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On July 10, in Boston, the External Research division of Microsoft Research will introduce the Microsoft Biology Initiative, resources designed to help biological scientists and programmers conduct research more efficiently and affordably. These include the first post-beta release of the Microsoft Biology Foundation (MBF), a language-neutral bioinformatics tool kit built as an extension to the Microsoft .NET Framework. In addition to a new genome assembler, performance enhancements, and other improvements, MBF builds upon the vision and goals that drove the development of the beta versions. Those included a commitment to community involvement, extensibility, cross-platform and interoperable functionality, language neutrality, and support for best practices. While there are other libraries of biological functionality available, MBF supports universally accepted standards of the bioinformatics community and implements a range of unique functionality derived from original Microsoft research. The code for MBF and supporting documents is available on CodePlex[RK1].
Like MBF itself, the audience during the 11th annual Bioinformatics Open Source Conference, held in conjunction with the 18th annual International Conference on Intelligent Systems for Molecular Biology, represents a powerful combination of technology and biology. To harness technology in support of biological discovery, MBF implements parsers for common bioinformatics file formats and algorithms used to manipulate DNA, RNA, and protein sequences. In addition, it provides a set of connectors to biologial Web services, such as the Basic Local Alignment Search Tool, as well as a utility that enables scientists to view their data within Excel easily and quickly.
From its core technology to the free availability of the code on which it is built, MBF is the result of collaboration between Microsoft Research and industrial and academic partners, with the aim of building the tools scientists need to pursue biological research. With Microsoft .NET as its base, MBF makes it easier for developers to leverage current technologies, with thousands of functions and a common code base that can be accessed and used with great flexibility.
One of the areas in which MBF is particularly valuable is the field of genomics, which has experienced tremendous advances since the human genome first was sequenced a decade ago. A full understanding of the human genome offers great potential for advances in health care. To reduce the computational complexity of reconstructing the the whole genome, MBF includes a new whole-genome-assembly algorithm, PaDeNA (Parallel de Novo Assembler). PaDeNA has the potential to reconstruct the DNA sequence of a patient rapidly from huge volumes of experimental data, the first step in using the genome in health care. While PaDeNA is provided freely as a part of MBF, it is designed to be modular and is fully documented, enabling experimental biologists and software developers to tweak the basic algorithm and add features to meet the needs of their research.
Another example of MBF at work is the research undertaken by David Heckerman, senior director of the eScience group within Microsoft Research. Heckerman, an expert in machine learning, is working on the design of HIV vaccines, which requires an understanding of how the virus evolves in each individual. The next versions of the biological applications Heckerman is developing will use functions built into MBF. Heckerman's applications will continue to be made available for free download on CodePlex[RK2] .
In keeping with the bioinformatics community's strong tradition of sharing expertise in support of ongoing discovery, I invite you to download it, use it for your work, and contribute your experience to the global research community.
Simon Mercer, director, Health & Wellbeing, External Research, a division of Microsoft Research
Rick Rashid, senior vice president of Microsoft Research, and Tony Hey, corporate vice president of the External Research division of Microsoft Research, join recipients of the 2010 Microsoft Research Faculty Fellows awards. Rashid (left) is accompanied by (left to right) Evimaria Terzi, Haiying (Helen) Shen, abhi shelat, Raanan Fattal, Doug Downey, Sinan Aral, and Hey. Not pictured: recipient Cyrill Stachniss. (Photo by Michael Nakamura)
This morning, on the second day of Faculty Summit 2010, we at Microsoft Research are proud to announce seven of the world's top university researchers as this year's awardees for the Microsoft Research Faculty Fellows grant program. In its sixth year, the rigorous application process was opened to an international audience, giving away $1.4 million, with no strings attached. This year's awards will help to further research in the exhilarating fields of mobile robotics, natural language processing, algorithmic data mining with an emphasis on social-network analysis, and cryptography.
Microsoft Research provides the fellows with support designed to have a tangible impact on their research. Each fellow receives a $200,000 award, to be used at his or her discretion for an unrestricted range of expenses that, in past years, have included planning research agendas, hiring graduate students, building labs, and purchasing equipment. Since the 2005 inception of the Faculty Fellows program, more than $7 million has been awarded to 37 professors from 22 universities. These funds are used to explore high-impact research that has the potential to solve some of today's most challenging problems.
This year's fellows were chosen as a result of a multitier selection process that includes more than 100 reviewers, whose goal is to identify the future leaders of academic research while they are at the beginning of their careers. From three continents, 120 initial nominees were narrowed to 18 finalists, chosen to be interviewed by a panel of Microsoft Research executives, researchers, and faculty members from leading universities. Of those 18 finalists, the following seven were announced as the Microsoft Research 2010 Faculty Fellows:
This year, the Microsoft Research Faculty Fellows program included international awardees for the first time, awarding Stachniss and Fattal with fellowships to enhance their research.
Fattal explores the application of elliptic-type operators such as derivatives and wavelet filters for problems such as edge-aware smoothing and interpolation, image sharpening, and resolution enhancement
Raanan Fattal of the Hebrew University of Jerusalem sketches the custom hardware needed for a new project in computational photography while talking with Floraine Grabler, a visiting graduate student from the University of California, Berkeley. Fattal has been named one of seven young faculty members to receive 2010 Microsoft Research Faculty Fellows.
After receiving his award, Stachniss told us: "Being a Microsoft Research Faculty Fellow is simply great for me and my research. First, the award gives me the opportunity to focus more on my research activities and less on writing grant proposals. Second, the group of Microsoft Research Faculty Fellows is a great platform of bright people, and I will enjoy discussions with them. Third, being a Microsoft Research Faculty Fellow is definitively great for the CV when applying for other faculty positions."
Cyrill Stachniss, one of seven recipients of the 2010 Microsoft Research Faculty Fellows awards, demonstrates a mobile manipulation task, in which a robot has to place objects on a table, to Barbara Frank, a Ph.D. student, in the Department of Computer Science’s Autonomous Intelligent Systems lab at the University of Freiburg.
When we asked Stachniss about his future plans, he replied: "The Microsoft grant allows me to react more flexibly on new developments and trends in robotics. I am considering spending parts of the grant on interesting new sensors to see how this will boost the performance of our robots."
Over the next year, the External Research Team Blog will feature a series of posts that take an in-depth look at our Faculty Fellows and what they have accomplished since winning their grants. Please check back to learn more about this program and how it benefits the academic research community.
Tony Hey, corporate vice president, Microsoft External Research, a division of Microsoft Research
During the Association for Computing Machinery's 33rd annual SIGIR Conference, on July 19-23, 2010 in Geneva, Microsoft Research is announcing enhancements to the Microsoft Web N-gram Services, available free via a cloud-based platform. Microsoft Research created Microsoft Web N-gram Services to help drive discovery and innovation by enabling scientists to conduct research on real-world, web data. Microsoft Web N-gram Services support many research areas that have the potential to change lives, including natural language processing and empowering people to take advantage of the vast amounts of information available on the Internet via new web search capabilities.
Introduced late last year, in partnership with Bing, the Microsoft Web N-gram Services public beta now is being extended beyond professors at accredited universities to include all researchers worldwide, provided they are using the service for non-commercial purposes. The service now also includes a predictive API in support of query-language models. By opening the service up to more researchers and making these important service enhancements, Microsoft Web N-gram Services will expand not only its audience, but also access to high-quality feedback
In the video below, Kuansan Wang, principal researcher at Microsoft Research Redmond, offers a more detailed explanation of Microsoft Web N-gram Services. Wang works with a team focused on developing technologies that provide a better understanding of human languages.
Professional gatherings such as the Web N-gram workshop during SIGIR 2010 serve as another important channel for using real-world expertise to enhance ongoing development of Microsoft Web N-gram Services. Research papers, selected by an international program committee, will be presented during the workshop and will be followed by discussions about the use of web-based data services for research. Workshops and other gatherings have been critical to the development of Microsoft Web N-gram Services from the beginning. After the expansion of beta availability announced during the International World Wide Web Conference in April 2010, for example, many researchers took advantage of the opportunity to work with the services. One such researcher, Li Ding of Rensselaer Polytechnic Institute, has his work on multiword tag clouds featured in this demo.
In addition to presentations, the workshop will include a panel discussion on issues related to query representation, including a rigorous definition of the task, modeling for the task, challenges and opportunities, implications for industrial research, and future research directions.
If you are attending SIGIR 2010, I cordially invite you to attend the workshop, at 9 a.m. July 23 and take advantage of this opportunity to share your perspectives and connect with other researchers in the field. To stay updated and to learn about opportunities to participate in ongoing development, please visit the Microsoft Web N-gram Services home page.
Evelyne Viegas, senior research program manager, Microsoft External Research, a division of Microsoft Research