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Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…

Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…

Long-document QA presents challenges with large-scale text and long-distance dependencies. Recent advances in Large Language Models (LLMs) enable entire documents to be processed in a single pass. However, their computational cost is…

Cross-View Geo-Localization (CVGL) involves determining the localization of drone images by retrieving the most similar GPS-tagged satellite images. However, the imaging gaps between platforms are often significant and the variations in…

We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…

In this work we present a performance exploration on Eager K-truss, a linear-algebraic formulation of the K-truss graph algorithm. We address performance issues related to load imbalance of parallel tasks in symmetric, triangular graphs by…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…

Generative Adversarial Networks (GAN) are cutting-edge algorithms for generating new data samples based on the learned data distribution. However, its performance comes at a significant cost in terms of computation and memory requirements.…

Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…

Performance optimization can be a daunting task especially as the hardware architecture becomes more and more complex. This paper takes a kernel from the Materials Science code BerkeleyGW, and demonstrates a few performance analysis and…

Large language models have led to state-of-the-art accuracies across a range of tasks. However, training these models efficiently is challenging for two reasons: a) GPU memory capacity is limited, making it impossible to fit large models on…

Low Autocorrelation Binary Sequences (LABS) is a particularly challenging binary optimization problem which quickly becomes intractable in finding the global optimum for problem sizes beyond 66. This aspect makes LABS appealing to use as a…

We propose GAN-Supervised Learning, a framework for learning discriminative models and their GAN-generated training data jointly end-to-end. We apply our framework to the dense visual alignment problem. Inspired by the classic Congealing…

We present an accurate and GPU-accelerated Stereo Visual SLAM design called Jetson-SLAM. It exhibits frame-processing rates above 60FPS on NVIDIA's low-powered 10W Jetson-NX embedded computer and above 200FPS on desktop-grade 200W GPUs,…

Enumerating simple cycles has important applications in computational biology, network science, and financial crime analysis. In this work, we focus on parallelising the state-of-the-art simple cycle enumeration algorithms by Johnson and…

Large scale graph optimization problems arise in many fields. This paper presents an extensible, high performance framework (named OpenGraphGym-MG) that uses deep reinforcement learning and graph embedding to solve large graph optimization…

Transformer models have achieved state-of-the-art performance on various domains of applications and gradually becomes the foundations of the advanced large deep learning (DL) models. However, how to train these models over multiple GPUs…

Graph Neural Networks (GNNs) are powerful deep learning models to generate node embeddings on graphs. When applying deep GNNs on large graphs, it is still challenging to perform training in an efficient and scalable way. We propose a novel…

The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…