Related papers: A Compressed Self-Index for Genomic Databases
A self-index is a compressed data structure that supports locate queries -- reporting all positions where a given pattern occurs in a string while maintaining the string in compressed form. While many self-indexes have been proposed,…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
Inspired by the recently proposed Magnetic Resonance Fingerprinting (MRF) technique, we develop a principled compressed sensing framework for quantitative MRI. The three key components are: a random pulse excitation sequence following the…
Shannon's entropy is a clear lower bound for statistical compression. The situation is not so well understood for dictionary-based compression. A plausible lower bound is $b$, the least number of phrases of a general bidirectional parse of…
In this paper, we present a compressed data structure for moving object trajectories in a road network, which are represented as sequences of road edges. Unlike existing compression methods for trajectories in a network, our method supports…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
In the modern era, large volumes of data are being produced continuously, especially in domain-specific fields such as medical records and clinical files, defence logs and HTML-based web traffic. Data with such volume and complexity needs…
We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion limited aggregation models on a Cayley tree. We point out that some aspects of these…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
The paper introduces a new lossless, highly robust compression algorithm that similar with LZW algorithm, yet the algorithm discards dictionary processing and uses irregular sequences with massive, random information instead. Then the paper…
Consider the case where consecutive blocks of N letters of a semi-infinite individual sequence X over a finite-alphabet are being compressed into binary sequences by some one-to-one mapping. No a-priori information about X is available at…
Detection of rare variants by resequencing is important for the identification of individuals carrying disease variants. Rapid sequencing by new technologies enables low-cost resequencing of target regions, although it is still prohibitive…
DNA has emerged as a promising alternative for long-term data storage due to its high capacity, durability, and low-energy potential. However, storing data in DNA presents several challenges. First, it requires complex and costly…
Traditional lossless text compression preserves every byte, but its gains on natural language are often modest in realistic operating regimes. We study \emph{lossy semantic text compression}, where the encoder strategically deletes parts of…
In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting…
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…
In this paper, a new compression scheme for text is presented. The same is efficient in giving high compression ratios and enables super fast searching within the compressed text. Typical compression ratios of 70-80% and reducing the search…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…