5th Accelerator Architecture in
Computational Biology and Bioinformatics workshop (AACBB-2023)

June 18th, 2023

In conjunction with the 50th
International Symposium on Computer Architecture (ISCA-2023)

Orlando, Florida, USA

Workshop website: https://aacbb-workshop.github.io/

Submission link: https://easychair.org/conferences/?conf=aacbb2023

Submission deadline: April 20, 2023, EoD AoE

Notifications: April 30, 2023

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.

 

Submission Guidelines

Interested authors are encouraged to submit papers (2-5 pages)
through EasyChair: https://easychair.org/conferences/?conf=aacbb2023

 

The full version should be a PDF file similar to ISCA-2023
submission format. For formatting instructions please refer to: https://www.iscaconf.org/isca2023/submit/guidelines.php  

 

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

 

 

Keynote Speakers

  • Katherine A. Yelick, Prof. of Electrical Engineering and Computer Science, UC Berkley.
  • Dominique Lavenier, CNRS Research Director, IRISA/INRIA.
  • Damla Senol, Bionano.

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

* Department of Engineering, Bar Ilan University

^ Department of Electrical and Computer Engineering, University
of California, San Diego

 

Important Notes

Presenting a paper in the workshop does not preclude publication in other venues 

Contact

All questions about submissions should be emailed to Leonid Yavits
(leonid.yavits@gmail.com or leonid.yavits@biu.ac.il) 

5th Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2023)