[hpc-announce] 4th Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2022)

Leonid Yavits leonid.yavits at nububbles.com
Mon Feb 21 01:00:26 CST 2022

4th Accelerator Architecture in Computational Biology and Bioinformatics
workshop (AACBB-2022)

June 12th 2022 


In conjunction with 49th IEEE International Symposium on Computer

New York City, New York, USA


Workshop website



Submission link



Submission deadline

April 15, 2022, EoD AoE



April 30, 2022


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 ongoing Covid-19 pandemic, where 

fast and reliable 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 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



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):

        - Bioinformatics

        - Genomics

        - Proteomics

        - Protein structure prediction

        - Covid-19 pandemic

    - Bioinformatics and computational biology accelerator architecture and
design based on (but not limited to):

        - 3D memory-logic stack 

        - Near-data (in-memory) processing

        - In-data processing

        - FPGAs

        - Reconfigurable architectures 

    - 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


Keynote Speakers

    - Tajana Rosing, Prof of Computer Science and Engineering, director of
System Energy Efficiency Lab, UCSD

    - Onur Mutlu, Prof of Computer Science, Zurich ETH and CMU 




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* (leonid.yavits at gmail.com)

    - Yatish Turakhia^ (yturakhia at eng.ucsd.edu) 

* 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



All questions about submissions should be emailed to Leonid Yavits
(leonid.yavits at gmail.com) 





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