Related papers: Faster and More Accurate Sequence Alignment with S…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
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…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Test-Time Adaptation (TTA) adjusts models using unlabeled test data to handle dynamic distribution shifts. However, existing methods rely on frequent adaptation and high computational cost, making them unsuitable for resource-constrained…
Spiking neural network (SNN) is a brain-inspired model which has more spatio-temporal information processing capacity and computational energy efficiency. However, with the increasing depth of SNNs, the memory problem caused by the weights…
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Spiking Neural Network (SNN) has been recognized as one of the next generation of neural networks. Conventionally, SNN can be converted from a pre-trained ANN by only replacing the ReLU activation to spike activation while keeping the…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…
Multi-bit spiking neural networks (SNNs) have recently become a heated research spot, pursuing energy-efficient and high-accurate AI. However, with more bits involved, the associated memory and computation demands escalate to the point…
Spiking neural networks (SNNs) have advantages in latency and energy efficiency over traditional artificial neural networks (ANNs) due to its event-driven computation mechanism and replacement of energy-consuming weight multiplications with…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…
Intracortical brain-machine interfaces demand low-latency, energy-efficient solutions for neural decoding. Spiking Neural Networks (SNNs) deployed on neuromorphic hardware have demonstrated remarkable efficiency in neural decoding by…
The ambition of brain-inspired Spiking Neural Networks (SNNs) is to become a low-power alternative to traditional Artificial Neural Networks (ANNs). This work addresses two major challenges in realizing this vision: the performance gap…
The exponential growth of DNA sequencing data has outpaced traditional heuristic-based methods, which struggle to scale effectively. Efficient computational approaches are urgently needed to support large-scale similarity search, a…
Spiking neural networks (SNNs) that enable low-power design on edge devices have recently attracted significant research. However, the temporal characteristic of SNNs causes high latency, high bandwidth and high energy consumption for the…