相关论文: Fast and sensitive read mapping with approximate s…

Background: Identifying all possible mapping locations of next-generation sequencing (NGS) reads is highly essential in several applications such as prediction of genomic variants or protein binding motifs located in repeat regions, isoform…

DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…

A common method to solve complex problems in software engineering, is to divide the problem into multiple sub-problems. Inspired by this, we propose a Modular Architecture for Software-engineering AI (MASAI) agents, where different…

Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of three key computational steps: Index Querying, Seed…

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…

fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components…

A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a variety of tools, e.g., the commonly-used CrossMap tool.…

Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…

Over the years, many frameworks and optimization techniques have been proposed to accelerate graph neural networks (GNNs). Compared to the optimizations explored in these systems, we observe that different matrix re-associations of GNN…

This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.

Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…

Modern deep neural networks must demonstrate state-of-the-art accuracy while exhibiting low latency and energy consumption. As such, neural architecture search (NAS) algorithms take these two constraints into account when generating a new…

Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and…

Classical autonomous driving systems connect perception and prediction modules via hand-crafted bounding-box interfaces, limiting information flow and propagating errors to downstream tasks. Recent research aims to develop end-to-end models…

Decision trees remain one of the most popular machine learning models today, largely due to their out-of-the-box performance and interpretability. In this work, we present a Bayesian approach to decision tree induction via maximum a…

DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…

We present FEAR, a family of fast, efficient, accurate, and robust Siamese visual trackers. We present a novel and efficient way to benefit from dual-template representation for object model adaption, which incorporates temporal information…

We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool…