Related papers: Concurrent and Accurate RNA Sequencing on Multicor…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

Maximizing parallelism level in applications can be achieved by minimizing overheads due to load imbalances and waiting time due to memory latencies. Compiler optimization is one of the most effective solutions to tackle this problem. The…

Hardware accelerators, such as those based on GPUs and FPGAs, offer an excellent opportunity to efficiently parallelize functionalities. Recently, modern embedded platforms started being equipped with such accelerators, resulting in a…

Background: Short-read aligners have recently gained a lot of speed by exploiting the massive parallelism of GPU. An uprising alternative to GPU is Intel MIC; supercomputers like Tianhe-2, currently top of TOP500, is built with 48,000 MIC…

The High Luminosity upgrade of the Large Hadron Collider (HL-LHC) will produce particle collisions with up to 200 simultaneous proton-proton interactions. These unprecedented conditions will create a combinatorial complexity for…

Accelerating Human Action Recognition (HAR) efficiently for real-time surveillance and robotic systems on edge chips remains a challenging research field, given its high computational and memory requirements. This paper proposed an…

While there have been many studies on hardware acceleration for deep learning on images, there has been a rather limited focus on accelerating deep learning applications involving graphs. The unique characteristics of graphs, such as the…

Convolutional Neural Networks (CNNs) combine large amounts of parallelizable computation with frequent memory access. Field Programmable Gate Arrays (FPGAs) can achieve low latency and high throughput CNN inference by implementing dataflow…

Neutral atom quantum computers (NAQCs) are among the most promising computational platforms for quantum computing. Controlling and measuring individual atoms and their states, which often requires multiple imaging and image-analysis…

In this paper, we describe a high-level synthesis (HLS) tool that automatically allows area/throughput trade-offs for implementing streaming task graphs (STG). Our tool targets a massively parallel processor array (MPPA) architecture, very…

We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-fly over the…

In the era of diminishing returns from Moores Law, heterogeneous computing systems have emerged as a vital approach to enhance computational efficiency. This paper introduces a novel MLIR-based dialect, named hyper, designed to optimize…

We present both a novel Convolutional Neural Network (CNN) accelerator architecture and a network compiler for FPGAs that outperforms all prior work. Instead of having generic processing elements that together process one layer at a time,…

The continually increasing volume of DNA sequence data has resulted in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments between candidate haplotypes and sequencing reads using Pair-HMMs is a…

This book focuses on the use of algorithmic high-level synthesis (HLS) to build application-specific FPGA systems. Our goal is to give the reader an appreciation of the process of creating an optimized hardware design using HLS. Although…

Nearest Neighbor Search (NNS) has recently drawn a rapid increase of interest due to its core role in managing high-dimensional vector data in data science and AI applications. The interest is fueled by the success of neural embedding,…

Heterogeneous MPSoCs comprise diverse processing units of varying compute capabilities. To date, the mapping strategies of neural networks (NNs) onto such systems are yet to exploit the full potential of processing parallelism, made…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segments using sequence alignment algorithms. Calculating the…