相关论文: Matching Statistics speed up BWT construction

In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…

Multi-parameter persistent homology is a recent branch of topological data analysis. In this area, data sets are investigated through the lens of homology with respect to two or more scale parameters. The high computational cost of many…

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…

Data subset selection aims to find a smaller yet informative subset of a large dataset that can approximate the full-dataset training, addressing challenges associated with training neural networks on large-scale datasets. However, existing…

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…

Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…

Selecting appropriate values for the configurable parameters of Database Management Systems (DBMS) to improve performance is a significant challenge. Recent machine learning (ML)-based tuning systems have shown strong potential, but their…

The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…

In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…

We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…

The Burrows Wheeler transform has applications in data compression as well as full text indexing. Despite its important applications and various existing algorithmic approaches the construction of the transform for large data sets is still…

Topological invariants of a dataset, such as the number of holes that survive from one length scale to another (persistent Betti numbers) can be used to analyze and classify data in machine learning applications. We present an improved…

The Tsetlin Machine (TM) is an interpretable mechanism for pattern recognition that constructs conjunctive clauses from data. The clauses capture frequent patterns with high discriminating power, providing increasing expression power with…

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…

Given a string of characters, the Burrows-Wheeler Transform rearranges the characters in it so as to produce another string of the same length which is more amenable to compression techniques such as move to front, run-length encoding, and…

A new array based data structure named black-white array (BWA) is introduced as an effective and efficient alternative to the list or tree based data structures for dynamic data set. It consists of two sub-arrays, one white and one black of…

For general repeated measures designs the Wald-type statistic (WTS) is an asymptotically valid procedure allowing for unequal covariance matrices and possibly non-normal multivariate observations. The drawback of this procedure is the poor…

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…

With the growing scale of big data, probabilistic structures receive increasing popularity for efficient approximate storage and query processing. For example, Bloom filters (BF) can achieve satisfactory performance for approximate…

The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…