For Whom the Bell Tolls: Big D v. Big C

Posted on by David Patterson
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By: Peggy Aycinena

For whom the bell tolls: Big D v. Big C

Randy Royce died yesterday of cancer. You probably didn’t know him. I didn’t know him very well, but his wife and I went to high school together. The first time I met Randy, Yvette was sitting on his lap at our big noisy 10-year class reunion. I always remembered that, because you never saw two people who had more fun together, who loved each other more.

Randy was mayor of San Carlos in recent years, and worked for many years before that at HP and Agilent. A long time ago, we were with Randy and Yvette at a dinner party given by mutual friends. Randy mentioned that he knew Paul Otellini from college and I said, “Really? I’d like to meet Paul Otellini. I’d liked to interview him.”

Randy said, “You’re a journalist? So who do you write for?”

I told him I’d send him my credentials and he said he’d pass them along to Otellini. Sometime later, I heard back from Randy: No go. Otellini didn’t know who I was and wasn’t willing to submit to an interview. Oh well, you can’t win them all.

There is one thing I wish we could win, however, and that’s this blasted battle with cancer. I’m really sick of this disease and I’m sick of going to funerals. I went to a funeral last month in Sacramento for a family member who died of cancer at 59, I expect to go to another funeral next month in San Francisco for somebody who’s only 45,  and that doesn’t include Randy’s funeral sometime in the next few weeks. He was only 62.

Sitting here, writing this while overlooking the escalators in the Santa Clara Convention Center as SNUG 2013 unfolds below me, I’m reminded of seeing my brother-in-law in this place in November 1999. We met up here for lunch some weeks after his wife, my sister, died of cancer. He was still a walking zombie, still living in a state of shock. My sister was only 51 when she died after a brief 6-month battle with cancer, and he didn’t know where to start to put his life back on track, how to finish raising their kids.

I hate cancer. Particularly because it seems like everybody who dies of it, is so not done. They’re not done being married, raising their kids, meeting their grandchildren, saving the world. They’ve still got lots of irons in the fire, and lots more potential for making a difference in a world that they’re exiting way too soon. That was certainly true for my sister, and it was most certainly true for Randy Royce.

Anyway, that’s the voice of despair talking. If you want to hear the voice of hope and optimism, you should listen instead to U.C. Berkeley’s Dave Patterson. True, Prof. Patterson’s had previous successes in other areas of technology, but if his talk at the February 14th Berkeley EECS Annual Research Symposium is any indication, his future success is what he hopes to be remembered for in the long run, because he’s got a really big iron in the fire.

Big D.Patterson wants to use Big D.Data to beat the Big C.Cancer.

He wants to use the same number crunching concepts – gathering, sorting, analyzing – to track Killer Cancers that other crunchers of Big Data use to track Killer Weather, to predict Killer Bugs on billion-transistor chips, and to design Killer Apps that benefit from Crowd Sourcing.

In other words, phenomenon which up-close are hard to understand, but looked at from way-far-away are characterized by zillions of data points that seem to show patterns of behavior that could possibly be used to predict and, in some cases, prevent that behavior.

Things like Cancer – a complex systemic problem, but also a point problem. Every cancer is different because every single person is different, but there are patterns there – at the molecular level, at the organelle level, at the cellular level, at the organ level, and at the organism level.

If manipulating Big D could give us a better handle on how to predict Big C, perhaps with time and determination it would allow us to prevent the disease in the first place, or at least stop its spread even after it’s got a foothold in the host. At least that’s how it’s supposed to work.

Of course, Prof. Patterson’s not the only researcher working on these ideas, but he’s the one I most recently heard talking about it. And he’s certainly one of the people who seems hellbent on making a difference by stopping the carnage that Big C is causing in the Big W  –  a Big World which is a sadder and less brilliant place for the loss of Randy Royce yesterday, and my sister 13 years ago.

I wish Big D.Patterson and his colleagues every success in their efforts.

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Berkeley wields big data to beat cancer

Posted on by David Patterson
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Researchers showed progress accelerating the search for gene-based cures for cancer and expanding the field of computer theory at an annual event sponsored by the University of California at Berkeley. They also discussed work on next-generation processor architectures and an effort to speed the development of an Internet of Things.

Computer scientist David A. Patterson called for a million genome warehouse to advance work on a cure for cancer. Today separate repositories hold less than 10,000 pieces of genetic information, many of them only partial representations of genes.

“There’s a chance for computer science to help build fast and accurate genetic pipelines and accelerate the move to personalized therapies–I want this in time to help me and my family,” he said, noting researchers today often delete genetic data after completing experiments.

Patterson helped develop a tool called SNAP that provides significantly faster and more accurate genetic analysis that tools typically used by cancer researchers today (see below). Benchmarking tools are still needed to improve what are still highly subjective methods used in the field, he said.

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New $28M Center will Develop Computers of 2025

Posted on by Krste Asanovic
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ANN ARBOR – Designing the computers of 2025 is the focus of a new $28 million, five-year research center led by the University of Michigan.

The Center for Future Architectures Research (C-FAR) opens today, and involves 14 other major research institutions. C-FAR aims to harness the power and boost the reliability of the tiniest transistors that will emerge over the next decade. Transistors are the fundamental building blocks of modern electronics, and more than a billion of them compose each integrated circuit in today’s cell phones and personal computers. C-FAR will support the design of the next generation of computers that will enable applications such as computer vision, speech recognition, enhanced graphics, and “big data” analysis.

C-FAR is one of six new centers announced today by the Semiconductor Research Corporation, a non-profit collaboration between government and industry with support from the Defense Advanced Research Projects Agency and major firms. In addition to leadership of C-FAR, U-M researchers are involved in three of the other five new Semiconductor Technology Advanced Research network (STARnet) centers.

Together, the STARnet centers are charged with guiding the field through the approaching sunset of Moore’s law, named for the Intel co-founder who in 1965 identified a trend that has fueled the semiconductor industry for the past 50 years. The law observes that the industry is able to shrink transistors enough to double the number that fit on an integrated circuit, or chip, every 18 months. With this increased density comes a doubling of computing power, which has transformed the room-sized computers of the ‘50’s to the significantly more powerful smartphones of today. But the field is reaching the limit to miniaturization.

“It’s a challenging time as we approach the end of Moore’s law – not tomorrow, but soon,” said Todd Austin, professor of electrical engineering and computer science and C-FAR director. “The dimensions of the transistors of today are in the tens of atoms. We can still make them smaller, but not without challenges that threaten the progress of the computing industry.”

In addition to Austin, other U-M co-investigators in C-FAR are Scott Mahlke, professor; Valeria Bertacco, associate professor; and Kevin Fu, associate professor, all in the Department of Electrical Engineering and Computer Science.

Researchers predict about another decade of squeezing silicon, and that will bring challenges along with opportunities. As nanoscale transistors shrink, they become less reliable. And in some cases, they offer more computational power than other parts of the system are capable of using.

“Industry is adding more and more cores. Last year, your cell phone had two, next year it will have four. The problem is your cell phone doesn’t do much more than it did before because harnessing all those cores is a challenge,” Bertacco said.

The researchers at C-FAR will work to overcome these challenges on three fronts. They will design specialized chips tailored for different applications. They’ll rethink how to build computers so they’re capable of analyzing massive data sets more efficiently, which will be a key application in the next decade. And they’ll explore how to integrate tomorrow’s technologies into conventional silicon processing techniques to ease the transition for industry. These advanced technologies include three-dimensional stacked chips and phase-change memory, which uses heat to store information in the molecules of a glass-like material.

“If we can build better systems with these smaller and less reliable transistors, we have an opportunity to make the next generation of faster, more energy-efficient computers. Imagine your tablet of tomorrow running high-end applications, like real-time medical imaging or computer vision, without needing a recharge for days,” Bertacco said.

While the center is headquartered at U-M, it includes researchers from top universities across the nation.

“The center provides a unique environment to collaborate closely with other researchers and our sponsors to create rule-breaking technologies that are both effective and relevant,” Austin said.

“If we can’t continue to improve the speed and energy efficiency of tomorrow’s computers, the computing industry will stagnate,” Bertacco concluded. “It’s important that we find ways to move the industry forward, even in the face of all these great challenges.”

Other universities in C-FAR are Columbia University; Duke University; Georgia Institute of Technology; Harvard University; Massachusetts Institute of Technology; Northeastern

University; Princeton University; Stanford University; the University of California, Berkeley; the University of California, Los Angeles, the University of California, San Diego; University of Illinois at Urbana-Champaign; the University of Virginia; and the University of Washington, Seattle.

The other MARCO centers U-M researchers are involved in are:

The TerraSwarm Research Center, led by the University of California, Berkeley. TerraSwarm will address the potential and risks of pervasively integrating smart, networked sensors and actuators into our connected world. While such integration could have benefits such as better traffic control, energy efficiency and emergency response, those must be balanced with safety and privacy concerns. In the U-M Department of Electrical Engineering and Computer Science, Prabal Dutta, assistant professor; David Blaauw, professor; and Kevin Fu, associate professor, are involved.
The Systems on Nanoscale Information fabriCs (SONIC) is led by the University of Illinois at Urbana-Champaign. SONIC aims to develop next-generation computing platforms with advanced circuit and device technology inspired by the robustness and energy efficiency of communication devices such as cell phones and biological systems such as the brain. David Blaauw, a professor of electrical engineering and computer science, is a principal investigator.
The Center for Spintronic Materials, Interfaces and Novel Architectures (C-SPIN), led by the University of Minnesota. C-SPIN will develop new material systems and transistor types that are based on the spin state of electrons, a quantum mechanical phenomenon. These could eventually complement or even replace traditional transistors. Dennis Sylvester, a professor of electrical engineering and computer science, is an investigator.
For more information:

C-FAR center: http://www.futurearchs.org

STARnet centers: http://www.src.org/program/starnet/