Showing posts with label Corona virus. Show all posts
Showing posts with label Corona virus. Show all posts

COVID-19 High Performance Computing Consortium



The COVID-19 High Performance Computing Consortium Bringing together the Federal government, industry, and academic leaders to provide access to the world’s most powerful high-performance computing resources in support of COVID-19 research. Over 402 petaflops, 105,334 nodes, 3,539,044 CPU cores, 41,286 GPUs, and counting.






The world's leading medical researchers are rushing to find a treatment for COVID-19 with the help of the most powerful and advanced supercomputers in the world.
Researchers aross the globe are submitting potential treatments and cures to the COVID-19 High Performance Computing Consortium.
The consortium, using a network of supercomputers and laboratotires, can run through simulations to narrow down or rule out drug compounds to use in a cure much faster than traditional methods.
"It's a means by which one can begin to analyze tremendously complex or large problems," says Vice President of Technical Computing at IBM Cognitive Systems Dave Turek. "Pharmaceutical companies may have billions of compounds that could be potential drugs."
Any researcher can submit proposals to the consortium for the supercomputes to run through.
"So, there are very novel techniques, specifically using A.I. on these supercomputers that are beginnign to speculate about new kinds of molecules that could be created to treat COVID-19," says Turek.

The COVID-19 High Performance Computing Consortium is a unique private-public effort spearheaded by the White House Office of Science and Technology Policy, the U.S. Department of Energy and IBM to bring together federal government, industry, and academic leaders who are volunteering free compute time and resources on their world-class machines.


Consortium partners include:

  • Industry
    • IBM
    • Amazon Web Services
    • AMD
    • Google Cloud
    • Hewlett Packard Enterprise
    • Microsoft
    • NVIDIA
  • Academia
    • Massachusetts Institute of Technology
    • Rensselaer Polytechnic Institute
    • University of Illinois
    • University of Texas at Austin
    • University of California - San Diego
    • Carnegie Mellon University
    • University of Pittsburgh
    • Indiana University
    • University of Wisconsin-Madison
  • Department of Energy National Laboratories
    • Argonne National Laboratory
    • Lawrence Livermore National Laboratory
    • Los Alamos National Laboratory
    • Oak Ridge National Laboratory
    • National Energy Research Scientific Computing Center
    • Sandia National Laboratories
  • Federal Agencies
    • National Science Foundation
      • XSEDE
      • Pittsburgh Supercomputing Center (PSC)
      • Texas Advanced Computing Center (TACC)
      • San Diego Supercomputer Center (SDSC)
      • National Center for Supercomputing Applications (NCSA)
      • Indiana University Pervasive Technology Institute (IUPTI)
      • Open Science Grid (OSG)
      • National Center for Atmospheric Research (NCAR)
    • NASA
Researchers are invited to submit COVID-19 related research proposals to the consortium via this online portal, which will then be reviewed for matching with computing resources from one of the partner institutions. An expert panel comprised of top scientists and computing researchers will work with proposers to assess the public health benefit of the work, with emphasis on projects that can ensure rapid results.
Fighting COVID-19 will require extensive research in areas like bioinformatics, epidemiology, and molecular modeling to understand the threat we’re facing and form strategies to address it. This work demands a massive amount of computational capacity. The COVID-19 High Performance Computing Consortium helps aggregate computing capabilities from the world's most powerful and advanced computers to help COVID-19 researchers execute complex computational research programs to help fight the virus.
About the Consortium, the HPC Systems & How to Join
Consortium members manage a range of computing capabilities that span from small clusters to some of the largest supercomputers in the world. As a member, you would support this crucial work by not only offering your computational resources, but also your deep technical capabilities and expertise to help COVID-19 researchers execute complex computational research programs. We hope that you will join us in this crucial mission.
We are currently providing broad access to portions of over 30 supercomputing systems, representing over over 402 petaflops, 105,334 nodes, 3,539,044 CPU cores, 41,286 GPUs, and counting. Their basic specifications are described below. Additional resources will be added as our consortium grows; please check back for updates.


Analyzing Corona Virus data with AI



Fully understanding and solving the coronavirus pandemic will be about the data. There’s no shortage of data sources that are growing hourly. Now nine organizations, business and academic, have formed a coalition to bring coronavirus data sources together, and added incentives for researchers who can apply modern data analysis and artificial intelligence to it. Leading this effort is the Silicon Valley company C3.ai

C3.ai, Microsoft Corporation, the University of Illinois at Urbana-Champaign (UIUC), the University of California, Berkeley, Princeton University, the University of Chicago, the Massachusetts Institute of Technology, Carnegie Mellon University, and the National Center for Supercomputing Applications at UIUC announced two major initiatives:

  • C3.ai Digital Transformation Institute (C3.ai DTI), a research consortium dedicated to accelerating the application of artificial intelligence to speed the pace of digital transformation in business, government, and society. Jointly managed by UC Berkeley and UIUC, C3.ai DTI will sponsor and fund world-leading scientists in a coordinated effort to advance the digital transformation of business, government, and society.
  • C3.ai DTI First Call for Research Proposals: C3.ai DTI invites scholars, developers, and researchers to embrace the challenge of abating COVID-19 and advance the knowledge, science, and technologies for mitigating future pandemics using AI. This is the first in what will be a series of bi-annual calls for Digital Transformation research proposals.
“The C3.ai Digital Transformation Institute is a consortium of leading scientists, researchers, innovators, and executives from academia and industry, joining forces to accelerate the social and economic benefits of digital transformation,” said Thomas M. Siebel, CEO of C3.ai. “We have the opportunity through public-private partnership to change the course of a global pandemic,” Siebel continued. “I cannot imagine a more important use of AI.”

Immediate Call for Proposals: AI Techniques to Mitigate Pandemic
Topics for Research Awards may include but are not limited to the following:
  1. Applying machine learning and other AI methods to mitigate the spread of the COVID-19 pandemic
  2. Genome-specific COVID-19 medical protocols, including precision medicine of host responses
  3. Biomedical informatics methods for drug design and repurposing
  4. Design and sharing of clinical trials for collecting data on medications, therapies, and interventions
  5. Modeling, simulation, and prediction for understanding COVID-19 propagation and efficacy of interventions
  6. Logistics and optimization analysis for design of public health strategies and interventions
  7. Rigorous approaches to designing sampling and testing strategies
  8. Data analytics for COVID-19 research harnessing private and sensitive data
  9. Improving societal resilience in response to the spread of the COVID-19 pandemic
  10. Broader efforts in biomedicine, infectious disease modeling, response logistics and optimization, public health efforts, tools, and methodologies around the containment of rising infectious diseases and response to pandemics, so as to be better prepared for future infectious diseases
The first call for proposals is open now, with a deadline of May 1, 2020. Researchers are invited to learn more about C3.ai DTI and how to submit their proposals for consideration at C3DTI.ai. Selected proposals will be announced by June 1, 2020.
Up to $5.8 million in awards will be funded from this first call, ranging from $100,000 to $500,000 each. In addition to cash awards, C3.ai DTI recipients will be provided with significant cloud computing, supercomputing, data access, and AI software resources and technical support provided by Microsoft and C3.ai. This will include unlimited use of the C3 AI Suite and access to the Microsoft Azure cloud platform and access to the Blue Waters supercomputer at the National Center for Supercomputing Applications (NCSA) at UIUC.
“We are collecting a massive amount of data about MERS, SARS, and now COVID-19,” said Condoleezza Rice, former US Secretary of State. “We have a unique opportunity before us to apply the new sciences of AI and digital transformation to learn from these data how we can better manage these phenomena and avert the worst outcomes for humanity,” Rice continued. “I can think of no work more important and no response more cogent and timely than this important public-private partnership.”
“We’re excited about the C3.ai Digital Transformation Institute and are happy to join on a shared mission to accelerate research at these eminent research institutions,” said Eric Horvitz, Chief Scientist at Microsoft and C3.ai DTI Advisory Board Member. “As we launch this exciting private-public partnership, we’re enthusiastic about aiming the broader goals of the Institute at urgent challenges with the COVID-19 pandemic, as well as on longer-term research that could help to minimize future pandemics.”
"At UC Berkeley, we are thrilled to help co-lead this important endeavor to establish and advance the science of digital transformation at the nexus of machine learning, IoT, and cloud computing,” said Carol Christ, Chancellor, UC Berkeley. “We believe this Institute has the potential to make tremendous contributions by including ethics, new business models, and public policy to the technologies for transforming societal scale systems globally."
“The C3.ai Digital Transformation Institute, with its vision of cross-institutional and multi-disciplinary collaboration, represents an exciting model to help accelerate innovation in this important new field of study,” said Robert J. Jones, Chancellor of the University of Illinois at Urbana-Champaign. “At this time of a global health crisis, the Institute’s initial research focus will be on applying AI to mitigate the COVID-19 pandemic and to learn from it how to protect the world from future pandemics. C3.ai DTI is an important addition to the world’s fight against this disease and a powerful new resource in developing solutions to all societal challenges.”
“Together with the other C3.ai Digital Transformation Institute partners, we look forward to creating a powerful ecosystem of scholars and educators committed to applying 21st century technologies to the benefit of all,” said Chris Eisgruber, President of Princeton University. “This public-private partnership with innovators like C3.ai and Microsoft, providing support to world-class researchers across a range of disciplines, promises to bring rapid innovation to an exciting new frontier.”
“By strongly supporting multidisciplinary research and multi-institution projects, the C3.ai DTI represents a new avenue to develop breakthrough scientific results with a positive impact on society at a time of great need,” said Robert Zimmer, President of the University of Chicago. “I’m very pleased that the University of Chicago is part of this formidable collaboration between academia and industry to lead crucial innovation with great purpose and urgency.”
“The vision of C3.ai DTI is driven by the recognition of digital transformation as both a science as well as a scientific imperative for this pivotal time, applicable to every sector of our economy across the public and private sectors, including in healthcare, education, and public health,” said Farnam Jahanian, President of Carnegie Mellon University. “We are excited to participate in building out the Institute’s structure, program and further alliances. This is just the beginning of an ambitious journey that can have enormous positive impact on the world.”
"At MIT, we share the commitment of C3.ai DTI to advancing the frontiers of AI, cybersecurity and related fields while building into every inquiry a deep concern for ethics, privacy, equity and the public interest,” said Rafael Reif, President of the Massachusetts Institute of Technology. “At this moment of national emergency, we are proud to be part of this intensive effort to apply these sophisticated tools to better analyze the COVID-19 epidemic and devise effective ways to stop it. We look forward to accelerating this work both by collaborating with the companies and institutions in the initiative, and by drawing on the frontline experience and clinical data of our colleagues in Boston's world-class hospitals."


Building Community
At the heart of C3.ai DTI will be the constant flow of new ideas and expertise provided by ongoing research, visiting professors and research scholars, and faculty and scholars in residence, many of whom will come from beyond the member institutions. This rich ecosystem will form the foundational structure of a new Science of Digital Transformation.
“This is about global innovation based on multinational collaboration to accelerate the positive impact of AI by providing researchers access to real world data and to massive resources,” said Jim Snabe, Chairman, Siemens. “This is exactly the kind of multinational public-private partnership that is required to address this critical issue.”
“I could not be more proud of our association with C3.ai and Microsoft,” said Lorenzo Simonelli, CEO of Baker Hughes. “This is exactly the kind of leadership that is required to bring together the best of us to address this critical need.”
“We are at war and we must win it! Using all means,” said Jacques Attali, French statesman. “This great project will organize global scientific collaboration for accelerating the social impact of AI, and help to win this war, using new weapons, for the best of mankind.”
“In these difficult times, we need – now more than ever – to join our forces with scholars, innovators, and industry experts to propose solutions to complex problems. I am convinced that digital, data science and AI are a key answer,” said Gwenaëlle Avice-Huet, Executive Vice President of ENGIE. “The C3.ai Digital Transformation Institute is a perfect example of what we can do together to make the world better.”


Establishing the New Science of Digital Transformation
C3.ai DTI will focus its research on AI, Machine Learning, IoT, Big Data Analytics, human factors, organizational behavior, ethics, and public policy. The Institute will support the development of ML algorithms, data security, and cybersecurity techniques. C3.ai DTI research will analyze new business operation models, develop methods of implementing organizational change management and protecting privacy, and amplify the dialogue around the ethics and public policy of AI.
C3.ai Digital Transformation Institute is a Research Initiative that Includes:
  • Research Awards: Up to 26 cash awards annually, ranging from $100,000 to $500,000 each
  • Computing Resources: Access to free Azure Cloud and C3 AI Suite resources
  • Visiting Professors & Research Scientists: $750,000 per year to support C3.ai DTI Visiting Scholars
  • Curriculum Development: Annual awards to faculty at member institutions to develop curricula that teach the emerging field of Digital Transformation Science
  • Data Analytics Platform: C3.ai DTI will host an elastic cloud, big data, development, and operating platform, including the C3 AI Suite hosted on Microsoft Azure for the purpose of supporting C3.ai DTI research, curriculum development, and teaching.
  • Educational Program: $750,000 a year to support an annual conference, annual report, newsletters, published research, and website
  • Industry Alignment: C3.ai DTI Industry Partners will be established to assure the institute’s operations are aligned to the needs of the private sector.
  • Open Source: C3.ai DTI will strongly favor proposals that promise to publish their research in the public domain.
To support the Institute, C3.ai will provide C3.ai DTI $57,250,000 in cash contributions over the first five years of operation. C3.ai and Microsoft will contribute an additional $310 million in-kind, including use of the C3 AI Suite and Microsoft Azure computing, storage, and technical resources to support C3.ai DTI research.
To learn more about C3.ai DTI’s program, award opportunities, and call for proposals, please visit C3DTI.ai.

About C3.ai Digital Transformation Institute
C3.ai Digital Transformation Institute represents an innovative vision to take AI, ML, IoT, and big data research in a consortium model to a level that cannot be achieved at any one institution alone. Jointly managed and hosted by the University of California, Berkeley and the University of Illinois at Urbana-Champaign, C3.ai DTI will attract the world’s leading scientists to join in a coordinated and innovative effort to advance the digital transformation of business, government, and society, and establish the new Science of the Digital Transformation of Societal Systems.
About C3.ai
C3.ai is a leading AI software provider for accelerating digital transformation. C3.ai delivers the C3 AI Suite for developing, deploying, and operating large-scale AI, predictive analytics, and IoT applications in addition to an increasingly broad portfolio of turn-key AI applications. The core of the C3.ai offering is a revolutionary, model-driven AI architecture that dramatically enhances data science and application development. Learn more at: www.c3.ai.


Use of Artificial Intelligence during the COVID19 Pandemic




Here are some of the projects using AI to address the coronavirus outbreak:



AI in Drug Discovery




A number of research projects are using AI to identify drugs that were developed to fight other diseases but which could now be repurposed to take on coronavirus. By studying the molecular setup of existing drugs with AI, companies want to identify which ones might disrupt the way COVID-19 works. 

BenevolentAI, a London-based drug-discovery company, began turning its attentions towards the coronavirus problem in late January. The company's AI-powered knowledge graph can digest large volumes of scientific literature and biomedical research to find links between the genetic and biological properties of diseases and the composition and action of drugs. 


The company had previously been focused on chronic disease, rather than infections, but was able to retool the system to work on COVID-19 by feeding it the latest research on the virus. "Because of the amount of data that's being produced about COVID-19 and the capabilities we have in being able to machine-read large amounts of documents at scale, we were able to adapt [the knowledge graph] so to take into account the kinds of concepts that are more important in biology, as well as the latest information about COVID-19 itself," says Olly Oechsle, lead software engineer at BenevolentAI. 

While a large body of biomedical research has built up around chronic diseases over decades, COVID-19 only has a few months' worth of studies attached to it. But researchers can use the information that they have to track down other viruses with similar elements, see how they function, and then work out which drugs could be used to inhibit the virus. 

"The infection process of COVID-19 was identified relatively early on. It was found that the virus binds to a particular protein on the surface of cells called ACE2. And what we could with do with our knowledge graph is to look at the processes surrounding that entry of the virus and its replication, rather than anything specific in COVID-19 itself. That allows us to look back a lot more at the literature that concerns different coronaviruses, including SARS, etc. and all of the kinds of biology that goes on in that process of viruses being taken in cells," Oechsle says. 

The system suggested a number of compounds that could potentially have an effect on COVID-19 including, most promisingly, a drug called Baricitinib. The drug is already licensed to treat rheumatoid arthritis. The properties of Baricitinib mean that it could potentially slow down the process of the virus being taken up into cells and reduce its ability to infect lung cells. More research and human trials will be needed to see whether the drug has the effects AI predicts.




Shedding light on the structure of COVID-19


Human epidemiologists at ProMed, an infectious-disease-reporting group, published their own alert just half an hour after HealthMap, and Brownstein also acknowledged the importance of human virologists in studying the spread of the outbreak. 
"What we quickly realised was that as much it's easy to scrape the web to create a really detailed line list of cases around the world, you need an army of people, it can't just be done through machine learning and webscraping," he said. HealthMap also drew on the expertise of researchers from universities across the world, using "official and unofficial sources" to feed into the line list
The data generated by HealthMap has been made public, to be combed through by scientists and researchers looking for links between the disease and certain populations, as well as containment measures. The data has already been combined with data on human movements, gleaned from Baidu, to see how population mobility and control measures affected the spread of the virus in China. 
HealthMap has continued to track the spread of coronavirus throughout the outbreak, visualising its spread across the world by time and location




Spotting signs of a COVID-19 infection in medical images


Canadian startup DarwinAI has developed a neural network that can screen X-rays for signs of COVID-19 infection. While using swabs from patients is the default for testing for coronavirus, analysing chest X-rays could offer an alternative to hospitals that don't have enough staff or testing kits to process all their patients quickly.
DarwinAI released COVID-Net as an open-source system, and "the response has just been overwhelming", says DarwinAI CEO Sheldon Fernandez. More datasets of X-rays were contributed to train the system, which has now learnt from over 17,000 images, while researchers from Indonesia, Turkey, India and other countries are all now working on COVID-19. "Once you put it out there, you have 100 eyes on it very quickly, and they'll very quickly give you some low-hanging fruit on ways to make it better," Fernandez said.
The company is now working on turning COVID-Net from a technical implementation to a system that can be used by healthcare workers. It's also now developing a neural network for risk-stratifying patients that have contracted COVID-19 as a way of separating those with the virus who might be better suited to recovering at home in self-isolation, and those who would be better coming into hospital. 




Monitoring how the virus and lockdown is affecting mental health


Johannes Eichstaedt, assistant professor in Stanford University's department of psychology, has been examining Twitter posts to estimate how COVID-19, and the changes that it's brought to the way we live our lives, is affecting our mental health. 
Using AI-driven text analysis, Eichstaedt queried over two million tweets hashtagged with COVID-related terms during February and March, and combined it with other datasets on relevant factors including the number of cases, deaths, demographics and more, to illuminate the virus' effects on mental health.
The analysis showed that much of the COVID-19-related chat in urban areas was centred on adapting to living with, and preventing the spread of, the infection. Rural areas discussed adapting far less, which the psychologist attributed to the relative prevalence of the disease in urban areas compared to rural, meaning those in the country have had less exposure to the disease and its consequences.
There are also differences in how the young and old are discussing COVID-19. "In older counties across the US, there's talk about Trump and the economic impact, whereas in young counties, it's much more problem-focused coping; the one language cluster that stand out there is that in counties that are younger, people talk about washing their hands," Eichstaedt said.
"We really need to measure the wellbeing impact of COVID-19, and we very quickly need to think about scalable mental healthcare and now is the time to mobilise resources to make that happen," Eichstaedt told the Stanford virtual conference. 





Forecasting how coronavirus cases and deaths will spread across cities – and why


Google-owned machine-learning community Kaggle is setting a number of COVID-19-related challenges to its members, including forecasting the number of cases and fatalities by city as a way of identifying exactly why some places are hit worse than others. 


"The goal here isn't to build another epidemiological model… there are lots of good epidemiological models out there. Actually, the reason we have launched this challenge is to encourage our community to play with the data and try and pick apart the factors that are driving difference in transmission rates across cities," Kaggle's CEO Anthony Goldbloom told the Stanford conference.
Currently, the community is working on a dataset of infections in 163 countries from two months of this year to develop models and interrogate the data for factors that predict spread. 
Most of the community's models have been producing feature-importance plots to show which elements may be contributing to the differences in cases and fatalities. So far, said Goldbloom, latitude and longitude are showing up as having a bearing on COVID-19 spread. The next generation of machine-learning-driven feature-importance plots will tease out the real reasons for geographical variances. 
"It's not the country that is the reason that transmission rates are different in different countries; rather, it's the policies in that country, or it's the cultural norms around hugging and kissing, or it's the temperature. We expect that as people iterate on their models, they'll bring in more granular datasets and we'll start to see these variable-importance plots becoming much more interesting and starting to pick apart the most important factors driving differences in transmission rates across different cities. This is one to watch," Goldbloom added.

~ Jai Krishna Ponnappan