[hpc-announce] 3rd Accelerator Architecture in Computational Biology and Bioinformatics workshop (in conjunction with HPCA-26): Call for papers

Yatish Turakhia yatisht at stanford.edu
Mon Dec 2 22:21:56 CST 2019

3rd Accelerator Architecture in Computational Biology and Bioinformatics
workshop (AACBB-2020)

February 23rd, 2020

In conjunction with 26th IEEE International Symposium on

High-Performance Computer Architecture (HPCA-2020)

San Diego, USA

Workshop website


Submission link


Submission deadline

December 15, 2019, EoD AoE


December 25, 2019

Over the last decade, the advent of high-throughput sequencing techniques
has brought exponential growth in biosequence database sizes. With
increased throughput demand and popularity of computational biology tools,
reducing time-to-solution during computational analysis has become a
significant challenge in the path to scientific discovery.

Conventional computer architecture has been proven to be inefficient for
computational biology and bioinformatics tasks. For example, 3rd generation
de-novo assembly of a human genome may take hundreds of hours on a high
performance computer. Hence, computational biology and bioinformatics
increasingly rely on hardware accelerators.

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 makes computational biology a prime
candidate to benefit from accelerator architecture research. Potential
directions include 3D integration, near-data processing, automata
processing and reconfigurable architectures.

This workshop will focus on the 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

Submission Guidelines

Interested authors are encouraged to submit papers (2-5 pages) through
EasyChair: https://easychair.org/conferences/?conf=aacbb2020

The full version should be a PDF file similar to HPCA26 submission format.
For formatting instructions please refer to:

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

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

        ◦ 3D memory-logic stack

        ◦ Automata processing

        ◦ Near-data (in-memory) processing

        ◦ 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

Keynote Speakers

    • James Larus, Dean of the School of Computer and Communication
Sciences at EPFL

    • Daniel Jacobson, Chief Scientist for Computational Systems Biology at
the Oak Ridge National Laboratory

    • Benedict Paten, Associate Director, UC Santa Cruz Genomics Institute


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^ (yatisht at stanford.edu)

    • Naor Granik* (naorgranik at gmail.com)

    • Sneha Goenka^ (gsneha at stanford.edu)

* Department of Electrical Engineering, Technion

^ Department of Electrical Engineering, Stanford University

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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