The 3rd HPCA Workshop on
Accelerator Architecture in
Computational Biology and Bioinformatics

February 23rd, 2020

San Diego, CA, USA

About

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 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.

Call For Participation

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

Registration information


Workshop registration (minimum requirement is 1-day workshop registration)

HPCA Venue and hotel information

Workshop will be held in room Capri

Schedule

7:00 - 8:30 Breakfast


8:30 - 8:40 Opening Remarks


8:40-9:40 James Larus, EPFL
"Protein Clustering: Parallelizing an Expensive Irregular Computation " (slides)
9:40 - 10:00 Farzaneh Zokaee and Lei Jiang
"FindeR: Accelerating FM-Index-based Exact Pattern Matching in Genomic Sequences through ReRAM technology " (slides, paper)


10:00 - 10:30 Coffee break


10:30 - 11:30 Daniel Jacobson, Oak Ridge National Laboratory
"Exascale Biology: From Genome to Climate with a Few Steps Along the Way"
11:30 - 11:50 Fan Chen, Linghao Song, Hai Li and Yiran Chen
"PARC: A Processing-in-CAM Architecture for Genomic Long Read Pairwise Alignment using ReRAM"


11:50 - 13:00 Lunch


13:00 - 14:00 Benedict Paten, UC Santa Cruz Genomics Institute
"Building the Human Pangenome " (slides)
14:00 - 14:20 Wenqin Huangfu, Xueqi Li, Shuangchen Li, Xing Hu, Peng Gu and Yuan Xie
"MEDAL: Scalable DIMM based Near Data Processing Accelerator for DNA Seeding Algorithm"
14:20 - 14:40 Saransh Gupta, Mohsen Imani, Behnam Khaleghi, Venkatesh Kumar and Tajana Rosing
"RAPID: A ReRAM Processing in-Memory Architecture for DNA Sequence Alignment"


14:40 - 15:00 Coffee break


15:00 - 15:20 Zheming Jin, Kazutomo Yoshii and Hal Finkel
"Optimizing the Performance of the Needleman-Wunsch Benchmark using SYCL"
15:20 - 15:40 Chih-Han Yang, Jhih-Wun Zeng, Cheng-Yueh Liu and Shih-Hao Hung
"Accelerating Variant Calling via Performance Analysis and Optimization of DeepVariant"
15:40 - 16:00 Roman Snytsar and Yatish Turakhia
"Parallel acceleration of ntHash"
16:00 - 16:05 Closing remarks


Keynote Speakers

  • James Larus, EPFL

    "Protein Clustering: Parallelizing an Expensive Irregular Computation"

    Short Bio: James Larus is Professor and Dean of the School of Computer and Communication Sciences (IC) at EPFL (École Polytechnique Fédérale de Lausanne). Prior to joining IC in October 2013, Larus was a researcher, manager, and director in Microsoft Research for over 16 years and an assistant and associate professor in the Computer Sciences Department at the University of Wisconsin, Madison. Larus has been an active contributor to numerous communities. He published over 100 papers (with 9 best and most influential paper awards), received over 40 US patents. Larus received a National Science Foundation Young Investigator award in 1993 and became an ACM Fellow in 2006. Larus received his MS and PhD in Computer Science from the University of California, Berkeley in 1989, and an AB in Applied Mathematics from Harvard in 1980.

  • Benedict Paten, UC Santa Cruz Genomics Institute

    "Building the Human Pangenome"

    Short Bio: Dr. Benedict Paten is an assistant professor in the department of Biomolecular Engineering at the University of California Santa Cruz (UCSC) and an associate director of the UC Santa Cruz Genomics Institute. He directs the Computational Genomics Lab at UCSC, which is broadly focused on computational genomics, creating algorithms, software and services addressing biomolecular challenges. He has a PhD from the University of Cambridge and the European Molecular Biology Laboratory in computational biology.

  • Daniel Jacobson, Oak Ridge National Laboratory

    "Exascale Biology: From Genome to Climate with a Few Steps Along the Way"

    Short Bio: Dr. Jacobson is the Chief Scientist for Computational Systems Biology at the Oak Ridge National Laboratory. His lab was the first group to break the Exascale barrier and is happy to have done so for a biology project. At present, this (2.41 Exaops) calculation is the fastest scientific calculation ever done anywhere in the world. This project led to his team being awarded the 2018 Gordon Bell Prize (the first ever for Systems Biology).
    Dr. Jacobson's career as a computational systems biologist has included leadership roles in academic, corporate, NGO and national lab settings. His lab focuses on the development and subsequent application of mathematical, statistical and computational methods to biological datasets in order to yield new insights into complex biological systems. His lab’s approaches include the use of Network Theory and Topology Discovery/Clustering, Wavelet Theory, and explainable-AI, together with traditional and more advanced supercomputing architectures. Areas of statistics of particular interest to his lab include the use of both frequentist (parametric and non-parametric) and Bayesian methods as well as the development of new methods for Genome-Wide Epistasis Studies (GWES). These mathematical and statistical methods are applied to various population and (meta)multiomics data sets (Genomics, Phylogenomics, Transcriptomics, Proteomics, Metabolomics, Microbiomics, Viriomics, Phytobiomics, Chemiomics, etc.) individually as well as in combination in an attempt to better understand the functional relationships as well as biosynthesis, signaling, transcriptional, translational, degradation and kinetic regulatory networks at play in biological organisms and communities. His group takes a broad view of biological complexity and evolution that stretches from viruses to microbes to plants to humans. ORNL is home to some of the world’s largest supercomputers and thus his lab uses petascale and exascale computing to analyze and model complex biological systems.

Program Committee

Workshop Organizers

From Technion, Israel Institute of Technology

Leonid Yavits

leonid.yavits@nububbles.com

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

Naor Granik

naorgranik@gmail.com

Short bio: Naor received his BSc from the faculty of Electrical Engineering, and MSc from the faculty of Biomedical Engineering, Technion, Israel in 2017 and 2019, respectively. He is now a PhD candidate in the faculty of Applied Mathematics under the supervision of Prof. Roee Amit.
Naor's research interests are near-data processing, deep-learning and biological computing.

From Stanford

Yatish Turakhia

yatisht@stanford.edu

Short bio: Yatish is a final year PhD student in Electrical Engineering at Stanford University, where he is co-advised by Prof. Bill Dally and Prof. Gill Bejerano. He is interested in the hardware-acceleration of genome sequence alignment and its application to biomedicine and comparative genomics. His work has won the best paper award at ASPLOS 2018 and IEEE Micro Top picks 2018 award. He is also a recipient of the NVIDIA graduate fellowship. He has served as a reviewer in a number of top-tier computer architecture journals, including Transactions on Computers, Transactions on Architecture and Code Optimization (TACO) and ComputerArchitecture Letters (CAL)

Sneha Goenka

gsneha@stanford.edu

Short bio: Sneha is a third year Ph.D. Candidate at Stanford University where she is advised by Prof. Mark Horowitz and Prof. Gill Bejerano. Previously, she received her B. Tech. and M. Tech. in Electrical Engineering at the Indian Institute of Technology, Bombay. She is interested in developing co-processors for genomic applications.