The Burrows-Wheeler Transform:


Book Description

The Burrows-Wheeler Transform is one of the best lossless compression me- ods available. It is an intriguing — even puzzling — approach to squeezing redundancy out of data, it has an interesting history, and it has applications well beyond its original purpose as a compression method. It is a relatively late addition to the compression canon, and hence our motivation to write this book, looking at the method in detail, bringing together the threads that led to its discovery and development, and speculating on what future ideas might grow out of it. The book is aimed at a wide audience, ranging from those interested in learning a little more than the short descriptions of the BWT given in st- dard texts, through to those whose research is building on what we know about compression and pattern matching. The ?rst few chapters are a careful description suitable for readers with an elementary computer science ba- ground (and these chapters have been used in undergraduate courses), but later chapters collect a wide range of detailed developments, some of which are built on advanced concepts from a range of computer science topics (for example, some of the advanced material has been used in a graduate c- puter science course in string algorithms). Some of the later explanations require some mathematical sophistication, but most should be accessible to those with a broad background in computer science.




Genome-Scale Algorithm Design


Book Description

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 Algorithms


Book Description




Understanding Compression


Book Description

If you want to attract and retain users in the booming mobile services market, you need a quick-loading app that won’t churn through their data plans. The key is to compress multimedia and other data into smaller files, but finding the right method is tricky. This witty book helps you understand how data compression algorithms work—in theory and practice—so you can choose the best solution among all the available compression tools. With tables, diagrams, games, and as little math as possible, authors Colt McAnlis and Aleks Haecky neatly explain the fundamentals. Learn how compressed files are better, cheaper, and faster to distribute and consume, and how they’ll give you a competitive edge. Learn why compression has become crucial as data production continues to skyrocket Know your data, circumstances, and algorithm options when choosing compression tools Explore variable-length codes, statistical compression, arithmetic numerical coding, dictionary encodings, and context modeling Examine tradeoffs between file size and quality when choosing image compressors Learn ways to compress client- and server-generated data objects Meet the inventors and visionaries who created data compression algorithms




A Concise Introduction to Data Compression


Book Description

This clearly written book offers readers a succinct foundation to the most important topics in the field of data compression. Part I presents the basic approaches to data compression and describes a few popular techniques and methods that are commonly used to compress data. The reader will discover essential concepts. Part II concentrates on advanced techniques, such as arithmetic coding, orthogonal transforms, subband transforms and Burrows-Wheeler transform. This book is the perfect reference for advanced undergraduates in computer science and requires a minimum of mathematics. An author-maintained website provides errata and auxiliary material.




Algorithm Theory - SWAT 2004


Book Description

This book constitutes the refereed proceedings of the 9th Scandinavian Workshop on Algorithm Theory, SWAT 2004, held in Humlebaek, Denmark in July 2004. The 40 revised full papers presented together with an invited paper and the abstract of an invited talk were carefully reviewed and selected from 121 submissions. The papers span the entire range of theoretical algorithmics and applications in various fields including graph algorithms, computational geometry, scheduling, approximation algorithms, network algorithms, data storage and manipulation, bioinformatics, combinatorics, sorting, searching, online algorithms, optimization, etc.







Data Compression


Book Description

A comprehensive reference for the many different types and methods of compression, including a detailed and helpful taxonomy, an analysis of the most common methods, and discussions on their use and comparative benefits. The presentation is organized into the main branches of the field: run length encoding, statistical methods, dictionary-based methods, image compression, audio compression, and video compression. Detailed descriptions and explanations of the most well- known and frequently used methods are covered in a self-contained fashion, with an accessible style and technical level for specialists and nonspecialists. In short, the book provides an invaluable reference and guide for all computer scientists, computer engineers, electrical engineers, signal/image processing engineers and other scientists needing a comprehensive compilation for a broad range of compression methods.




String Processing and Information Retrieval


Book Description

This book constitutes the refereed proceedings of the 11th International Conference on String Processing and Information Retrieval, SPIRE 2004, held in Padova, Italy, in October 2004. The 28 revised full papers and 16 revised short papers presented were carefully reviewed and selected from 123 submissions. The papers address current issues in string pattern searching and matching, string discovery, data compression, data mining, text mining, machine learning, information retrieval, digital libraries, and applications in various fields, such as bioinformatics, speech and natural language processing, Web links and communities, and multilingual data.




Pearls of Functional Algorithm Design


Book Description

Richard Bird takes a radical approach to algorithm design, namely, design by calculation. These 30 short chapters each deal with a particular programming problem drawn from sources as diverse as games and puzzles, intriguing combinatorial tasks, and more familiar areas such as data compression and string matching. Each pearl starts with the statement of the problem expressed using the functional programming language Haskell, a powerful yet succinct language for capturing algorithmic ideas clearly and simply. The novel aspect of the book is that each solution is calculated from an initial formulation of the problem in Haskell by appealing to the laws of functional programming. Pearls of Functional Algorithm Design will appeal to the aspiring functional programmer, students and teachers interested in the principles of algorithm design, and anyone seeking to master the techniques of reasoning about programs in an equational style.