相关论文: Algorithms to compute the Burrows-Wheeler Similari…

Code-switching (CSW) text generation has been receiving increasing attention as a solution to address data scarcity. In light of this growing interest, we need more comprehensive studies comparing different augmentation approaches. In this…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…

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…

The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…

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…

In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…

Large bilingual parallel texts (also known as bitexts) are usually stored in a compressed form, and previous work has shown that they can be more efficiently compressed if the fact that the two texts are mutual translations is exploited.…

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…

A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…

We propose a new model for learning bilingual word representations from non-parallel document-aligned data. Following the recent advances in word representation learning, our model learns dense real-valued word vectors, that is, bilingual…

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…

Dynamic time warping (DTW) can be used to compute the similarity between two sequences of generally differing length. We propose a modification to DTW that performs individual and independent pairwise alignment of feature trajectories. The…

Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…

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…

In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…

As an essential operation in data cleaning, the similarity join has attracted considerable attention from the database community. In this paper, we study string similarity joins with edit-distance constraints, which find similar string…

Cross-lingual semantic textual similarity systems estimate the degree of the meaning similarity between two sentences, each in a different language. State-of-the-art algorithms usually employ machine translation and combine vast amount of…

Bearing data compression is vital to manage the large volumes of data generated during condition monitoring. In this paper, a novel asymmetrical autoencoder with a lifting wavelet transform (LWT) layer is developed to compress bearing…

Binary search trees (BST) are a popular type of data structure when dealing with ordered data. Indeed, they enable one to access and modify data efficiently, with their height corresponding to the worst retrieval time. From a probabilistic…