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December, 2011

Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

December, 2011

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    Coping with Data Deluge

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    Overwhelmed by data? You’re not alone.

    Data mining has become one of the most critical research processes in this era of data-intensive science. There are, however, many areas of science where the usefulness of data mining is limited by the massive nature of the datasets. Consequently, scientists are desperately looking for new tools that can dig into the data faster and deeper. In the rapidly developing field of synoptic sky surveys, for example, transient signals from a variety of interesting astrophysical phenomena must be detected and characterized in (near) real-time. The resulting wealth of data is invaluable to researchers seeking new discoveries, but they need better computational methods to help them manage and analyze so much data.

    Coping with Data Deluge

    It was in response to such needs that Caltech’s Keck Institute for Space Studies sponsored a workshop, Digging Faster and Deeper:  Algorithms for Computationally Limited Problems in Time-Domain Astronomy, from December 12 to 13. Bringing together more than 50 distinguished participants, the workshop focused on some of the unresolved data mining issues for future studies in time-domain astronomy and related fields.

    I was privileged to give two talks during day two of the workshop. In “Discovery of Hidden Patterns in Data through Interactive Search,” I presented the Environmental Informatics Framework (EIF), a strategy and technology platform that the Microsoft Research Connections Earth, Energy, and Environment group developed to help advance data exploration in environmental research. I demonstrated Microsoft PivotViewer, a faceted search technology included in EIF that enables users to visually and interactively search and discover hidden patterns in massive data or image sets.

    I was pleased to receive positive feedback from attendees about the work that Microsoft Research is doing for data-intensive sciences. As one participant noted to me in email, “I have to admit that I wasn’t aware of the work that Microsoft Research was doing, but I was very impressed with what I saw yesterday. The work you’ve been doing on data visualization can only be described as stunning!”

    In “Building a Better Scientist,” my second talk of the day, I discussed how the fourth paradigm for data-intensive scientific discovery is changing the way scientists conduct research, and is, therefore, creating a need for a new generation of scientists with advanced computational mindsets. The presentation stimulated passionate discussions, and, as event chair George Djorgovski pointed out, it is a topic closely related to how fast and deep we can go with our data.

    Yan Xu, Senior Research Program Manager, Microsoft Research Connections

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    Readers’ Choice: Top 10 Blogs of 2011

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    Microsoft Research Connections: Top 10 Blogs of 2011Recaps of the top 10 news stories of the year—it’s a New Year’s tradition that rivals Dick Clark’s “New Year’s Rockin’ Eve” show. So who are we to buck convention? Therefore, without further ado, here are the top 10 Microsoft Research Connections blogs of 2011, as chosen by your clicks.


    Number 10:
    Kinect for Windows SDK Beta Refresh Available 

    Who can resist building apps for the latest and greatest Kinect sensor? Apparently not the developers who are avid readers of our blog. So let’s raise a cup of cheer, or eggnog, to the intrepid innovators who are using the Kinect for Windows Software Development Kit (SDK) to push the boundaries of natural user interface applications.

    Number 9: Night at the Museum—sans Ben Stiller

    A planetarium show plus a demonstration of the new earth-sciences applications of Microsoft Research’s WorldWide Telescope (WWT) took center stage at the California Academy of Sciences. If you thought turning your computer into a world-class telescope was cool, you’ll be blown away by WWT’s ability to create earth-science narratives.

    Number 8: Introducing Chemistry Add-in for Word

    The ancient Egyptians had nothing on us: using chemistry symbols in digital documents can be every bit as cumbersome as carving hieroglyphics into stone. And then came Chemistry Add-in for Word, which makes it easier for students, chemists, and researchers to insert and modify chemical information, such as labels, formulas, and 2-D depictions, from within Microsoft Word.

    Number 7: Digital Research Libraries Get a Boost with Latest Zentity Release

    Research archivists, librarians, and others who have grappled with organizing and accessing voluminous research collections asked for it—and Microsoft Research Connections delivered: the 2.1 release of Zentity. A repository platform designed to manage research objects—such as journal articles, reports, datasets, projects, and people—as well as the relationships among them, Zentity supports arbitrary data models and provides semantically rich functionality that enables users to find and visually explore interesting relationships between elements.

    Number 6: Parallel Processing Software Gets a Boost in Barcelona

    Today, it seems that everything—from smart phones and tablets to PCs and supercomputers—is sprouting extra cores so users can do more. Can Microsoft Research Connections help create parallel code to make the most efficient use of these ubiquitous multi-core processors? Need you ask? A joint venture of the Barcelona Supercomputing Center and Microsoft Research Centre (BSCMSRC) is bringing together the expertise of hardware and software researchers to do just that.

    Number 5: Building a .NET Quality Control Tool for Next-Generation Sequencing Technologies

    Quality control—it’s vital in food inspections and DNA sequencing. Unfortunately, not all sequencing technologies produce reliable and accurate results, and experimental data will always contain varying rates of error. That’s where Sequence Quality Control Studio (SeQCoS) can help. A Microsoft .NET software suite designed to perform an array of QC evaluations and post-QC manipulation of sequencing data, SeQCoS generates a series of standard plots that illustrate the quality of the input data.

    Number 4: Women in Technology Hop to It in Portland

    Every year, the annual Grace Hopper Celebration of Women in Technology brings the research and career interests of women in computing to the forefront. This past year was no exception, as some 2,000 attendees descended on Portland, Oregon, to hear about the latest research and explore the roles of women in computer science, information technology, research, and engineering. Microsoft Research Connections was there, too, offering support and free epiphytes (really)!

    Number 3: Chinese University Students Push the Boundaries of Kinect for Windows

    Chinese university students took the Kinect for Windows SDK and pushed it hard, applying the sensor’s depth sensing, voice and object recognition, and human motion tracking capabilities to diverse topics: from education to commerce to culture and history. Their creative and elegant applications far surpass traditional games, demonstrating Kinect’s potential in diverse areas.

    Number 2: Microsoft Research and the Kinect Effect

    Our blog readers are very interested in Kinect! And why not? Thanks to contributions from Microsoft Research, Kinect has state-of-the-art audio, skeletal-tracking, and facial-recognition capabilities. Microsoft built Kinect to revolutionize the way you play games and how you experience entertainment. But along the way, people started applying the “Kinect Effect” in ways we never imagined—from helping children with autism to assisting doctors in the operating room.

    Number 1: Unlocking Academic Success with Frame Games for Learning

    Drumroll please: the top-ranked Microsoft Research Connections blog explored—what else?—a game. But, surprisingly, it isn’t Kinect based! Instead, it’s a learning game that was developed in collaboration with the Rochester Institute of Technology. Called Just Press Play, the game helps students earn a digital reward for the ultimate achievement: collegiate success. Just Press Play encourages students to venture out of their comfort zone and get involved in all aspects of school—including (gasp) interactions with school faculty and staff.

    So there they are: 2011’s most-read Microsoft Research Connections blogs. Why Robots Invade Upstate New York didn’t make the list is beyond us. Go figure. Happy New Year from your friends at Microsoft Research Connections!

    —Lisa Clawson, Senior Manager, Microsoft Research Connections

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    On World AIDS Day, HIV Research Provides a Ray of Hope

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    On World AIDS Day, HIV Research Provides a Ray of HopeThe first documented case of HIV was in 1981. Today, HIV is viewed as a treatable, chronic disease by many in developed nations where treatments are readily available. Yet HIV continues to devastate, claiming the lives of 1.8 million people annually—about 5,000 deaths per day. Those fortunate enough to have access to treatment must arrange their lives around a strict treatment regime that can overshadow everyday activities. On this World AIDS Day, we are taking time to focus on this global crisis, and to remember that the battle is not over. We would also like to shine a light on a possible weapon in the battle to stop the virus: an HIV vaccine.

    HIV remains a threat throughout the world. It has been particularly devastating in the sub-Saharan region of Africa, where two-thirds of the population is HIV positive by age 25. The occurrence of HIV is higher for women than men; an estimated one in three women seeking care during pregnancy is HIV positive. By age 35, the infection rate for men rivals that of women in the region.

    The South African government offers free antiretroviral (AVR) therapy for HIV-positive residents. The precision timing required by AVR therapy is a dominant factor in the life of any HIV-positive individual. For Purity, a 30-year-old resident of the KwaZulu-Natal province in South Africa, it is a constant struggle. “Early in the morning at 8:00, I take Tenofovir and Lamivudine. After I eat my breakfast, I take Bactrim and vitamins. In the evening, at 8:00, I take Stocrin and Lamivudine.”

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    Purity does not know exactly when she contracted HIV. She knew she was ill, and sought treatment at the hospital. She was diagnosed with tuberculosis and then soon after, HIV. “I thought my life was over,” she remembers. “People told us that if you are HIV positive, you’re dead—you’re not going to live. But there is always hope. There is always a way. And I’m here today. I’m fine.”

    Purity hopes for a cure for those who already have HIV. She also hopes that a vaccine will be developed to prevent others from contracting HIV and suffering the physical, mental, and emotional pain that HIV has inflicted upon her life. Until that time, she has a message of hope for those who contract the virus.

    “If I met somebody [who was] HIV positive, I would tell them to hold on. They are still alive. There’s hope,” she said. “They must dream, because that’s what keeps me going. Dreams—dreams and hopes. Because if you don’t have hope and dreams, you see yourself as good as dead.”

    The Search for a Vaccine

    Researchers are working hard to make Purity’s dream of a cure—or at least a vaccine—come true. A number of HIV vaccines are in various stages of development. A notable HIV vaccine effort is being led by Bruce Walker, director of the Ragon Institute at Massachusetts General Hospital, MIT and Harvard, and a professor of medicine at the University of KwaZulu-Natal. Walker is leading a multi-organizational effort to test a vaccine in Durban, South Africa—the epicenter of the African HIV epidemic. Joining Walker and the Ragon Institute are the Centre for the AIDS Programme of Research in South Africa (CAPRISA) and the KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH). Microsoft Research is working with the Ragon Institute to quantify how the immune system attacks various fragments of HIV—data that we hope will, one day, lead to a vaccine or possibly even a cure.

    Understanding HIV

    One of the biggest challenges we face in building a vaccine for HIV is that HIV mutates a lot. How much? Well, consider this: if you look at all the mutations that have ever occurred in the influenza virus—the virus that causes the flu—you’ll see about the same amount of mutation of HIV in a single individual who has contracted the virus. You’ve heard how difficult it has been to develop an effective flu vaccine. Imagine how difficult it is to create a vaccine for HIV.

    Difficult does not mean impossible, however. While HIV does have a strong evolutionary advantage—its ability to mutate—we believe it also has an “Achilles heel.” There are certain fragments of HIV that, we believe, when attacked by our immune system, will become sick and die. We are cataloguing those fragments of HIV that we know are vulnerable to attacks by the immune system. Once that is done, we plan to develop a vaccine that will train our immune systems to attack just those fragments of HIV, and ignore all the other parts of the virus that are not vulnerable.

    To catalog the vulnerable fragments of HIV, we’re taking data from many individuals in South Africa and correlating that data with how the patient’s body is reacting to the virus. Is it controlling HIV? Or is the virus continuing to copy itself and survive? We’re also sorting through the different mutations of HIV to identify when and where the immune system attacks, and how HIV mutates in response.

    It’s an incredibly daunting task: there are millions of possible combinations to sort through. It would take years to process the volume of data we receive on a single computer. Therefore, we’re committing thousands of machines to this task, using an algorithm we developed at Microsoft Research called PhyloD. Combined, our hardware and software can complete the analysis in just hours—a critical advantage in the fight against HIV. We send the information back to Ragon in Africa and we then work together to identify follow-up experiments. In addition to our targeted research, we have also made some general discoveries that are applicable to all immune system research—not just HIV.

    Fighting More Than Just HIV

    We are continuing to work towards a better understanding of the breadth and complexity of the immune system—not just how it reacts to HIV and the virus’ mutations. For example, over the course of this research, we have discovered that some fragments of the immune system are stronger than others. We have also uncovered another component of our immune system that attacks HIV: natural killer cells.

    These and other discoveries made through our research have the potential to help millions through the prevention of HIV and perhaps, one day, a cure. It could also have ramifications for research on how the immune system responds to other diseases, such as cancer and diabetes. Until the day we find a vaccine and perhaps even a cure, World AIDS Day will continue to remind us that the fight against HIV has not yet been won.

    David Heckerman, Distinguished Scientist, Microsoft Research Connections

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