NSF Awards Funding for a Semantic Integration Platform to Combat COVID-19

June 2, 2020

June 2, 2020 — The Convergence Accelerator Office in the Office of Integrative Activities at the National Science Foundation (NSF) has awarded two researchers at the San Diego Supercomputer Center (SDSC) funding to organize COVID-19 information into a transdisciplinary knowledge network that integrates health, pathogen, and environmental data to better track cases to improve analysis and forecasting across the greater San Diego region.

The award, funded under the NSF’s Rapid Response Research or RAPID program, is valued at $200,000 and set to run between mid-May and the end of October. It will allow the researchers to quickly launch a comprehensive semantic integration platform for data-driven analysis and development of policy interventions that take into account up-to-date health, social-economic, and demographic characteristics of populations in different areas as well as biomedical information such as virus strains and genetic profiles.

Complementary knowledge graph themes to be integrated into a comprehensive Open Knowledge Network (OKN) by project partners: UC San Diego (blue), UC Santa Barbara (green), and UC San Francisco (orange). Gradients represent areas of overlapping expertise and integration. Credit: Krzysztof Janowicz (UC Santa Barbara), Peter Rose and Ilya Zaslavsky Image courtesy of San Diego Supercomputer Center, UC San Diego.

“The project will be based on our knowledge graph prototype linking information about pathogens, health data, and environmental indicators and enabling cross-domain inferencing,” said Peter Rose, director of SDSC’s Structural Bioinformatics Laboratory and principal investigator (PI) for the project, called ‘COVID-19-Net: Integrating Health, Pathogen and Environmental Data into a Knowledge Graph for Case Tracking, Analysis, and Forecasting.’ “Such a graph lets researchers trace the spread of the coronavirus in different geographic conditions, focusing on specific virus strains and transmissions.”

The COVID-19-Net grant  is one of 13 RAPID awards made by the NSF Convergence Accelerator to Track A: Open Knowledge Network-related projects. This project will be coordinated with another RAPID program led by Krzysztof Janowicz, a  professor of Geographic Information Science at UC Santa Barbara, with focuses on infrastructure resilience, supply chain disruptions, and local policy decisions designed to combat the pandemic.

Specifically, the COVID-19 Net project will refine the knowledge graph and integrate it with other complementary graphs being developed by the Open Knowledge Network (OKN) that was funded in September 2019 under the NSF’s Convergence Accelerator program. Tasks include refining methodology for populating the knowledge graph using Jupyter-based data-to-knowledge ingestion pipeline, continuously extending the knowledge graph content with additional data, and developing efficient data markup using recent schema.org COVID-19 extensions.

“The main goal is to make these datasets easier to find, index, and integrate,” said Ilya Zaslavsky, director of Spatial Information Systems Laboratory at SDSC and UC San Diego, and co-PI of the award. Zaslavsky also specializes in geoscience data discovery and develops visual exploratory gateways into advanced data science and machine learning tools, which will serve as one of the user dashboards for querying the graph.

“The NSF COVID RAPID awards program focuses on research that can be used immediately to explore how to model and understand the spread of COVID-19, to inform and educate about the science of virus transmission and prevention, and to encourage the development of processes and actions to address this global challenge,” said Lara Campbell, Program Director, Convergence Accelerator Office, NSF. “The project exemplifies how the NSF research community is able to respond to societal challenges in a timely manner, and also demonstrates the power of the “track” concept in the Accelerator, where independent projects collaborate as a cohort, which is enabling PIs Rose and Zaslavsky to leverage investments made by the NSF in the other Open Knowledge Network projects. We look forward to the valuable information and services that these efforts will be able to provide to benefit the American public during this pandemic.”

The project team has planned for continued collaboration with industry, university, and community efforts focused on COVID-19 data assimilation and analysis, including local government agencies in San Diego County, citizen scientists (Open San Diego), global initiatives (Graphs4Good), and industrial partners such as Microsoft and Neo4J. Together with many other UC San Diego experts who refocused their work on COVID-19, they regularly communicate with County health officials and researchers on issues critical for the County’s response to the pandemic, including tracing the spread of the infection and analysis of at-risk populations.

“The current pandemic has shown that we must all work together to overcome this crisis,” said UC San Diego Vice Chancellor for Research Sandra Brown. “This means bringing together the best minds in academia, industry, and the community, and it also means bringing together discrete data in unique ways to reveal a fuller picture of how SARS-CoV-2 is spread and how we can stem transmission. We are grateful to the NSF for their essential support in this effort.”

“I am pleased to join UC San Diego in announcing that federal funding will go to local researchers at the San Diego Supercomputer Center to help us combat the coronavirus pandemic,” said U.S. Representative Mike Levin (D-CA). “Since the beginning of this crisis, I have emphasized that we must listen to the scientists and the experts in order to beat this disease, and I am incredibly proud that UC San Diego researchers are playing a leading role in that effort.”

Added SDSC Director Michael Norman: “This project will result in a crucial resource among researchers dedicating their time and expertise to ending this pandemic by creating a data-driven analysis resource that can be widely shared to accelerate findings. It is among several COVID research initiatives that are currently using SDSC’s expertise as we provide priority access to our Comet supercomputer, coordinated through the recently announced COVID-19 HPC Consortium national alliance.”

Zaslavsky and Rose also offered a Directed Group Study course for data science seniors this quarter (DSC198), where several student teams developed additional components of the knowledge graph and created dashboards and markup that assist researchers in finding answers about the spread of COVID-19 as well asbiomedical and environmental aspects.


Source: Jan Zverina, San Diego Supercomputer Center, UC San Diego

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Xilinx Announces First Adaptive Computing Challenge

July 9, 2020

A new contest is challenging the computing world. Xilinx has announced the first Xilinx Adaptive Computing Challenge, a competition that will task developers and startups with finding creative workload acceleration solutions. Xilinx is running the Adaptive Computing Challenge in partnership with Hackster.io, a developing community... Read more…

By Staff report

Reviving Moore’s Law? LBNL Researchers See Promise in Heterostructure Oxides

July 9, 2020

The reality of Moore’s law’s decline is no longer doubted for good empirical reasons. That said, never say never. Recent work by Lawrence Berkeley National Laboratory researchers suggests heterostructure oxides may b Read more…

By John Russell

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: 1) Industries of the Future (IotF), chaired be Dario Gil (d Read more…

By John Russell

Penguin Computing Brings Cascade Lake-AP to OCP Form Factor

July 7, 2020

Penguin Computing, a subsidiary of SMART Global Holdings, Inc., announced yesterday (July) a new Tundra server, Tundra AP, that is the first to implement the Intel Xeon Scalable 9200 series processors (codenamed Cascade Read more…

By Tiffany Trader

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia's Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 "Accelerator Optimized" VM A2 instance family on Google Compute Engine. The instances are powered by t Read more…

By Tiffany Trader

AWS Solution Channel

Best Practices for Running Computational Fluid Dynamics (CFD) Workloads on AWS

The scalable nature and variable demand of CFD workloads makes them well-suited for a cloud computing environment. Many of the AWS instance types, such as the compute family instance types, are designed to include support for this type of workload.  Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial research. Can you discuss key developments in recent years? Read more…

By Steve Conway, Hyperion

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia's Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 "Accelerator Optimized" VM A2 instance fam Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

ISC 2020 Keynote: Hope for the Future, Praise for Fugaku and HPC’s Pandemic Response

June 24, 2020

In stark contrast to past years Thomas Sterling’s ISC20 keynote today struck a more somber note with the COVID-19 pandemic as the central character in Sterling’s annual review of worldwide trends in HPC. Better known for his engaging manner and occasional willingness to poke prickly egos, Sterling instead strode through the numbing statistics associated... Read more…

By John Russell

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers

Contributors

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This