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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…

Genomics · Quantitative Biology 2018-05-02 Nathaniel McVicar , Akina Hoshino , Anna La Torre , Thomas A. Reh , Walter L. Ruzzo , Scott Hauck

High-throughput imaging workflows, such as Parallel Rapid Imaging with Spectroscopic Mapping (PRISM), generate data at rates that exceed conventional real-time processing capabilities. We present a scalable FPGA-based preprocessing pipeline…

Hardware Architecture · Computer Science 2025-11-26 Weichien Liao

To cope with the increasing demand and computational intensity of deep neural networks (DNNs), industry and academia have turned to accelerator technologies. In particular, FPGAs have been shown to provide a good balance between performance…

Hardware Architecture · Computer Science 2018-07-12 Yongming Shen , Tianchu Ji , Michael Ferdman , Peter Milder

The increasing complexity of transformer models in artificial intelligence expands their computational costs, memory usage, and energy consumption. Hardware acceleration tackles the ensuing challenges by designing processors and…

Hardware Architecture · Computer Science 2023-12-21 Alireza Amirshahi , Giovanni Ansaloni , David Atienza

Graph Neural Networks (GNNs) have shown great success in many applications such as recommendation systems, molecular property prediction, traffic prediction, etc. Recently, CPU-FPGA heterogeneous platforms have been used to accelerate many…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-12-23 Yi-Chien Lin , Bingyi Zhang , Viktor Prasanna

AI acceleration has been dominated by GPUs, but the growing need for lower latency, energy efficiency, and fine-grained hardware control exposes the limits of fixed architectures. In this context, Field-Programmable Gate Arrays (FPGAs)…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-11-18 Arturo Urías Jiménez

Large Language Models (LLMs) increasingly require processing long text sequences, but GPU memory limitations force difficult trade-offs between memory capacity and bandwidth. While HBM-based acceleration offers high bandwidth, its capacity…

Hardware Architecture · Computer Science 2025-04-25 Qingyuan Liu , Liyan Chen , Yanning Yang , Haocheng Wang , Dong Du , Zhigang Mao , Naifeng Jing , Yubin Xia , Haibo Chen

Memory bandwidth is known to be a performance bottleneck for FPGA accelerators, especially when they deal with large multi-dimensional data-sets. A large body of work focuses on reducing of off-chip transfers, but few authors try to improve…

Hardware Architecture · Computer Science 2024-01-23 Corentin Ferry , Nicolas Derumigny , Steven Derrien , Sanjay Rajopadhye

Implementing convolutional neural networks (CNNs) on field-programmable gate arrays (FPGAs) has emerged as a promising alternative to GPUs, offering lower latency, greater power efficiency and greater flexibility. However, this development…

Hardware Architecture · Computer Science 2025-10-21 Philippe Magalhães , Virginie Fresse , Benoît Suffran , Olivier Alata

Energy-efficiency is a key concern for neural network applications. To alleviate this issue, hardware acceleration using FPGAs or GPUs can provide better energy-efficiency than general-purpose processors. However, further improvement of the…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-06-29 Seyed Morteza Nabavinejad , Behzad Salami

High Bandwidth Memory with Processing-in-Memory (HBM-PIM) offers an opportunity to reduce data movement by executing computation directly inside memory, but current commercial platforms expose limited instruction sets and require…

Hardware Architecture · Computer Science 2026-05-01 Emanuele Venieri , Simone Manoni , Alberto Florian , Jaehyun Park , Kyomin Sohn , Andrea Bartolini

The conventional von Neumann architecture has been revealed as a major performance and energy bottleneck for rising data-intensive applications. %, due to the intensive data movements. The decade-old idea of leveraging in-memory processing…

Hardware Architecture · Computer Science 2019-06-18 Bing Li , Bonan Yan , Hai , Li

The attention layer, a core component of Transformer-based LLMs, brings out inefficiencies in current GPU systems due to its low operational intensity and the substantial memory requirements of KV caches. We propose a High-bandwidth…

Hardware Architecture · Computer Science 2025-12-19 Myunghyun Rhee , Joonseop Sim , Taeyoung Ahn , Seungyong Lee , Daegun Yoon , Euiseok Kim , Kyoung Park , Youngpyo Joo , Hoshik Kim

Mixed-precision quantization is a popular approach for compressing deep neural networks (DNNs). However, it is challenging to scale the performance efficiently with mixed-precision DNNs given the current FPGA architecture and conventional…

Hardware Architecture · Computer Science 2023-11-07 Yuzong Chen , Jordan Dotzel , Mohamed S. Abdelfattah

Power-spectrum analysis is an important tool providing critical information about a signal. The range of applications includes communication-systems to DNA-sequencing. If there is interference present on a transmitted signal, it could be…

Instrumentation and Methods for Astrophysics · Physics 2015-03-18 Yogindra Abhyankar , Sajish C. , Yogesh Agarwal , C. R. Subrahmanya , Peeyush Prasad

Reducing energy consumption is a challenge that is faced on a daily basis by teams from the High-Performance Computing as well as the Embedded domain. This issue is mostly attacked from an hardware perspective, by devising architectures…

Performance · Computer Science 2015-11-30 Baptiste Delporte , Roberto Rigamonti , Alberto Dassatti

Deep convolution Neural Network (DCNN) has been widely used in computer vision tasks. However, for edge devices even inference has too large computational complexity and data access amount. The inference latency of state-of-the-art models…

Hardware Architecture · Computer Science 2025-09-09 Kuan-Ting Lin , Ching-Te Chiu , Jheng-Yi Chang , Shi-Zong Huang , Yu-Ting Li

The edge computing paradigm has emerged to handle cloud computing issues such as scalability, security and low response time among others. This new computing trend heavily relies on ubiquitous embedded systems on the edge. Performance and…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-01-28 Mohammad Hosseinabady , Mohd Amiruddin Bin Zainol , Jose Nunez-Yanez

Power awareness is fast becoming immensely important in computing, ranging from the traditional High Performance Computing applications, to the new generation of data centric workloads. In this work we describe our efforts towards a power…

Mathematical Software · Computer Science 2014-05-20 Pavel Klavík , A. Cristiano I. Malossi , Constantin Bekas , Alessandro Curioni

As the demand for computational power increases, high-bandwidth memory (HBM) has become a critical technology for next-generation computing systems. However, the widespread adoption of HBM presents significant thermal management challenges,…

Machine Learning · Computer Science 2025-03-07 Chengxin Zhang , Yujie Liu , Quan Chen
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