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Genome sequence analysis is a powerful tool in medical and scientific research. Considering the inevitable sequencing errors and genetic variations, approximate string matching (ASM) has been adopted in practice for genome sequencing.…

The second-order training methods can converge much faster than first-order optimizers in DNN training. This is because the second-order training utilizes the inversion of the second-order information (SOI) matrix to find a more accurate…

Hardware Architecture · Computer Science 2022-10-28 Yilong Zhao , Li Jiang , Mingyu Gao , Naifeng Jing , Chengyang Gu , Qidong Tang , Fangxin Liu , Tao Yang , Xiaoyao Liang

The continuous shift of computational bottlenecks to the memory access and data transfer, especially for AI applications, poses the urgent needs of re-engineering the computer architecture fundamentals. Many edge computing applications,…

Systems and Control · Electrical Eng. & Systems 2025-01-31 Georgios Papandroulidakis , Shady Agwa , Ahmet Cirakoglu , Themis Prodromakis

This paper presents GRAPHR, the first ReRAM-based graph processing accelerator. GRAPHR follows the principle of near-data processing and explores the opportunity of performing massive parallel analog operations with low hardware and energy…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-12-12 Linghao Song , Youwei Zhuo , Xuehai Qian , Hai Li , Yiran Chen

Database applications are increasingly bottlenecked by memory bandwidth and latency due to the memory wall and the limited scalability of DRAM. Join queries, central to analytical workloads, require intensive memory access and are…

Hardware Architecture · Computer Science 2025-08-13 Sabiha Tajdari , Anastasia Ailamaki , Sandhya Dwarkadas

Genome analysis has revolutionized fields such as personalized medicine and forensics. Modern sequencing machines generate vast amounts of fragmented strings of genome data called reads. The alignment of these reads into a complete DNA…

Hardware Architecture · Computer Science 2024-11-22 Rotem Ben-Hur , Orian Leitersdorf , Ronny Ronen , Lidor Goldshmidt , Idan Magram , Lior Kaplun , Leonid Yavitz , Shahar Kvatinsky

Resistive Random Access Memory (ReRAM) based Processing In Memory (PIM) Accelerator has emerged as a promising computing architecture for memory intensive applications, such as Deep Neural Networks (DNNs). However, due to its immaturity,…

Emerging Technologies · Computer Science 2023-12-19 Je-Woo Jang , Thai-Hoang Nguyen , Joon-Sung Yang

Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore…

Hardware Architecture · Computer Science 2020-08-10 Qian Lou , Sarath Janga , Lei Jiang

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…

Neural networks are an increasingly attractive algorithm for natural language processing and pattern recognition. Deep networks with >50M parameters are made possible by modern GPU clusters operating at <50 pJ per op and more recently,…

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…

Hardware Architecture · Computer Science 2023-11-01 Cenlin Duan , Jianlei Yang , Xiaolin He , Yingjie Qi , Yikun Wang , Yiou Wang , Ziyan He , Bonan Yan , Xueyan Wang , Xiaotao Jia , Weitao Pan , Weisheng Zhao

Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major…

Hardware Architecture · Computer Science 2022-05-31 Geraldo F. Oliveira , Amirali Boroumand , Saugata Ghose , Juan Gómez-Luna , Onur Mutlu

Due to the very rapidly growing use of Artificial Neural Networks (ANNs) in real-world applications related to machine learning and Artificial Intelligence (AI), several hardware accelerator de-signs for ANNs have been proposed recently. In…

Hardware Architecture · Computer Science 2021-03-09 Supreeth Mysore Shivanandamurthy , Ishan. G. Thakkar , Sayed Ahmad Salehi

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…

Machine Learning · Computer Science 2023-11-07 Marcel Khalifa , Barak Hoffer , Orian Leitersdorf , Robert Hanhan , Ben Perach , Leonid Yavits , Shahar Kvatinsky

Our ISCA 2015 paper provides a new programmable processing-in-memory (PIM) architecture and system design that can accelerate key data-intensive applications, with a focus on graph processing workloads. Our major idea was to completely…

Hardware Architecture · Computer Science 2023-06-28 Junwhan Ahn , Sungpack Hong , Sungjoo Yoo , Onur Mutlu , Kiyoung Choi

Processing In Memory (PIM) accelerators are promising architecture that can provide massive parallelization and high efficiency in various applications. Such architectures can instantaneously provide ultra-fast operation over extensive…

Hardware Architecture · Computer Science 2022-07-26 Kazi Abu Zubair , Sumit Kumar Jha , David Mohaisen , Clayton Hughes , Amro Awad

Large-scale genomic workflows used in precision medicine can process datasets spanning tens to hundreds of gigabytes per sample, leading to high memory spikes, intensive disk I/O, and task failures due to out-of-memory errors. Simple static…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-11-21 Daniel Mas Montserrat , Ray Verma , Míriam Barrabés , Francisco M. de la Vega , Carlos D. Bustamante , Alexander G. Ioannidis

Computation-in-Memory (CiM) is attracting attention as a technology that can perform MAC calculations required for AI accelerators, at high speed with low power consumption. However, there is a problem regarding power consumption and…

Hardware Architecture · Computer Science 2025-07-21 Fuyuki Kihara , Seiji Uenohara , Satoshi Awamura , Naoko Misawa , Chihiro Matsui , Ken Takeuchi

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…

Cryptography and Security · Computer Science 2023-10-04 Harshita Gupta , Mayank Kabra , Juan Gómez-Luna , Konstantinos Kanellopoulos , Onur Mutlu

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…

Hardware Architecture · Computer Science 2025-05-19 Feng Cheng , Tunhou Zhang , Junyao Zhang , Jonathan Hao-Cheng Ku , Yitu Wang , Xiaoxuan Yang , Hai , Li , Yiran Chen