40,6 Mb
Release : 2018-06-15
Category : Computers
ISBN : 9789811302008

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Evolutionary Approach to Machine Learning and Deep Neural Networks by Hitoshi Iba Pdf

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.

Author : Mauro Castelli,Lukas Sekanina,Mengjie Zhang,Stefano Cagnoni,Pablo García-Sánchez
Publisher : Springer
Page : 331 pages
File Size : 48,7 Mb
Release : 2018-03-23
Category : Computers
ISBN : 9783319775531

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Genetic Programming by Mauro Castelli,Lukas Sekanina,Mengjie Zhang,Stefano Cagnoni,Pablo García-Sánchez Pdf

This book constitutes the refereed proceedings of the 21st European Conference on Genetic Programming, EuroGP 2018, held in Parma, Italy, in April 2018, co-located with the Evo* 2018 events, EvoCOP, EvoMUSART, and EvoApplications. The 11 revised full papers presented together with 8 poster papers were carefully reviewed and selected from 36 submissions. The wide range of topics in this volume reflects the current state of research in the field. Thus, we see topics and applications including analysis of feature importance for metabolomics, semantic methods, evolution of boolean networks, generation of redundant features, ensembles of GP models, automatic design of grammatical representations, GP and neuroevolution, visual reinforcement learning, evolution of deep neural networks, evolution of graphs, and scheduling in heterogeneous networks.

Author : Hitoshi Iba,Nasimul Noman
Publisher : John Wiley & Sons
Page : 464 pages
File Size : 55,5 Mb
Release : 2016-02-23
Category : Computers
ISBN : 9781118911518

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Evolutionary Computation in Gene Regulatory Network Research by Hitoshi Iba,Nasimul Noman Pdf

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.

Author : Das, Sanjoy,Caragea, Doina,Welch, Stephen,Hsu, William H.
Publisher : IGI Global
Page : 740 pages
File Size : 48,6 Mb
Release : 2009-10-31
Category : Computers
ISBN : 9781605666860

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Handbook of Research on Computational Methodologies in Gene Regulatory Networks by Das, Sanjoy,Caragea, Doina,Welch, Stephen,Hsu, William H. Pdf

"This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.

Author : Iba Hitoshi,Noman Nasimul
Publisher : Imperial College Press
Page : 316 pages
File Size : 46,5 Mb
Release : 2011-08-26
Category : Computers
ISBN : 9781911299554

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New Frontier In Evolutionary Algorithms: Theory And Applications by Iba Hitoshi,Noman Nasimul Pdf

This book delivers theoretical and practical knowledge of Genetic Algorithms (GA) for the purpose of practical applications. It provides a methodology for a GA-based search strategy with the integration of several Artificial Life and Artificial Intelligence techniques, such as memetic concepts, swarm intelligence, and foraging strategies. The development of such tools contributes to better optimizing methodologies when addressing tasks from areas such as robotics, financial forecasting, and data mining in bioinformatics.The emphasis of this book is on applicability to the real world. Tasks from application areas - optimization of the trading rule in foreign exchange (FX) and stock prices, economic load dispatch in power system, exit/door placement for evacuation planning, and gene regulatory network inference in bioinformatics - are studied, and the resultant empirical investigations demonstrate how successful the proposed approaches are when solving real-world tasks of great importance.

Author : Eric H. Davidson
Publisher : Elsevier
Page : 304 pages
File Size : 42,9 Mb
Release : 2010-07-19
Category : Science
ISBN : 0080455573

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The Regulatory Genome by Eric H. Davidson Pdf

Gene regulatory networks are the most complex, extensive control systems found in nature. The interaction between biology and evolution has been the subject of great interest in recent years. The author, Eric Davidson, has been instrumental in elucidating this relationship. He is a world renowned scientist and a major contributor to the field of developmental biology. The Regulatory Genome beautifully explains the control of animal development in terms of structure/function relations of inherited regulatory DNA sequence, and the emergent properties of the gene regulatory networks composed of these sequences. New insights into the mechanisms of body plan evolution are derived from considerations of the consequences of change in developmental gene regulatory networks. Examples of crucial evidence underscore each major concept. The clear writing style explains regulatory causality without requiring a sophisticated background in descriptive developmental biology. This unique text supersedes anything currently available in the market. The only book in the market that is solely devoted to the genomic regulatory code for animal development Written at a conceptual level, including many novel synthetic concepts that ultimately simplify understanding Presents a comprehensive treatment of molecular control elements that determine the function of genes Provides a comparative treatment of development, based on principles rather than description of developmental processes Considers the evolutionary processes in terms of the structural properties of gene regulatory networks Includes 42 full-color descriptive figures and diagrams

Author : Johannes F. Knabe
Publisher : Springer
Page : 122 pages
File Size : 53,8 Mb
Release : 2012-08-14
Category : Technology & Engineering
ISBN : 9783642302961

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Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems by Johannes F. Knabe Pdf

Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting from a single cell interacting with its environment, eventually including a changing local neighbourhood of other cells. These methods may help us understand the genesis, organization, adaptive plasticity, and evolvability of differentiated biological systems, and may also provide a paradigm for transferring these principles of biology's success to computational and engineering challenges at a scale not previously conceivable.

Author : Rick Riolo,Bill Worzel
Publisher : Springer Science & Business Media
Page : 317 pages
File Size : 50,9 Mb
Release : 2012-12-06
Category : Computers
ISBN : 9781441989833

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Genetic Programming Theory and Practice by Rick Riolo,Bill Worzel Pdf

Genetic Programming Theory and Practice explores the emerging interaction between theory and practice in the cutting-edge, machine learning method of Genetic Programming (GP). The material contained in this contributed volume was developed from a workshop at the University of Michigan's Center for the Study of Complex Systems where an international group of genetic programming theorists and practitioners met to examine how GP theory informs practice and how GP practice impacts GP theory. The contributions cover the full spectrum of this relationship and are written by leading GP theorists from major universities, as well as active practitioners from leading industries and businesses. Chapters include such topics as John Koza's development of human-competitive electronic circuit designs; David Goldberg's application of "competent GA" methodology to GP; Jason Daida's discovery of a new set of factors underlying the dynamics of GP starting from applied research; and Stephen Freeland's essay on the lessons of biology for GP and the potential impact of GP on evolutionary theory.

Author : Isabelle Peter,Eric H. Davidson
Publisher : Academic Press
Page : 460 pages
File Size : 41,7 Mb
Release : 2015-01-21
Category : Science
ISBN : 9780124047464

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Genomic Control Process by Isabelle Peter,Eric H. Davidson Pdf

Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Author : Hamid Bolouri
Publisher : Imperial College Press
Page : 341 pages
File Size : 40,6 Mb
Release : 2008
Category : Medical
ISBN : 9781848162204

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Computational Modeling of Gene Regulatory Networks by Hamid Bolouri Pdf

This book serves as an introduction to the myriad computational approaches to gene regulatory modeling and analysis, and is written specifically with experimental biologists in mind. Mathematical jargon is avoided and explanations are given in intuitive terms. In cases where equations are unavoidable, they are derived from first principles or, at the very least, an intuitive description is provided. Extensive examples and a large number of model descriptions are provided for use in both classroom exercises as well as self-guided exploration and learning. As such, the book is ideal for self-learning and also as the basis of a semester-long course for undergraduate and graduate students in molecular biology, bioengineering, genome sciences, or systems biology.

Author : Anonim
Publisher : Unknown
Page : 128 pages
File Size : 44,9 Mb
Release : 2024-05-09
Category : Electronic
ISBN : 9789814466745

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Artificial Life and Evolutionary Computation by Anonim Pdf

Author : Sanjeev Kumar,Peter J. Bentley
Publisher : Elsevier
Page : 472 pages
File Size : 40,6 Mb
Release : 2003-10-03
Category : Mathematics
ISBN : 9780080497587

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On Growth, Form and Computers by Sanjeev Kumar,Peter J. Bentley Pdf

Conceived for both computer scientists and biologists alike, this collection of 22 essays highlights the important new role that computers play in developmental biology research. Essays show how through computer modeling, researchers gain further insight into developmental processes. Featured essays also cover their use in designing computer algorithms to tackle computer science problems in areas like neural network design, robot control, evolvable hardware, and more. Peter Bentley, noted for his prolific research on evolutionary computation, and Sanjeev Kumar head up a respected team to guide readers through these very complex and fascinating disciplines. * Covers both developmental biology and computational development -- the only book of its kind! * Provides introductory material and more detailed information on BOTH disciplines * Includes contribututions from Richard Dawkins, Lewis Wolpert, Ian Stewart, and many other experts

Author : Stefano Cagnoni,Marco Mirolli,Marco Villani
Publisher : Springer Science & Business Media
Page : 280 pages
File Size : 46,5 Mb
Release : 2013-12-21
Category : Computers
ISBN : 9783642375774

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Evolution, Complexity and Artificial Life by Stefano Cagnoni,Marco Mirolli,Marco Villani Pdf

Evolution and complexity characterize both biological and artificial life – by direct modeling of biological processes and the creation of populations of interacting entities from which complex behaviors can emerge and evolve. This edited book includes invited chapters from leading scientists in the fields of artificial life, complex systems, and evolutionary computing. The contributions identify both fundamental theoretical issues and state-of-the-art real-world applications. The book is intended for researchers and graduate students in the related domains.