相关论文: Accelerating K-mer Frequency Counting with GPU and…

Massive exploitation of next-generation sequencing technologies requires dealing with both: huge amounts of data and complex bioinformatics pipelines. Computing architectures have evolved to deal with these problems, enabling approaches…

A basic task in bioinformatics is the counting of $k$-mers in genome strings. The $k$-mer counting problem is to build a histogram of all substrings of length $k$ in a given genome sequence. We present the open source $k$-mer counting…

A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…

Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…

Kernel matrix-vector multiplication (KMVM) is a foundational operation in machine learning and scientific computing. However, as KMVM tends to scale quadratically in both memory and time, applications are often limited by these…

Machine learning algorithms are becoming increasingly prevalent and performant in the reconstruction of events in accelerator-based neutrino experiments. These sophisticated algorithms can be computationally expensive. At the same time, the…

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…

The rise of LLMs has driven demand for private serverless deployments, characterized by moderate-sized models and infrequent requests. While existing serverless solutions follow exclusive GPU allocation, we take a step back to explore…

Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…

In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…

The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…

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…

General matrix multiplication (GEMM) operations are the fundamental building blocks of computational domains including artificial intelligence (AI). As GPU architectures evolve and high-performance AI becomes increasingly important,…

Quantized Spiking Neural Networks (QSNNs) offer superior energy efficiency and are well-suited for deployment on resource-limited edge devices. However, limited bit-width weight and membrane potential result in a notable performance…

Modern computing platforms tend to deploy multiple GPUs (2, 4, or more) on a single node to boost system performance, with each GPU having a large capacity of global memory and streaming multiprocessors (SMs). GPUs are an expensive…

Modern transformer-based Large Language Models (LLMs) are constructed with a series of decoder blocks. Each block comprises three key components: (1) QKV generation, (2) multi-head attention, and (3) feed-forward networks. In batched…

Deep Neural Networks (DNNs) have revolutionized various fields, but their deployment on GPUs often leads to significant energy consumption. Unlike existing methods for reducing GPU energy consumption, which are either hardware-inflexible or…

This problem was solved within the framework of the grant project "Solving of problems of cluster analysis with application of parallel algorithms and cloud technologies" in the Institute of Mathematics and Mathematical Modelling in Almaty.…

In this paper we implemented the algorithm we developed in [1] called 3DPIFCM in a parallel environment by using CUDA on a GPU. In our previous work we introduced 3DPIFCM which performs segmentation of images in noisy conditions and uses…

Graph Neural Networks (GNNs) are becoming a promising technique in various domains due to their excellent capabilities in modeling non-Euclidean data. Although a spectrum of accelerators has been proposed to accelerate the inference of…