AWS: Updates and Early Lessons from our COVID-19 HPC Consortium Research Partners

May 22, 2020

May 22, 2020 — Dave Levy, vice president of U.S. government at Amazon Web Services, shared the lessons learned early on once the COVID-19 High Performance Computing Consortium was established. In addition, in the blog posted below, Levy provides an update and provides a summary of the projects that Amazon is collaborating with academia and industry alike as they tackle the challenges posed by COVID-19.


The concept of a COVID-19 High Performance Computing (HPC) Consortium emerged from a roundtable discussion at the White House in March and included input from industry, government, and academic leaders. Following the announcement of the consortium, AWS has been collaborating with teams on a growing number of projects to provide cloud computing resources from AWS.

I want to share three early learnings from this work.

  1. When empowered with the right tools, researchers can significantly accelerate the pace of their work. Tools including deep learning and artificial intelligence are reducing time to insight for researchers around the world.
  2. There is no silver bullet. The diversity of the efforts below reflects the many dimensions to the health challenge posed by COVID-19.
  3. We are only scratching the surface of what’s possible. The work of the HPC Consortium demonstrates the commitment of a community of researchers and public sector leaders to test new ideas, iterate on others, and tackle the challenge of COVID-19 head-on.

Today I would like to provide some insight into some of the innovative projects on which we are collaborating with the world’s leading researchers. Read more about each individual effort, below.

COVID Moonshot Request

Lead researcher: PostEra

PostEra is helping to lead Project Moonshot, an open science initiative to find a novel antiviral cure for COVID-19, tested in animals within four months. The worldwide scientific community suggests drug candidates that might bind to, and neutralize, the COVID-19 main protease. However, machine learning resources are necessary to predict how to synthesize these suggested compounds. This can reduce the time to determine optimal ways to make these compounds from weeks to days, and would be the first time that a drug was developed in an open-sourced fashion.

Designing virus-specific sACE2 mimics for competitive inhibition of SARS-CoV-2

Lead researcher: Massachusetts Institute of Technology

Soluble angiotensin-converting enzyme 2 (sACE2) can inhibit SARS and SARS2 coronaviruses. Although there is an ongoing clinical trial of sACE2 for this purpose, it has other properties that are likely to limit its safety and clinical effectiveness. The goal of this project is to design multiple sACE2 mutants that can be used as safe and effective antiviral therapeutics. This project uses deep learning to predict sACE2 variants that are effective with few to no side effects.

SARS-CoV-2 Detection in Sequence Read Archive Data

Lead researcher: Los Alamos National Lab (LANL)

This project uses a genomic data driven technique to analyze the temporal and spatial dynamics of the COVID-19 pandemic. Researchers will analyze all the data deposited over the last six months to the Sequence Read Archive (SRA), a repository of genomics data. Pathogen detection pipelines will detect which samples are likely to contain SARS-CoV-2. Results from these pipelines will be combined with sample metadata, providing a “map” of where the virus has been identified.

Target Identification for Broad Antiviral Therapy using Functional Genetic Screening Datasets

Lead researcher: Children’s National Medical Centre

It is important to understand how human genes interact with a virus to develop antiviral therapy. Functional genetic screening is a high-throughput and cost-effective way of studying how a virus interacts with the functions of many genes before and after infection. The goal of this proposal is to reanalyze public genetic screening datasets to identify genes that serve as potential targets of broad antiviral activity including COVID-19.

tmCOVID: a text mining tool for COVID-19 scientific literature

Lead researcher: Emory University

More than 2,700 peer-reviewed articles related to COVID-19 have been published since last December, which is too much information for researchers to explore manually in any reasonable timeframe. The goal of this project is to develop and host an interactive web-based text mining tool to be used for automated extraction and summarization of key bio-concepts (genes, chemicals, diseases, species, mutations, and cell lines) in COVID-19 scientific literature to make it easier to quickly extract information and summarize it. A prototype of this tool is available at www.tmcovid.com; this project will incorporate capabilities for full-text document summarization and generate textual summaries based on the user query.

The evolutionary history of SARS-CoV-2

Lead researcher: Iowa State University

The SARS-CoV-2 virus replicates and mutates as it spreads, and some variants impact how the virus impacts hosts. However, we do not know much about how different strains of the virus – some potentially more virulent than others – are distributed across the globe. Using a variety of evolutionary models together with publicly available genomic datasets, researchers will construct and release the phylogenetic relationship of strains of SARS-CoV-2 and make this available on a public website.

Combined virtual screening and machine learning approach to finding novel SARS-CoV-2 protease inhibitors.

Lead researcher: Kuano

The goal of this proposal is to combine machine learning and molecular modeling to improve virtual screening and drug discovery applications targeting COVID-19. The team has developed a genetic algorithm capable of searching the chemical space surrounding existing antiviral drugs, and a deep learning-based classification model based on existing binding data. These tools will be combined with docking and molecular dynamics simulations to enhance results. The output of this effort will be a set of machine learning models that can be used to score molecular designs for synthesis as antiviral compounds.

Compounds to prevent the spread of COVID-19

Lead researcher: Novel Tech Sciences

Novel Tech Sciences is applying molecular dynamics simulations to identify antiviral compounds from ayurvedic medicine that might bind to the SARS-CoV-2 protein targets. The goal is to create a blend of these phytochemicals derived from natural sources that can be used as a therapy and to help prevent spread of COVID-19.

Learn more about the COVID-19 High Performance Computing (HPC) Consortium.

About Amazon Web Services

For 14 years, Amazon Web Services has been the world’s most comprehensive and broadly adopted cloud platform. AWS offers over 175 fully featured services for compute, storage, databases, networking, analytics, robotics, machine learning and artificial intelligence (AI), Internet of Things (IoT), mobile, security, hybrid, virtual and augmented reality (VR and AR), media, and application development, deployment, and management from 76 Availability Zones (AZs) within 24 geographic regions, with announced plans for nine more Availability Zones and three more AWS Regions in Indonesia, Japan, and Spain. Millions of customers—including the fastest-growing startups, largest enterprises, and leading government agencies—trust AWS to power their infrastructure, become more agile, and lower costs. To learn more about AWS, visit aws.amazon.com.

About Amazon

Amazon is guided by four principles: customer obsession rather than competitor focus, passion for invention, commitment to operational excellence, and long-term thinking. Customer reviews, 1-Click shopping, personalized recommendations, Prime, Fulfillment by Amazon, AWS, Kindle Direct Publishing, Kindle, Fire tablets, Fire TV, Amazon Echo, and Alexa are some of the products and services pioneered by Amazon. For more information, visit www.amazon.com/about and follow @AmazonNews.


Source: Dave Levy, Amazon Web Services

 

Subscribe to HPCwire's Weekly Update!

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

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from its predecessors, including the red-hot H100 and A100 GPUs. Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. While Nvidia may not spring to mind when thinking of the quant Read more…

2024 Winter Classic: Meet the HPE Mentors

March 18, 2024

The latest installment of the 2024 Winter Classic Studio Update Show features our interview with the HPE mentor team who introduced our student teams to the joys (and potential sorrows) of the HPL (LINPACK) and accompany Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the field was normalized for boys in 1969 when the Apollo 11 missi Read more…

Apple Buys DarwinAI Deepening its AI Push According to Report

March 14, 2024

Apple has purchased Canadian AI startup DarwinAI according to a Bloomberg report today. Apparently the deal was done early this year but still hasn’t been publicly announced according to the report. Apple is preparing Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimization algorithms to iteratively refine their parameters until Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, code-named Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Nvidia Showcases Quantum Cloud, Expanding Quantum Portfolio at GTC24

March 18, 2024

Nvidia’s barrage of quantum news at GTC24 this week includes new products, signature collaborations, and a new Nvidia Quantum Cloud for quantum developers. Wh Read more…

Houston We Have a Solution: Addressing the HPC and Tech Talent Gap

March 15, 2024

Generations of Houstonian teachers, counselors, and parents have either worked in the aerospace industry or know people who do - the prospect of entering the fi Read more…

Survey of Rapid Training Methods for Neural Networks

March 14, 2024

Artificial neural networks are computing systems with interconnected layers that process and learn from data. During training, neural networks utilize optimizat Read more…

PASQAL Issues Roadmap to 10,000 Qubits in 2026 and Fault Tolerance in 2028

March 13, 2024

Paris-based PASQAL, a developer of neutral atom-based quantum computers, yesterday issued a roadmap for delivering systems with 10,000 physical qubits in 2026 a Read more…

India Is an AI Powerhouse Waiting to Happen, but Challenges Await

March 12, 2024

The Indian government is pushing full speed ahead to make the country an attractive technology base, especially in the hot fields of AI and semiconductors, but Read more…

Charles Tahan Exits National Quantum Coordination Office

March 12, 2024

(March 1, 2024) My first official day at the White House Office of Science and Technology Policy (OSTP) was June 15, 2020, during the depths of the COVID-19 loc Read more…

AI Bias In the Spotlight On International Women’s Day

March 11, 2024

What impact does AI bias have on women and girls? What can people do to increase female participation in the AI field? These are some of the questions the tech Read more…

Alibaba Shuts Down its Quantum Computing Effort

November 30, 2023

In case you missed it, China’s e-commerce giant Alibaba has shut down its quantum computing research effort. It’s not entirely clear what drove the change. Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Analyst Panel Says Take the Quantum Computing Plunge Now…

November 27, 2023

Should you start exploring quantum computing? Yes, said a panel of analysts convened at Tabor Communications HPC and AI on Wall Street conference earlier this y Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

DoD Takes a Long View of Quantum Computing

December 19, 2023

Given the large sums tied to expensive weapon systems – think $100-million-plus per F-35 fighter – it’s easy to forget the U.S. Department of Defense is a Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Intel’s Server and PC Chip Development Will Blur After 2025

January 15, 2024

Intel's dealing with much more than chip rivals breathing down its neck; it is simultaneously integrating a bevy of new technologies such as chiplets, artificia Read more…

Baidu Exits Quantum, Closely Following Alibaba’s Earlier Move

January 5, 2024

Reuters reported this week that Baidu, China’s giant e-commerce and services provider, is exiting the quantum computing development arena. Reuters reported � Read more…

Leading Solution Providers

Contributors

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Training of 1-Trillion Parameter Scientific AI Begins

November 13, 2023

A US national lab has started training a massive AI brain that could ultimately become the must-have computing resource for scientific researchers. Argonne N Read more…

Shutterstock 1179408610

Google Addresses the Mysteries of Its Hypercomputer 

December 28, 2023

When Google launched its Hypercomputer earlier this month (December 2023), the first reaction was, "Say what?" It turns out that the Hypercomputer is Google's t Read more…

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

Shutterstock 1606064203

Meta’s Zuckerberg Puts Its AI Future in the Hands of 600,000 GPUs

January 25, 2024

In under two minutes, Meta's CEO, Mark Zuckerberg, laid out the company's AI plans, which included a plan to build an artificial intelligence system with the eq Read more…

Google Introduces ‘Hypercomputer’ to Its AI Infrastructure

December 11, 2023

Google ran out of monikers to describe its new AI system released on December 7. Supercomputer perhaps wasn't an apt description, so it settled on Hypercomputer Read more…

China Is All In on a RISC-V Future

January 8, 2024

The state of RISC-V in China was discussed in a recent report released by the Jamestown Foundation, a Washington, D.C.-based think tank. The report, entitled "E Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire