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Algebraic And Combinatorial Computational Biology

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Algebraic and Combinatorial Computational Biology

Algebraic and Combinatorial Computational Biology Book
Author : Raina Robeva,Matthew Macauley
Publisher : Academic Press
Release : 2018-10-08
ISBN : 0128140690
Language : En, Es, Fr & De

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Book Description :

Algebraic and Combinatorial Computational Biology introduces students and researchers to a panorama of powerful and current methods for mathematical problem-solving in modern computational biology. Presented in a modular format, each topic introduces the biological foundations of the field, covers specialized mathematical theory, and concludes by highlighting connections with ongoing research, particularly open questions. The work addresses problems from gene regulation, neuroscience, phylogenetics, molecular networks, assembly and folding of biomolecular structures, and the use of clustering methods in biology. A number of these chapters are surveys of new topics that have not been previously compiled into one unified source. These topics were selected because they highlight the use of technique from algebra and combinatorics that are becoming mainstream in the life sciences. Integrates a comprehensive selection of tools from computational biology into educational or research programs Emphasizes practical problem-solving through multiple exercises, projects and spinoff computational simulations Contains scalable material for use in undergraduate and graduate-level classes and research projects Introduces the reader to freely-available professional software Supported by illustrative datasets and adaptable computer code

Algebraic Statistics for Computational Biology

Algebraic Statistics for Computational Biology Book
Author : L. Pachter,B. Sturmfels
Publisher : Cambridge University Press
Release : 2005-08-22
ISBN : 9780521857000
Language : En, Es, Fr & De

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Book Description :

This book, first published in 2005, offers an introduction to the application of algebraic statistics to computational biology.

Algebraic Combinatorics for Computational Biology

Algebraic Combinatorics for Computational Biology Book
Author : Nicholas Karl Eriksson
Publisher : Unknown
Release : 2006
ISBN : 9780542824098
Language : En, Es, Fr & De

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Book Description :

Algebraic statistics is the study of the algebraic varieties that correspond to discrete statistical models. Such statistical models are used throughout computational biology, for example to describe the evolution of DNA sequences. This perspective on statistics allows us to bring mathematical techniques to bear and also provides a source of new problems in mathematics.

Patterns in Permutations and Words

Patterns in Permutations and Words Book
Author : Sergey Kitaev
Publisher : Springer Science & Business Media
Release : 2011-08-30
ISBN : 3642173330
Language : En, Es, Fr & De

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Book Description :

There has been considerable interest recently in the subject of patterns in permutations and words, a new branch of combinatorics with its roots in the works of Rotem, Rogers, and Knuth in the 1970s. Consideration of the patterns in question has been extremely interesting from the combinatorial point of view, and it has proved to be a useful language in a variety of seemingly unrelated problems, including the theory of Kazhdan—Lusztig polynomials, singularities of Schubert varieties, interval orders, Chebyshev polynomials, models in statistical mechanics, and various sorting algorithms, including sorting stacks and sortable permutations. The author collects the main results in the field in this up-to-date, comprehensive reference volume. He highlights significant achievements in the area, and points to research directions and open problems. The book will be of interest to researchers and graduate students in theoretical computer science and mathematics, in particular those working in algebraic combinatorics and combinatorics on words. It will also be of interest to specialists in other branches of mathematics, theoretical physics, and computational biology. The author collects the main results in the field in this up-to-date, comprehensive reference volume. He highlights significant achievements in the area, and points to research directions and open problems. The book will be of interest to researchers and graduate students in theoretical computer science and mathematics, in particular those working in algebraic combinatorics and combinatorics on words. It will also be of interest to specialists in other branches of mathematics, theoretical physics, and computational biology.

Combinatorial Computational Biology of RNA

Combinatorial Computational Biology of RNA Book
Author : Christian Reidys
Publisher : Springer Science & Business Media
Release : 2010-10-29
ISBN : 9780387767314
Language : En, Es, Fr & De

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Book Description :

In this monograph, new combinatorial and computational approaches in the study of RNA structures are presented which enhance both mathematics and computational biology. It begins with an introductory chapter, which motivates and sets the background of this research. In the following chapter, all the concepts are systematically developed. The reader will find * integration of more than forty research papers covering topics like, RSK-algorithm, reflection principle, singularity analysis and random graph theory * systematic presentation of the theory of pseudo-knotted RNA structures including their generating function, uniform generation as well as central and discrete limit theorems * computational biology of pseudo-knotted RNA structures, including dynamic programming paradigms and a new folding algorithm * analysis of neutral networks of pseudo knotted RNA structures and their random graph theory, including neutral paths, giant components and connectivity All algorithms presented are freely available through springer.com and implemented in C. A proofs section at the end contains the necessary technicalities. This book will serve graduate students and researchers in the fields of discrete mathematics, mathematical and computational biology. It is suitable as a textbook for a graduate course in mathematical and computational biology.

Computing and Combinatorics

Computing and Combinatorics Book
Author : Joachim Gudmundsson,Julián Mestre,Taso Viglas
Publisher : Springer
Release : 2012-08-14
ISBN : 3642322417
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 18th Annual International Conference on Computing and Combinatorics, held in Sydney, Australia, in August 2012. The 50 revised full papers presented were carefully reviewed and selected from 121 submissions. Topics covered are algorithms and data structures; algorithmic game theory and online algorithms; automata, languages, logic, and computability; combinatorics related to algorithms and complexity; complexity theory; computational learning theory and knowledge discovery; cryptography, reliability and security, and database theory; computational biology and bioinformatics; computational algebra, geometry, and number theory; graph drawing and information visualization; graph theory, communication networks, and optimization.

Language and Automata Theory and Applications

Language and Automata Theory and Applications Book
Author : Adrian-Horia Dediu,Carlos Martín-Vide,Bianca Truthe
Publisher : Springer
Release : 2013-02-20
ISBN : 9783642370632
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 7th International Conference on Language and Automata Theory and Applications, LATA 2013, held in Bilbao, Spain in April 2013. The 45 revised full papers presented together with 5 invited talks were carefully reviewed and selected from 97 initial submissions. The volume features contributions from both classical theory fields and application areas (bioinformatics, systems biology, language technology, artificial intelligence, etc.). Among the topics covered are algebraic language theory; algorithms for semi-structured data mining; algorithms on automata and words; automata and logic; automata for system analysis and program verification; automata, concurrency and Petri nets; automatic structures; cellular automata; combinatorics on words; computability; computational complexity; computational linguistics; data and image compression; decidability questions on words and languages; descriptional complexity; DNA and other models of bio-inspired computing; document engineering; foundations of finite state technology; foundations of XML; fuzzy and rough languages; grammars (Chomsky hierarchy, contextual, multidimensional, unification, categorial, etc.); grammars and automata architectures; grammatical inference and algorithmic learning; graphs and graph transformation; language varieties and semigroups; language-based cryptography; language-theoretic foundations of artificial intelligence and artificial life; parallel and regulated rewriting; parsing; pattern recognition; patterns and codes; power series; quantum, chemical and optical computing; semantics; string and combinatorial issues in computational biology and bioinformatics; string processing algorithms; symbolic dynamics; symbolic neural networks; term rewriting; transducers; trees, tree languages and tree automata; weighted automata.

Combinatorial Algorithms

Combinatorial Algorithms Book
Author : Costas Iliopoulos,Hon Wai Leong,Wing-Kin Sung
Publisher : Springer
Release : 2018-08-03
ISBN : 3319946676
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed post-conference proceedings of the 29th International Workshop on Combinatorial Algorithms, IWOCA 2018, held in Singapore, Singapore, in July 2018. The 31 regular papers presented in this volume were carefully reviewed and selected from 69 submissions. They cover diverse areas of combinatorical algorithms, complexity theory, graph theory and combinatorics, combinatorial optimization, cryptography and information security, algorithms on strings and graphs, graph drawing and labelling, computational algebra and geometry, computational biology, probabilistic and randomised algorithms, algorithms for big data analytics, and new paradigms of computation.

Combinatorial Pattern Matching

Combinatorial Pattern Matching Book
Author : Moshe Lewenstein,Gabriel Valiente
Publisher : Springer
Release : 2006-07-01
ISBN : 3540354611
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006, held in Barcelona, Spain, July 2006. The book presents 33 revised full papers together with 3 invited talks, organized in topical sections on data structures, indexing data structures, probabilistic and algebraic techniques, applications in molecular biology, string matching, data compression, and dynamic programming.

Combinatorial Algorithms

Combinatorial Algorithms Book
Author : Charles J. Colbourn,Roberto Grossi,Nadia Pisanti
Publisher : Springer
Release : 2019-07-15
ISBN : 3030250059
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed post-conference proceedings of the 30th International Workshop on Combinatorial Algorithms, IWOCA 2019, held in Pisa, Italy, in July 2019. The 36 regular papers presented in this volume were carefully reviewed and selected from 73 submissions. They cover diverse areas of combinatorical algorithms, complexity theory, graph theory and combinatorics, combinatorial optimization, cryptography and information security, algorithms on strings and graphs, graph drawing and labelling, computational algebra and geometry, computational biology, probabilistic and randomized algorithms, algorithms for big data analytics, and new paradigms of computation.

Computing and Combinatorics

Computing and Combinatorics Book
Author : Dachuan Xu,Donglei Du,Dingzhu Du
Publisher : Springer
Release : 2015-06-23
ISBN : 3319213989
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 21st International Conference on Computing and Combinatorics, COCOON 2015, held in Beijing, China, in August 2015. The 49 revised full papers and 11 shorter papers presented were carefully reviewed and selected from various submissions. The papers cover various topics including algorithms and data structures; algorithmic game theory; approximation algorithms and online algorithms; automata, languages, logic and computability; complexity theory; computational learning theory; cryptography, reliability and security; database theory, computational biology and bioinformatics; computational algebra, geometry, number theory, graph drawing and information visualization; graph theory, communication networks, optimization and parallel and distributed computing.

Bulletin of the Institute of Combinatorics and Its Applications

Bulletin of the Institute of Combinatorics and Its Applications Book
Author : Anonim
Publisher : Unknown
Release : 2007
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Bulletin of the Institute of Combinatorics and Its Applications book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

First Joint International Meeting IMU SMM Program

First Joint International Meeting IMU SMM Program Book
Author : Fausto Andrés Trujillo García,Soluciones Empresariales Pantiger y Asociados SA de CV,Sociedad Matemática Mexicana
Publisher : Fausto Trujillo
Release : 2015-09-04
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

First Joint International Meeting of the Israel Mathematical Union and the Mexican Mathematical Society Program

Dissertation Abstracts International

Dissertation Abstracts International Book
Author : Anonim
Publisher : Unknown
Release : 2007
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Download Dissertation Abstracts International book written by , available in PDF, EPUB, and Kindle, or read full book online anywhere and anytime. Compatible with any devices.

Algebraic Statistics

Algebraic Statistics Book
Author : Karl-Heinz Zimmermann
Publisher : Unknown
Release : 2015
ISBN : 0987650XXX
Language : En, Es, Fr & De

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Book Description :

Algebraic statistics brings together ideas from algebraic geometry, commutative algebra, and combinatorics to address problems in statistics and its applications. Computer algebra provides powerful tools for the study of algorithms and software. However, these tools are rarely prepared to address statistical challenges and therefore new algebraic results need often be developed. This way of interplay between algebra and statistics fertilizes both disciplines. Algebraic statistics is a relatively new branch of mathematics that developed and changed rapidly over the last ten years. The seminal work in this field was the paper of Diaconis and Sturmfels (1998) introducing the notion of Markov bases for toric statistical models and showing the connection to commutative algebra. Later on, the connection between algebra and statistics spread to a number of different areas including parametric inference, phylogenetic invariants, and algebraic tools for maximum likelihood estimation. These connection were highlighted in the celebrated book Algebraic Statistics for Computational Biology of Pachter and Sturmfels (2005) and subsequent publications. In this report, statistical models for discrete data are viewed as solutions of systems of polynomial equations. This allows to treat statistical models for sequence alignment, hidden Markov models, and phylogenetic tree models. These models are connected in the sense that if they are interpreted in the tropical algebra, the famous dynamic programming algorithms (Needleman-Wunsch, Viterbi, and Felsenstein) occur in a natural manner. More generally, if the models are interpreted in a higher dimensional analogue of the tropical algebra, the polytope algebra, parametric versions of these dynamic programming algorithms can be established. Markov bases allow to sample data in a given fibre using Markov chain Monte Carlo algorithms. In this way, Markov bases provide a means to increase the sample size and make statistical tests in inferential statistics more reliable. We will calculate Markov bases using Groebner bases in commutative polynomial rings. The manuscript grew out of lectures on algebraic statistics held for Master students of Computer Science at the Hamburg University of Technology. It appears that the first lecture held in the summer term 2008 was the first course of this kind in Germany. The current manuscript is the basis of a four-hour introductory course. The use of computer algebra systems is at the heart of the course. Maple is employed for symbolic computations, Singular for algebraic computations, and R for statistical computations. The second edition at hand is just a streamlined version of the first one.$cen$dAbstract

LATIN 2012 Theoretical Informatics

LATIN 2012  Theoretical Informatics Book
Author : David Fernández-Baca
Publisher : Springer
Release : 2012-04-25
ISBN : 9783642293450
Language : En, Es, Fr & De

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Book Description :

This book constitutes the proceedings of the 10th Latin American Symposium on Theoretical Informatics, LATIN 2012, held in Arequipa, Peru, in April 2012. The 55 papers presented in this volume were carefully reviewed and selected from 153 submissions. The papers address a variety of topics in theoretical computer science with a certain focus on algorithms, automata theory and formal languages, coding theory and data compression, algorithmic graph theory and combinatorics, complexity theory, computational algebra, computational biology, computational geometry, computational number theory, cryptography, theoretical aspects of databases and information retrieval, data structures, networks, logic in computer science, machine learning, mathematical programming, parallel and distributed computing, pattern matching, quantum computing and random structures.

Linear Algebraic Primitives for Parallel Computing on Large Graphs

Linear Algebraic Primitives for Parallel Computing on Large Graphs Book
Author : Aydin Buluç
Publisher : Unknown
Release : 2010
ISBN : 9781109726589
Language : En, Es, Fr & De

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Book Description :

This dissertation presents a scalable high-performance software library to be used for graph analysis and data mining. Large combinatorial graphs appear in many applications of high-performance computing, including computational biology, informatics, analytics, web search, dynamical systems, and sparse matrix methods.

Computing and Combinatorics

Computing and Combinatorics Book
Author : Thang N. Dinh,My T. Thai
Publisher : Springer
Release : 2016-07-20
ISBN : 9783319426334
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 22nd International Conference on Computing and Combinatorics, COCOON 2016, held in Ho Chi Minh City, Vietnam, in August 2016. The 50 revised full papers papers presented in this book were carefully reviewed and selected from various submissions. The papers cover various topics including: Theory and Algorithms; Parameterized Complexity and Algorithms; Database and Data Structures; Computational Complexity; Approximation Algorithms; Cryptography; Network and Algorithms; Graph Theory and Algorithms; Computational Geometry; Scheduling Algorithms and Circuit Complexity; Computational Geometry and Computational Biology; and Logic, Algebra and Automata.

Discrete and Topological Models in Molecular Biology

Discrete and Topological Models in Molecular Biology Book
Author : Nataša Jonoska,Masahico Saito
Publisher : Springer Science & Business Media
Release : 2013-12-23
ISBN : 3642401937
Language : En, Es, Fr & De

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Book Description :

Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.

Language and Automata Theory and Applications

Language and Automata Theory and Applications Book
Author : Adrian-Horia Dediu,Jan Janoušek,Carlos Martín-Vide,Bianca Truthe
Publisher : Springer
Release : 2016-04-03
ISBN : 9783319299990
Language : En, Es, Fr & De

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Book Description :

This book constitutes the refereed proceedings of the 10th International Conference on Language and Automata Theory and Applications, LATA 2016, held in Prague, Czech Republic, in March 2016. The 42 revised full papers presented together with 5 invited talks were carefully reviewed and selected from 119 submissions. The papers cover the following topics: algebraic language theory; algorithms for semi-structured data mining, algorithms on automata and words; automata and logic; automata for system analysis and program verification; automata networks, concurrency and Petri nets; automatic structures; cellular automata, codes, combinatorics on words; computational complexity; data and image compression; descriptional complexity; digital libraries and document engineering; foundations of finite state technology; foundations of XML; fuzzy and rough languages; grammatical inference and algorithmic learning; graphs and graph transformation; language varieties and semigroups; parallel and regulated rewriting; parsing; patterns; string and combinatorial issues in computational biology and bioinformatics; string processing algorithms; symbolic dynamics; term rewriting; transducers; trees, tree languages and tree automata; weighted automata.