Institute of Information Systems and Applications |
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Speaker: |
Prof. Chien-Chung Ho(何建忠教授), National Cheng Kung University |
Topic: |
UpPipe: A Novel Pipeline Management on In-Memory Processors for RNA-seq Quantification |
Date: |
13:20-15:00 Wednesday 8-Mar-2023 |
QR Code: |
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Link: |
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Location: |
Delta 103 |
Hosted by: |
Prof. Te-Chuan Chiu |
Abstract
RNA sequence quantification is an important analysis method to measure
transcript abundances. A key overhead in RNA-seq quantification is to map a set of
RNA reads to multiple reference transcripts, i.e., transcriptome. Besides, the
performance of RNAseq quantification is strictly limited by the excessive amounts of
data movement between CPU and memory, i.e., memory wall problem on the
conventional architecture. As the first publicly commercial processing-in-memory
(PIM) system, UPMEM DPU, is proposed, the PIM gradually becomes a promising
solution to overcome the memory wall problem. DPUs show great potential to
accelerate data-intensive workloads by minimizing off-chip data movement between
CPU and memory. This talk is about how to improve the performance of RNA-seq
quantification by fully exploiting the strengths of DPU. I will present a novel DPU-
aware pipeline design “UpPipe” built on the software layer to address the hardware
constraints of DPU. In addition, DPU-friendly transcriptome allocation policy and
DPU-aware pipeline management with considering the quantification characteristics
and DPU’s constraints are also presented.
Bio.
Dr. Ho is an Assistant Professor in the Department of Computer Science and
Information Engineering (CSIE), National Cheng Kung University (NCKU). Before
joining NCKU CSIE, he worked in the Department of Computer Science and
Information Engineering (CSIE), National Chung Cheng University (CCU) from 2017 to
2021, and as a Postdoctoral Researcher in the Institute of Information Science (IIS),
Academia Sinica from 2016 to 2017. He received his Ph.D. degree in the Department
of Computer Science and Information Engineering from National Taiwan University
in June 2016. His primary research interests include emerging non-volatile memory
and storage technologies, memory and storage systems, and next-generation
memory/storage architecture designs.
faculty and students are welcome to join.