Compressed Data Structures For Strings

Data compression is mandatory to manage massive datasets, indexing is fundamental to query them. However, their goals appear as counterposed: the former aims at minimizing data redundancies, whereas the latter augments the dataset with auxiliary information to speed up the query resolution. In this monograph we introduce solutions that overcome this dichotomy. We start by presenting the use of optimization techniques to improve the compression of classical data compression algorithms, then we move to the design of compressed data structures providing fast random access or efficient pattern matching queries on the compressed dataset. These theoretical studies are supported by experimental evidences of their impact in practical scenarios.

This books reviews recent theoretical and practical advances on suffix sorting and introduces algorithmic solutions to problems of wide interest for the construction of fundamental data structures that operate efficiently on strings namely, constructing the suffix array, the longest common prefix (LCP) array, the document array and the Lyndon array. These data structures are the cornerstone of many algorithmic solutions in Bioiformatics, Information Retrieval and Data Compression. This book introduces the relevant problem areas, their importance, the notation and related algorithms and then presents the algorithmic solutions for indexing data structure constructions. This book is intended for graduate students, researchers and practitioners from Computer Science and Bioinformatics with a strong interest in algorithmic aspects.

This practical, applications-oriented book describes essential tools for efficiently handling massive amounts of data.

This volume constitutes the refereed proceedings of the 26th International Symposium on String Processing and Information Retrieval, SPIRE 2019, held in Segovia, Spain, in October 2019. The 28 full papers and 8 short papers presented in this volume were carefully reviewed and selected from 59 submissions. They cover topics such as: data compression; information retrieval; string algorithms; algorithms; computational biology; indexing and compression; and compressed data structures.

Compact data structures help represent data in reduced space while allowing it to be queried, navigated, and operated in compressed form. They are essential tools for efficiently handling massive amounts of data by exploiting the memory hierarchy. They also reduce the resources needed in distributed deployments and make better use of the limited memory in low-end devices. The field has developed rapidly, reaching a level of maturity that allows practitioners and researchers in application areas to benefit from the use of compact data structures. This first comprehensive book on the topic focuses on the structures that are most relevant for practical use. Readers will learn how the structures work, how to choose the right ones for their application scenario, and how to implement them. Researchers and students in the area will find in the book a definitive guide to the state of the art in compact data structures.

This book constitutes the refereed proceedings of the 14th International Symposium on String Processing and Information Retrieval, SPIRE 2007. Coverage in the 27 revised full papers includes dictionary algorithms, text searching, pattern matching, text compression, text mining, natural language processing, sequence driven protein structure prediction, XML, SGML, information retrieval from semi-structured data, text mining and generation of structured data from text.

This book constitutes the refereed proceedings of the 19th International Symposium on String Processing and Information Retrieval, SPIRE 2012, held in Cartagena de Indias, Colombia, in October 2012. The 26 full papers, 13 short papers, and 3 keynote speeches were carefully reviewed and selected from 81 submissions. The following topics are covered: fundamentals algorithms in string processing and information retrieval; SP and IR techniques as applied to areas such as computational biology, DNA sequencing, and Web mining.

This book constitutes the refereed proceedings of the 23rd Annual European Symposium on Algorithms, ESA 2015, held in Patras, Greece, in September 2015, as part of ALGO 2015. The 86 revised full papers presented together with two invited lectures were carefully reviewed and selected from 320 initial submissions: 71 out of 261 in Track A, Design and Analysis, and 15 out of 59 in Track B, Engineering and Applications. The papers present real-world applications, engineering, and experimental analysis of algorithms.