arXiv subjects

Zheyu Li

Publications and source records attributed to Zheyu Li.

9 recordsLinked to original sources

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↗

arXiv2026

Compiler-Driven Approximation Tuning for Hyperdimensional Computing

As Moore's law reaches its physical and economic limits, domain-specific approaches are increasingly employed to accelerate machine learning workloads. Hyperdimensional Computing (HDC) represents one such emerging paradigm, offering an alternative to conventional deep learning techniques. Rooted in cognitive models of computation, HDC is designed bottom-up with hardware efficiency as a first-class objective. HDC workloads map naturally to heterogeneous hardware platforms, including CPUs, GPUs, and FPGAs, as well as emerging in-memory computing technologies such as Resistive RAM (ReRAM) and Phase-Change Memory (PCM). HDC algorithms are intrinsically tolerant to noise and approximation, enabling substantial performance gains with minimal accuracy loss. In this work, we introduce ApproxHDC, a framework for automated identification and application of domain-specific approximations in HDC workloads. ApproxHDC extends the HPVM-HDC compiler infrastructure to enable retargetable compilation across diverse hardware backends, including CPUs, GPUs, and simulated ReRAM and PCM-based accelerators. The space of possible approximations is exponentially large; ApproxHDC employs efficient search and analysis to navigate it and identify high-impact configurations spanning both software and hardware levels.

cs.PL↗

arXiv2026

GEN-Graph: Heterogeneous PIM Accelerator for General Computational Patterns in Graph-based Dynamic Programming

While graph-based dynamic programming (DP) is a cornerstone of genomics and network analytics, its efficiency is hampered by fundamentally conflicting computational patterns. Matrix-centric DP drives regular, compute-bound network analytics, while topology-centric DP handles irregular, memory-bound genomic traversals. These two categories of DP have substantially different computation patterns and dataflows, which makes it difficult for a single homogeneous processing-in-memory (PIM) architecture to efficiently support both. This work presents GEN-Graph, a novel heterogeneous PIM chiplet that integrates two types of specialized compute tiles within a 2.5D package: Matrix-tile, a processing-using-memory (PUM) tile optimized for matrix-centric workloads, such as all-pairs shortest path (APSP); and traversal-tile, a processing-near-memory (PNM) tile optimized for traversal-centric DP workloads, such as DNA sequence alignment. Our hardware-software co-design employs recursive partitioning and reconfigurable windowed bit-parallel logic to ensure exact computation. Results show the matrix tile achieves 42.8x speedup and 392x energy efficiency over the NVIDIA H100 GPU for APSP. For sequence-to-graph alignment, the traversal tile sustains 2.56 million reads/s (short-reads) and 39.3 thousand reads/s (long-reads), outperforming state-of-the-art accelerators by up to 2.56x in throughput. GEN-Graph provides the first scalable, exact solution for general DP dataflows by matching hardware specialization to algorithmic structure.

cs.AR↗

arXiv2025

PIM-FW: Hardware-Software Co-Design of All-pairs Shortest Paths in DRAM

All-pairs shortest paths (APSP) is a fundamental algorithm used for routing, logistics, and network analysis, but the cubic time complexity and heavy data movement of the canonical Floyd-Warshall (FW) algorithm severely limits its scalability on conventional CPUs or GPUs. In this paper, we propose PIM-FW, a novel co-designed hardware architecture and dataflow that leverages processing in and near memory architecture designed to accelerate blocked FW algorithm on an HBM3 stack. To enable fine-grained parallelism, we propose a massively parallel array of specialized bit-serial bank PE and channel PE designed to accelerate the core min-plus operations. Our novel dataflow complements this hardware, employing an interleaved mapping policy for superior load balancing and hybrid in and near memory computing model for efficient computation and reduction. The novel in-bank computing approach allows all distance updates to be performed and stored in memory bank, a key contribution is that eliminates the data movement bottleneck inherent in GPU-based approaches. We implement a full software and hardware co-design using a cycle-accurate simulator to simulate an 8-channel, 4-Hi HBM3 PIM stack on real road-network traces. Experimental results show that, for a 8192 x 8192 graph, PIM-FW achieves a 18.7x speedup in end-to-end execution, and consumes 3200x less DRAM energy compared to a state-of-the-art GPU-only Floyd-Warshall.

cs.AR↗

arXiv2025

RAPID-Graph: Recursive All-Pairs Shortest Paths Using Processing-in-Memory for Dynamic Programming on Graphs

All-pairs shortest paths (APSP) remains a major bottleneck for large-scale graph analytics, as data movement with cubic complexity overwhelms the bandwidth of conventional memory hierarchies. In this work, we propose RAPID-Graph to address this challenge through a co-designed processing-in-memory (PIM) system that integrates algorithm, architecture, and device-level optimizations. At the algorithm level, we introduce a recursion-aware partitioner that enables an exact APSP computation by decomposing graphs into vertex tiles to reduce data dependency, such that both Floyd-Warshall and Min-Plus kernels execute fully in-place within digital PIM arrays. At the architecture and device levels, we design a 2.5D PIM stack integrating two phase-change memory compute dies, a logic die, and high-bandwidth scratchpad memory within a unified advanced package. An external non-volatile storage stack stores large APSP results persistently. The design achieves both tile-level and unit-level parallel processing to sustain high throughput. On the 2.45M-node OGBN-Products dataset, RAPID-Graph is 5.8x faster and 1,186x more energy efficient than state-of-the-art GPU clusters, while exceeding prior PIM accelerators by 8.3x in speed and 104x in efficiency. It further delivers up to 42.8x speedup and 392x energy savings over an NVIDIA H100 GPU.

cs.AR↗

arXiv2025

CHIME: Chiplet-based Heterogeneous Near-Memory Acceleration for Edge Multimodal LLM Inference

The proliferation of large language models (LLMs) is accelerating the integration of multimodal assistants into edge devices, where inference is executed under stringent latency and energy constraints, often exacerbated by intermittent connectivity. These challenges become particularly acute in the context of multimodal LLMs (MLLMs), as high-dimensional visual inputs are transformed into extensive token sequences, thereby inflating the key-value (KV) cache and imposing substantial data movement overheads to the LLM backbone. To address these issues, we present CHIME, a chiplet-based heterogeneous near-memory acceleration for edge MLLMs inference. CHIME leverages the complementary strengths of integrated monolithic 3D (M3D) DRAM and RRAM chiplets: DRAM supplies low-latency bandwidth for attention, while RRAM offers dense, non-volatile storage for weights. This heterogeneous hardware is orchestrated by a co-designed mapping framework that executes fused kernels near data, minimizing cross-chiplet traffic to maximize effective bandwidth. On FastVLM (0.6B/1.7B) and MobileVLM (1.7B/3B), CHIME achieves up to 54x speedup and up to 246x better energy efficiency per inference as compared to the edge GPU NVIDIA Jetson Orin NX. It sustains 116.5-266.5 token/J compared to Jetson's 0.7-1.1 token/J. Furthermore, it delivers up to 69.2x higher throughput than the state-of-the-art PIM accelerator FACIL. Compared to the M3D DRAM-only design, CHIME's heterogeneous memory further improves energy efficiency by 7% and performance by 2.4x.

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

SpecPCM: A Low-power PCM-based In-Memory Computing Accelerator for Full-stack Mass Spectrometry Analysis

Mass spectrometry (MS) is essential for proteomics and metabolomics but faces impending challenges in efficiently processing the vast volumes of data. This paper introduces SpecPCM, an in-memory computing (IMC) accelerator designed to achieve substantial improvements in energy and delay efficiency for both MS spectral clustering and database (DB) search. SpecPCM employs analog processing with low-voltage swing and utilizes recently introduced phase change memory (PCM) devices based on superlattice materials, optimized for low-voltage and low-power programming. Our approach integrates contributions across multiple levels: application, algorithm, circuit, device, and instruction sets. We leverage a robust hyperdimensional computing (HD) algorithm with a novel dimension-packing method and develop specialized hardware for the end-to-end MS pipeline to overcome the non-ideal behavior of PCM devices. We further optimize multi-level PCM devices for different tasks by using different materials. We also perform a comprehensive design exploration to improve energy and delay efficiency while maintaining accuracy, exploring various combinations of hardware and software parameters controlled by the instruction set architecture (ISA). SpecPCM, with up to three bits per cell, achieves speedups of up to 82x and 143x for MS clustering and DB search tasks, respectively, along with a four-orders-of-magnitude improvement in energy efficiency compared with state-of-the-art CPU/GPU tools.

cs.AR↗