SAY AH-HA!

February 2, 2001

by Karen Green, NCSA Senior Writer

Champaign, IL — Scientific research is often a game of strategy, with research teams constantly devising new ways to outmaneuver the challenges that inhibit their progress. Every new tool, every improved process is a chance to gain a competitive advantage. Algorithms that can better analyze field data, codes that promise to speed up the analysis of datasets, new visualization techniques — all are eagerly put to the test. Cancer researchers, for example, covet tools and techniques that can help them deal with large volumes of data from human subjects. The best of these tools become part of the best strategies and methods used to help medical science get a competitive edge on a formidable opponent: cancer.

The research team led by Kenneth Watkin at the University of Illinois at Urbana-Champaign is typical of cancer research teams. Watkin, a U of I professor of medicine and applied life studies, is one of two principal investigators on a project that aims to understand the content of ultrasonic images taken of tissue in cancer patients. His co-PI is Tanya Gallagher, dean of the U of I College of Applied Life Studies. Watkin realized he needed more computing power to analyze his group’s research data, so he began looking for solutions — a tool or a process that could cut the team’s computing time. When he turned to NCSA and learned that the center’s Origin2000 supercomputer could meet his data analysis challenges, he seized the opportunity.

“When we started our work, we were using an 800 MHz desktop computer, and it took at least several hours to process one ultrasonic image,” says Watkin. “We needed to process 400 to 600 images a year, and there was just no way we were going to accomplish that. We needed something faster-something that could process medical images at very high speeds.”

Help came in the form of Faisal Saied and Sirpa Saarinen in NCSA’s Performance Engineering group. They developed a parallel version of the team’s algorithm that analyzes textures in ultrasonic images and ported it to the Origin2000. The researchers received an allotment of time on the Origin2000 and now, a five- to six-hour computing and imaging process can be completed in about five minutes. The collaboration, says Watkin, means he is free to concentrate on the science of his research, knowing that the computational aspects are being handled.

Watkin’s team looks at tissue changes in the tongues of cancer patients, determining how much of the tissue is muscle and fat and how much is a stiff fibrous tissue normally not present in healthy individuals. Healthy tongue tissue is mostly muscle with some fatty tissue, says Watkin. However, in patients who receive radiation treatments for head or neck cancer, some of that muscle tissue often becomes fibrous and inflexible, a process known as fibrosis. The tissue changes can cause other problems in the patient such as dysphagia, or difficulty swallowing. In the most serious dysphagia cases, the patient is unable to swallow food and liquids often get rerouted to the windpipe, causing breathing problems. Sometimes swallowing becomes so difficult that the patient needs a feeding tube.

“When people are radiated, muscle tissue is heated up and begins to change,” explains Watkin. “Our study involves treatment strategies. Ultimately, we are looking at what is the best treatment we can provide while still maintaining muscle quality.”

The team, funded by the National Institutes of Health’s National Cancer Institute, uses ultrasound images of tongue tissue from patients at 10 cancer research centers nationwide. The data, which are transmitted electronically as image files to Watkin’s laboratory at Carle Foundation Hospital in Urbana, IL, include images from patients receiving different radiation doses. The images are ultrasounds taken at different times in patients’ treatments and up to a year after treatment has finished. By studying changes in tissue over time and comparing tissue changes in patients receiving different dosages of radiation, the researchers hope to develop treatment strategies for head and neck cancer patients that cause the least amount of damage to healthy tissue while still killing cancerous cells.

To analyze the ultrasound images and determine the textures of the tissues represented in each, the researchers developed a tissue analysis algorithm called the Gray Level Texture Parameter computation. To compute the textures, the code divides each image into kernels that are 8 x 8 pixels in size. A tool called the Spatial Gray Level Dependence (SGLD) matrix then computes a correlation number for each pixel within each 8-x-8 kernel of the image. This correlation number identifies whether the tissue is muscle, fat, or fibrous tissue. The SGLD correlation number for muscle ranges from 0 to .40, for fibrous tissue it ranges from .41 to .85, while the correlation number for fat is .85 or above. The end result is a color-coded image of the tongue tissue in which red represents muscle, yellow represents fat, and blue represents other tissue types, including fibrous tissue.

“The correlation number that the computer generates for each pixel identifies what [tissue] type is at that particular point in the image,” says Ibrahima Diouf, a postdoctoral fellow in speech and hearing science and a member of the research team. “Generating a correlation matrix for each pixel is a computationally intensive process. It could be done on a PC, but it was taking us a whole day to get a full analysis of one image. ”

When the team’s code was ported to the Origin2000, tissue analysis of the images made a giant leap in speed. NCSA’s Saarinen developed a parallel version of the Gray Level Texture Parameter computation algorithm, which allowed image analysis to be distributed to a number of Origin processors. According to Diouf, each ultrasound image is now subdivided into two, four, eight, or 16 segments. Each segment is then analyzed by an individual Origin processor, and the segments are recombined into one color coded image. So far, analysis of a single image has been done on up to 16 Origin processors, which cuts the compute time to about five minutes. In the months to come, the team plans to port its code to NCSA’s NT supercluster. According to Diouf, computing on the NT supercluster is a logical move for the research team since the lab’s computers run Windows NT.

Texture analysis algorithms and faster ways of analyzing medical images benefit not only researchers. In the long run, the combination of new analysis methods and supercomputing power could assist radiologists and pathologists, who are often the first medical professionals to identify cancerous tissue. These days, radiologists and pathologists deal with hundreds of diagnostic images a day taken from a wide range of imaging devices, including computerized tomography, magnetic resonance imaging, positron emission tomography, ultrasound, light and electron microscopy, and 3D imaging. Examining and sorting through all these images to identify specific types of cells, including cancer cells, is labor intensive and fatiguing, says Watkin. He hopes for a future in which high-speed networks or satellites transmit medical imaging data to a supercomputing system for processing. Processing would take only minutes, and results could be displayed remotely for the technicians at hospitals and clinics.

“This kind of image analysis methodology on a large scale would mean that professionals in the hospital setting would be able to quickly identify differences in tissue and know what areas of an image need to be looked at closely,” says Watkin.

This research is supported by the National Institutes of Health’s National Cancer Institute.

============================================================

Subscribe to HPCwire's Weekly Update!

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

Supercomputer Modeling Shows How COVID-19 Spreads Through Populations

May 30, 2020

As many states begin to loosen the lockdowns and stay-at-home orders that have forced most Americans inside for the past two months, researchers are poring over the data, looking for signs of the dreaded second peak of t Read more…

By Oliver Peckham

SODALITE: Towards Automated Optimization of HPC Application Deployment

May 29, 2020

Developing and deploying applications across heterogeneous infrastructures like HPC or Cloud with diverse hardware is a complex problem. Enabling developers to describe the application deployment and optimising runtime p Read more…

By the SODALITE Team

What’s New in HPC Research: Astronomy, Weather, Security & More

May 29, 2020

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

DARPA Looks to Automate Secure Silicon Designs

May 28, 2020

The U.S. military is ramping up efforts to secure semiconductors and its electronics supply chain by embedding defenses during the chip design phase. The automation effort also addresses the high cost and complexity of s Read more…

By George Leopold

COVID-19 HPC Consortium Expands to Europe, Reports on Research Projects

May 28, 2020

The COVID-19 HPC Consortium, a public-private effort delivering free access to HPC processing for scientists pursuing coronavirus research – some utilizing AI-based techniques – has expanded to more than 56 research Read more…

By Doug Black

AWS Solution Channel

Computational Fluid Dynamics on AWS

Over the past 30 years Computational Fluid Dynamics (CFD) has grown to become a key part of many engineering design processes. From aircraft design to modelling the blood flow in our bodies, the ability to understand the behaviour of fluids has enabled countless innovations and improved the time to market for many products. Read more…

What’s New in Computing vs. COVID-19: IceCube, TACC, Watson & More

May 28, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

COVID-19 HPC Consortium Expands to Europe, Reports on Research Projects

May 28, 2020

The COVID-19 HPC Consortium, a public-private effort delivering free access to HPC processing for scientists pursuing coronavirus research – some utilizing AI Read more…

By Doug Black

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

IBM Boosts Deep Learning Accuracy on Memristive Chips

May 27, 2020

IBM researchers have taken another step towards making in-memory computing based on phase change (PCM) memory devices a reality. Papers in Nature and Frontiers Read more…

By John Russell

Hats Over Hearts: Remembering Rich Brueckner

May 26, 2020

HPCwire and all of the Tabor Communications family are saddened by last week’s passing of Rich Brueckner. He was the ever-optimistic man in the Red Hat presiding over the InsideHPC media portfolio for the past decade and a constant presence at HPC’s most important events. Read more…

Nvidia Q1 Earnings Top Expectations, Datacenter Revenue Breaks $1B

May 22, 2020

Nvidia’s seemingly endless roll continued in the first quarter with the company announcing blockbuster earnings that exceeded Wall Street expectations. Nvidia Read more…

By Doug Black

Microsoft’s Massive AI Supercomputer on Azure: 285k CPU Cores, 10k GPUs

May 20, 2020

Microsoft has unveiled a supercomputing monster – among the world’s five most powerful, according to the company – aimed at what is known in scientific an Read more…

By Doug Black

HPC in Life Sciences 2020 Part 1: Rise of AMD, Data Management’s Wild West, More 

May 20, 2020

Given the disruption caused by the COVID-19 pandemic and the massive enlistment of major HPC resources to fight the pandemic, it is especially appropriate to re Read more…

By John Russell

AMD Epyc Rome Picked for New Nvidia DGX, but HGX Preserves Intel Option

May 19, 2020

AMD continues to make inroads into the datacenter with its second-generation Epyc "Rome" processor, which last week scored a win with Nvidia's announcement that Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
ASROCK RACK
ASROCK RACK
AWS
AWS
CEJN
CJEN
CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
IBM
IBM
MELLANOX
MELLANOX
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

Contributors

Fujitsu A64FX Supercomputer to Be Deployed at Nagoya University This Summer

February 3, 2020

Japanese tech giant Fujitsu announced today that it will supply Nagoya University Information Technology Center with the first commercial supercomputer powered Read more…

By Tiffany Trader

Tech Conferences Are Being Canceled Due to Coronavirus

March 3, 2020

Several conferences scheduled to take place in the coming weeks, including Nvidia’s GPU Technology Conference (GTC) and the Strata Data + AI conference, have Read more…

By Alex Woodie

Exascale Watch: El Capitan Will Use AMD CPUs & GPUs to Reach 2 Exaflops

March 4, 2020

HPE and its collaborators reported today that El Capitan, the forthcoming exascale supercomputer to be sited at Lawrence Livermore National Laboratory and serve Read more…

By John Russell

Cray to Provide NOAA with Two AMD-Powered Supercomputers

February 24, 2020

The United States’ National Oceanic and Atmospheric Administration (NOAA) last week announced plans for a major refresh of its operational weather forecasting supercomputers, part of a 10-year, $505.2 million program, which will secure two HPE-Cray systems for NOAA’s National Weather Service to be fielded later this year and put into production in early 2022. Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This