Related papers: GateKeeper: A New Hardware Architecture for Accele…
Addressing the growing demands of artificial intelligence (AI) and data analytics requires new computing approaches. In this paper, we propose a reconfigurable hardware accelerator designed specifically for AI and data-intensive…
With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
Approximate computing offers promising energy efficiency benefits for error-tolerant applications, but discovering optimal approximations requires extensive design space exploration (DSE). Predicting the accuracy of circuits composed of…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…
Hardware prefetching is one of the most widely-used techniques for hiding long data access latency. To address the challenges faced by hardware prefetching, architects have proposed to detect and exploit the spatial locality at the…
Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…
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…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Packet classification is a vital and complicated task as the processing of packets should be done at a specified line speed. In order to classify a packet as belonging to a particular flow or set of flows, network nodes must perform a…
Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
Molecular similarity search has been widely used in drug discovery to identify structurally similar compounds from large molecular databases rapidly. With the increasing size of chemical libraries, there is growing interest in the efficient…
The development of cancer is largely driven by the gain or loss of subsets of the genome, promoting uncontrolled growth or disabling defenses against it. Identifying genomic regions whose DNA copy number deviates from the normal is…
Graph-based Approximate Nearest Neighbor Search (ANNS) is widely adopted in numerous applications, such as recommendation systems, natural language processing, and computer vision. While recent works on GPU-based acceleration have…
6DoF object pose estimation is fundamental to robotic grasp tasks. While recent learning-based methods achieve high accuracy, their computational demands hinder deployment on resource-constrained mobile platforms. In this work, we revisit…
Accurate indoor localization is crucial for enabling spatial context in smart environments and navigation systems. Wi-Fi Received Signal Strength (RSS) fingerprinting is a widely used indoor localization approach due to its compatibility…