DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

Zuher Jahshan; Itay Merlin; Esteban Garzón; Leonid Yavits

doi:10.1145/3613424.3614262

DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

Zuher Jahshan, Itay Merlin, Esteban Garzón, Leonid Yavits

Bar-Ilan University - The Alexander Kofkin Faculty of Engineering

University of Calabria

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

11 Scopus citations

Abstract

We propose a novel dynamic storage-based approximate search content addressable memory (DASH-CAM) for computational genomics applications, particularly for identification and classification of viral pathogens of epidemic significance. DASH-CAM provides 5.5 × better density compared to state-of-the-art SRAM-based approximate search CAM. This allows using DASH-CAM as a portable classifier that can be applied to pathogen surveillance in low-quality field settings during pandemics, as well as to pathogen diagnostics at points of care. DASH-CAM approximate search capabilities allow a high level of flexibility when dealing with a variety of industrial sequencers with different error profiles. DASH-CAM achieves up to 30% and 20% higher F1 score when classifying DNA reads with 10% error rate, compared to state-of-the-art DNA classification tools MetaCache-GPU and Kraken2 respectively. Simulated at 1GHz, DASH-CAM provides 1, 178 × and 1, 040 × average speedup over MetaCache-GPU and Kraken2 respectively.

Original language	English
Title of host publication	Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023
Publisher	Association for Computing Machinery, Inc
Pages	1453-1465
Number of pages	13
ISBN (Electronic)	9798400703294
DOIs	https://doi.org/10.1145/3613424.3614262
State	Published - 28 Oct 2023
Event	56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023 - Toronto, Canada Duration: 28 Oct 2023 → 1 Nov 2023

Publication series

Name	Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023

Conference

Conference	56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023
Country/Territory	Canada
City	Toronto
Period	28/10/23 → 1/11/23

Bibliographical note

Publisher Copyright:
© 2023 Owner/Author.

Funding

This work was supported by the European Union's Horizon Europe programme for research and innovation under grant agreement No. 101047160. The work of Esteban Garzón was supported by the Italian MUR under the call "Horizon Europe 2021-2027 programme - H25F21001420001" This work was supported by the European Union’s Horizon Europe programme for research and innovation under grant agreement No. 101047160. The work of Esteban Garzón was supported by the Italian MUR under the call “Horizon Europe 2021-2027 programme – H25F21001420001”

Funders	Funder number
European Union's Horizon Europe Programme for Research and Innovation
European Union’s Horizon Europe programme for research and innovation	101047160
Horizon Europe 2021-2027 programme	H25F21001420001
Ministero dell’Istruzione, dell’Università e della Ricerca

Keywords

Approximate search
Content Addressable Memory
Dynamic approximate search
GC-eDRAM
Pathogen classification
Pathogen detection

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1145/3613424.3614262

Cite this

Jahshan, Z., Merlin, I., Garzón, E., & Yavits, L. (2023). DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification. In Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023 (pp. 1453-1465). (Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023). Association for Computing Machinery, Inc. https://doi.org/10.1145/3613424.3614262

Jahshan, Zuher ; Merlin, Itay ; Garzón, Esteban et al. / DASH-CAM : Dynamic Approximate SearcH Content Addressable Memory for genome classification. Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023. Association for Computing Machinery, Inc, 2023. pp. 1453-1465 (Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023).

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title = "DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification",

abstract = "We propose a novel dynamic storage-based approximate search content addressable memory (DASH-CAM) for computational genomics applications, particularly for identification and classification of viral pathogens of epidemic significance. DASH-CAM provides 5.5 × better density compared to state-of-the-art SRAM-based approximate search CAM. This allows using DASH-CAM as a portable classifier that can be applied to pathogen surveillance in low-quality field settings during pandemics, as well as to pathogen diagnostics at points of care. DASH-CAM approximate search capabilities allow a high level of flexibility when dealing with a variety of industrial sequencers with different error profiles. DASH-CAM achieves up to 30% and 20% higher F1 score when classifying DNA reads with 10% error rate, compared to state-of-the-art DNA classification tools MetaCache-GPU and Kraken2 respectively. Simulated at 1GHz, DASH-CAM provides 1, 178 × and 1, 040 × average speedup over MetaCache-GPU and Kraken2 respectively.",

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Jahshan, Z, Merlin, I, Garzón, E & Yavits, L 2023, DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification. in Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023. Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023, Association for Computing Machinery, Inc, pp. 1453-1465, 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023, Toronto, Canada, 28/10/23. https://doi.org/10.1145/3613424.3614262

DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification. / Jahshan, Zuher; Merlin, Itay; Garzón, Esteban et al.
Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023. Association for Computing Machinery, Inc, 2023. p. 1453-1465 (Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Jahshan Z, Merlin I, Garzón E, Yavits L. DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification. In Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023. Association for Computing Machinery, Inc. 2023. p. 1453-1465. (Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, MICRO 2023). doi: 10.1145/3613424.3614262

DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

Abstract

Publication series

Conference

Bibliographical note

Funding

Keywords

UN SDGs

Access to Document

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Cite this