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research-article

EDAM: edit distance tolerant approximate matching content addressable memory

Authors:

Esteban Garzón,

Leonid YavitsAuthors Info & Claims

ISCA '22: Proceedings of the 49th Annual International Symposium on Computer Architecture

Pages 495 - 507

https://doi.org/10.1145/3470496.3527424

Published: 11 June 2022 Publication History

Abstract

We propose a novel edit distance-tolerant content addressable memory (EDAM) for energy-efficient approximate search applications. Unlike state-of-the-art approximate search solutions that tolerate certain Hamming distance between the query pattern and the stored data, EDAM tolerates edit distance, which makes it especially efficient in applications such as text processing and genome analysis. EDAM was designed using a commercial 65 nm 1.2 V CMOS technology and evaluated through extensive Monte Carlo simulations, while considering different process corners. Simulation results show that EDAM can achieve robust approximate search operation with a wide range of edit distance threshold levels. EDAM is functionally evaluated as a pathogen DNA detection and classification accelerator. EDAM achieves up to 1.7× higher F₁ score for high-quality DNA reads and up to 19.55× higher F₁ score for DNA reads with 15% error rate, compared to state-of-the-art DNA classification tool Kraken2. Simulated at 667 MHz, EDAM provides 1, 214× average speedup over Kraken2. This makes EDAM suitable for hardware acceleration of genomic surveillance of outbreaks, such as the ongoing Covid-19 pandemic.

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Cited By

Taco RGarzón EHanhan RTeman AYavits LLanuzza M(2024)Designing Precharge-Free Energy-Efficient Content-Addressable MemoriesIEEE Transactions on Very Large Scale Integration (VLSI) Systems10.1109/TVLSI.2024.347503632:12(2303-2314)Online publication date: Dec-2024
https://doi.org/10.1109/TVLSI.2024.3475036
Shaban AHou TSuri M(2024)SOT-MRAM-Based Approximate Content Addressable Memory for DNA ClassificationIEEE Transactions on Electron Devices10.1109/TED.2024.342381271:9(5732-5738)Online publication date: Sep-2024
https://doi.org/10.1109/TED.2024.3423812
Merlin IGarzón EFish AYavits L(2024)DIPER: Detection and Identification of Pathogens Using Edit Distance-Tolerant Resistive CAMIEEE Transactions on Computers10.1109/TC.2023.331582973:10(2463-2473)Online publication date: Oct-2024
https://doi.org/10.1109/TC.2023.3315829
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cover image ACM Conferences

ISCA '22: Proceedings of the 49th Annual International Symposium on Computer Architecture

June 2022

1097 pages

ISBN:9781450386104

DOI:10.1145/3470496

General Chairs:
Valentina Salapura
Google
,
Mohamed Zahran
New York University
,
Program Chairs:
Fred Chong
The University of Chicago
,
Lingjia Tang
The University of Michigan

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Taco RGarzón EHanhan RTeman AYavits LLanuzza M(2024)Designing Precharge-Free Energy-Efficient Content-Addressable MemoriesIEEE Transactions on Very Large Scale Integration (VLSI) Systems10.1109/TVLSI.2024.347503632:12(2303-2314)Online publication date: Dec-2024
https://doi.org/10.1109/TVLSI.2024.3475036
Shaban AHou TSuri M(2024)SOT-MRAM-Based Approximate Content Addressable Memory for DNA ClassificationIEEE Transactions on Electron Devices10.1109/TED.2024.342381271:9(5732-5738)Online publication date: Sep-2024
https://doi.org/10.1109/TED.2024.3423812
Merlin IGarzón EFish AYavits L(2024)DIPER: Detection and Identification of Pathogens Using Edit Distance-Tolerant Resistive CAMIEEE Transactions on Computers10.1109/TC.2023.331582973:10(2463-2473)Online publication date: Oct-2024
https://doi.org/10.1109/TC.2023.3315829
Jahshan ZYavits L(2024) MajorK: Majority Based k mer Matching in Commodity DRAM IEEE Computer Architecture Letters10.1109/LCA.2024.338425923:1(83-86)Online publication date: Jan-2024
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Ghiasi NSadrosadati MMustafa HGollwitzer AFirtina CEudine JMao HLindegger JCavlak MAlser MPark JMutlu O(2024)MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA)10.1109/ISCA59077.2024.00054(660-677)Online publication date: 29-Jun-2024
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Walia SYe CBera ALodhavia DTurakhia Y(2024)TALCO: Tiling Genome Sequence Alignment Using Convergence of Traceback Pointers2024 IEEE International Symposium on High-Performance Computer Architecture (HPCA)10.1109/HPCA57654.2024.00044(91-107)Online publication date: 2-Mar-2024
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Khalifa MHoffer BLeitersdorf OHanhan RPerach BYavits LKvatinsky S(2023)ClaPIM: Scalable Sequence Classification Using Processing-in-MemoryIEEE Transactions on Very Large Scale Integration (VLSI) Systems10.1109/TVLSI.2023.329303831:9(1347-1357)Online publication date: 1-Sep-2023
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Garzón EGolman RLanuzza MTeman AYavits L(2023)A Low-Complexity Sensing Scheme for Approximate Matching Content-Addressable MemoryIEEE Transactions on Circuits and Systems II: Express Briefs10.1109/TCSII.2023.328625770:10(3867-3871)Online publication date: Oct-2023
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