Sumukh Pinge

Sumukh Pinge, Weihong Xu, Jaeyoung Kang et al.

Mass spectrometry-based proteomics is a key enabler for personalized healthcare, providing a deep dive into the complex protein compositions of biological systems. This technology has vast applications in biotechnology and biomedicine but faces significant computational bottlenecks. Current methodologies often require multiple hours or even days to process extensive datasets, particularly in the domain of spectral clustering. To tackle these inefficiencies, we introduce SpecHD, a hyperdimensional computing (HDC) framework supplemented by an FPGA-accelerated architecture with integrated near-storage preprocessing. Utilizing streamlined binary operations in an HDC environment, SpecHD capitalizes on the low-latency and parallel capabilities of FPGAs. This approach markedly improves clustering speed and efficiency, serving as a catalyst for real-time, high-throughput data analysis in future healthcare applications. Our evaluations demonstrate that SpecHD not only maintains but often surpasses existing clustering quality metrics while drastically cutting computational time. Specifically, it can cluster a large-scale human proteome dataset-comprising 25 million MS/MS spectra and 131 GB of MS data-in just 5 minutes. With energy efficiency exceeding 31x and a speedup factor that spans a range of 6x to 54x over existing state of-the-art solutions, SpecHD emerges as a promising solution for the rapid analysis of mass spectrometry data with great implications for personalized healthcare.

Weihong Xu, Junwei Chen, Po-Kai Hsu et al.

Approximate nearest neighbor search (ANNS) plays an indispensable role in a wide variety of applications, including recommendation systems, information retrieval, and semantic search. Among the cutting-edge ANNS algorithms, graph-based approaches provide superior accuracy and scalability on massive datasets. However, the best-performing graph-based ANN search solutions incur tens of hundreds of memory footprints as well as costly distance computation, thus hindering their efficient deployment at scale. The 3D NAND flash is emerging as a promising device for data-intensive applications due to its high density and nonvolatility. In this work, we present the near-storage processing (NSP)-based ANNS solution Proxima, to accelerate graph-based ANNS with algorithm-hardware co-design in 3D NAND flash. Proxima significantly reduces the complexity of graph search by leveraging the distance approximation and early termination. On top of the algorithmic enhancement, we implement Proxima search algorithm in 3D NAND flash using the heterogeneous integration technique. To maximize 3D NAND's bandwidth utilization, we present customized dataflow and optimized data allocation scheme. Our evaluation results show that: compared to graph ANNS on CPU and GPU, Proxima achieves a magnitude improvement in throughput or energy efficiency. Proxima yields 7x to 13x speedup over existing ASIC designs. Furthermore, Proxima achieves a good balance between accuracy, efficiency and storage density compared to previous NSP-based accelerators.