Related papers: Accelerating DNA Read Mapping with Digital Process…
Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms.…
Processing-in-memory (PIM), as a novel computing paradigm, provides significant performance benefits from the aspect of effective data movement reduction. SRAM-based PIM has been demonstrated as one of the most promising candidates due to…
Digital processing-in-memory (PIM) architectures are rapidly emerging to overcome the memory-wall bottleneck by integrating logic within memory elements. Such architectures provide vast computational power within the memory itself in the…
Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…
The performance bottleneck of deep-learning-based recommender systems resides in their backbone Deep Neural Networks. By integrating Processing-In-Memory~(PIM) architectures, researchers can reduce data movement and enhance energy…
Decoder-only Transformer models such as GPT have demonstrated exceptional performance in text generation, by autoregressively predicting the next token. However, the efficacy of running GPT on current hardware systems is bounded by low…
The excellent performance of modern deep neural networks (DNNs) comes at an often prohibitive training cost, limiting the rapid development of DNN innovations and raising various environmental concerns. To reduce the dominant data movement…
Approximate nearest neighbor search (ANNS) is essential for applications like recommendation systems and retrieval-augmented generation (RAG) but is highly I/O-intensive and memory-demanding. CPUs face I/O bottlenecks, while GPUs are…
Neural networks (NNs) are growing in importance and complexity. A neural network's performance (and energy efficiency) can be bound either by computation or memory resources. The processing-in-memory (PIM) paradigm, where computation is…
Computing on encrypted data is a promising approach to reduce data security and privacy risks, with homomorphic encryption serving as a facilitator in achieving this goal. In this work, we accelerate homomorphic operations using the…
With the widespread use of deep neural networks(DNNs) in intelligent systems, DNN accelerators with high performance and energy efficiency are greatly demanded. As one of the feasible processing-in-memory(PIM) architectures,…
Deep Neural Networks (DNNs) have transformed the field of machine learning and are widely deployed in many applications involving image, video, speech and natural language processing. The increasing compute demands of DNNs have been widely…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…
Processing-in-memory (PIM) architecture is an inherent match for data analytics application, but we observe major challenges to address when accelerating it using PIM. In this paper, we propose Darwin, a practical LRDIMM-based multi-level…
The widespread integration of embedded systems across various industries has facilitated seamless connectivity among devices and bolstered computational capabilities. Despite their extensive applications, embedded systems encounter…
With Von-Neumann computing architectures struggling to address computationally- and memory-intensive big data analytic task today, Processing-in-Memory (PIM) platforms are gaining growing interests. In this way, processing-in-DRAM…
The performance and efficiency of running large-scale datasets on traditional computing systems exhibit critical bottlenecks due to the existing "power wall" and "memory wall" problems. To resolve those problems, processing-in-memory (PIM)…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
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…