Related papers: Variant tolerant read mapping using min-hashing
Due to the crossbar array architecture, the sneak-path problem severely degrades the data integrity in the resistive random access memory (ReRAM). In this letter, we investigate the channel quantizer design for ReRAM arrays with multiple…
Most pattern recognition models are developed on pre-proce\-ssed data. In computer vision, for instance, RGB images processed through image signal processing (ISP) pipelines designed to cater to human perception are the most frequent input…
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…
As DRAM and other transistor-based memory technologies approach their scalability limits, alternative storage solutions like Phase-Change Memory (PCM) are gaining attention for their scalability, fast access times, and zero leakage power.…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
We propose a novel Hamming distance tolerant content-addressable memory (HD-CAM) for energy-efficient in memory approximate matching applications. HD-CAM implements approximate search using matchline charge redistribution rather than its…
Large-scale Vision-Language Models (VLMs) have achieved notable progress in aligning visual inputs with text. However, their ability to deeply understand the unique physical properties of non-RGB vision sensor images remains limited. In…
Self-supervised learning methods for computer vision have demonstrated the effectiveness of pre-training feature representations, resulting in well-generalizing Deep Neural Networks, even if the annotated data are limited. However,…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
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…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
Modern DRAM chips are subject to read disturbance errors. State-of-the-art read disturbance mitigations rely on accurate and exhaustive characterization of the read disturbance threshold (RDT) (e.g., the number of aggressor row activations…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed…
Recent DNA pre-alignment filter designs employ DRAM for storing the reference genome and its associated meta-data. However, DRAM incurs increasingly high energy consumption background and refresh energy as devices scale. To overcome this…
DNA barcoding has emerged as a cost-effective approach for species identification. However, the scarcity of tools used for searching the booming reference database becomes an obstacle, currently with BLAST as the only practical choice.…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Vision Transformers (ViTs) have shown significant promise in computer vision applications. However, their performance in few-shot learning is limited by challenges in refining token-level interactions, struggling with limited training data,…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…