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

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped…

Inverted file structure is a common technique for accelerating dense retrieval. It clusters documents based on their embeddings; during searching, it probes nearby clusters w.r.t. an input query and only evaluates documents within them by…

Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be applied to a non-model organism without a reference genome,…

Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…

In order to help in the identification of INTEGRAL/ISGRI sources, we have developed a software package which allows a rapid and detailed cross-correlation to be performed between various source catalogues. It allows subsets of catalogues to…

Neural models have transformed the fundamental information retrieval problem of mapping a query to a giant set of items. However, the need for efficient and low latency inference forces the community to reconsider efficient approximate…

FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…

High throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis and interpretation of…

The fitting or parameter estimation of complex ecological models is a challenging optimisation task, with a notable lack of tools for fitting complex, long runtime or stochastic models. calibrar is an R package that is dedicated to the…

RGB-Infrared (IR) person re-identification aims to retrieve person-of-interest from heterogeneous cameras, easily suffering from large image modality discrepancy caused by different sensing wavelength ranges. Existing work usually minimizes…

Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…

In order to speed-up classification models when facing a large number of categories, one usual approach consists in organizing the categories in a particular structure, this structure being then used as a way to speed-up the prediction…

Index structures are one of the most important tools that DBAs leverage to improve the performance of analytics and transactional workloads. However, building several indexes over large datasets can often become prohibitive and consume…

This work addresses the problem of billion-scale nearest neighbor search. The state-of-the-art retrieval systems for billion-scale databases are currently based on the inverted multi-index, the recently proposed generalization of the…

Motivation: Protein-ligand affinity prediction is an important part of structure-based drug design. It includes molecular docking and affinity prediction. Although molecular dynamics can predict affinity with high accuracy at present, it is…

This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…

A search query consists of several words. In a proximity full-text search, we want to find documents that contain these words near each other. This task requires much time when the query consists of high-frequently occurring words. If we…

Improvements of entity-relationship (E-R) search techniques have been hampered by a lack of test collections, particularly for complex queries involving multiple entities and relationships. In this paper we describe a method for generating…

This paper investigates the application of consensus clustering and meta-clustering to the set of all possible partitions of a data set. We show that when using a "complement" of Rand Index as a measure of cluster similarity, the…