Evolutionary Computation In Gene Regulatory Network Research

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Evolutionary Computation in Gene Regulatory Network Research

Author : Hitoshi Iba
Publisher : John Wiley & Sons
ISBN 13 : 1119079780
Total Pages : 464 pages
Book Rating : 4.1/5 (19 download)

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Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Hitoshi Iba

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-01-21 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Computation in Gene Regulatory Network Research

Author : Andy Goodwin
Publisher : Createspace Independent Publishing Platform
ISBN 13 : 9781975978105
Total Pages : 428 pages
Book Rating : 4.9/5 (781 download)

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Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Andy Goodwin

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Andy Goodwin and published by Createspace Independent Publishing Platform. This book was released on 2017-05-23 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Evolutionary Approach to Machine Learning and Deep Neural Networks

Author : Hitoshi Iba
Publisher : Springer
ISBN 13 : 9811302006
Total Pages : 245 pages
Book Rating : 4.8/5 (113 download)

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Book Synopsis Evolutionary Approach to Machine Learning and Deep Neural Networks by : Hitoshi Iba

Download or read book Evolutionary Approach to Machine Learning and Deep Neural Networks written by Hitoshi Iba and published by Springer. This book was released on 2018-06-15 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Genetic Programming

Author : Mauro Castelli
Publisher : Springer
ISBN 13 : 3319775537
Total Pages : 331 pages
Book Rating : 4.3/5 (197 download)

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Book Synopsis Genetic Programming by : Mauro Castelli

Download or read book Genetic Programming written by Mauro Castelli and published by Springer. This book was released on 2018-03-23 with total page 331 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Evolutionary Computation in Gene Regulatory Network Research

Author : Hitoshi Iba
Publisher : John Wiley & Sons
ISBN 13 : 1118911512
Total Pages : 464 pages
Book Rating : 4.1/5 (189 download)

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Book Synopsis Evolutionary Computation in Gene Regulatory Network Research by : Hitoshi Iba

Download or read book Evolutionary Computation in Gene Regulatory Network Research written by Hitoshi Iba and published by John Wiley & Sons. This book was released on 2016-02-23 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Handbook of Research on Computational Methodologies in Gene Regulatory Networks

Author : Das, Sanjoy
Publisher : IGI Global
ISBN 13 : 1605666866
Total Pages : 740 pages
Book Rating : 4.6/5 (56 download)

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Book Synopsis Handbook of Research on Computational Methodologies in Gene Regulatory Networks by : Das, Sanjoy

Download or read book Handbook of Research on Computational Methodologies in Gene Regulatory Networks written by Das, Sanjoy and published by IGI Global. This book was released on 2009-10-31 with total page 740 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book focuses on methods widely used in modeling gene networks including structure discovery, learning, and optimization"--Provided by publisher.

New Frontier In Evolutionary Algorithms: Theory And Applications

Author : Iba Hitoshi
Publisher : Imperial College Press
ISBN 13 : 1911299557
Total Pages : 316 pages
Book Rating : 4.9/5 (112 download)

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Book Synopsis New Frontier In Evolutionary Algorithms: Theory And Applications by : Iba Hitoshi

Download or read book New Frontier In Evolutionary Algorithms: Theory And Applications written by Iba Hitoshi and published by Imperial College Press. This book was released on 2011-08-26 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems

Author : Johannes F. Knabe
Publisher : Springer
ISBN 13 : 3642302963
Total Pages : 122 pages
Book Rating : 4.6/5 (423 download)

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

Download or read book Computational Genetic Regulatory Networks: Evolvable, Self-organizing Systems written by Johannes F. Knabe and published by Springer. This book was released on 2012-08-14 with total page 122 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

The Regulatory Genome

Author : Eric H. Davidson
Publisher : Elsevier
ISBN 13 : 9780080455570
Total Pages : 304 pages
Book Rating : 4.4/5 (555 download)

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Book Synopsis The Regulatory Genome by : Eric H. Davidson

Download or read book The Regulatory Genome written by Eric H. Davidson and published by Elsevier. This book was released on 2010-07-19 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Proceedings of the ... Congress on Evolutionary Computation

Author :
Publisher :
ISBN 13 :
Total Pages : 788 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Proceedings of the ... Congress on Evolutionary Computation by :

Download or read book Proceedings of the ... Congress on Evolutionary Computation written by and published by . This book was released on 2003 with total page 788 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Artificial Life and Evolutionary Computation

Author :
Publisher :
ISBN 13 : 9814466743
Total Pages : pages
Book Rating : 4.8/5 (144 download)

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Book Synopsis Artificial Life and Evolutionary Computation by :

Download or read book Artificial Life and Evolutionary Computation written by and published by . This book was released on with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Genomic Control Process

Author : Isabelle Peter
Publisher : Academic Press
ISBN 13 : 0124047467
Total Pages : 460 pages
Book Rating : 4.1/5 (24 download)

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Book Synopsis Genomic Control Process by : Isabelle Peter

Download or read book Genomic Control Process written by Isabelle Peter and published by Academic Press. This book was released on 2015-01-21 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Computational Modeling of Gene Regulatory Networks

Author : Hamid Bolouri
Publisher : Imperial College Press
ISBN 13 : 1848162200
Total Pages : 341 pages
Book Rating : 4.8/5 (481 download)

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Book Synopsis Computational Modeling of Gene Regulatory Networks by : Hamid Bolouri

Download or read book Computational Modeling of Gene Regulatory Networks written by Hamid Bolouri and published by Imperial College Press. This book was released on 2008 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Artificial Life and Evolutionary Computation

Author : Roberto Serra
Publisher : World Scientific
ISBN 13 : 981428744X
Total Pages : 341 pages
Book Rating : 4.8/5 (142 download)

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Book Synopsis Artificial Life and Evolutionary Computation by : Roberto Serra

Download or read book Artificial Life and Evolutionary Computation written by Roberto Serra and published by World Scientific. This book was released on 2010 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Italian community in Artificial Life and Evolutionary computation has grown remarkably in recent years, and this book is the first broad collection of its major interests and achievements (including contributions from foreign countries). The contributions in Artificial Life as well as in Evolutionary Computation allow one to see the deep connections between the two fields. The topics addressed are extremely relevant for present day research in Artificial Life and in Evolutionary Computation, which include important contributions from very well-known researchers. The volume provides a very broad picture of the Italian activities in this field.

Frontiers of Evolutionary Computation

Author : Anil Menon
Publisher : Springer Science & Business Media
ISBN 13 : 1402077823
Total Pages : 271 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Frontiers of Evolutionary Computation by : Anil Menon

Download or read book Frontiers of Evolutionary Computation written by Anil Menon and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: Frontiers of Evolutionary Computation brings together eleven contributions by international leading researchers discussing what significant issues still remain unresolved in the field of Evolutionary Computation (Ee. They explore such topics as the role of building blocks, the balancing of exploration with exploitation, the modeling of EC algorithms, the connection with optimization theory and the role of EC as a meta-heuristic method, to name a few. The articles feature a mixture of informal discussion interspersed with formal statements, thus providing the reader an opportunity to observe a wide range of EC problems from the investigative perspective of world-renowned researchers. These prominent researchers include: Heinz M]hlenbein, Kenneth De Jong, Carlos Cotta and Pablo Moscato, Lee Altenberg, Gary A. Kochenberger, Fred Glover, Bahram Alidaee and Cesar Rego, William G. Macready, Christopher R. Stephens and Riccardo Poli, Lothar M. Schmitt, John R. Koza, Matthew J. Street and Martin A. Keane, Vivek Balaraman, Wolfgang Banzhaf and Julian Miller.

Genetic Programming Theory and Practice

Author : Rick Riolo
Publisher : Springer Science & Business Media
ISBN 13 : 1441989838
Total Pages : 317 pages
Book Rating : 4.4/5 (419 download)

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Book Synopsis Genetic Programming Theory and Practice by : Rick Riolo

Download or read book Genetic Programming Theory and Practice written by Rick Riolo and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Evolution, Complexity and Artificial Life

Author : Stefano Cagnoni
Publisher : Springer Science & Business Media
ISBN 13 : 3642375774
Total Pages : 280 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Evolution, Complexity and Artificial Life by : Stefano Cagnoni

Download or read book Evolution, Complexity and Artificial Life written by Stefano Cagnoni and published by Springer Science & Business Media. This book was released on 2013-12-21 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.