AACBB-2023

5th Accelerator Architecture in Computational Biology and Bioinformatics workshop (AACBB-2023)
June 18th, 2023 Orlando, Florida, USA
In conjunction with the 50th International Symposium on Computer Architecture (ISCA-2023)
Workshop website: https://aacbb-workshop.github.io/

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.

Keynote Speakers

• Katherine A. Yelick, Prof. of Electrical Engineering and Computer Science, UC Berkley. Genomic Analysis at Scale: Mapping Irregular Computations to Advanced Architectures
• Dominique Lavenier, CNRS Research Director, IRISA/INRIA. Exploring genomic algorithms on UPMEM Processing-in-Memory Architecture
• Damla Senol, Bionano. Accelerating the Transformation in How We Analyze the Human Genome

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:

1. 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
• Antimicrobial resistance

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

• Heterogeneous architectures
• 3D memory-logic stack
• Near-memory and in-memory processing
• FPGAs and reconfigurable

3. Emerging memory technologies and their impact on bioinformatics and computational biology

4. Impact of bioinformatics and biology applications on computer architecture research

5. Bioinformatics and computational biology-inspired hardware/software trade-offs

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

• Leonid Yavits* (leonid.yavits@biu.ac.il)
• Yatish Turakhia^ (yturakhia@eng.ucsd.edu)

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

Contact

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