相关论文: Matching reads to many genomes with the $r$-index

We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…

In this paper, the mining of hybrid association rules with rough set approach is investigated as the algorithm RSHAR.The RSHAR algorithm is constituted of two steps mainly. At first, to join the participant tables into a general table to…

Iris recognition systems transform an iris image into a feature vector. The seminal pipeline segments an image into iris and non-iris pixels, normalizes this region into a fixed-dimension rectangle, and extracts features which are stored…

The method of Probability Density Profile Analysis has been introduced previously as a tool to find the best match between a set of experimentally generated Residual Dipolar Couplings and a set of known protein structures. While it proved…

Finding patterns in data and being able to retrieve information from those patterns is an important task in Information retrieval. Complex search requirements which are not fulfilled by simple string matching and require exploring certain…

Nearest neighbor searching of large databases in high-dimensional spaces is inherently difficult due to the curse of dimensionality. A flavor of approximation is, therefore, necessary to practically solve the problem of nearest neighbor…

Rotary Indexing Machines (RIMs) are widely used in manufacturing due to their ability to perform multiple production steps on a single product without manual repositioning, reducing production time and improving accuracy and consistency.…

We present Masai, a read mapper representing the state of the art in terms of speed and sensitivity. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2--3 times faster and more accurate than Bowtie 2 and BWA. The novelties…

This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing,…

Domains like bioinformatics, version control systems, collaborative editing systems (wiki), and others, are producing huge data collections that are very repetitive. That is, there are few differences between the elements of the collection.…

Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for…

The emerging class of instance-optimized systems has shown potential to achieve high performance by specializing to a specific data and query workloads. Particularly, Machine Learning (ML) techniques have been applied successfully to build…

The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, the lack of standardized,…

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…

Relative Lempel-Ziv (RLZ) is a popular algorithm for compressing databases of genomes from individuals of the same species when fast random access is desired. With Kuruppu et al.'s (SPIRE 2010) original implementation, a reference genome is…

The interAdapt R package is designed to be used by statisticians and clinical investigators to plan randomized trials. It can be used to determine if certain adaptive designs offer tangible benefits compared to standard designs, in the…

Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…

Impact craters are a cornerstone of planetary surface analysis. However, while most deep learning pipelines treat craters solely as a detection problem, critical scientific workflows such as catalog deduplication, cross-observation…

Information retrieval (IR) is a user approach to obtain relevant information which meets needs with the help of a IR system (IRS). However, the IRS shows certain differences between user relevance and system relevance. These gaps are…

User identity linkage is a task of recognizing the identities of the same user across different social networks (SN). Previous works tackle this problem via estimating the pairwise similarity between identities from different SN, predicting…