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In the field of digital signal processing, the fast Fourier transform (FFT) is a fundamental algorithm, with its processors being implemented using either the pipelined architecture, well-known for high-throughput applications but weak in…
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…
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and…
Motivation: Eugene Myers in his string graph paper (Myers, 2005) suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a…
Over the years, many frameworks and optimization techniques have been proposed to accelerate graph neural networks (GNNs). Compared to the optimizations explored in these systems, we observe that different matrix re-associations of GNN…
A high-dimensional and incomplete (HDI) matrix can describe the complex interactions among numerous nodes in various big data-related applications. A stochastic gradient descent (SGD)-based latent factor analysis (LFA) model is remarkably…
Current Artificial Intelligence (AI) computation systems face challenges, primarily from the memory-wall issue, limiting overall system-level performance, especially for Edge devices with constrained battery budgets, such as smartphones,…
Radio frequency fingerprint identification (RFFI) can classify wireless devices by analyzing the signal distortions caused by the intrinsic hardware impairments. State-of-the-art neural networks have been adopted for RFFI. However, many…
The Square Kilometre Array (SKA) project will be the world largest radio telescope array. With its large number of antennas, the number of signals that need to be processed is dramatic. One important element of the SKA's Central Signal…
Large language models (LLMs) have demonstrated remarkable performance across a wide range of language processing tasks. However, this success comes at the cost of substantial computation and memory requirements, which significantly impedes…
Hyperspectral image (HSI) classification has been widely adopted in applications involving remote sensing imagery analysis which require high classification accuracy and real-time processing speed. Methods based on Convolutional neural…
Existing approximate nearest neighbor search systems suffer from two fundamental problems that are of practical importance but have not received sufficient attention from the research community. First, although existing systems perform well…
Due to the ability to implement customized topology, FPGA is increasingly used to deploy SNNs in both embedded and high-performance applications. In this paper, we survey state-of-the-art SNN implementations and their applications on FPGA.…
A miniaturized full-frequency encoded illumination (mini-FEI) chip is presented for high-throughput super-resolution imaging using the spatial frequency shift (SFS) effect. A tunable full SFS scheme is achieved through propagating and…
The escalating challenges of managing vast sensor-generated data, particularly in audio applications, necessitate innovative solutions. Current systems face significant computational and storage demands, especially in real-time applications…
Low-precision is the first order knob for achieving higher Artificial Intelligence Operations (AI-TOPS). However the algorithmic space for sub-8-bit precision compute is diverse, with disruptive changes happening frequently, making FPGAs a…
We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
In this paper, the field programmable gate array (FPGA) implementation of a fetal heart rate (FHR) monitoring system is presented. The system comprises of a preprocessing unit to remove various types of noise, followed by a fetal…
Computing-in-memory (CIM) is renowned in deep learning due to its high energy efficiency resulting from highly parallel computing with minimal data movement. However, current SRAM-based CIM designs suffer from long latency for loading…