Metaheuristics for String Problems in Bio-informatics PDF Download

Author: Christian Blum
Publisher: John Wiley & Sons
ISBN: 1848218125
Category : Computers
Languages : en
Pages : 243

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Book Description
So-called string problems are abundant in bioinformatics and computational biology. New optimization problems dealing with DNA or protein sequences are constantly arising and researchers are highly in need of efficient optimization techniques for solving them. One obstacle for optimization practitioners is the atypical nature of these problems which require an interdisciplinary approach in order to solve them efficiently and accurately.

Author: Christian Blum
Publisher: John Wiley & Sons
ISBN: 1119136806
Category : Computers
Languages : en
Pages : 228

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Book Description
So-called string problems are abundant in bioinformatics and computational biology. New optimization problems dealing with DNA or protein sequences are constantly arising and researchers are highly in need of efficient optimization techniques for solving them. One obstacle for optimization practitioners is the atypical nature of these problems which require an interdisciplinary approach in order to solve them efficiently and accurately.

Author: Elisa Pappalardo
Publisher: Springer Science & Business Media
ISBN: 1461490537
Category : Mathematics
Languages : en
Pages : 57

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Book Description
Optimization Approaches for Solving String Selection Problems provides an overview of optimization methods for a wide class of genomics-related problems in relation to the string selection problems. This class of problems addresses the recognition of similar characteristics or differences within biological sequences. Specifically, this book considers a large class of problems, ranging from the closest string and substring problems, to the farthest string and substring problems, to the far from most string problem. Each problem includes a detailed description, highlighting both biological and mathematical features and presents state-of-the-art approaches. This Brief provides a quick introduction of optimization methods for string selection problems for young scientists and a detailed description of the mathematical and computational methods developed for experts in the field of optimization who want to deepen their understanding of the string selection problems. Researchers, practitioners and graduate students in the field of Computer Science, Operation Research, Mathematics, Computational Biology and Biomedicine will find this book useful. ​

Author: Venkatram Vishwanath
Publisher:
ISBN:
Category :
Languages : en
Pages : 58

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Book Description

Author: Maria José Blesa
Publisher: Springer Science & Business Media
ISBN: 3642160530
Category : Computers
Languages : en
Pages : 231

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Book Description
This book constitutes the refereed proceedings of the 7th International Workshop on Hybrid Metaheuristics, HM 2010, held in Vienna, Austria, in October 2010. The 14 revised full papers presented were carefully reviewed and selected from 29 submissions.

Author: Cesar Rego
Publisher: Springer Science & Business Media
ISBN: 0387236678
Category : Business & Economics
Languages : en
Pages : 472

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Book Description
Tabu Search (TS) and, more recently, Scatter Search (SS) have proved highly effective in solving a wide range of optimization problems, and have had a variety of applications in industry, science, and government. The goal of Metaheuristic Optimization via Memory and Evolution: Tabu Search and Scatter Search is to report original research on algorithms and applications of tabu search, scatter search or both, as well as variations and extensions having "adaptive memory programming" as a primary focus. Individual chapters identify useful new implementations or new ways to integrate and apply the principles of TS and SS, or that prove new theoretical results, or describe the successful application of these methods to real world problems.

Author: El-Ghazali Talbi
Publisher: John Wiley & Sons
ISBN: 0470496908
Category : Computers
Languages : en
Pages : 625

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Book Description
A unified view of metaheuristics This book provides a complete background on metaheuristics and shows readers how to design and implement efficient algorithms to solve complex optimization problems across a diverse range of applications, from networking and bioinformatics to engineering design, routing, and scheduling. It presents the main design questions for all families of metaheuristics and clearly illustrates how to implement the algorithms under a software framework to reuse both the design and code. Throughout the book, the key search components of metaheuristics are considered as a toolbox for: Designing efficient metaheuristics (e.g. local search, tabu search, simulated annealing, evolutionary algorithms, particle swarm optimization, scatter search, ant colonies, bee colonies, artificial immune systems) for optimization problems Designing efficient metaheuristics for multi-objective optimization problems Designing hybrid, parallel, and distributed metaheuristics Implementing metaheuristics on sequential and parallel machines Using many case studies and treating design and implementation independently, this book gives readers the skills necessary to solve large-scale optimization problems quickly and efficiently. It is a valuable reference for practicing engineers and researchers from diverse areas dealing with optimization or machine learning; and graduate students in computer science, operations research, control, engineering, business and management, and applied mathematics.

Author: Roberto Battiti
Publisher: Springer
ISBN: 3030053482
Category : Computers
Languages : en
Pages : 487

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Book Description
This book constitutes the thoroughly refereed post-conference proceedings of the 12th International Conference on Learning and Intelligent Optimization, LION 12, held in Kalamata, Greece, in June 2018. The 28 full papers and 12 short papers presented have been carefully reviewed and selected from 62 submissions. The papers explore the advanced research developments in such interconnected fields as mathematical programming, global optimization, machine learning, and artificial intelligence. Special focus is given to advanced ideas, technologies, methods, and applications in optimization and machine learning.

Author: Volker Sperschneider
Publisher: Springer Science & Business Media
ISBN: 3540785051
Category : Computers
Languages : en
Pages : 302

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Book Description
"There are fundamental principles for problem analysis and algorithm design that are continuously used in bioinformatics. This book concentrates on a clear presentation of these principles, presenting them in a self-contained, mathematically clear and precise manner, and illustrating them with lots of case studies from main fields of bioinformatics. Emphasis is laid on algorithmic "pearls" of bioinformatics, showing that things may get rather simple when taking a proper view into them. The book closes with a thorough bibliography, ranging from classic research results to very recent findings, providing many pointers for future research. Overall, this volume is ideally suited for a senior undergraduate or graduate course on bioinformatics, with a strong focus on its mathematical and computer science background."--BOOK JACKET.

Author: Sahar Hooshmand
Publisher:
ISBN:
Category :
Languages : en
Pages : 73

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Book Description
The work presented in this dissertation deals with establishing efficient methods for solving some algorithmic problems, which have applications to Bioinformatics. After a short introduction in Chapter 1, an algorithm for genome mappability problem is presented in Chapter 2. Genome mappability is a measure for the approximate repeat structure of the genome with respect to substrings of specific length and a tolerance to define the number of mismatches. The similarity between reads is measured by using the Hamming distance function. Genome mappability is computed for each position in the string and has several applications in designing high-throughput short-read sequencing experiments. Chapter 3, presents an algorithm to compute the Average Common Substring of two input sequences in their run-length encoded format. The distance between them based on the Average Common Substring measure can be computed in linearithmic time and linear space proportional to the total length of sequences after run-length encoding. Chapter 4, presents a method that produces a better approximation for Average Common Substring calculations where we are allowed to have mismatches. This method is applicable to the alignmentfree comparison of biological sequences at highly competitive speed. Finally, in Chapter 5, we present two algorithms to efficiently decode the Suffix Array/Inverse Suffix Array of the reveres text, by using the FM-index of the forward text. Additionally, our experimental results are competitive when compared to the standard approach of maintaining the FM-Index for both the forward and the reverse text in approximate string-matching applications.