Call for Papers:

AACBB 2020: Workshop on Accelerator Architecture in Computational Biology and Bioinformatics

Abstract or Paper Registration Deadline
December 15, 2019
Final Submission Deadline
December 15, 2019


3rd Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2020)
In conjunction with the 26th IEEE International Symposium on High-Performance Computer Architecture (HPCA-2020)

February 23, 2020
San Diego, USA

Submissions Due: December 15, 2019

Workshop website
Submission link
Submission deadline December 15, 2019, EoD AoE
Notifications 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 biology.


Submission Guidelines

Interested authors are encouraged to submit papers (2-5 pages) through EasyChair:


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 trade-offs

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, 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

* 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 venues



All questions about submissions should be emailed to Leonid Yavits (