Doe Science news source
The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2017-07-31 14:05:38
  • Article ID: 678786

Argonne Goes Deep to Crack Cancer Code

  • Credit: Argonne National Laboratory

    Rick Stevens is Associate Laboratory Director for Computing, Environment and Life Sciences. Stevens is helping to develop the CANDLE computer architecture on the patient level which is meant to help guide drug treatment choices for tumors based on a much wider assortment of data than currently used.

  • Credit: David Kashatus/ National Cancer Institute / Univ. of Virginia Cancer Center

    Ras-Driven Cancer. About a third of all human cancers are driven by mutations in RAS genes. When Ras genes are mutated, cells grow uncontrollably and evade death signals. Argonne is part of a multi-institutional effort advancing an exascale computing framework focused on the development of the deep neural network code called CANDLE, to help understand these mutations.

  • Credit: National Institutes of Health

    Eric Stahlberg is director of the High Performance Computing Initiative at Frederick National Laboratory and Co-principal Investigator on the Exascale Computing Project.

  • Credit: Argonne National Laboratory

    Rick Stevens is Associate Laboratory Director for Computing, Environment and Life Sciences. Stevens is helping to develop the CANDLE computer architecture on the patient level which is meant to help guide drug treatment choices for tumors based on a much wider assortment of data than currently used.

  • Credit: David Kashatus/ National Cancer Institute / Univ. of Virginia Cancer Center

    Ras-Driven Cancer. About a third of all human cancers are driven by mutations in RAS genes. When Ras genes are mutated, cells grow uncontrollably and evade death signals. Argonne is part of a multi-institutional effort advancing an exascale computing framework focused on the development of the deep neural network code called CANDLE, to help understand these mutations.

  • Credit: National Institutes of Health

    Eric Stahlberg is director of the High Performance Computing Initiative at Frederick National Laboratory and Co-principal Investigator on the Exascale Computing Project.

  • Credit: Argonne National Laboratory

    Rick Stevens is Associate Laboratory Director for Computing, Environment and Life Sciences. Stevens is helping to develop the CANDLE computer architecture on the patient level which is meant to help guide drug treatment choices for tumors based on a much wider assortment of data than currently used.

  • Credit: David Kashatus/ National Cancer Institute / Univ. of Virginia Cancer Center

    Ras-Driven Cancer. About a third of all human cancers are driven by mutations in RAS genes. When Ras genes are mutated, cells grow uncontrollably and evade death signals. Argonne is part of a multi-institutional effort advancing an exascale computing framework focused on the development of the deep neural network code called CANDLE, to help understand these mutations.

  • Credit: National Institutes of Health

    Eric Stahlberg is director of the High Performance Computing Initiative at Frederick National Laboratory and Co-principal Investigator on the Exascale Computing Project.

  • Credit: Argonne National Laboratory

    Rick Stevens is Associate Laboratory Director for Computing, Environment and Life Sciences. Stevens is helping to develop the CANDLE computer architecture on the patient level which is meant to help guide drug treatment choices for tumors based on a much wider assortment of data than currently used.

  • Credit: David Kashatus/ National Cancer Institute / Univ. of Virginia Cancer Center

    Ras-Driven Cancer. About a third of all human cancers are driven by mutations in RAS genes. When Ras genes are mutated, cells grow uncontrollably and evade death signals. Argonne is part of a multi-institutional effort advancing an exascale computing framework focused on the development of the deep neural network code called CANDLE, to help understand these mutations.

  • Credit: National Institutes of Health

    Eric Stahlberg is director of the High Performance Computing Initiative at Frederick National Laboratory and Co-principal Investigator on the Exascale Computing Project.

A cancer diagnosis is overwhelming, the treatment often complex and uncertain. Doctors have yet to understand how a specific cancer will affect an individual, and a drug that may hold promise for one patient, may not work for another.

But a melding of medical research and high-performance computing is taking a more personalized approach to treatment by creating precise therapy options based on genetics.

"We are trying to devise a means of automating the search through machine learning so that you’d start with an initial model and then automatically find models that perform better than the initial one."

“Precision medicine is the ability to fine tune a treatment for each patient based on specific variations, whether it’s their genetics, their environment or their history. To do that in cancer, demands large amounts of data, not only from the patient, but the tumor, as well, because cancer changes the genetics of the tissue that it surrounds,” said Rick Stevens, Associate Laboratory Director for Computing, Environment and Life Sciences for the U.S. Department of Energy’s (DOE) Argonne National Laboratory.

In a typical cancer study today, more than eight million measurements are taken from the biopsy of a single tumor. But even as current technologies allow us to characterize the biological components of cancer with greater levels of accuracy, the massive amounts of data they produce have out-paced our ability to quickly and accurately analyze them.

To tackle these complicated and consequential precision medicine problems, researchers globally are looking toward the promise of exascale computing. Stevens is principal investigator of a multi-institutional effort advancing an exascale computing framework focused on the development of the deep neural network code CANDLE (CANcer Distributed Learning Environment).

Part of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C), a DOE and National Cancer Institute (NCI) collaboration, CANDLE will address three key cancer challenges to accelerate research at the molecular, cellular and population levels.

The challenges will test CANDLE’s advanced machine learning approach—deep learning—that, in combination with novel data acquisition and analysis techniques, model formulation and simulation, will help arrive at a prognosis and treatment plan designed specifically for an individual patient.

“Deep learning is the use of multi-layered neural networks to do machine learning, a program that gets smarter or more accurate as it gets more data to make predictions. It’s very successful at learning to solve problems,” said Stevens.

The model stores data that has already been observed and uses it later to quickly infer the solution to similar or recurring events or problems. Speech recognition, image recognition and text translation are examples of machine learning that many of us utilize every day without realizing it.

“Every time you talk to SIRI or Alexa, you’re encountering deep learning,” he added.

This framework will be built upon available open-source deep learning platforms that can be adapted to address different aspects of the cancer process as represented by JDACS4C’s challenge topics: 1) understand the molecular basis of key protein interactions; 2) develop predictive models for drug response; and 3) automate the extraction and analysis of information from millions of cancer patient records to determine optimal cancer treatment strategies.

The process begins by compiling all the known data on how cancer functions, reacts to drugs and behaves within individuals, and creating a virtual approximation of it. While the numbers of molecular configurations, drug combinations and patient datasets are staggering, the exascale-anticipating framework will progressively “learn” to manage it.

For example, the goal of the drug response challenge is to predict how a tumor will respond to a drug based on the characteristics of both the tumor and the drug, the information for which is identified through previously available data, such as tumor samples and previous drug screens.

The CANDLE network code will be trained to assimilate millions of previous drug screen results. An open-source content management system then would search through upwards of a billion drug combinations to find those with the greatest potential to inhibit a given tumor, or a billion hypothetical compounds to identify candidates for new drug development.

Through another technique called data mining, researchers working on the treatment strategy problem can train the network to sift through and automatically interpret millions of clinical reports and patient records. From those, it can pull data related directly to a specific patient and build predictive models of treatment and outcome trajectories for that individual.

Until now, cancer researchers have been doing this in small teams, maintaining massive databases of different factors characteristic of the cancer’s growth. But much of this information is peripheral. The most helpful information is buried within and among the millions of data points collected.

“This is a huge part of the challenge, because humans do this now, but by hand,” explained Stevens. “We are trying to devise a means of automating the search through machine learning so that you’d start with an initial model and then automatically find models that perform better than the initial one. We then could repeat this process for each individual patient.”

While the computational solutions for these training problems alone will require the largest available high-performance computers, Stevens and his team believe that the resulting models are likely to require exascale or near-exascale systems to advance each of the cancer problem areas.

CANDLE is one of three unique Argonne National Laboratory programs funded by the DOE’s Exascale Computing Project (ECP), launched in 2015 to promote the design and integration of application, software and hardware technologies into exascale systems.

These systems will be able to run applications such as CANDLE 50 to 100 times faster than today’s most powerful supercomputers, like those housed at the Argonne Leadership Computing Facility (ALCF) a DOE Office of Science User Facility. Theta, ALCF’s new 9.65 petaflops Intel-Cray system, delivers high performance on traditional modeling and simulation applications and was developed to more quickly and efficiently handle advanced software and data analysis methods.

“The types of things researchers would like to accomplish now require a lot more data, capacity and computing power than we have. That’s why there is this effort to build a whole new framework, one focused more on data,” said Paul Messina, director of ECP. “CANDLE will play an essential role in the development of applications that drive this framework, creating the ability to analyze hundreds of millions of items of data to come up with individual cancer treatments.”

With the unique collaboration of JDACS4C, the CANDLE team has immediate access to NCI’s formidable subject matter and domain experts on cancer. And as partners with the DOE and, specifically, CORAL (a collaboration comprising Oak Ridge, Argonne and Lawrence Livermore National Laboratories), CANDLE enlists some of the nation’s leading computational scientists to provide the computational and data science expertise.

Vendors involved with the labs and ECP are among the leading designers of high-performance computing architecture in the world. Companies like Intel, Nvidia, IBM, and Cray are interested in collaborating on cancer research, and are fully vested in the idea that the convergence between simulation, data and machine learning is the future, noted Stevens.

“There is a tremendous level of team work and sharing across the enterprise. Cancer is something that people can relate to personally, so having the opportunity to develop a capability that will eventually help somebody else can be very motivating,” said Eric Stahlberg, director of the Frederick National Laboratory for Cancer Research’s strategic and data science initiatives.

“It’s a Herculean task. But even incremental progress toward that goal will have a significant impact on many more people affected by cancer, as a result.”

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.

X
X
X
  • Filters

  • × Clear Filters

Discovered: A Quick and Easy Way to Shut Down Instabilities in Fusion Devices

Article describes use of second neutral beam injector to suppress instabilities on the NSTX-U

Researchers Create Molecular Movie of Virus Preparing to Infect Healthy Cells

A research team has created for the first time a movie with nanoscale resolution of the three-dimensional changes a virus undergoes as it prepares to infect a healthy cell. The scientists analyzed thousands of individual snapshots from intense X-ray flashes, capturing the process in an experiment at the Department of Energy's SLAC National Accelerator Laboratory.

Nanotechnology Gives Green Energy a Green Color

Solar panels have tremendous potential to provide affordable renewable energy, but many people see traditional black and blue panels as an eyesore. Architects, homeowners and city planners may be more open to the technology if they could install colorful, efficient solar panels, and a new study, published this week in Applied Physics Letters, brings us one step closer. Researchers have developed a method for imprinting existing solar panels with silicon nanopatterns that scatter green light back toward an observer.

New 3-D Simulations Show How Galactic Centers Cool Their Jets

Scientists at Berkeley Lab and Purdue University developed new theories and 3-D simulations to explain what's at work in the mysterious jets of energy and matter beaming from the center of galaxies at nearly the speed of light.

Are Your Tweets Feeling Well?

Study finds opinion and emotion in tweets change when you get sick, a method public health workers could use to track health trends.

"Getting to 80%" on Energy Cutbacks Cannot Occur Unless Behaviors Change

California's plan to cut energy consumption by 80 percent by 2050 cannot be achieved with current proposed policy changes because most solutions focus on changing technologies rather than changing behavior, a new UC Davis study suggests.

New Battery Material Goes with the Flow

Scientists at the U.S. Department of Energy's (DOE) Argonne National Laboratory have engineered a new material to be used in redox flow batteries, which are particularly useful for storing electricity for the grid. The material consists of carefully structured molecules designed to be particularly electrochemically stable in order to prevent the battery from losing energy to unwanted reactions.

Simulation Demonstrates How Exposure to Plasma Makes Carbon Nanotubes Grow

PPPL research performed with collaborators from Princeton University and the Institute for Advanced Computational Science at the State University of New York at Stony Brook has shown how plasma causes exceptionally strong, microscopic structures known as carbon nanotubes to grow.

Night Vision for Bird- & Bat-Friendly Offshore Wind Power

The ThermalTracker software analyzes video with night vision, the same technology that helps soldiers see in the dark, to help birds and bats near offshore wind turbines.

Drone Tech Offers New Ways to Manage Climate Change

An innovation providing key clues to how humans might manage forests and cities to cool the planet is taking flight. Cornell researchers are using drone technology to more accurately measure surface reflectivity on the landscape, a technological advance that could offer a new way to manage climate change.


  • Filters

  • × Clear Filters

Kathryn Hastie Wins Spicer Award for Lassa Virus Work at SLAC's X-Ray Synchrotron

Kathryn Hastie, staff scientist at The Scripps Research Institute, has spent the last decade studying how the deadly Lassa virus - which causes up to half a million cases of Lassa fever each year in West Africa - enters human cells via a cell surface receptor.

Southern Research to Play Key Role in Low Cost Carbon Fiber Project

Southern Research's Energy & Environment division (E&E) will participate as a subcontractor to WRI to provide renewable acrylonitrile -- the key raw material needed to produce the highest quality carbon fibers -- produced from biomass-derived second generation sugars.

Newly Upgraded Laser Allows Scientists to Peer Further Into the Extreme Universe at SLAC's LCLS

Scientists at the Department of Energy's SLAC National Accelerator Laboratory recently upgraded a powerful optical laser system used to create shockwaves that generate high-pressure conditions like those found within planetary interiors. The laser system now delivers three times more energy for experiments with SLAC's ultrabright X-ray laser, providing a more powerful tool for probing extreme states of matter in our universe.

Three Brookhaven Lab Scientists Selected to Receive Early Career Research Program Funding

Three scientists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory have been selected by DOE's Office of Science to receive significant research funding through its Early Career Research Program.

Upcoming 232nd ECS Meeting to Feature International Energy Summit, Nobel Laureate Lecture

The 232nd ECS Meeting will include 49 topical symposia and over 2,300 technical presentations, including the 7th International Electrochemical Energy Summit, the Society's inaugural OpenCon and Hack Day events, and plenary lecture delivered by former U.S. Secretary of Energy and Nobel Prize Laureate Steven Chu.

PNNL Scientist Jiwen Fan Receives DOE Early Career Research Award

Jiwen Fan of the Department of Energy's Pacific Northwest National Laboratory has been selected to receive a 2017 Early Career Research Program award from the U.S. Department of Energy. Fan will use the award to study severe thunderstorms in the central United States - storms that produce large hail, damaging winds, tornadoes, and torrential rainfall.

Three SLAC Scientists Receive DOE Early Career Research Grants

Three scientists at the Department of Energy's SLAC National Accelerator Laboratory will receive DOE Early Career Research Program grants for research to find evidence of cosmic inflation, understand how plasmas excite particles to high energies and develop a way to accelerate particles in much shorter distances with terahertz radiation.

Four ORNL Researchers Receive DOE Early Career Funding Awards

Four Oak Ridge National Laboratory researchers specializing in nuclear physics, fusion energy, advanced materials and environmental science are among 59 recipients of Department of Energy's Office of Science Early Career Research Program awards.

Missouri S&T Professor Earns Patent for Energy Storage Technology

ceramic engineering professor at Missouri University of Science and Technology has received a federal patent for his latest innovation, a multi-layer ceramic capacitor that could help boost energy storage in applications ranging from pulse power devices to military hardware.

James Peery Named Chief Scientist of the Global Security Directorate at Oak Ridge National Laboratory

James Peery, who has led critical national security programs at Sandia National Laboratories and Los Alamos National Laboratory, has been selected as the chief scientist of the Global Security Directorate at Oak Ridge National Laboratory.


  • Filters

  • × Clear Filters

Creating a Molecular Super Sponge, From the Ground Up

A new uranium-based metal-organic framework, NU-1301, could aid energy producers and industry.

Physicists Move Closer to Listening in on Sub-Atomic Conversation

Calculations of a subatomic particle called the sigma provide insight into the communication between subatomic particles deep inside the heart of matter.

Meet the Director: Chuck Black

This is a continuing profile series on the directors of the Department of Energy (DOE) Office of Science User Facilities. These scientists lead a variety of research institutions that provide researchers with the most advanced tools of modern science including accelerators, colliders, supercomputers, light sources and neutron sources, as well as facilities for studying the nano world, the environment, and the atmosphere.

Making an Ultra-small Silicon "Chip"

A new polymer, created with a structure inspired by crystalline silicon, may make it easier to build better computers and solar cells.

How to Keep a Vital Diagnostic Isotope in Stock

Researchers succeed in producing larger quantities of a long-lived radioisotope, titanium-44, that generates a needed isotope, scandium-44g, on demand.

When Strontium Is Away, Iridium Comes Out to Play

Developing a highly active and acid-stable catalyst for water splitting could significantly impact solar energy technologies.

On Track Towards a Zika Virus Vaccine

Antibody's molecular structure reveals how it recognizes the Zika virus

Quantum Computing Building Blocks

Scientists invented an approach to creating ordered patterns of nitrogen-vacancy centers in diamonds, a promising approach to storing and computing quantum data.

Scientists Program Yeast to Turn Plant Sugars into Biodiesel

Redox metabolism was engineered in Yarrowia lipolytica to increase the availability of reducing molecules needed for lipid production.

Soils Could Release Much More Carbon than Expected as Climate Warms

Deeper soil layers are more sensitive to warming than previously thought.


Spotlight

Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

Rensselaer Polytechnic Institute (RPI)

Wednesday September 16, 2009, 10:00 AM

College Presidents Flock to D.C., Urge Senate to Pass Clean Energy Bill

National Wildlife Federation (NWF)

Wednesday July 01, 2009, 04:15 PM

Northeastern Announces New Professional Master's in Energy Systems

Northeastern University

Friday October 12, 2007, 09:35 AM

Kansas Rural Schools To Receive Wind Turbines

Kansas State University

Thursday August 17, 2006, 05:30 PM

High Gas Prices Here to Stay, Says Engineering Professor

Rowan University

Wednesday May 17, 2006, 06:45 PM

Time Use Expert's 7-Year Fight for Better Gas Mileage

University of Maryland, College Park





Showing results

0-4 Of 2215