相关论文: Efficient Architecture-Aware Acceleration of BWA-M…

In-memory database query processing frequently involves substantial data transfers between the CPU and memory, leading to inefficiencies due to Von Neumann bottleneck. Processing-in-Memory (PIM) architectures offer a viable solution to…

In-DRAM Processing-In-Memory (DRAM-PIM) has emerged as a promising approach to accelerate memory-intensive workloads by mitigating data transfer overhead between DRAM and the host processor. Bit-serial DRAM-PIM architectures, further…

Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…

High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…

Computationally intensive Inference tasks of Deep neural networks have enforced revolution of new accelerator architecture to reduce power consumption as well as latency. The key figure of merit in hardware inference accelerators is the…

Generalized linear mixed-effects models in the context of genome-wide association studies (GWAS) represent a formidable computational challenge: the solution of millions of correlated generalized least-squares problems, and the processing…

The high computational and memory demands of modern deep learning (DL) workloads have led to the development of specialized hardware devices from cloud to edge, such as AMD's Ryzen AI XDNA NPUs. Optimizing general matrix multiplication…

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…

State Space Model (SSM)-based machine learning architectures have recently gained significant attention for processing sequential data. Mamba, a recent sequence-to-sequence SSM, offers competitive accuracy with superior computational…

The distributed shared memory (DSM) architecture is widely used in today's computer design to mitigate the ever-widening processing-memory gap, and inevitably exhibits non-uniform memory access (NUMA) to shared-memory parallel applications.…

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…

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…

This paper advocates for an intertwined design of the dense linear algebra software stack that breaks down the strict barriers between the high-level, blocked algorithms in LAPACK (Linear Algebra PACKage) and the low-level,…

Advances in hybrid bonding and packaging have driven growing interest in 3D DRAM-stacked accelerators with higher memory bandwidth and capacity. As LLMs scale to hundreds of billions or trillions of parameters, distributed inference across…

Spiking Neural Networks (SNNs) are extensively utilized in brain-inspired computing and neuroscience research. To enhance the speed and energy efficiency of SNNs, several many-core accelerators have been developed. However, maintaining the…

The co-design of neural network architectures, quantization precisions, and hardware accelerators offers a promising approach to achieving an optimal balance between performance and efficiency, particularly for model deployment on…

As spiking-based deep learning inference applications are increasing in embedded systems, these systems tend to integrate neuromorphic accelerators such as $\mu$Brain to improve energy efficiency. We propose a $\mu$Brain-based scalable…

Designing a unified neural network to efficiently and inherently process sequential data with arbitrary lengths is a central and challenging problem in sequence modeling. The design choices in Transformer, including quadratic complexity and…

Next-generation wireless technologies (for immersive-massive communication, joint communication and sensing) demand highly parallel architectures for massive data processing. A common architectural template scales up by grouping tens to…

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…