Related papers: Self-Index Based on LZ77
Domains like bioinformatics, version control systems, collaborative editing systems (wiki), and others, are producing huge data collections that are very repetitive. That is, there are few differences between the elements of the collection.…
Advances in DNA sequencing technology will soon result in databases of thousands of genomes. Within a species, individuals' genomes are almost exact copies of each other; e.g., any two human genomes are 99.9% the same. Relative Lempel-Ziv…
Indexing highly repetitive collections has become a relevant problem with the emergence of large repositories of versioned documents, among other applications. These collections may reach huge sizes, but are formed mostly of documents that…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
We show how to compress string dictionaries using the Lempel-Ziv (LZ78) data compression algorithm. Our approach is validated experimentally on dictionaries of up to 1.5 GB of uncompressed text. We achieve compression ratios often…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
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…
Lempel-Ziv (LZ77 or, briefly, LZ) is one of the most effective and widely-used compressors for repetitive texts. However, the existing efficient methods computing the exact LZ parsing have to use linear or close to linear space to index the…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
For decades, computing the LZ factorization (or LZ77 parsing) of a string has been a requisite and computationally intensive step in many diverse applications, including text indexing and data compression. Many algorithms for LZ77 parsing…
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…
The Lempel--Ziv 78 (LZ78) factorization is a well-studied technique for data compression. It and its derivatives are used in compression formats such as "compress" or "gif". Although most research focuses on the factorization of plain data,…
Compression techniques that support fast random access are a core component of any information system. Current state-of-the-art methods group documents into fixed-sized blocks and compress each block with a general-purpose adaptive…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
Simple and fast decoding is one of the main advantages of LZ77-type text encoding used in many popular file compressors such as gzip and 7zip. With the recent introduction of external memory algorithms for Lempel-Ziv factorization there is…
One of the most famous and investigated lossless data-compression scheme is the one introduced by Lempel and Ziv about 40 years ago. This compression scheme is known as "dictionary-based compression" and consists of squeezing an input…
Compressed indexing enables powerful queries over massive and repetitive textual datasets using space proportional to the compressed input. While theoretical advances have led to highly efficient index structures, their practical…