Hamming Distance Tolerant Content-Addressable Memory (HD-CAM) for DNA Classification

Garzón, Esteban; Golman, Roman; Zuher, Jahshan,; Hanhan, Robert; Vinshtok-Melnik, Natan; Lanuzza, Marco; Teman, Adam; Yavits, Leonid

doi:10.1109/access.2022.3158305

Cited by 25 publications

(26 citation statements)

References 66 publications

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“…In such a configuration, the approximate search utilizes the matchline charge redistribution rather than its rise or fall time. By tuning this gate voltage (possibly automatically), we can set a desired level of Hamming distance without adjusting the ML sampling time [34], [35].…”

Section: F Approximate Search Cam (Acam)mentioning

confidence: 99%

“…A small Hamming distance tolerance (≤ 2 bits) approximate CAM is proposed in [62], [63]. Garzón, et al [34] and Hanhan, et al [35] use the combination of the voltage, controlling the speed of the matchline discharge, and the sense amplifier reference voltage to define the Hamming distance threshold. These designs are capable of tolerating very large Hamming distances.…”

Section: Related Workmentioning

confidence: 99%

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AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

Garzón

Lanuzza

Teman

et al. 2023

IEEE J. Emerg. Sel. Topics Circuits Syst.

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In-memory computing seeks to minimize data movement and alleviate the memory wall by computing in-situ, in the same place that the data is located. One of the key emerging technologies that promises to enable such computing-inmemory is spin-transfer torque magnetic tunnel junction (STT-MTJ). This paper proposes AM 4 , a combined STT-MTJ-based Content Addressable Memory (CAM), Ternary CAM (TCAM), approximate matching (similarity search) CAM (ACAM), and in-memory Associative Processor (AP) design, inspired by the recently announced Samsung MRAM crossbar. We demonstrate and evaluate the performance and energy-efficiency of the AM 4based AP using a variety of data intensive workloads. We show that an AM 4 -based AP outperforms state-of-the-art solutions both in performance (with the average speedup of about 10 ×) and energy-efficiency (by about 60 × on average).

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Section: F Approximate Search Cam (Acam)mentioning

confidence: 99%

Section: Related Workmentioning

confidence: 99%

AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

Garzón

Lanuzza

Teman

et al. 2023

IEEE J. Emerg. Sel. Topics Circuits Syst.

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“…Some of the approximate search CAM designs use timing (i.e., the matching score signal delay, or the speed of the matchline discharge) as a measure of Hamming distance. HD-CAM [27], a Hamming distance tolerant CAM, uses the combination of the voltage, controlling the speed of the matchline discharge, and the sense amplifier reference voltage to define the Hamming distance threshold. HD-CAM is capable of tolerating very large Hamming distances.…”

Section: Approximate Search Content-addressable Memorymentioning

confidence: 99%

Edam

Hanhan

Garzón

Zuher

et al. 2022

Proceedings of the 49th Annual International Symposium on Computer Architecture

Self Cite

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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 𝐹 1 score for high-quality DNA reads and up to 19.55× higher 𝐹 1 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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“…CAM cells, sense ampli ers, decoders, encoder, write drivers and pre-charge circuits make up a memory array [5]. Decoders are used for accessing a particular CAM cell in the array and are placed along row as well as column.…”

Section: Structure Of Memory Arraymentioning

confidence: 99%

A Novel Design of Low Power, Modified Pre-charge free Binary CAM Array with Pre-computation for Search-Intensive Applications

Gavaskar¹,

Surendar²,

S³

et al. 2022

Preprint

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Memory is a storage space that is essential for storing the repetitive data and the instructions to perform an operation. In modern processors speed has been increased significantly but memory enhancements are mainly focusing on the ability to store more data in less space and to reduce the latency. Content Addressable Memory (CAM) cells are preferred over SRAM cells as they are faster and gives the address of the matched data whereas SRAM uses address to access particular data. The circuit of Modified Pre-charge free CAM cell proposed in this paper is made up of basic 6T SRAM cell (2 cross-coupled inverters and 2 access transistors) and separate comparison circuit (1 PMOS and 1 NMOS transistor). The 8X8 memory array consists of memory cells, row and column decoders, encoder, pre-charge circuits, sense amplifiers and write driver circuits. The various parameters like delay, dynamic power and power delay product are measured and compared with other CAM cells. CADENCE Virtuoso Tool is used for designing the various circuits in 90 nm technology. The simulation results demonstrate that the suggested CAM cell outperforms other cells, hence it is employed to create the array structure. The 8X8 CAM array based on MPF CAM cell has less power and less delay when compared with other array structures.

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Hamming Distance Tolerant Content-Addressable Memory (HD-CAM) for DNA Classification

Cited by 25 publications

References 66 publications

AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

Edam

A Novel Design of Low Power, Modified Pre-charge free Binary CAM Array with Pre-computation for Search-Intensive Applications

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Hamming Distance Tolerant Content-Addressable Memory (HD-CAM) for DNA Classification

Cited by 25 publications

References 66 publications

AM4: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

AM4: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

Edam

A Novel Design of Low Power, Modified Pre-charge free Binary CAM Array with Pre-computation for Search-Intensive Applications

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Product

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AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing

AM⁴: MRAM Crossbar Based CAM/TCAM/ACAM/AP for In-Memory Computing