Big Data meets big healthcare for veteransBy Ronald Walli • August 7, 2017
Veterans will be the ultimate winners in the U.S. Department of Veterans Affairs (VA) - Department of Energy (DOE) MVP-CHAMPION (Million Veteran Program Computational Health Analytics for Medical Precision to Improve Outcomes Now) initiative, a collaborative research effort that aligns DOE national laboratories with VA researchers, including Argonne National Laboratory (ANL) in a prominent role.
The partnership brings together VA’s unparalleled and vast array of healthcare and genomic data with DOE’s world class high performance computing, artificial intelligence and data analytics to push the frontiers of next-generation computing, precision health, genomic sciences, and health care delivery. In addition to ANL, the partnering DOE laboratories include Brookhaven, Lawrence Livermore, Los Alamos, Oak Ridge, Pacific Northwest and Sandia National Laboratories.
“This is truly the humanization of computing. We have an opportunity to touch thousands of people on a very personal level and make their lives better.” - Ravi Madduri, Argonne computer scientist
For Argonne, its extensive track record of successes with big data and big computers make it a quintessential partner in this multi-faceted research team to improve healthcare for millions of veterans, advance supercomputing, and solve some of the nation’s biggest scientific challenges. A team led by Argonne’s Rick Stevens, associate laboratory director for Computing, Environment and Life Sciences, was instrumental in moving the effort from concept to reality.
“We hosted a daylong workshop last year that led to the creation of a working group from the U.S. Department of Veterans Affairs and the U.S. Department of Energy,” Stevens said. “We met every two weeks and led the discussions of the overarching goals that have culminated in a project we are confident will lead to transformational science.”
Specifically, the VA-DOE partnership supports:
- Innovation to design and develop DOE research that will merge big data, artificial intelligence and high-performance computing
- Better healthcare by using high-performance computing to improve outcomes and reduce costs
- Better science through a team of researchers and clinicians who specialize in healthcare with DOE experts in high-performance computing, artificial intelligence and big data
- Better government through interagency collaborations that take advantage of public-private partnerships
At a two-day joint VA-DOE summit in Washington, D.C., earlier this year, joint agency multi-laboratory teams shaped discussions focused on cardiovascular diseases, the leading cause of death for men and women in the U.S., prostate cancer, and suicide prevention. Suicide is currently the 10th leading cause of death in the U.S. and claims 20 to 22 veterans per day.
Armed with never-before-available data from more than half a million veterans, made available through the VA-DOE partnership, Argonne researchers will collaborate with VA clinicians and scientists to build predictive tools that identify improved sets of risk factors for specific types of cardiovascular disease. To combat suicide, researchers will develop patient-specific mathematical models designed to help identify veterans at risk. The third focus of these pilot projects, all to be done while ensuring security and privacy of veterans, is on prostate cancer and helping to discern lethal and non-lethal forms of the disease.
Argonne computer scientist Ravi Madduri emphasized that this project has multiple levels of complexity, but it’s the perfect marriage of the VA’s enormous repository of health and genomic data and DOE’s world-class high-performance computing capabilities and ability to manage big data.
“Ultimately, we’re leveraging the latest DOE expertise and technologies in big data, artificial intelligence and high-performance computing to identify trends that will lead to new treatments and preventive strategies,” Madduri said. His focus is on building software for data management and analysis to improve patient outcomes by linking researchers, physicians and patients.
The recent explosion of genetics data combined with the VA’s end-to-end records of veterans are especially valuable, as are its extensive records of treatments and outcomes. Health data will also be made available from the Department of Defense, Centers for Medicare and Medicaid Services and the Center for Disease Control’s National Death Index. With this information and the expertise of Argonne and other collaborating DOE labs, clinicians will be able to perform genome-wide association studies, develop pattern recognition techniques and ultimately better treatments for cardiovascular and other diseases.
While Madduri is quick to acknowledge the significant contributions of supercomputing in areas that include jet engine design, fusion and nanomaterials, he’s especially excited about the human element of this initiative.
“This is truly the humanization of computing,” Madduri said. “We have an opportunity to touch thousands of people on a very personal level and make their lives better.”
Another key member of the Argonne team is Strategic Program Manager Tom Brettin, who attended a VA-DOE strategy and planning meeting at the VA’s Jamaica Plain Campus in Boston last year. He quickly realized that the challenge facing the VA was something Argonne has been focused on for more than a decade and noted the special synergy that positions Argonne to be an important intellectual partner.
“Using big computers to solve problems like what our veterans and the Department of Veterans Affairs are facing is something we know how to do, and we know how to provide solutions that will make the most of limited resources,” Brettin said.
Although supercomputers have been making strides in a number of scientific areas for more than two decades, genomics hasn’t traditionally been part of the equation. Computers simply weren’t designed for that purpose, but that’s been changing and this project will serve as a catalyst as researchers work together to determine the best computer architectures.
“We’re at a point where genomics-based medicine and high-performance computing are coming together because of discussions about architecture of next-generation machines,” said Brettin, who has studied genomics for 20 years. He envisions a time soon when doctors will have a wealth of patient information at their fingertips.
“We are entering a whole new era when we’ll have the best of both – historic advances in medicine and high-performance computing,” he said. Teaming with the University of Chicago, Brettin is confident that researchers will make great strides.
“Twenty years ago, when I was working on the human genome project, my co-workers and I could imagine what human medicine might be like in the future, but it was only a dream,” Brettin said. “But I realized even then that computing would play a vital role in that future, and today it’s coming true right before my eyes.”
Another challenge involves moving huge amounts of data efficiently and securely. The DOE’s ESnet, which provides high bandwidth and reliable connections that link scientists at national laboratories, universities and other research institutions, solves that problem. The ability to transmit data is an essential component of the effort, and the payoff will happen on multiple levels as experts in diverse fields engage.
On the computational front, Theta, a 9.65-petaflops system designed in collaboration with Intel and Cray, will aid the MVP-CHAMPION initiative. Aurora will be the next star of the Argonne Leadership Computing Facility (ALCF) and will play a prominent role in this data analysis challenge.
Ultimately, Aurora’s configuration will enable researchers, clinicians and others to devise complex work flows tailored to producing results that will yield diagnoses and treatments that take into account genetic factors and likely outcomes. Brettin sees a future of doing genomics at scale and looking at individual chromosomes of people to figure out the best treatment.
“Physicians will have a central database that includes data about statistical associations of diseases, treatments and outcomes, all of which they can use to make real-world decisions,” Brettin said.
What began in 2011 with the VA’s Million Veteran Program, designed to study how genes affect health, has blossomed into something with an enrollment of more than 560,000 veterans and a partnership with DOE, its state-of-the-art computing and scientists who are the best in the world. Argonne scientists are confident that veterans and people throughout the nation will reap benefits as the DOE national laboratory enterprise works with the VA to provide an unparalleled opportunity to advance veterans’ health.
Established by Congress in 2000, the National Nuclear Security Administration (NNSA) is a semi-autonomous agency within the U.S. Department of Energy responsible for enhancing national security through the military application of nuclear science. NNSA maintains and enhances the safety, security, and effectiveness of the U.S. nuclear weapons stockpile without nuclear explosive testing; works to reduce the global danger from weapons of mass destruction; provides the U.S. Navy with safe and effective nuclear propulsion; and responds to nuclear and radiological emergencies in the U.S. and abroad. Visit nnsa.energy.gov for more information.
Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.
The U.S. Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the Office of Science website.