Spaces, trees, and colors: The algorithmic landscape of document retrieval on sequences

G Navarro - ACM Computing Surveys (CSUR), 2014 - dl.acm.org
Document retrieval is one of the best-established information retrieval activities since
the'60s, pervading all search engines. Its aim is to obtain, from a collection of text …

Compressing IP forwarding tables: Towards entropy bounds and beyond

G Rétvári, J Tapolcai, A Kőrösi, A Majdán… - Proceedings of the …, 2013 - dl.acm.org
Lately, there has been an upsurge of interest in compressed data structures, aiming to pack
ever larger quantities of information into constrained memory without sacrificing the …

Optimized succinct data structures for massive data

S Gog, M Petri - Software: Practice and Experience, 2014 - Wiley Online Library
Succinct data structures provide the same functionality as their corresponding traditional
data structure in compact space. We improve on functions rank and select, which are the …

Lightweight data indexing and compression in external memory

P Ferragina, T Gagie, G Manzini - Algorithmica, 2012 - Springer
In this paper we describe algorithms for computing the Burrows-Wheeler Transform (bwt)
and for building (compressed) indexes in external memory. The innovative feature of our …

Prospects and limitations of full-text index structures in genome analysis

M Vyverman, B De Baets, V Fack… - Nucleic acids …, 2012 - academic.oup.com
The combination of incessant advances in sequencing technology producing large amounts
of data and innovative bioinformatics approaches, designed to cope with this data flood, has …

Systems, methods and computer-accessible mediums for utilizing pattern matching in stringomes

B Mishra, P Ferragina - US Patent 10,346,551, 2019 - Google Patents
Navarro, Gonzalo.“Wavelet trees for all,” In Proc. of the Sympo sium on Combinatorial
Pattern Matching (CPM), vol. 7354 of Lecture Notes in Computer Science, pp. 2-26 …

Wavelet trees: From theory to practice

R Grossi, JS Vitter, B Xu - 2011 first international conference on …, 2011 - ieeexplore.ieee.org
The wavelet tree data structure is a space-efficient technique for rank and select queries that
generalizes from binary characters to an arbitrary multicharacter alphabet. It has become a …

Wavelet trees: A survey

C Makris - Computer Science and Information Systems, 2012 - doiserbia.nb.rs
The topic of this paper is the exploration of the various characteristics of the wavelet tree
data structure, a data structure that was initially proposed for text compression applications …

Top-k Document Retrieval in External Memory

R Shah, C Sheng, SV Thankachan, JS Vitter - European Symposium on …, 2013 - Springer
Let D be a given set of (string) documents of total length n. The top-k document retrieval
problem is to index D such that when a pattern P of length p, and a parameter k come as a …

Large-scale pattern search using reduced-space on-disk suffix arrays

S Gog, A Moffat, JS Culpepper… - IEEE transactions on …, 2013 - ieeexplore.ieee.org
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can
also be used for external-memory pattern search, via two-level structures that use an internal …