HPCA 2018 Workshop on
Accelerator Architecture in
Computational Biology and Bioinformatics

February 24th, 2018

Vienna, Austria


Over the last decade, the advent of high-throughput sequencing techniques brought an 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 is proven to be inefficient for computational biology and bioinformatics tasks. For example, aligning even several hundred DNA or protein sequences using progressive multiple alignment tools consumes several CPU hours on high performance computer. Hence, computational biology and bioinformatics rely on hardware accelerators to allow processing to keep up with the increasing amount of data generated from biology applications.

In a typical application, 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 prime candidate to benefit from accelerator architecture research. Potential directions include 3D integration, near-data processing, automata processing, associative processing and reconfigurable architectures.

Call For Papers

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.
Topics of interest include, but are not limited to:

  • Impact of bioinformatics and biology applications on computer architecture research
  • Bioinformatics and computational biology accelerator architecture and design
  • 3D memory-logic stack based accelerators
  • Automata processing in bioinformatics and computational biology applications
  • Associative processing in bioinformatics and computational biology applications
  • Near-data (in-memory) acceleration bioinformatics and computational biology applications
  • Emerging memory technologies and their impact on bioinformatics and computational biology
  • Embedded and reconfigurable architectures
  • Field programmable logic based accelerators
  • Bioinformatics and computational biology-inspired hardware/software trade-offs

Submission Guidelines

Interested authors are encouraged to submit papers (2-5 pages) through EasyChair: https://easychair.org/conferences/?conf=aacbb2018
For a PDF version of the CFP click here: Download CFP

All papers will be evaluated based on their relation to the subject, novelty, fundamental insights, experimental evaluation, and potential for long-term impact.

The full version should be a PDF file in HPCA24 submission format. For formatting instructions please refer to: HPCA Guidelines for Submission

Important Dates

Submission deadline: November 30, 2017. Friday, December 15, 2017.
Notification by: December 20, 2017.


8:45 - 9:00 Opening Remarks
9:00 - 10:00 Keynote 1 - Onur Mutlu: “Accelerating Genome Analysis: A Primer on an Ongoing Journey”
10:00 - 10:30 Invited Talk - Bertil Schmidt: “Next Generation Sequencing: Big Data meets High Performance Computing Architectures”
10:30 - 11:00 Break
11:00 - 12:00 Paper session 1 (3 papers)
12:00 - 13:30 Lunch
13:30 - 14:30 Keynote 2 - Srinivas Aluru: “Automata Processor and its Applications in Bioinformatics”
14:30 - 15:10 Paper Session 2 (2 papers)
15:10 - 15:30 Break
15:30 - 16:10 Paper session 3 (2 papers)
16:10 - 16:50 Invited Talk - Can Alkan
16:50 - 17:00 Closing remarks

Keynote Talks

Invited Talks

  • Bertil Schmidt, JGU Mainz

    “Next Generation Sequencing: Big Data meets High Performance Computing Architectures”


    Talk abstract: TBD

  • Can Alkan, Bilkent University

    "Addressing Computational Burden to Realize Precision Medicine"


    Talk abstract: TBD

Workshop Organizers

From Technion, Israel Institute of Technology

Leonid Yavits


Short bio: Leonid received his MSc and PhD in Electrical Engineering from the Technion. After graduating, he co-founded VisionTech where he co-designed a single chip MPEG2 codec. Following VisionTech’s acquisition by Broadcom, he co-founded Horizon Semiconductors where he co-designed a Set Top Box on chip for cable and satellite TV.
Leonid is a postdoc fellow in Electrical Engineering in the Technion. He co-authored a number of patents and research papers on SoC and ASIC. His research interests include non von Neumann computer architectures and processing in memory

Roman Kaplan


Short bio: Roman received his BSC and MSc from the faculty of Electrical Engineering, Technion, Israel in 2009 and 2015, respectively. He is now a PhD candidate in the same faculty under the supervision of Prof. Ran Ginosar.
Roman's research interests are parallel computer architectures, in-data processing, accelerators for machine learning and big data, and novel computer architectures for bioinformatics applications.