arXiv subjects

Sumukh Pinge

Publications and source records attributed to Sumukh Pinge.

10 recordsLinked to original sources

arXiv2026

D-NOVA: In-Storage Retrieval Accelerator via Dual-Bound 3D NAND-Optimized Similarity Search with Vector Adaptation

Retrieval-Augmented Generation (RAG) enhances the factual grounding of large language model (LLM) inference by retrieving relevant information from external knowledge bases. However, its dense vector retrieval introduces significant latency and energy overhead, becoming the primary performance bottleneck. Although recent in-storage accelerators aim to reduce data movement, they still rely on host or embedded processors outside the memory, where nearly 70% of the total retrieval time is spent. As a result, they cannot fully overcome the bandwidth limitations, leading to yet another memory bottleneck. To tackle these limitations, we present D-NOVA, a hardware-software co-designed in-storage retrieval accelerator. D-NOVA executes an inverted file (IVF)-based hierarchical retrieval pipeline by deeply embedding the search functionality directly into the NAND memory array. This is achieved by incorporating a new distance metric, Dual-Bound Tight Similarity Sensing (DTS), which is specifically tailored for searching within the NAND string. In addition, we introduce a lightweight contrastive adapter that maps embedding vectors into a DTS-friendly domain, recovering near-software recall while improving performance and energy efficiency. D-NOVA is up to 41.7x faster and 71x more energy-efficient than a CPU baseline, and achieves 12.13x higher throughput while being up to 1.26x more energy-efficient than state-of-the-art in-storage RAG accelerators, demonstrating the potential of fully in-storage vector search for scalable RAG acceleration.

cs.AR↗

arXiv2026

Cross-Domain Acceleration of Open Modification Search: From Commodity Platforms to Emerging Memory and Storage Devices

Open modification search (OMS) in mass spectrometry (MS) is a data-intensive workload whose performance is dominantly limited by reference data movement rather than computation. Prior OMS accelerators have largely been evaluated in isolation, making it difficult to understand system-level trade-offs across platforms. This paper presents the first workload-driven, cross-platform survey of accelerators for MS search by studying not only commodity platforms, but also emerging memory- and storage-centric architectures, including GPUs, near-storage FPGAs, DRAM near-memory processing, ReRAM/PCM in-memory processing, and 3D NAND/FeNAND in-storage processing, under consistent algorithmic and accuracy assumptions. Leveraging a binary hyperdimensional computing (HDC)-based OMS formulation that reduces similarity evaluation to lightweight bitwise primitives and tolerates device-level non-idealities, we enable a robust execution on memory-centric architectures despite device-level non-idealities and limited computing capability. Overall, this study identifies memory- and storage-centric architectures as a key architectural breakthrough for large-scale, high-speed search acceleration, delivering up to >100x speedup and >40,000x improvement in energy efficiency.

cs.AR↗

arXiv2025

HDDB: Efficient In-Storage SQL Database Search Using Hyperdimensional Computing on Ferroelectric NAND Flash

Hyperdimensional Computing (HDC) encodes information and data into high-dimensional distributed vectors that can be manipulated using simple bitwise operations and similarity searches, offering parallelism, low-precision hardware friendliness, and strong robustness to noise. These properties are a natural fit for SQL database workloads dominated by predicate evaluation and scans, which demand low energy and low latency over large fact tables. Notably, HDC's noise-tolerance maps well onto emerging ferroelectric NAND (FeNAND) memories, which provide ultra-high density and in-storage compute capability but suffer from elevated raw bit-error rates. In this work, we propose HDDB, a hardware-software co-design that combines HDC with FeNAND multi-level cells (MLC) to perform in-storage SQL predicate evaluation and analytics with massive parallelism and minimal data movement. Particularly, we introduce novel HDC encoding techniques for standard SQL data tables and formulate predicate-based filtering and aggregation as highly efficient HDC operations that can happen in-storage. By exploiting the intrinsic redundancy of HDC, HDDB maintains correct predicate and decode outcomes under substantial device noise (up to 10% randomly corrupted TLC cells) without explicit error-correction overheads. Experiments on TPC-DS fact tables show that HDDB achieves up to 80.6x lower latency and 12,636x lower energy consumption compared to conventional CPU/GPU SQL database engines, suggesting that HDDB provides a practical substrate for noise-robust, memory-centric database processing.

cs.AR↗

arXiv2025

HERP: Hardware for Energy Efficient and Realtime DB Search and Cluster Expansion in Proteomics

Database search and clustering are fundamental components of many data analytics problems, such as mass spectrometry-driven proteomics. Traditional full clustering and search algorithms suffer from high resource usage and long latencies. We introduce HERP, a lightweight incremental clustering method and a highly parallelizable database (DB) search platform that utilizes 3T2MTJ SOT-MRAM based CAM in 7nm technology for in-memory acceleration. A single hardware initialization using pre-clustered proteomics data allows for continuous DB searching and local re-clustering, providing a more practical and efficient alternative to clustering from scratch. Heuristics derived from the initial pre-clustered data guide the incremental process, accelerating clustering by 20x at a cost of 0.3% increase in clustering error where DB search results overlap by 96% with SOTA algorithms validating search quality. For a 131GB human genome proteomics dataset HERP setup requires 1.19mJ for 2M spectra while 1000 query search consumes only 1.1uJ at SOTA accuracy. Bucket-wise parallelization and query scheduling provides additional 100x speedup.

cs.DB↗

arXiv2025

FeNOMS: Enhancing Open Modification Spectral Library Search with In-Storage Processing on Ferroelectric NAND (FeNAND) Flash

The rapid expansion of mass spectrometry (MS) data, now exceeding hundreds of terabytes, poses significant challenges for efficient, large-scale library search - a critical component for drug discovery. Traditional processors struggle to handle this data volume efficiently, making in-storage computing (ISP) a promising alternative. This work introduces an ISP architecture leveraging a 3D Ferroelectric NAND (FeNAND) structure, providing significantly higher density, faster speeds, and lower voltage requirements compared to traditional NAND flash. Despite its superior density, the NAND structure has not been widely utilized in ISP applications due to limited throughput associated with row-by-row reads from serially connected cells. To overcome these limitations, we integrate hyperdimensional computing (HDC), a brain-inspired paradigm that enables highly parallel processing with simple operations and strong error tolerance. By combining HDC with the proposed dual-bound approximate matching (D-BAM) distance metric, tailored to the FeNAND structure, we parallelize vector computations to enable efficient MS spectral library search, achieving 43x speedup and 21x higher energy efficiency over state-of-the-art 3D NAND methods, while maintaining comparable accuracy.

cs.AR↗

arXiv2024

HPVM-HDC: A Heterogeneous Programming System for Accelerating Hyperdimensional Computing

Hyperdimensional Computing (HDC), a technique inspired by cognitive models of computation, has been proposed as an efficient and robust alternative basis for machine learning. HDC programs are often manually written in low-level and target specific languages targeting CPUs, GPUs, and FPGAs -- these codes cannot be easily retargeted onto HDC-specific accelerators. No previous programming system enables productive development of HDC programs and generates efficient code for several hardware targets. We propose a heterogeneous programming system for HDC: a novel programming language, HDC++, for writing applications using a unified programming model, including HDC-specific primitives to improve programmability, and a heterogeneous compiler, HPVM-HDC, that provides an intermediate representation for compiling HDC programs to many hardware targets. We implement two tuning optimizations, automatic binarization and reduction perforation, that exploit the error resilient nature of HDC. Our evaluation shows that HPVM-HDC generates performance-competitive code for CPUs and GPUs, achieving a geomean speed-up of 1.17x over optimized baseline CUDA implementations with a geomean reduction in total lines of code of 1.6x across CPUs and GPUs. Additionally, HPVM-HDC targets an HDC Digital ASIC and an HDC ReRAM accelerator simulator, enabling the first execution of HDC applications on these devices.

cs.PL↗

arXiv2024

RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing

Mass spectrometry (MS) is essential for protein analysis but faces significant challenges with large datasets and complex post-translational modifications, resulting in difficulties in spectral identification. Open Modification Search (OMS) improves the analysis of these modifications. We present RapidOMS, a solution leveraging the Samsung SmartSSD, which integrates SSD and FPGA in a near-storage configuration to minimize data movement and enhance the efficiency of large-scale database searching. RapidOMS employs hyperdimensional computing (HDC), a brain-inspired, high-dimensional data processing approach, exploiting the parallel processing and low-latency capabilities of FPGAs, making it well-suited for MS. Utilizing the parallelism and efficiency of bitwise operations in HDC, RapidOMS delivers up to a 60x speedup over the state-of-the-art (SOTA) CPU tool ANN-Solo and is 2.72x faster than the GPU tool HyperOMS. Furthermore, RapidOMS achieves an 11x improvement in energy efficiency compared to conventional systems, providing scalable, energy-efficient solutions for large-scale proteomics applications and advancing the efficient processing of proteomic data.

cs.DC↗

arXiv2024

Efficient Open Modification Spectral Library Searching in High-Dimensional Space with Multi-Level-Cell Memory

Open Modification Search (OMS) is a promising algorithm for mass spectrometry analysis that enables the discovery of modified peptides. However, OMS encounters challenges as it exponentially extends the search scope. Existing OMS accelerators either have limited parallelism or struggle to scale effectively with growing data volumes. In this work, we introduce an OMS accelerator utilizing multi-level-cell (MLC) RRAM memory to enhance storage capacity by 3x. Through in-memory computing, we achieve up to 77x faster data processing with two to three orders of magnitude better energy efficiency. Testing was done on a fabricated MLC RRAM chip. We leverage hyperdimensional computing to tolerate up to 10% memory errors while delivering massive parallelism in hardware.

cs.AR↗

arXiv2023

Proxima: Near-storage Acceleration for Graph-based Approximate Nearest Neighbor Search in 3D NAND

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.

cs.AR↗

arXiv2023

SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering

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.

q-bio.QM↗