Related papers: SOAP3-dp: Fast, Accurate and Sensitive GPU-based S…

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…

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…

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…

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…

We explore different ways to simplify the evaluation of the smooth overlap of atomic positions (SOAP) many-body atomic descriptor [Bart\'{o}k et al., Phys. Rev. B 87, 184115 (2013)]. Our aim is to improve the computational efficiency of…

With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…

We consider the problem of cross-sensor domain adaptation in the context of LiDAR-based 3D object detection and propose Stationary Object Aggregation Pseudo-labelling (SOAP) to generate high quality pseudo-labels for stationary objects. In…

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…

PPG-based Blood Pressure (BP) estimation is a challenging biosignal processing task for low-power devices such as wearables. State-of-the-art Deep Neural Networks (DNNs) trained for this task implement either a PPG-to-BP signal-to-signal…

Photoplethysmography (PPG)-based blood pressure (BP) estimation is a challenging task, particularly on resource-constrained wearable devices. However, fully on-board processing is desirable to ensure user data confidentiality. Recent deep…

Depthwise separable convolutions are a fundamental component in efficient Deep Neural Networks, as they reduce the number of parameters and operations compared to traditional convolutions while maintaining comparable accuracy. However,…

3D object detection from LiDAR sensor data is an important topic in the context of autonomous cars and drones. In this paper, we present the results of experiments on the impact of backbone selection of a deep convolutional neural network…

The rapid growth of artificial intelligence (AI) has made low-precision formats such as FP16, FP8, and, most recently, block-scaled FP4 the primary focus of modern GPUs, where Tensor Cores now deliver orders-of-magnitude higher throughput…

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…

Implicit neural representations have become pivotal in robotic perception, enabling robots to comprehend 3D environments from 2D images. Given a set of camera poses and associated images, the models can be trained to synthesize novel,…

Deploying deep neural networks (DNNs) across homogeneous edge devices (the devices with the same SKU labeled by the manufacturer) often assumes identical performance among them. However, once a device model is widely deployed, the…

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…

In recent years, the rapidly increasing number of reads produced by next-generation sequencing (NGS) technologies has driven the demand for efficient implementations of sequence alignments in bioinformatics. However, current…

Real-time Deep Neural Network (DNN) inference with low-latency requirement has become increasingly important for numerous applications in both cloud computing (e.g., Apple's Siri) and edge computing (e.g., Google/Waymo's driverless car).…

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…