EDAM: Edit Distance tolerant Approximate Matching content addressable memory

Robert Hanhan, Esteban Garzón, Zuher Jahshan, Adam Teman, Marco Lanuzza, Leonid Yavits

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

10 Scopus citations

Abstract

We propose a novel edit distance-tolerant content addressable memory (EDAM) for energy-efcient 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 efcient 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 classifcation 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 classifcation 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.

Original languageEnglish
Title of host publicationISCA 2022 - Proceedings of the 49th Annual International Symposium on Computer Architecture
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages495-507
Number of pages13
ISBN (Electronic)9781450386104
DOIs
StatePublished - 18 Jun 2022
Event49th IEEE/ACM International Symposium on Computer Architecture, ISCA 2022 - New York, United States
Duration: 18 Jun 202222 Jun 2022

Publication series

NameProceedings - International Symposium on Computer Architecture
ISSN (Print)1063-6897

Conference

Conference49th IEEE/ACM International Symposium on Computer Architecture, ISCA 2022
Country/TerritoryUnited States
CityNew York
Period18/06/2222/06/22

Bibliographical note

Publisher Copyright:
© 2022 Copyright held by the owner/author(s). Publication rights licensed to ACM.

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