Related papers: BWT for string collections
In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts…
In recent years, the continuous wavelet transform (CWT) has been employed as a spectral feature extractor for acoustic recognition tasks in conjunction with machine learning and deep learning models. However, applying the CWT to each…
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…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…
Intelligent selection of training data has proven a successful technique to simultaneously increase training efficiency and translation performance for phrase-based machine translation (PBMT). With the recent increase in popularity of…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Contextual bandits are a core technology for personalized mobile health interventions, where decision-making requires adapting to complex, non-linear user behaviors. While Thompson Sampling (TS) is a preferred strategy for these problems,…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
Cognitive Behavioral Therapy (CBT) is a goal-oriented psychotherapy for mental health concerns implemented in a conversational setting with broad empirical support for its effectiveness across a range of presenting problems and client…
We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW…
Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…
Entropy quantifies the number of bits required to store objects under certain given assumptions. While this is a well established concept for strings, in the context of tries the state-of-the-art regarding entropies is less developed. The…
The minimizers sampling mechanism is a popular mechanism for string sampling introduced independently by Schleimer et al. [SIGMOD 2003] and by Roberts et al. [Bioinf. 2004]. Given two positive integers $w$ and $k$, it selects the…
A bit catastrophe, loosely defined, is when a change in just one character of a string causes a significant change in the size of the compressed string. We study this phenomenon for the Burrows-Wheeler Transform (BWT), a string transform at…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…