Indexing highly repetitive string collections, part II: Compressed indexes

G Navarro - ACM Computing Surveys (CSUR), 2021 - dl.acm.org
Two decades ago, a breakthrough in indexing string collections made it possible to
represent them within their compressed space while at the same time offering indexed …

Optimal-time dictionary-compressed indexes

AR Christiansen, MB Ettienne, T Kociumaka… - ACM Transactions on …, 2020 - dl.acm.org
We describe the first self-indexes able to count and locate pattern occurrences in optimal
time within a space bounded by the size of the most popular dictionary compressors. To …

Random access to grammar-compressed strings and trees

P Bille, GM Landau, R Raman, K Sadakane… - SIAM Journal on …, 2015 - SIAM
Grammar-based compression, where one replaces a long string by a small context-free
grammar that generates the string, is a simple and powerful paradigm that captures …

Balancing straight-line programs

M Ganardi, A Jeż, M Lohrey - Journal of the ACM (JACM), 2021 - dl.acm.org
We show that a context-free grammar of size that produces a single string of length (such a
grammar is also called a string straight-line program) can be transformed in linear time into a …

Computing MEMs and Relatives on Repetitive Text Collections

G Navarro - arXiv preprint arXiv:2210.09914, 2022 - arxiv.org
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given
pattern $ P [1.. m] $ on a large repetitive text collection $ T [1.. n] $, which is represented as a …

Self-indexed grammar-based compression

F Claude, G Navarro - Fundamenta Informaticae, 2011 - content.iospress.com
Self-indexes aim at representing text collections in a compressed format that allows
extracting arbitrary portions and also offers indexed searching on the collection. Current self …

Optimal dynamic strings

P Gawrychowski, A Karczmarz, T Kociumaka… - Proceedings of the …, 2018 - SIAM
In this paper, we study the fundamental problem of maintaining a dynamic collection of
strings under the following operations:• make_string–add a string of constant length,• concat …

Improved grammar-based compressed indexes

F Claude, G Navarro - International Symposium on String Processing and …, 2012 - Springer
We introduce the first grammar-compressed representation of a sequence that supports
searches in time that depends only logarithmically on the size of the grammar. Given a text T …

Grammar-compressed indexes with logarithmic search time

F Claude, G Navarro, A Pacheco - Journal of Computer and System …, 2021 - Elsevier
Abstract Let a text T [1.. n] be the only string generated by a context-free grammar with g
(terminal and nonterminal) symbols, and of size G (measured as the sum of the lengths of …

Grammar-based graph compression

S Maneth, F Peternek - Information Systems, 2018 - Elsevier
We present a new graph compressor that works by recursively detecting repeated
substructures and representing them through grammar rules. We show that for a large …