Related papers: A Fast and Small Subsampled R-index
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
We consider the problem of creating document representations in which inter-document similarity measurements correspond to semantic similarity. We first present a novel subspace-based framework for formalizing this task. Using this…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
We consider the problem of decompressing the Lempel--Ziv 77 representation of a string $S$ of length $n$ using a working space as close as possible to the size $z$ of the input. The folklore solution for the problem runs in $O(n)$ time but…
Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…
For multiple index models, it has recently been shown that the sliced inverse regression (SIR) is consistent for estimating the sufficient dimension reduction (SDR) space if and only if $\rho=\lim\frac{p}{n}=0$, where $p$ is the dimension…
Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query RMQ$(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n +…
An optimal index solving top-k document retrieval [Navarro and Nekrich, SODA12] takes O(m + k) time for a pattern of length m, but its space is at least 80n bytes for a collection of n symbols. We reduce it to 1.5n to 3n bytes, with…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
Finding desired information from large data set is a difficult problem. Information retrieval is concerned with the structure, analysis, organization, storage, searching, and retrieval of information. Index is the main constituent of an IR…
Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…
The Lempel-Ziv parsing of a string (LZ77 for short) is one of the most important and widely-used algorithmic tools in data compression and string processing. We show that the Lempel-Ziv parsing of a string of length $n$ on an alphabet of…
Although several grammar-based self-indexes have been proposed thus far, their applicability is limited to offline settings where whole input texts are prepared, thus requiring to rebuild index structures for given additional inputs, which…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
The sheer increase in volume of RDF data demands efficient solutions for the triple indexing problem, that is devising a compressed data structure to compactly represent RDF triples by guaranteeing, at the same time, fast pattern matching…
We present a novel compressed dynamic self-index for highly repetitive text collections. Signature encoding is a compressed dynamic self-index for highly repetitive texts and has a large disadvantage that the pattern search for short…