@inproceedings{ee823d1a6fac40b8827ac5463908cd4a,
title = "PIM-Quantifier: A Processing-in-Memory Platform for mRNA Quantification",
abstract = "Processing-in-memory (PIM) architecture has been considered as a promising solution for the 'memory-wall' issue in many data-intensive applications, especially in bioinformatics. Recent works of developing PIM for genome alignment and assembling have achieved tremendous improvement, while another important genome analysis-mRNA quantification has not been explored. Efficient and accurate mRNA quantification is a crucial step for molecular signature identification, disease outcome prediction and drug development. In this paper, for the first time, we propose a SOT-MRAM based PIM platform, named PIM-Quantifier, for efficient mRNA quantification. A PIM-friendly alignment-free quantification algorithm is first proposed. Then, we present the optimized PIM architecture/circuit designs and mapping method to efficiently accelerate mRNA quantification. Extensive experiments show that PIM-Quantifier significantly improves mRNA quantification performance than CPU and recent other PIM platforms in efficiency defined as throughput/power.",
keywords = "MRAM, Processing-in-memory, mRNA-seq",
author = "Fan Zhang and Shaahin Angizi and Fahmi, {Naima Ahmed} and Wei Zhang and Deliang Fan",
note = "Publisher Copyright: {\textcopyright} 2021 IEEE.; 58th ACM/IEEE Design Automation Conference, DAC 2021 ; Conference date: 05-12-2021 Through 09-12-2021",
year = "2021",
month = dec,
day = "5",
doi = "10.1109/DAC18074.2021.9586144",
language = "English (US)",
series = "Proceedings - Design Automation Conference",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "43--48",
booktitle = "2021 58th ACM/IEEE Design Automation Conference, DAC 2021",
address = "United States",
}