Related papers: SquiggleFilter: An Accelerator for Portable Virus …
The Oxford Nanopore Technologies's MinION is the first portable DNA sequencing device. It is capable of producing long reads, over 100 kBp were reported. However, it has significantly higher error rate than other methods. In this study, we…
Third-generation nanopore sequencers offer a feature called selective sequencing or 'Read Until' that allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to a genomic region of 'interest'. This selective…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Oxford Nanopore MinION sequencer is currently the smallest sequencing device available. While being able to produce very long reads (reads of up to 100~kbp were reported), it is prone to high sequencing error rates of up to 30%. Since most…
Convolutional neural network (CNN) offers significant accuracy in image detection. To implement image detection using CNN in the internet of things (IoT) devices, a streaming hardware accelerator is proposed. The proposed accelerator…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
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…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
This paper describes a novel idea of a fine-grained fully-active plastic scintillator detector made of many optically independent $1\times1\times1~\text{cm}^3$ cubes with readout on three orthogonal projections by wavelength shifting…
We present and discuss the development and performance of a compact scintillating fiber (SciFi) detector for timing to be used in the Mu3e experiment at very high particle rates. The SciFi detector is read out with multichannel silicon…
The MiniCLEAN dark matter experiment will exploit a single-phase liquid-argon detector instrumented with photomultiplier tubes submerged in the cryogen with nearly 4pi coverage of a 500 kg (150 kg) target (fiducial) mass. The high light…
We present VitaLLM, a mixed precision accelerator that enables ternary weight large language models to run efficiently on edge devices. The design combines two compute cores, a multiplier free TINT core for ternary-INT projections and a…
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…
Muon tomography is a non-destructive imaging technique that uses cosmic-ray muons to probe dense materials. Bar scintillator and scintillating fiber detectors equipped with one-dimensional SiPM arrays offer compact, high-resolution…
TRION is a sub-mm spatial resolution fast neutron imaging detector, which employs an integrative optical time-of-flight technique. The detector was developed for fast neutron resonance radiography, a method capable of detecting a broad…
Advances in lightweight neural networks have revolutionized computer vision in a broad range of IoT applications, encompassing remote monitoring and process automation. However, the detection of small objects, which is crucial for many of…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
Deep Convolutional Neural Networks (CNNs) have become state-of-the art for computer vision and other signal processing tasks due to their superior accuracy. In recent years, large efforts have been made to reduce the computational costs of…