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.
  • 2018-03-06 10:45:51
  • Article ID: 690589

Teaching Computers to Guide Science: New Machine Learning Method Sees the Forests and the Trees

Berkeley Lab and UC Berkeley researchers say "iterative Random Forests" will deliver powerful scientific insights

  • Credit: iStock

While it may be the era of supercomputers and “big data,” without smart methods to mine all that data, it’s only so much digital detritus. Now researchers at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley have come up with a novel machine learning method that enables scientists to derive insights from systems of previously intractable complexity in record time. 

In a paper published recently in the Proceedings of the National Academy of Sciences (PNAS), the researchers describe a technique called “iterative Random Forests,” which they say could have a transformative effect on any area of science or engineering with complex systems, including biology, precision medicine, materials science, environmental science, and manufacturing, to name a few. 

“Take a human cell, for example. There are 10170 possible molecular interactions in a single cell. That creates considerable computing challenges in searching for relationships,” said Ben Brown, head of Berkeley Lab’s Molecular Ecosystems Biology Department. “Our method enables the identification of interactions of high order at the same computational cost as main effects – even when those interactions are local with weak marginal effects.” 

Brown and Bin Yu of UC Berkeley are lead senior authors of “Iterative Random Forests to Discover Predictive and Stable High-Order Interactions.” The co-first authors are Sumanta Basu (formerly a joint postdoc of Brown and Yu and now an assistant professor at Cornell University) and Karl Kumbier (a Ph.D. student of Yu in the UC Berkeley Statistics Department). The paper is the culmination of three years of work that the authors believe will transform the way science is done. “With our method we can gain radically richer information than we’ve ever been able to gain from a learning machine,” Brown said. 

The needs of machine learning in science are different from that of industry, where machine learning has been used for things like playing chess, making self-driving cars, and predicting the stock market. 

“The machine learning developed by industry is great if you want to do high-frequency trading on the stock market,” Brown said. “You don’t care why you’re able to predict the stock will go up or down. You just want to know that you can make the predictions.” 

But in science, questions surrounding why a process behaves in certain ways are critical. Understanding “why” allows scientists to model or even engineer processes to improve or attain a desired outcome. As a result, machine learning for science needs to peer inside the black box and understand why and how computers reached the conclusions they reached. A long-term goal is to use this kind of information to model or engineer systems to obtain desired outcomes. 

In highly complex systems – whether it’s a single cell, the human body, or even an entire ecosystem – there are a large number of variables interacting in nonlinear ways. That makes it difficult if not impossible to build a model that can determine cause and effect. “Unfortunately, in biology, you come across interactions of order 30, 40, 60 all the time,” Brown said. “It’s completely intractable with traditional approaches to statistical learning.” 

The method developed by the team led by Brown and Yu, iterative Random Forests (iRF), builds on an algorithm called random forests, a popular and effective predictive modeling tool, translating the internal states of the black box learner into a human-interpretable form. Their approach allows researchers to search for complex interactions by decoupling the order, or size, of interactions from the computational cost of identification. 

“There is no difference in the computational cost of detecting an interaction of order 30 versus an interaction of order two,” Brown said. “And that’s a sea change.” 

In the PNAS paper, the scientists demonstrated their method on two genomics problems, the role of gene enhancers in the fruit fly embryo and alternative splicing in a human-derived cell line. In both cases, using iRF confirmed previous findings while also uncovering previously unidentified higher-order interactions for follow-up study. 

Brown said they’re now using their method for designing phased array laser systems and optimizing sustainable agriculture systems. 

“We believe this is a different paradigm for doing science,” said Yu, a professor in the departments of Statistics and Electrical Engineering & Computer Science at UC Berkeley. “We do prediction, but we introduce stability on top of prediction in iRF to more reliably learn the underlying structure in the predictors.” 

“This enables us to learn how to engineer systems for goal-oriented optimization and more accurately targeted simulations and follow-up experiments,” Brown added. 

In a PNAS commentary on the technique, Danielle Denisko and Michael Hoffman of the University of Toronto wrote: “iRF holds much promise as a new and effective way of detecting interactions in a variety of settings, and its use will help us ensure no branch or leaf is ever left unturned.” 

The research was supported by grants from DOE’s Small Business Technology Transfer (STTR) program, the Laboratory Directed Research and Development (LDRD) program, the National Human Genome Research Institute, the Army Research Office, the Office of Naval Research, and the National Science Foundation. 

# # # 

Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel Prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit

DOE’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, please visit

  • Filters

  • × Clear Filters

Engineering Yeast Tolerance to a Promising Biomass Deconstruction Solvent

Chemical genomic-guided engineering of gamma-valerolactone-tolerant yeast.

Beyond the WIMP: Unique Crystals Could Expand the Search for Dark Matter

A new particle detector design proposed at the U.S. Department of Energy's Berkeley Lab could greatly broaden the search for dark matter - which makes up 85 percent of the total mass of the universe yet we don't know what it's made of - into an unexplored realm.

20 Percent of Americans Responsible for Almost Half of US Food-Related Greenhouse Gas Emissions

On any given day, 20 percent of Americans account for nearly half of U.S. diet-related greenhouse gas emissions, and high levels of beef consumption are largely responsible, according to a new study from researchers at the University of Michigan and Tulane University.

Saplings Survive Droughts via Storage

Certain species of trees retain stored water, limit root growth to survive three months without water.

Study Reveals New Insights into How Hybrid Perovskite Solar Cells Work

Scientists have gained new insights into a fundamental mystery about hybrid perovskites, low-cost materials that could enhance or even replace conventional solar cells made of silicon.

Want to Clean Up the Environment? Make Credit Easier to Get.

Research by Berkeley Haas Prof. Ross Levine, the Willis H. Booth Chair in Banking and Finance, is the first to show that when lending conditions ease, businesses invest more in projects to cut pollution.

A Reference Catalog for the Rumen Microbiome

In Nature Biotechnology, an international team including JGI scientists presents a reference catalog of rumen microbial genomes and isolates, one of the largest targeted cultivation and sequencing projects to date.

Scientists Have a New Way to Gauge the Growth of Nanowires

n a new study, researchers from the U.S. Department of Energy's Argonne and Brookhaven National Laboratories observed the formation of two kinds of defects in individual nanowires, which are smaller in diameter than a human hair.

A Future Colorfully Lit by Mystifying Physics of Paint-On Semiconductors

It defies conventional wisdom about semiconductors. It's baffling that it even works. It eludes physics models that try to explain it. This newly tested class of light-emitting semiconductors is so easy to produce from solution that it could be painted onto surfaces to light up our future in myriad colors shining from affordable lasers, LEDs, and even window glass.

Liquid-to-Glass Transition Process Gains Clarity

Paul Voyles, the Beckwith-Bascom Professor in materials science and engineering at the University of Wisconsin-Madison, and collaborators in Madison and at Yale University have made significant experimental strides in understanding how, when and where the constantly moving atoms in molten metal "lock" into place as the material transitions from liquid to solid glass.

  • Filters

  • × Clear Filters

Rensselaer Polytechnic Institute Professor Jian Shi Receives Air Force Young Investigator Research Program Award

Jian Shi, assistant professor of materials science and engineering at Rensselaer Polytechnic Institute, has won a Young Investigator Research Program (YIP) award from the Air Force Office of Scientific Research (AFOSR). Shi will use the three-year, $450,000 grant to pursue fundamental research on nanoscale complex materials that could lead to the development of next-generation resilient and high-performance energy conversion and sensing technologies.

Kerstin Kleese van Dam Receives 32nd Town of Brookhaven Annual Women's Recognition Award for Science

The award recognizes the contributions Kleese van Dam--director of Brookhaven Lab's Computational Science Initiative since 2015--has made to scientific computing and data management over the past three decades.

Jefferson Lab Announces New Accelerator Science Leader

The Department of Energy's Thomas Jefferson National Accelerator Facility has announced that Andrei Seryi will become its new associate director for accelerator operations, research and development in June.

First Plasma for New Machine to Study Puzzling Process That Occurs Throughout the Universe

Announcement describes completion of construction of FLARE, a powerful new machine to study magnetic reconnection.

Rensselaer Polytechnic Institute Professor Jian Sun Receives Power Electronics Achievement Award

Jian Sun, professor of electrical, computer, and systems engineering and director the New York State Center for Future Energy Systems at Rensselaer Polytechnic Institute, received the 2017 R. David Middlebrook Outstanding Achievement Award from the IEEE Power Electronics Society (PELS). He was recognized for "contributions to modeling and control of power electronic converters and systems."

FGC Plasma Solutions Wins Top NASA Innovation Award

Argonne Chain Reaction Innovator Felipe Gomez del Campo has received the 2018 NASA iTech award for X-Factor Innovation.

Sandia Researcher Jacqueline Chen Elected to National Academy of Engineering

LIVERMORE, Calif. -- Jacqueline Chen, a distinguished member of the technical staff at Sandia National Laboratories, has been elected to the National Academy of Engineering. Chen is among the 99 new members from around the globe in the 2018 class.Election to the National Academy of Engineering is the highest professional distinction for an engineer in the United States.

PNNL Helps Form International Energy Storage Organization

News Release DALIAN, China -- Energy storage allows power operators across the nation to balance electricity supply and demand instantaneously, affording ratepayers a more resilient power supply.Now the focus on energy storage is global. In January, energy storage experts at the Department of Energy's Pacific Northwest National Laboratory joined forces with their counterparts around the world to forge the International Coalition for Energy Storage and Innovation, or ICESI.

University Partnership to Help Nevada Scientists Commercialize Discovery

UNLV's Office of Technology Transfer and the Desert Research are partnering to help faculty and students leverage each other's talent and resources to transform inventionsĀ into new products and services.

DOE Seeks Industry Partners for HPC Research on Materials in Applied Energy Technologies

The Department of Energy (DOE) today announced a funding opportunity totaling $3 million to support projects between U.S. industry and DOE national laboratories related to improving materials in severe or complex environments through the new High Performance Computing for Materials in Applied Energy Technologies (HPC4Mtls) Program.

  • Filters

  • × Clear Filters

Engineering Yeast Tolerance to a Promising Biomass Deconstruction Solvent

Chemical genomic-guided engineering of gamma-valerolactone-tolerant yeast.

Saplings Survive Droughts via Storage

Certain species of trees retain stored water, limit root growth to survive three months without water.

Unlocking On-Package Memory's Effects on High-Performance Computing's Scientific Kernels

Intuitive visual analytical model better explains complex architectural scenarios and offers general design principles.

Data Dive: How Microbes Handle Poor Nutrition in Tropical Soil

High-performance computing reveals the relationship between DNA and phosphorous uptake.

The Secret Lives of Cells

Supercomputer simulations predict how E. coli adapts to environmental stresses.

It's Not Part of the Problem, but Part of the Solution

Americium(III) is selectively and efficiently separated from europium(III) by an extractant in an ionic liquid.

Buckyball Marries Graphene

Electronic and structure richness arise from the merger of semiconducting molecules of carbon buckyballs and 2-D graphene.

Atomic Movies Explain Why Perovskite Solar Cells Are More Efficient

Tracking atoms is crucial to improving the efficiency of next-generation perovskite solar cells.

Catalysts: High Performance Lies on the Edge

Iron may be more valuable than platinum. Sometimes.

Discovery of a New Microbe that Produces Methane in Oxygenated Soils

Global models may be underestimating net wetland methane emissions.


Wednesday March 14, 2018, 02:05 PM

Q&A: Al Ashley Reflects on His Efforts to Diversify SLAC and Beyond

SLAC National Accelerator Laboratory

Thursday February 15, 2018, 12:05 PM

Insights on Innovation in Energy, Humanitarian Aid Highlight UVA Darden's Net Impact Week

University of Virginia Darden School of Business

Friday February 09, 2018, 11:05 AM

Ivy League Graduate, Writer and Activist with Dyslexia Visits CSUCI to Reframe the Concept of Learning Disabilities

California State University, Channel Islands

Wednesday January 17, 2018, 12:05 PM

Photographer Adam Nadel Selected as Fermilab's New Artist-in-Residence for 2018

Fermi National Accelerator Laboratory (Fermilab)

Wednesday January 17, 2018, 12:05 PM

Fermilab Computing Partners with Argonne, Local Schools for Hour of Code

Fermi National Accelerator Laboratory (Fermilab)

Wednesday December 20, 2017, 01:05 PM

Q&A: Sam Webb Teaches X-Ray Science from a Remote Classroom

SLAC National Accelerator Laboratory

Monday December 18, 2017, 01:05 PM

The Future of Today's Electric Power Systems

Rensselaer Polytechnic Institute (RPI)

Monday December 18, 2017, 12:05 PM

Supporting the Development of Offshore Wind Power Plants

Rensselaer Polytechnic Institute (RPI)

Tuesday October 03, 2017, 01:05 PM

Stairway to Science

Argonne National Laboratory

Thursday September 28, 2017, 12:05 PM

After-School Energy Rush

Argonne National Laboratory

Thursday September 28, 2017, 10:05 AM

Bringing Diversity Into Computational Science Through Student Outreach

Brookhaven National Laboratory

Thursday September 21, 2017, 03:05 PM

From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

SLAC National Accelerator Laboratory

Thursday September 07, 2017, 02:05 PM

Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

SLAC National Accelerator Laboratory

Thursday August 31, 2017, 05:05 PM

Binghamton University Opens $70 Million Smart Energy Building

Binghamton University, State University of New York

Wednesday August 23, 2017, 05:05 PM

Widening Horizons for High Schoolers with Code

Argonne National Laboratory

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)

Showing results

0-4 Of 2215