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 …

Compressed full-text indexes

G Navarro, V Mäkinen - ACM Computing Surveys (CSUR), 2007 - dl.acm.org
Full-text indexes provide fast substring search over large text collections. A serious problem
of these indexes has traditionally been their space consumption. A recent trend is to develop …

Fully functional suffix trees and optimal text searching in BWT-runs bounded space

T Gagie, G Navarro, N Prezza - Journal of the ACM (JACM), 2020 - dl.acm.org
Indexing highly repetitive texts—such as genomic databases, software repositories and
versioned text collections—has become an important problem since the turn of the …

Opportunistic data structures with applications

P Ferragina, G Manzini - Proceedings 41st annual symposium …, 2000 - ieeexplore.ieee.org
We address the issue of compressing and indexing data. We devise a data structure whose
space occupancy is a function of the entropy of the underlying data set. We call the data …

Indexing compressed text

P Ferragina, G Manzini - Journal of the ACM (JACM), 2005 - dl.acm.org
We design two compressed data structures for the full-text indexing problem that support
efficient substring searches using roughly the space required for storing the text in …

On prediction using variable order Markov models

R Begleiter, R El-Yaniv, G Yona - Journal of Artificial Intelligence Research, 2004 - jair.org
This paper is concerned with algorithms for prediction of discrete sequences over a finite
alphabet, using variable order Markov models. The class of such algorithms is large and in …

Fully functional static and dynamic succinct trees

G Navarro, K Sadakane - ACM Transactions on Algorithms (TALG), 2014 - dl.acm.org
We propose new succinct representations of ordinal trees and match various space/time
lower bounds. It is known that any n-node static tree can be represented in 2 n+ o (n) bits so …

[HTML][HTML] Wavelet trees for all

G Navarro - Journal of Discrete Algorithms, 2014 - Elsevier
The wavelet tree is a versatile data structure that serves a number of purposes, from string
processing to computational geometry. It can be regarded as a device that represents a …

Compressed representations of sequences and full-text indexes

P Ferragina, G Manzini, V Mäkinen… - ACM Transactions on …, 2007 - dl.acm.org
Given a sequence S= s 1 s 2… sn of integers smaller than r= O (polylog (n)), we show how S
can be represented using nH 0 (S)+ o (n) bits, so that we can know any sq, as well as …

Space-efficient preprocessing schemes for range minimum queries on static arrays

J Fischer, V Heun - SIAM Journal on Computing, 2011 - SIAM
Given a static array of n totally ordered objects, the range minimum query problem is to build
a data structure that allows us to answer efficiently subsequent on-line queries of the form …