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 …
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 …
time within a space bounded by the size of the most popular dictionary compressors. To …
Random access to grammar-compressed strings and trees
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 …
grammar that generates the string, is a simple and powerful paradigm that captures …
Balancing straight-line programs
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 …
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 …
pattern $ P [1.. m] $ on a large repetitive text collection $ T [1.. n] $, which is represented as a …
Self-indexed grammar-based compression
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 …
extracting arbitrary portions and also offers indexed searching on the collection. Current self …
Optimal dynamic strings
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 …
strings under the following operations:• make_string–add a string of constant length,• concat …
Improved grammar-based compressed indexes
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 …
searches in time that depends only logarithmically on the size of the grammar. Given a text T …
Grammar-compressed indexes with logarithmic search time
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 …
(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 …
substructures and representing them through grammar rules. We show that for a large …