Related papers: A Compressed Self-Index for Genomic Databases
Gagie, Navarro and Prezza's $r$-index (SODA, 2018) promises to speed up DNA alignment and variation calling by allowing us to index entire genomic databases, provided certain obstacles can be overcome. In this paper we first strengthen and…
The compression-complexity trade-off of lossy compression algorithms that are based on a random codebook or a random database is examined. Motivated, in part, by recent results of Gupta-Verd\'{u}-Weissman (GVW) and their underlying…
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,…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
With the recent advances in DNA sequencing, it is now possible to have complete genomes of individuals sequenced and assembled. This rich and focused genotype information can be used to do different population-wide studies, now first time…
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…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can…
We describe a data structure that stores a string $S$ in space similar to that of its Lempel-Ziv encoding and efficiently supports access, rank and select queries. These queries are fundamental for implementing succinct and compressed data…
We present a Compression Tool, "GenBit Compress", for genetic sequences based on our new proposed "GenBit Compress Algorithm". Our Tool achieves the best compression ratios for Entire Genome (DNA sequences) . Significantly better…
We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions…
Data compression continues to evolve, with traditional information theory methods being widely used for compressing text, images, and videos. Recently, there has been growing interest in leveraging Generative AI for predictive compression…
Given a string $S$, the \emph{compressed indexing problem} is to preprocess $S$ into a compressed representation that supports fast \emph{substring queries}. The goal is to use little space relative to the compressed size of $S$ while…
The LZ-End parsing [Kreft & Navarro, 2011] of an input string yields compression competitive with the popular Lempel-Ziv 77 scheme, but also allows for efficient random access. Kempa and Kosolobov showed that the parsing can be computed in…
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…
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…
Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…
We propose a universal ensemble for random selection of rate-distortion codes, which is asymptotically optimal in a sample-wise sense. According to this ensemble, each reproduction vector, $\hbx$, is selected independently at random under…
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…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…