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!

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing components with Intel Xeon, AMD Epyc, IBM Power, and Arm server ch Read more…

By Tiffany Trader

SIA Recognizes Robert Dennard with 2019 Noyce Award

November 12, 2019

If you don’t know what Dennard Scaling is, the chances are strong you don’t labor in electronics. Robert Dennard, longtime IBM researcher, inventor of the DRAM and the fellow for whom Dennard Scaling was named, is th Read more…

By John Russell

Leveraging Exaflops Performance to Remediate Nuclear Waste

November 12, 2019

Nuclear waste storage sites are a subject of intense controversy and debate; nobody wants the radioactive remnants in their backyard. Now, a collaboration between Berkeley Lab, Pacific Northwest National University (PNNL Read more…

By Oliver Peckham

Using HPC and Machine Learning to Predict Traffic Congestion

November 12, 2019

Traffic congestion is a never-ending logic puzzle, dictated by commute patterns, but also by more stochastic accidents and similar disruptions. Traffic engineers struggle to model the traffic flow that occurs after accid Read more…

By Oliver Peckham

Mira Supercomputer Enables Cancer Research Breakthrough

November 11, 2019

Dynamic partial-wave spectroscopic (PWS) microscopy allows researchers to observe intracellular structures as small as 20 nanometers – smaller than those visible by optical microscopes – in three dimensions at a mill Read more…

By Staff report

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quantum annealing) – ion trap technology is edging into the QC Read more…

By John Russell

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. Th Read more…

By Jan Rowell

MLPerf Releases First Inference Benchmark Results; Nvidia Touts its Showing

November 6, 2019

MLPerf.org, the young AI-benchmarking consortium, today issued the first round of results for its inference test suite. Among organizations with submissions wer Read more…

By John Russell

Azure Cloud First with AMD Epyc Rome Processors

November 6, 2019

At Ignite 2019 this week, Microsoft's Azure cloud team and AMD announced an expansion of their partnership that began in 2017 when Azure debuted Epyc-backed ins Read more…

By Tiffany Trader

Nvidia Launches Credit Card-Sized 21 TOPS Jetson System for Edge Devices

November 6, 2019

Nvidia has launched a new addition to its Jetson product line: a credit card-sized (70x45mm) form factor delivering up to 21 trillion operations/second (TOPS) o Read more…

By Doug Black

In Memoriam: Steve Tuecke, Globus Co-founder

November 4, 2019

HPCwire is deeply saddened to report that Steve Tuecke, longtime scientist at Argonne National Lab and University of Chicago, has passed away at age 52. Tuecke Read more…

By Tiffany Trader

Spending Spree: Hyperscalers Bought $57B of IT in 2018, $10B+ by Google – But Is Cloud on Horizon?

October 31, 2019

Hyperscalers are the masters of the IT universe, gravitational centers of increasing pull in the emerging age of data-driven compute and AI.  In the high-stake Read more…

By Doug Black

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

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