Call for participation: 5th Accelerator Architecture in
Computational Biology and Bioinformatics workshop (AACBB-2023)
June 18th, 2023 Orlando, Florida, USA
In conjunction with the 50th International Symposium on
Computer Architecture (ISCA-2023)
Workshop website https://aacbb-workshop.github.io/
Over the last decade, the advent of high-throughput
sequencing techniques brought an exponential growth in sequenced data. At the
same time, the single-thread performance continued to improve by only a few
percent point annually. The growing gap between the performance demand to
performance supply became a significant challenge in the path to scientific
discovery. The computational bottleneck of genome analysis pipelines became
even more apparent during the Covid-19 pandemic, where fast and accurate virus
detection and classification tools have been critical for the worldwide genomic
surveillance system.
The gap between the performance of a conventional
computer architecture and the biological data processing requirements is
growing. For example, assembling a human genome from 3rd generation sequenced
data may require hundreds of CPU hours. Hence, computational biology and
bioinformatics will have to rely on hardware accelerators to allow processing
to keep up with the exploding amount of sequenced data.
In a typical application, the dominant portion of the
runtime is spent in a small number of computational kernels, making it an
excellent target for hardware acceleration. The combination of increasingly
large datasets and high-performance computing requirements make computational
biology a prime candidate to benefit from accelerator architecture research.
Potential directions include heterogeneous architectures, 3D integration,
near-data processing, in-data processing, and reconfigurable architectures.
This workshop will focus on architecture and design of
hardware accelerators for computational biology and bioinformatics problems. We
plan to present and discuss a variety of acceleration techniques, accelerator
architectures and their implications on the development of computational
biology. This year, we plan to extend the industry angle, by providing a
keynote and invited talks from leading industry research specialists.
Keynote Speakers
• Katherine A. Yelick, Prof. of Electrical Engineering and Computer Science, UC Berkley.
Genomic Analysis at Scale: Mapping Irregular Computations to Advanced Architectures
• Dominique Lavenier, CNRS Research Director, IRISA/INRIA.
Exploring genomic algorithms on UPMEM Processing-in-Memory Architecture
• Damla Senol, Bionano.
Accelerating the Transformation in How We Analyze the Human Genome
List of Topics
This workshop focuses on architecture and design of hardware and software accelerators for computational biology and bioinformatics
problems.
Topics of interest include, but are not limited to the following:
• Hardware and software algorithms/applications in the fields of computational biology, such as (but not limited to):
o Bioinformatics
o Genomics
o Proteomics
o Protein structure prediction
o Covid-19 pandemic
o Antimicrobial resistance
• Bioinformatics and computational biology accelerator architecture and design based on (but not limited to):
o Heterogeneous architectures
o 3D memory-logic stack
o Near-memory and in-memory processing
o FPGAs and reconfigurable
• Emerging memory technologies and their impact on bioinformatics and computational biology
• Impact of bioinformatics and biology applications on computer architecture research
• Bioinformatics and computational biology-inspired hardware/software trade-offs
Committees
Program Committee
• Ananth Kalyanaraman, WSU
• Can Alkan, Bilkent University
• Engin Ipek, University of Rochester
• Jason Cong, UCLA
• Mattan Erez, UT Austin
• Mircea Stan, UVA
• Onur Mutlu, ETH/CMU
• Ran Ginosar, Technion
• Ronnie Ronen, Technion
• Yuan Xie, UCSB
Organizing committee
• Leonid Yavits* (mailto:leonid.yavits@biu.ac.il)
• Yatish Turakhia^ (mailto:yturakhia@eng.ucsd.edu)
* Department of Engineering, Bar Ilan University ^
Department of Electrical and Computer Engineering, University of California, San Diego
Contact
All questions about submissions should be emailed to
Leonid Yavits (mailto:leonid.yavits@gmail.com
or mailto:leonid.yavits@biu.ac.il)