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Finding A Fitness Function To Be Used With Genetic Algorithms To Solve A Protein Folding Problem
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Book Synopsis Finding a Fitness Function to be Used with Genetic Algorithms to Solve a Protein Folding Problem by : Noni McCullough Bohonak
Download or read book Finding a Fitness Function to be Used with Genetic Algorithms to Solve a Protein Folding Problem written by Noni McCullough Bohonak and published by . This book was released on 2000 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genetic Algorithms in Optimisation, Simulation and Modelling by : Joachim Stender
Download or read book Genetic Algorithms in Optimisation, Simulation and Modelling written by Joachim Stender and published by IOS Press. This book was released on 1994 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book examines the implementation and applications of genetic algorithms (GA) to the domain of AI.In recent years the trend towards, real world applications is fgaining ground especially in GA. The general purpose nature of GA is examined from an interdiciplinary point of view. Despite the differences that may exist in between representations across domain problems the commonality of in the design of GA is upheld. This work provides an overview of the current developments in Europe a section is devoted to the progrmamming of Parallel Genetic Algorithms (including GAME) and a section on Optimisation and Complex Modelling. Readers: researchers in AI, mathematics and computing.
Book Synopsis Automated Optimization Methods for Scientific Workflows in e-Science Infrastructures by : Sonja Holl
Download or read book Automated Optimization Methods for Scientific Workflows in e-Science Infrastructures written by Sonja Holl and published by Forschungszentrum Jülich. This book was released on 2014 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientific workflows have emerged as a key technology that assists scientists with the design, management, execution, sharing and reuse of in silico experiments. Workflow management systems simplify the management of scientific workflows by providing graphical interfaces for their development, monitoring and analysis. Nowadays, e-Science combines such workflow management systems with large-scale data and computing resources into complex research infrastructures. For instance, e-Science allows the conveyance of best practice research in collaborations by providing workflow repositories, which facilitate the sharing and reuse of scientific workflows. However, scientists are still faced with different limitations while reusing workflows. One of the most common challenges they meet is the need to select appropriate applications and their individual execution parameters. If scientists do not want to rely on default or experience-based parameters, the best-effort option is to test different workflow set-ups using either trial and error approaches or parameter sweeps. Both methods may be inefficient or time consuming respectively, especially when tuning a large number of parameters. Therefore, scientists require an effective and efficient mechanism that automatically tests different workflow set-ups in an intelligent way and will help them to improve their scientific results. This thesis addresses the limitation described above by defining and implementing an approach for the optimization of scientific workflows. In the course of this work, scientists’ needs are investigated and requirements are formulated resulting in an appropriate optimization concept. In a following step, this concept is prototypically implemented by extending a workflow management system with an optimization framework, including general mechanisms required to conduct workflow optimization. As optimization is an ongoing research topic, different algorithms are provided by pluggable extensions (plugins) that can be loosely coupled with the framework, resulting in a generic and quickly extendable system. In this thesis, an exemplary plugin is introduced which applies a Genetic Algorithm for parameter optimization. In order to accelerate and therefore make workflow optimization feasible at all, e-Science infrastructures are utilized for the parallel execution of scientific workflows. This is empowered by additional extensions enabling the execution of applications and workflows on distributed computing resources. The actual implementation and therewith the general approach of workflow optimization is experimentally verified by four use cases in the life science domain. All workflows were significantly improved, which demonstrates the advantage of the proposed workflow optimization. Finally, a new collaboration-based approach is introduced that harnesses optimization provenance to make optimization faster and more robust in the future.
Book Synopsis Protein Structure Prediction by : David Webster
Download or read book Protein Structure Prediction written by David Webster and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 425 pages. Available in PDF, EPUB and Kindle. Book excerpt: The number of protein sequences grows each year, yet the number of structures deposited in the Protein Data Bank remains relatively small. The importance of protein structure prediction cannot be overemphasized, and this volume is a timely addition to the literature in this field. Protein Structure Prediction: Methods and Protocols is a departure from the normal Methods in Molecular Biology series format. By its very nature, protein structure prediction demands that there be a greater mix of theoretical and practical aspects than is normally seen in this series. This book is aimed at both the novice and the experienced researcher who wish for detailed inf- mation in the field of protein structure prediction; a major intention here is to include important information that is needed in the day-to-day work of a research scientist, important information that is not always decipherable in scientific literature. Protein Structure Prediction: Methods and Protocols covers the topic of protein structure prediction in an eclectic fashion, detailing aspects of pred- tion that range from sequence analysis (a starting point for many algorithms) to secondary and tertiary methods, on into the prediction of docked complexes (an essential point in order to fully understand biological function). As this volume progresses, the authors contribute their expert knowledge of protein structure prediction to many disciplines, such as the identification of motifs and domains, the comparative modeling of proteins, and ab initio approaches to protein loop, side chain, and protein prediction.
Book Synopsis Applications of Evolutionary Computation in Chemistry by : H.M. Cartwright
Download or read book Applications of Evolutionary Computation in Chemistry written by H.M. Cartwright and published by Springer Science & Business Media. This book was released on 2004-03-12 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: H. M. Cartwright: An Introduction to Evolutionary Computation andEvolutionary Algorithms; B. Hartke: Application of Evolutionary Algorithms to Global Cluster Geometry Optimization; K.D.M. Harris, R.L. Johnston, S. Habershon: Application of Evolutionary Computation in Structure Solution from Diffraction Data; S. M.
Book Synopsis Solving the Protein Structure Prediction Problem with Fast Messy Genetic Algorithms (Scaling the Fast Messy Genetic Algorithm to Medium-Sized Peptides by Detecting Secondary Structures) by : Steven R. Michaud
Download or read book Solving the Protein Structure Prediction Problem with Fast Messy Genetic Algorithms (Scaling the Fast Messy Genetic Algorithm to Medium-Sized Peptides by Detecting Secondary Structures) written by Steven R. Michaud and published by . This book was released on 2001-03-01 with total page 259 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ability to accurately predict a polypeptide's molecular structure given its amino acid sequence is important to numerous scientific, medical, and engineering applications. Studies have been conducted in the application of Genetic Algorithms (GAs) to this problem with promising initial results. In this thesis report, we use the fast messy Genetic Algorithm (fmGA) to attempt to find the minimization of an empirical CHARMM energy model and generation of the associated conformation. Previous work has shown that the fmGA provided favorable results, at least when applied to the pentapeptide Met-Enkephalin. We extend these results to a larger Polyalinine peptide by utilizing secondary structure information as both searching constraints and seeding the initial population. Additional efforts where conducted to improve the performance of the algorithm with respect to solving the Protein Structure Prediction (PSP) problem through a short-circuiting operator--where complete evaluation of the fitness function is halted if initial results are not promising, and by conducting additional searches on faster machines in a heterogeneous environment. Results indicate that, on average, this localized search tends to produce better final solutions. Finally, the fmGA as applied to the PSP problem is analyzed and shown to have improved performance and effectiveness.
Book Synopsis Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions by : Agnes Dittel
Download or read book Protein Folding and Self-Avoiding Walks Polyhedral Studies and Solutions written by Agnes Dittel and published by Logos Verlag Berlin GmbH. This book was released on 2008 with total page 362 pages. Available in PDF, EPUB and Kindle. Book excerpt: The protein folding problem refers to the correlation of a protein's amino acid sequence and its native three-dimensional structure which is essential for functionality. It still constitutes one of the major challenges in computational biology. One commonly studied model for the protein folding problem is the HP lattice model in which proteins are considered in a fairly abstract representation. However, the HP model proteins exhibit significant parallels to proteins occurring in nature. The solution of the HP lattice mode as a combinatorial optimization problem has been proven to be NP-complete, and there have already been developed various different approaches for efficient algorithms. We study an integer programming formulation of the problem. Starting with an analysis of this model, where we concentrate on symmetry issues, we show how the model can be consolidated by exploiting symmetry properties of the underlying lattice. The main focus lies in the development of specific components of a branch-and-cut framework for the computation of solutions for the HP model by means of integer programming methods. In order to understand the structure of the model, we perform a series of polyhedral studies from which we derive two main classes of cutting planes. Furthermore, we exploit the knowledge of folding principles which are also valid for HP model proteins for the development of related branching strategies. For the solution of a special class of instances, we present an implementation of a genetic algorithm for the generation of primal feasible start solutions. Finally, we document the performance of the methods developed for each of the four topics (model consolidation, primal method, branching strategy and cutting planes) within the branch-and-cut procedure. We present computational results for different types of lattices, where we both consider known benchmark instances from literature and random instances.
Book Synopsis Biological and Medical Data Analysis by : José Luis Oliveira
Download or read book Biological and Medical Data Analysis written by José Luis Oliveira and published by Springer. This book was released on 2005-10-24 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Evolutionary Algorithms in Molecular Design by : David E. Clark
Download or read book Evolutionary Algorithms in Molecular Design written by David E. Clark and published by John Wiley & Sons. This book was released on 2008-11-21 with total page 288 pages. Available in PDF, EPUB and Kindle. Book excerpt: When trying to find new methods and problem-solving strategies for their research, scientists often turn to nature for inspiration. An excellent example of this is the application of Darwin's Theory of Evolution, particularly the notion of the 'survival of the fittest', in computer programs designed to search for optimal solutions to many kinds of problems. These 'evolutionary algorithms' start from a population of possible solutions to a given problem and, by applying evolutionary principles, evolve successive generations with improved characteristics until an optimal, or near-optimal, solution is obtained. This book highlights the versatility of evolutionary algorithms in areas of relevance to molecular design with a particular focus on drug design. The authors, all of whom are experts in their field, discuss the application of these computational methods to a wide range of research problems including conformational analysis, chemometrics and quantitative structure-activity relationships, de novo molecular design, chemical structure handling, combinatorial library design, and the study of protein folding. In addition, the use of evolutionary algorithms in the determination of structures by X-ray crystallography and NMR spectroscopy is also covered. These state-of-the-art reviews, together with a discussion of new techniques and future developments in the field, make this book a truly valuable and highly up-to-date resource for anyone engaged in the application or development of computer-assisted methods in scientific research.
Book Synopsis Molecular Bioinformatics by : Steffen Schulze-Kremer
Download or read book Molecular Bioinformatics written by Steffen Schulze-Kremer and published by Walter de Gruyter. This book was released on 2011-07-20 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Computational Science and Its Applications - ICCSA 2003 by : Vipin Kumar
Download or read book Computational Science and Its Applications - ICCSA 2003 written by Vipin Kumar and published by Springer Science & Business Media. This book was released on 2003-05-08 with total page 1093 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-volume set, LNCS 2667, LNCS 2668, and LNCS 2669, constitutes the refereed proceedings of the International Conference on Computational Science and Its Applications, ICCSA 2003, held in Montreal, Canada, in May 2003. The three volumes present more than 300 papers and span the whole range of computational science from foundational issues in computer science and mathematics to advanced applications in virtually all sciences making use of computational techniques. The proceedings give a unique account of recent results in computational science.
Book Synopsis Mathematical Methods for Knowledge Discovery and Data Mining by : Felici, Giovanni
Download or read book Mathematical Methods for Knowledge Discovery and Data Mining written by Felici, Giovanni and published by IGI Global. This book was released on 2007-10-31 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: "This book focuses on the mathematical models and methods that support most data mining applications and solution techniques, covering such topics as association rules; Bayesian methods; data visualization; kernel methods; neural networks; text, speech, and image recognition; an invaluable resource for scholars and practitioners in the fields of biomedicine, engineering, finance, manufacturing, marketing, performance measurement, and telecommunications"--Provided by publisher.
Book Synopsis The Application of Hybridized Genetic Algorithms to the Protein Folding Problem by : Robert L. Gaulke
Download or read book The Application of Hybridized Genetic Algorithms to the Protein Folding Problem written by Robert L. Gaulke and published by . This book was released on 1995 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author :Management Association, Information Resources Publisher :IGI Global ISBN 13 :1522556443 Total Pages :2390 pages Book Rating :4.5/5 (225 download)
Book Synopsis Intelligent Systems: Concepts, Methodologies, Tools, and Applications by : Management Association, Information Resources
Download or read book Intelligent Systems: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2018-06-04 with total page 2390 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ongoing advancements in modern technology have led to significant developments in intelligent systems. With the numerous applications available, it becomes imperative to conduct research and make further progress in this field. Intelligent Systems: Concepts, Methodologies, Tools, and Applications contains a compendium of the latest academic material on the latest breakthroughs and recent progress in intelligent systems. Including innovative studies on information retrieval, artificial intelligence, and software engineering, this multi-volume book is an ideal source for researchers, professionals, academics, upper-level students, and practitioners interested in emerging perspectives in the field of intelligent systems.
Book Synopsis Multiobjective Problem Solving from Nature by : Joshua Knowles
Download or read book Multiobjective Problem Solving from Nature written by Joshua Knowles and published by Springer Science & Business Media. This book was released on 2008-01-28 with total page 413 pages. Available in PDF, EPUB and Kindle. Book excerpt: This text examines how multiobjective evolutionary algorithms and related techniques can be used to solve problems, particularly in the disciplines of science and engineering. Contributions by leading researchers show how the concept of multiobjective optimization can be used to reformulate and resolve problems in areas such as constrained optimization, co-evolution, classification, inverse modeling, and design.
Book Synopsis An Introduction to Genetic Algorithms by : Melanie Mitchell
Download or read book An Introduction to Genetic Algorithms written by Melanie Mitchell and published by MIT Press. This book was released on 1998-03-02 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genetic algorithms have been used in science and engineering as adaptive algorithms for solving practical problems and as computational models of natural evolutionary systems. This brief, accessible introduction describes some of the most interesting research in the field and also enables readers to implement and experiment with genetic algorithms on their own. It focuses in depth on a small set of important and interesting topics—particularly in machine learning, scientific modeling, and artificial life—and reviews a broad span of research, including the work of Mitchell and her colleagues. The descriptions of applications and modeling projects stretch beyond the strict boundaries of computer science to include dynamical systems theory, game theory, molecular biology, ecology, evolutionary biology, and population genetics, underscoring the exciting "general purpose" nature of genetic algorithms as search methods that can be employed across disciplines. An Introduction to Genetic Algorithms is accessible to students and researchers in any scientific discipline. It includes many thought and computer exercises that build on and reinforce the reader's understanding of the text. The first chapter introduces genetic algorithms and their terminology and describes two provocative applications in detail. The second and third chapters look at the use of genetic algorithms in machine learning (computer programs, data analysis and prediction, neural networks) and in scientific models (interactions among learning, evolution, and culture; sexual selection; ecosystems; evolutionary activity). Several approaches to the theory of genetic algorithms are discussed in depth in the fourth chapter. The fifth chapter takes up implementation, and the last chapter poses some currently unanswered questions and surveys prospects for the future of evolutionary computation.
Author :Management Association, Information Resources Publisher :IGI Global ISBN 13 :1522507892 Total Pages :1810 pages Book Rating :4.5/5 (225 download)
Book Synopsis Nature-Inspired Computing: Concepts, Methodologies, Tools, and Applications by : Management Association, Information Resources
Download or read book Nature-Inspired Computing: Concepts, Methodologies, Tools, and Applications written by Management Association, Information Resources and published by IGI Global. This book was released on 2016-07-26 with total page 1810 pages. Available in PDF, EPUB and Kindle. Book excerpt: As technology continues to become more sophisticated, mimicking natural processes and phenomena also becomes more of a reality. Continued research in the field of natural computing enables an understanding of the world around us, in addition to opportunities for man-made computing to mirror the natural processes and systems that have existed for centuries. Nature-Inspired Computing: Concepts, Methodologies, Tools, and Applications takes an interdisciplinary approach to the topic of natural computing, including emerging technologies being developed for the purpose of simulating natural phenomena, applications across industries, and the future outlook of biologically and nature-inspired technologies. Emphasizing critical research in a comprehensive multi-volume set, this publication is designed for use by IT professionals, researchers, and graduate students studying intelligent computing.
