Integer Linear Programming In Computational And Systems Biology

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Integer Linear Programming in Computational and Systems Biology

Author : Dan Gusfield
Publisher : Cambridge University Press
ISBN 13 : 1108386253
Total Pages : 431 pages
Book Rating : 4.1/5 (83 download)

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Book Synopsis Integer Linear Programming in Computational and Systems Biology by : Dan Gusfield

Download or read book Integer Linear Programming in Computational and Systems Biology written by Dan Gusfield and published by Cambridge University Press. This book was released on 2019-06-13 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: Integer linear programming (ILP) is a versatile modeling and optimization technique that is increasingly used in non-traditional ways in biology, with the potential to transform biological computation. However, few biologists know about it. This how-to and why-do text introduces ILP through the lens of computational and systems biology. It uses in-depth examples from genomics, phylogenetics, RNA, protein folding, network analysis, cancer, ecology, co-evolution, DNA sequencing, sequence analysis, pedigree and sibling inference, haplotyping, and more, to establish the power of ILP. This book aims to teach the logic of modeling and solving problems with ILP, and to teach the practical 'work flow' involved in using ILP in biology. Written for a wide audience, with no biological or computational prerequisites, this book is appropriate for entry-level and advanced courses aimed at biological and computational students, and as a source for specialists. Numerous exercises and accompanying software (in Python and Perl) demonstrate the concepts.

Linear Programming

Author : Saul I. Gass
Publisher : Courier Corporation
ISBN 13 : 048643284X
Total Pages : 545 pages
Book Rating : 4.4/5 (864 download)

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Book Synopsis Linear Programming by : Saul I. Gass

Download or read book Linear Programming written by Saul I. Gass and published by Courier Corporation. This book was released on 2003-01-01 with total page 545 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive, well-organized volume, suitable for undergraduates, covers theoretical, computational, and applied areas in linear programming. Expanded, updated edition; useful both as a text and as a reference book. 1995 edition.

Linear and Integer Optimization

Author : Gerard Sierksma
Publisher : CRC Press
ISBN 13 : 1498743129
Total Pages : 676 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis Linear and Integer Optimization by : Gerard Sierksma

Download or read book Linear and Integer Optimization written by Gerard Sierksma and published by CRC Press. This book was released on 2015-05-01 with total page 676 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting a strong and clear relationship between theory and practice, Linear and Integer Optimization: Theory and Practice is divided into two main parts. The first covers the theory of linear and integer optimization, including both basic and advanced topics. Dantzig's simplex algorithm, duality, sensitivity analysis, integer optimization models

Mixed Integer Nonlinear Programming

Author : Jon Lee
Publisher : Springer Science & Business Media
ISBN 13 : 1461419271
Total Pages : 692 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Mixed Integer Nonlinear Programming by : Jon Lee

Download or read book Mixed Integer Nonlinear Programming written by Jon Lee and published by Springer Science & Business Media. This book was released on 2011-12-02 with total page 692 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many engineering, operations, and scientific applications include a mixture of discrete and continuous decision variables and nonlinear relationships involving the decision variables that have a pronounced effect on the set of feasible and optimal solutions. Mixed-integer nonlinear programming (MINLP) problems combine the numerical difficulties of handling nonlinear functions with the challenge of optimizing in the context of nonconvex functions and discrete variables. MINLP is one of the most flexible modeling paradigms available for optimization; but because its scope is so broad, in the most general cases it is hopelessly intractable. Nonetheless, an expanding body of researchers and practitioners — including chemical engineers, operations researchers, industrial engineers, mechanical engineers, economists, statisticians, computer scientists, operations managers, and mathematical programmers — are interested in solving large-scale MINLP instances.

Systems Biology

Author : Bernhard Palsson
Publisher : Cambridge University Press
ISBN 13 : 1107038855
Total Pages : 551 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Systems Biology by : Bernhard Palsson

Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Algorithms for Computational Biology

Author : Carlos Martín-Vide
Publisher : Springer
ISBN 13 : 9783030422653
Total Pages : 199 pages
Book Rating : 4.4/5 (226 download)

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Book Synopsis Algorithms for Computational Biology by : Carlos Martín-Vide

Download or read book Algorithms for Computational Biology written by Carlos Martín-Vide and published by Springer. This book was released on 2020-02-20 with total page 199 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the proceedings of the 7th International Conference on Algorithms for Computational Biology, AlCoB 2020, held in Missoula, MT, USA in April 2020. The 15 full papers included in this volume were carefully reviewed and selected from 24 submissions. They were organized in topical sections on genomics, phylogenetics, and RNA-Seq and other biological processes.

Computational Phylogenetics

Author : Tandy Warnow
Publisher : Cambridge University Press
ISBN 13 : 1107184711
Total Pages : 399 pages
Book Rating : 4.1/5 (71 download)

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Book Synopsis Computational Phylogenetics by : Tandy Warnow

Download or read book Computational Phylogenetics written by Tandy Warnow and published by Cambridge University Press. This book was released on 2017-11-02 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.

Applied Integer Programming

Author : Der-San Chen
Publisher : John Wiley & Sons
ISBN 13 : 1118210026
Total Pages : 489 pages
Book Rating : 4.1/5 (182 download)

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Book Synopsis Applied Integer Programming by : Der-San Chen

Download or read book Applied Integer Programming written by Der-San Chen and published by John Wiley & Sons. This book was released on 2011-09-20 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: An accessible treatment of the modeling and solution of integer programming problems, featuring modern applications and software In order to fully comprehend the algorithms associated with integer programming, it is important to understand not only how algorithms work, but also why they work. Applied Integer Programming features a unique emphasis on this point, focusing on problem modeling and solution using commercial software. Taking an application-oriented approach, this book addresses the art and science of mathematical modeling related to the mixed integer programming (MIP) framework and discusses the algorithms and associated practices that enable those models to be solved most efficiently. The book begins with coverage of successful applications, systematic modeling procedures, typical model types, transformation of non-MIP models, combinatorial optimization problem models, and automatic preprocessing to obtain a better formulation. Subsequent chapters present algebraic and geometric basic concepts of linear programming theory and network flows needed for understanding integer programming. Finally, the book concludes with classical and modern solution approaches as well as the key components for building an integrated software system capable of solving large-scale integer programming and combinatorial optimization problems. Throughout the book, the authors demonstrate essential concepts through numerous examples and figures. Each new concept or algorithm is accompanied by a numerical example, and, where applicable, graphics are used to draw together diverse problems or approaches into a unified whole. In addition, features of solution approaches found in today's commercial software are identified throughout the book. Thoroughly classroom-tested, Applied Integer Programming is an excellent book for integer programming courses at the upper-undergraduate and graduate levels. It also serves as a well-organized reference for professionals, software developers, and analysts who work in the fields of applied mathematics, computer science, operations research, management science, and engineering and use integer-programming techniques to model and solve real-world optimization problems.

Genome-Scale Algorithm Design

Author : Veli Mäkinen
Publisher : Cambridge University Press
ISBN 13 : 1009341219
Total Pages : 470 pages
Book Rating : 4.0/5 (93 download)

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Book Synopsis Genome-Scale Algorithm Design by : Veli Mäkinen

Download or read book Genome-Scale Algorithm Design written by Veli Mäkinen and published by Cambridge University Press. This book was released on 2023-10-12 with total page 470 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guided by standard bioscience workflows in high-throughput sequencing analysis, this book for graduate students, researchers, and professionals in bioinformatics and computer science offers a unified presentation of genome-scale algorithms. This new edition covers the use of minimizers and other advanced data structures in pangenomics approaches.

Bioinformatics and Phylogenetics

Author : Tandy Warnow
Publisher : Springer
ISBN 13 : 3030108376
Total Pages : 410 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Bioinformatics and Phylogenetics by : Tandy Warnow

Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.

Algorithms in Structural Molecular Biology

Author : Bruce R. Donald
Publisher : MIT Press
ISBN 13 : 0262548798
Total Pages : 497 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Algorithms in Structural Molecular Biology by : Bruce R. Donald

Download or read book Algorithms in Structural Molecular Biology written by Bruce R. Donald and published by MIT Press. This book was released on 2023-08-15 with total page 497 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

Control Theory and Systems Biology

Author : Pablo A. Iglesias
Publisher : MIT Press
ISBN 13 : 0262013347
Total Pages : 359 pages
Book Rating : 4.2/5 (62 download)

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Book Synopsis Control Theory and Systems Biology by : Pablo A. Iglesias

Download or read book Control Theory and Systems Biology written by Pablo A. Iglesias and published by MIT Press. This book was released on 2010 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: A survey of how engineering techniques from control and systems theory can be used to help biologists understand the behavior of cellular systems.

Algebraic Statistics for Computational Biology

Author : L. Pachter
Publisher : Cambridge University Press
ISBN 13 : 9780521857000
Total Pages : 440 pages
Book Rating : 4.8/5 (57 download)

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Book Synopsis Algebraic Statistics for Computational Biology by : L. Pachter

Download or read book Algebraic Statistics for Computational Biology written by L. Pachter and published by Cambridge University Press. This book was released on 2005-08-22 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, first published in 2005, offers an introduction to the application of algebraic statistics to computational biology.

Feasibility and Infeasibility in Optimization:

Author : John W. Chinneck
Publisher : Springer Science & Business Media
ISBN 13 : 0387749322
Total Pages : 274 pages
Book Rating : 4.3/5 (877 download)

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Book Synopsis Feasibility and Infeasibility in Optimization: by : John W. Chinneck

Download or read book Feasibility and Infeasibility in Optimization: written by John W. Chinneck and published by Springer Science & Business Media. This book was released on 2007-10-25 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by a world leader in the field and aimed at researchers in applied and engineering sciences, this brilliant text has as its main goal imparting an understanding of the methods so that practitioners can make immediate use of existing algorithms and software, and so that researchers can extend the state of the art and find new applications. It includes algorithms on seeking feasibility and analyzing infeasibility, as well as describing new and surprising applications.

Exact and Fast Algorithms for Mixed-integer Nonlinear Programming

Author : Ambros Gleixner
Publisher :
ISBN 13 : 9783832541903
Total Pages : 0 pages
Book Rating : 4.5/5 (419 download)

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Book Synopsis Exact and Fast Algorithms for Mixed-integer Nonlinear Programming by : Ambros Gleixner

Download or read book Exact and Fast Algorithms for Mixed-integer Nonlinear Programming written by Ambros Gleixner and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The discipline of mixed-integer nonlinear programming (MINLP) deals with finite-dimensional optimization problems featuring both discrete choices and nonlinear functions. By this combination, it facilitates more accurate models of real-world systems than possible with purely continuous or purely linear models alone. This book presents new methods that improve the numerical reliability and the computational performance of global MINLP solvers. The author addresses numerical accuracy directly at the linear programming level by means of LP iterative refinement: a new algorithm to solve linear programs to arbitrarily high levels of precision. The computational performance of LP-based MINLP solvers is enhanced by efficient methods to execute and approximate optimization-based bound tightening and by new branching rules that exploit the presence of nonlinear integer variables, i.e., variables both contained in nonlinear terms and required to be integral. The new algorithms help to solve problems which could not be solved before, either due to their numerical complexity or because of limited computing resources.

Bayesian Networks in R

Author : Radhakrishnan Nagarajan
Publisher : Springer Science & Business Media
ISBN 13 : 1461464463
Total Pages : 157 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Bayesian Networks in R by : Radhakrishnan Nagarajan

Download or read book Bayesian Networks in R written by Radhakrishnan Nagarajan and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 157 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.

Computational Techniques of the Simplex Method

Author : István Maros
Publisher : Springer Science & Business Media
ISBN 13 : 1461502578
Total Pages : 335 pages
Book Rating : 4.4/5 (615 download)

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Book Synopsis Computational Techniques of the Simplex Method by : István Maros

Download or read book Computational Techniques of the Simplex Method written by István Maros and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Techniques of the Simplex Method is a systematic treatment focused on the computational issues of the simplex method. It provides a comprehensive coverage of the most important and successful algorithmic and implementation techniques of the simplex method. It is a unique source of essential, never discussed details of algorithmic elements and their implementation. On the basis of the book the reader will be able to create a highly advanced implementation of the simplex method which, in turn, can be used directly or as a building block in other solution algorithms.