Related papers: Accelerating K-mer Frequency Counting with GPU and…

The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…

Approximate Nearest Neighbor Search (ANNS) underpins modern applications such as information retrieval and recommendation. With the rapid growth of vector data, efficient indexing for real-time vector search has become rudimentary. Existing…

Spiking neural networks (SNNs) are the third generation of neural networks and can explore both rate and temporal coding for energy-efficient event-driven computation. However, the decision accuracy of existing SNN designs is contingent…

Developing kernels for Processing-In-Memory (PIM) platforms poses unique challenges in data management and parallel programming on limited processing units. Although software development kits (SDKs) for PIM, such as the UPMEM SDK, provide…

Cost of serving large language models (LLM) is high, but the expensive and scarce GPUs are poorly efficient when generating tokens sequentially, unless the batch of sequences is enlarged. However, the batch size is limited by some…

Clustering is an important tool in data analysis, with K-means being popular for its simplicity and versatility. However, it cannot handle non-linearly separable clusters. Kernel K-means addresses this limitation but requires a large kernel…

Generating texts with a large language model (LLM) consumes massive amounts of memory. Apart from the already-large model parameters, the key/value (KV) cache that holds information about previous tokens in a sequence can grow to be even…

The rapid development of deep neural networks (DNNs) is inherently accompanied by the problem of high computational costs. To tackle this challenge, dynamic voltage frequency scaling (DVFS) is emerging as a promising technology for…

K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of…

Drawing on the intricate structures of the brain, Spiking Neural Networks (SNNs) emerge as a transformative development in artificial intelligence, closely emulating the complex dynamics of biological neural networks. While SNNs show…

Recent advances in self-supervised learning and the Transformer architecture have significantly improved natural language processing (NLP), achieving remarkably low perplexity. However, the growing size of NLP models introduces a memory…

Spiking Neural Networks (SNNs) offer a biologically inspired computational paradigm, enabling energy-efficient data processing through spike-based information transmission. Despite notable advancements in hardware for SNNs, spike encoding…

Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…

Variant calling is the first step in analyzing a human genome and aims to detect variants in an individual's genome compared to a reference genome. Due to the computationally-intensive nature of variant calling, genomic data are…

Large language models~(LLMs) are known for their high demand on computing resources and memory due to their substantial model size, which leads to inefficient inference on moderate GPU systems. Techniques like quantization or pruning can…

Spiking Neural Networks (SNNs) have emerged as a biologically inspired alternative to conventional deep networks, offering event-driven and energy-efficient computation. However, their throughput remains constrained by the serial update of…

We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions,…

Efficiently harnessing GPU compute is critical to improving user experience and reducing operational costs in large language model (LLM) services. However, current inference engine schedulers overlook the attention backend's sensitivity to…

As inference on Large Language Models (LLMs) emerges as an important workload in machine learning applications, weight quantization has become a standard technique for efficient GPU deployment. Quantization not only reduces model size, but…

Solving quantifier-free non-linear real arithmetic (NRA) problems is a computationally hard task. To tackle this problem, prior work proposed a promising approach based on gradient descent. In this work, we extend their ideas and combine…