Computing Research Policy Blog

Computing Research Challenges in Biomedicine


Last June, CRA and he National Institutes of Health jointly hosted a workshop motivated by the following two observations (from the 2004 NIH Roadmap):

The success of computational biology is shown by the fact that computation has become integral and critical to modern biomedical research.

Because computation is integral to biomedical research, its deficiencies have become significant limiters on the rate of progress of biomedical research.

It seems rational to conclude (as the attendees of the workshop concluded) that the productive synergies between the two fields can accelerate research in both, but only if the challenges are addressed through cooperative effort. So, the workshop attendees — leaders in computing and biomedicine, along with NIH Program Directors — aimed to address these challenges by developing a “list of focused recommendations and action items that would guide the NIH and computing communities in addressing current impediments to fully realizing effective collaborations at the interface between computing and biomedical research.” Those recommendations are now available (pdf) as a 14 page report.
The workshop participants ultimately came to agreement on six recommendations, which are listed in some detail in the report but that I’ll attempt to summarize here:

  • Recommendation 1: NIH, the National Science Foundation and Department of Energy Office of Science should support biomedicine and computing research collaborations by:
    • Initiating small, interdisciplinary planning grants that require conceptual proof-of-principal, but minimal or no preliminary results and that involve both computing and biomedical researchers as full partners;
    • creating (or expanding current programs) to fund computing and biomedicine research projects at the PI level, as well as larger collaborative projects with multiple PIs, that reflect the maturation of teams and projects from the small grants above;
    • establishing a cross-disciplinary, multiagency working group to identify, explore and recommend individual agency opportunities and define and coordinate joint agency programs.
  • Recommendation 2: Federal agencies should enhance support for “training at the interface.” These mechanisms would include summer schools for students, post-docs, and professors; increased emphasis on extant undergrad and grad training programs; and funding to transform existing “silo” disciplinary education into new, multidisciplinary structures that support the integration of computing and biomedicine.
  • Recommendation 3: NIH should create a cross-institute software program to create and maintain high-quality, well-engineered biomedical computing software, to assess the quality of existing software, and to create and support for repositories.
  • Recommendation 4: NIH should fund a number of large, distributed transformational centers — distinct from and somewhat orthogonal to the NIH National Centers for Biomedical Computing program — to act as “expeditions to the future.
  • Recommendation 5: NIH should invest in a range of computing research technologies (specified in detail in the report) that are motivated by current and future biomedical research and healthcare needs.
  • Recommendation 6: NIH, NSF, DOE and CRA should create a joint “Interface Task Force” (ITF) — perhaps using the Computing Community Consortium to involve the community — to recommend specific ways to support advances at the interface between computing and biomedicine.

The report includes much more detail for each of the recommendations, including a timeline for implementation and an estimated cost for each. The report also includes more detail on the particular computing research areas the participants thought deserved particular attention.
The whole thing is only 14 pages and is a quick read — well worth it.

  • CRA-NIH Computing Research Challenges in Biomedicine Workshop Recommendations.
    Update: (5/29/07) — Dan Reed has a lot more of the backstory for the report on his blog today.

  • CCC at FCRC


    The following is brought to you by your friends at the CCC…:
    Under an agreement with the National Science Foundation, the Computing Research Association (CRA) has established the Computing Community Consortium (CCC) to engage the computing research community in articulating and pursuing longer-term research visions – visions that will capture the imagination of our community and of the public at large.
    The CCC invites your engagement in this process! At the Federated Computing Research Conference in San Diego during the second week in June, five special talks will sketch the possibilities. These talks are intended to be inspirational, motivational, and accessible. Please join us!
    Monday June 11, 6-7 p.m., Grand Exhibit Hall
    Christos Papadimitriou, UC Berkeley
    The Algorithmic Lens: How the Sciences are Being Transformed by the Computational Perspective
    Abstract
    Tuesday June 12, 6-7 p.m., Grand Exhibit Hall
    Bob Colwell, Independent Consultant
    Future of Computer Architecture ’07
    Abstract
    Wednesday June 13, 6-7 p.m., Grand Exhibit Hall
    Randal Bryant, Carnegie Mellon University
    Data-Intensive Super Computing: Taking Google-Style Computing Beyond Web Search
    Abstract
    Thursday June 14, 6-7 p.m., Grand Exhibit Hall
    Scott Shenker, UC Berkeley
    We Dream of GENI: Exploring Radical Network Designs
    Abstract
    Friday June 15, 11:30 a.m. – 12:30 p.m., Grand Exhibit Hall (FCRC Keynote Talk)
    Ed Lazowska, University of Washington and Chair, Computing Community Consortium
    Computer Science: Past, Present and Future
    Abstract
    More info here.

    A Little Bit of Press for America COMPETES Act


    David Broder writes about the America COMPETES Act in his column today at the Washington Post. It contains this great quote from Sen. Lamar Alexander (R-TN), one of the sponsors of the Act:

    “Last week,” he said, “while the media covered Iraq and U.S. attorneys, the Senate spent three days debating and passing perhaps the most important piece of legislation of this two-year session. Almost no one noticed.”
    Alexander has a point. The bill, boldly named the America Competes Act, authorized an additional $16 billion over four years as part of a $60 billion effort to “double spending for physical sciences research, recruit 10,000 new math and science teachers and retrain 250,000 more, provide grants to researchers and invest more in high-risk, high-payoff research.”

    Read the whole thing.

    NSF Authorization on the Floor Today


    The National Science Foundation Authorization Act of 2007 (H.R. 1867), which we’ve discussed previously, will be on the House floor today. The bill authorizes appropriations at the agency (which is not the same as actually funding the agency — only the appropriations committee can do that — but is still a necessary (and symbolic) step in getting funding for the agency) at the levels called for in the President’s American Competitiveness Initiative and the Democratic Innovation Agenda — a trajectory that would double the agency’s budget over the next seven years.
    It’s likely the bill will pass today without much difficulty. There are, however, a whole slate of amendments proposed, some of which are pretty awful (though not likely to pass). For example, there are amendments from Reps. Scott Garrett (R-NJ) and John Campbell (R-CA) that would specifically prohibit funding of nine already-funded grants in NSF’s Social, Behavioral and Economics directorate, based apparently on their “silly” titles. Here are the grants targeted:

  • the reproductive aging and symptom experience at midlife among Bangladeshi Immigrants, Sedentees, and White London Neighbors;
  • the diet and social stratification in ancient Puerto Rico;
  • archives of Andean Knotted-String Records;
  • the accuracy in the cross-cultural understanding of others’ emotions;
  • bison hunting on the late prehistoric Great Plains;
  • team versus individual play;
  • sexual politics of waste in Dakar, Senegal;
  • social relationships and reproductive strategies of Phayre’s Leaf Monkeys; and
  • cognitive model of superstitious belief.
  • There are a number of reasons amendments like this are a bad idea. The primary one is that the NSF peer-review system, while arguably not perfect (well, far from perfect), is still likely a much more reliable way of choosing meritorious research than Congressional intervention. It’s also pretty reasonable to assert that titles are not the best way to judge the worthiness of research.
    Additionally, there’s an interesting (and bad) amendment proposed by Rep. Dave Weldon (R-FL) that would tie any increases in the NSF budget to proportional increases at the National Aeronautics and Space Administration. The amendment, Weldon says in a press release, would “ensure that NASA’s budget is not raided to fund the NSF increase.” As someone who has been doing science policy work for the better part of a decade, it amuses a little to think of NASA in the role of victim to NSF, as I’ve watched innumerable times in the past as NASA increases swallowed up all the available funding room in VA/HUD appropriations bills that shortchanged NSF and NIST. But the Weldon amendment is an innovative approach to “protecting” NASA, by trying to link the two agencies’ budgets. It might, however, set an awkward precedent. One could imagine linking the National Institutes of Health and NASA, or NIH and NSF, or NSF and DOE, or NSF and NIST and NIH…the number of permutations just among the science agencies are enormous. But why stop there? We could link NSF and the Veterans Administration. The Department of Labor to NIH. Or NASA and the Department of Transportation (wait, that could almost make sense). In any case, the idea of linking two agencies with disparate missions together is probably not sound policy, and I would argue that the best way to “protect” NASA funding (which isn’t actually at risk because of the NSF Authorization) is to ensure NASA is pursuing a compelling mission for the Nation.
    You can find a complete list of amendments being considered today on THOMAS. We’ll try to keep score here throughout the day.
    One other piece of news about the bill is that it appears H.R. 1867 will get conferenced with the Senate as part of the S. 761 (the “America COMPETES Act“) conference. This is actually very good news as it means the NSF Authorization has a real chance of enactment. While the bill is expected to pass the House without much difficulty, it wasn’t clear that the Senate had much of an interest in moving it’s own version of the bill, simply because they’d already passed an NSF authorization as part of S. 761. Now it appears that there’s an inclination to take the NSF-specific portions of that bill out and use them as a conference vehicle for H.R. 1867. We’ll have more as we learn more, but in short, this means that there’s a potential path to enactment that is relatively free of big bumps….
    Update: (5/3/07 12:20 am) — The bill passed overwhelmingly (399-17). The Garrett and Campbell amendments both failed, and the Weldon amendment was subject to a point of order that the NASA provisions weren’t germane to the bill — a point of order that was sustained. So great news all around!

    Two Interesting Posts…


    …on Jim Horning’s Nothing is as simple as we hope it will be blog. The first, on a recent cyber security hearing on the Hill has a nice extended quote from the Chairman of the Subcommittee on Emerging Threats, Cybersecurity, and S&T of the House Committee on Homeland Security, complaining about the gutting of the cyber security R&D budget at DHS.
    The second is a summary of a paper by Robert Meyer and Michel Cukier on the impact of (perceived) user gender on the cyber attack threat (quick summary: “females” are much more likely to get attacked), which concludes with this great quote from Jim:

    If this hostility is anywhere near the typical Internet experience, is it any wonder that computing and IT are increasingly losing the women?”

    Frances Allen Honored by House of Representatives


    A resolution to honor Frances E. Allen, the 2006 recipient of ACM’s A.M. Turing Award, passed the House today. House Concurrent Resolution 95 was introduced by Rep. Lynn Woolsey (D-CA) and reported out of the House Science and Technology Committee last week.
    We wrote about Dr. Allen here when the Turning Award was announced in February. She was the first woman to receive the award since it was first given forty years ago. Dr. Allen was an IBM Fellow at the TJ Watson Research Center.
    A press release from the House Science and Technology Committee stated:

    H. Con. Res. 95 recognizes her achievements in computer research and development while working at IBM Corporation, and salutes the Turing Award Committee for recognizing the contributions of women to the field of computing.
    “It is certainly telling that women, who earn more than half of all undergraduate degrees in this country and make up more than half of the professional workforce, represent only 25% percent of all information technology workers,” Woolsey said. “Dr. Allen has been an inspirational mentor to younger researchers and a leader within the computing community and it is clear that Dr. Allen deserves recognition for all of the tireless work she has done to promote women’s role in computing.”

    Another Article on the Innovation Agenda


    Interesting article (requires free registration) on the innovation agenda in the San Jose Mercury News. While it does focus mostly on the energy and environmental areas that could be helped, it also touches on almost all aspects of the overall innovation agenda such as funding basic research and increasing STEM K-12 teachers. There is also a good quote from Sen. John Ensign (R-NV) who said, “I’m a fiscal conservative, but the dollars we invest in basic research will come back to us in spades in terms of stimulating economic activity and helping the United States remain at the forefront of global innovation.”

    Graduate Education and Innovation


    The Council of Graduate Schools yesterday released a report regarding the role of graduate education in America’s competitiveness. The report makes five key findings:

    1. A highly skilled workforce operating at the frontiers of knowledge creation and professional practice is key to America’s competitiveness and national security. Universities, governments, and private industry each play an essential role in providing the expertise and resources necessary to achieve this objective.
    2. The expanded participation of U.S. citizens, particularly from underrepresented minority groups, should be a priority in fields that are essential to our nation’s success. Development of STEM careers should be emphasized.
    3. Interdisciplinary research preparation and education are central to future competitiveness, because knowledge creation and innovation frequently occur at the interface of disciplines.
    4. U.S. graduate schools must be able to attract the best and brightest students from around the world.
    5. The quality of graduate programs drives the success of America’s higher education system. Efforts to evaluate and improve all aspects of the quality of the U.S. graduate education enterprise must be advanced and supported in order to foster innovation.

    The report makes a series of recommendations for policymakers, calling for:

  • Collaboration among leaders in government, business, and higher education to develop a highly-educated workforce and encourage entrepreneurship in graduate education.
  • The creation of incentives for students, particularly from underrepresented groups, to pursue graduate education in STEM fields, the social sciences, and humanities, and identify “best practices” to reduce attrition and shorten the time required to complete a degree.
  • Support for innovative graduate education programs, such as professional master’s degrees, which respond to workforce needs in such critical fields as science, engineering, technology and mathematics (STEM), as well as in social sciences and the humanities.
  • Expanding opportunities for graduate students to pursue interdisciplinary study at the frontier of knowledge creation, using models such as those pioneered by the National Science Foundation and National Institutes of Health.
  • Continuing to improve and reform the visa process so that the world’s top international talent can pursue graduate study in the U.S. and contribute to our nation’s research and innovation.
  • Increasing federal funds for graduate education programs by at least 10% at every agency.
  • Enhancing the quality of graduate education through ongoing evaluation and research, and supporting risk-taking research programs that prepare highly-trained professionals for a knowledge-based global economy.
  • While the findings and recommendations echo a lot of recent reports — the National Academies Rising Above the Gathering Storm, the Council on Competitiveness’ Innovate America, the Task Force on the Future of American Innovation’s Measuring the Moment — it’s very useful to have another perspective on innovation policy from another “sector” of the U.S. innovation ecosystem. And as innovation policy continues to swirl around the Hill, these reports provide the sort of buttressing policymakers need to continue to champion pro-innovation ideas.

    House Innovation Agenda


    Speaker Pelosi has re-released the House Democrats Innovation Agenda, which we have talked about before in this space. The Agenda was first announced in November 2005 and includes many of the provisions called for in the National Academies Rising Above the Gathering Storm report and that subsequently ended up in the American Competitiveness Initiative. With this re-release of the Agenda, Speaker Pelosi also released a statement saying:

    “To meet the challenges of today and to create the jobs and economic security of tomorrow, the time to act is now,” Speaker Nancy Pelosi said. “This week, the House is taking the first steps in an Innovation Agenda that will help spur the next generation of discovery and invention. Democrats will continue throughout the 110th Congress to move forward on legislation that asserts our global economic leadership, creates new business ventures and jobs, and gives future generations increased opportunity to achieve the American Dream.”

    The re-release is in support of three bills that are going to the House floor this week—HR 362 the 10,000 Teachers, 10 Million Minds Science and Math Scholarship Act, HR 1332 the Small Business Lending Improvements Act of 2007, and HR 363 the Sowing the Seeds Through Science and Engineering Research Act. Rep. George Miller (D-CA), chairman of the House Education and Labor Committee, and Rep. Bart Gordon (D-TN), chairman of the House Science and Technology Committee, each released a statement supporting the Innovation Agenda and the three bills.
    This happens at the same time that the Senate is voting on S. 761, the America COMPETES Act, and could mean that a conference between the two chambers’ innovation bills might not be as problematic as it initially appeared…. We’ll keep you posted.

    PCAST Approves Draft IT R&D Recommendations


    The President’s Council of Advisors for Science and Technology met today to approve a draft set of recommendations concerning the federal Networking and Information Technology Research and Development (NITRD) program. In reviewing the program and the overall IT “ecosystem” in the U.S. and abroad for the first time since the PITAC review in 1999, the committee came to the conclusion that while the U.S. continues to hold a dominant leadership position in the IT sector, that leadership is at risk unless steps are taken now to shore up our innovation footing long-term.
    The committee, composed of 35 leaders of industry and academia appointed by the President, approved recommendations in four general areas:

    • Revamp networking and information technology education and training;
    • Rebalance the federal NITRD portfolio;
    • Re-prioritize some NITRD topics;
    • Improve interagency planning and coordination.

    PCAST members Dan Reed (Director of the Renaissance Computing Institute at UNC, and Chair of CRA) and George Scalise (President, Semiconductor Industry Association) both co-chair the subcommittee charged with producing the report and led the other members of PCAST through the draft recommendations during PCAST’s meeting today at the National Academies.
    Reed began by noting that America’s current global success relies in large part on our lead in IT, but that our favorable position in developing and adopting new networking and IT technologies is not assured. Other nations have recognized the value of leadership in IT and are mounting challenges. Our current success rests on our leadership throughout the IT ecosystem — in the market positions of US IT firms, in our IT commercialization systems, and in the position of U.S. higher education and research systems. The enabling foundation for that ecosystem is clear — early and continuing federal investments.
    Three independent areas must be strengthened to ensure continued leadership, Reed said: education and training; the structure of the federal NITRD portfolio; and prioritization among research areas.
    Education and Training: The U.S. demand for IT professionals in the coming decade is likely to grow more rapidly than most other employment categories. The current IT curricula do not adequately meet employer and student needs. In addition, women and other underrepresented groups constitute a declining proportion of new IT graduates. The committee recommends assessing the current state of and future requirements for IT graduate and undergraduate education, revising IT curricula, increasing fellowship opportunities, and ease visa processes for students and R&D visitors and green card processes for IT professionals.
    Evolving Nature of IT R&D: The committee finds (as the PITAC did in 1999) that the NITRD program is currently imbalanced in favor of projects that are low risk, small-scale and short term. In addition, universities continue to miss research opportunities because of organizational structures and incentives that emphasize disciplinary studies rather than inter-disciplinary research. The committee will call on NITRD and federal agencies to identify important IT problems and put in place appropriately balanced programs that stress innovation and longer term, multidisciplinary projects. The committee also concluded that universities must rethink their structures — their organizations as well as their merit and tenure systems — to become more open to and rewarding of multidisciplinary work.
    Technology R&D Priorities for NITRD: The committee identified eight general research areas it deemed worthy of priority in the NITRD portfolio:

    • Networking and IT systems connecting with the physical world. This includes software monitoring/control via sensors and actuators. The committee recommends that the National Science and Technology Council develop a federal plan for a coordinated multi-agency R&D effort to maximize the effectiveness of federal investments and ensure future U.S. competitiveness in this area.
    • Software. Software is at the center of everything and rapid changes in hardware, like the advent and widespread use of multiple processors per chip, has “strong implications for how we produce software.” The committee recommends that academia, industry and government jointly identify the critical issues limiting advances in reliable, efficient software design and development.
    • Networking: The committee simply endorsed the call by the Director of OSTP for an interagency federal plan for Advanced Networking R&D and noted that a key element of the plan should be R&D for advancing the internet.
    • Data/Data Stores and Data Streams: Recognizing that we’re facing a “data deluge,” the committee recommends that the federal government should develop and implement a national strategy and associated plan to assure the long-term preservation, stewardship, and widespread availability of data important to scientific engineering and technology R&D.
    • High-end Computing: Essentially just reiterated that it should remain a strategic priority and echoed the recommendations of the previous PITAC report (pdf) that called for the development of a federal HPC strategic plan and roadmap.
    • Cyber Security and Information Assurance: Accelerate the activities called for in the Federal Plan for Cybersecurity and Information Assurance R&D.
    • Human Computer Interaction: The science and engineering of HCI underlies nearly all IT applications.
    • IT and the Social Sciences: NITRD should continue to inform public understanding and policymaking.

    The Federal NITRD Program: The committee found that, in general, NITRD has been very effective. However, the NITRD program’s current coordination process are inadequate to meet anticipated national needs and to maintain U.S. leadership in a globally competitive world. The NITRD program must evolve to support the challenges of developing and applying advanced networking and IT capabilities that require larger scale, longer term and multidisciplinary R&D. PCAST will call upon the NSTC NITRD Subcommittee to develop a strategic plan — a vision — and the roadmap to get it done. To help this process along, the PCAST is calling on the NITRD subcommittee to meet annually with broad agency participation to discuss the plan and roadmap.
    Technology Transfer: Scalise delivered this portion of the presentation and noted that the ability to transition ideas from the nation’s R&D institutions to the marketplace has been a key strength of America’s science and technology base. However, it wasn’t clear to PCAST that there was adequate structure within the NITRD program to maximize transfer possibilities. Scalise said the program needs a technology strategy committee, with representatives from industry and academia, to manage the process of technology transfer, not just oversee it. He sees the FOCUS Center Research Program — a research partnership between the federal government, the semiconductor industry, and academia — as a good model. With such a management structure in place, he argued, “the technology transfer problem becomes moot, because it becomes imbedded in the process.”
    Scalise also noted that there’s one key issue that is missing from the draft report and that’s whether the current federal investment of $3.1 billion per year in IT R&D is adequate. It’s missing, he said, because the committee didn’t feel like it had enough information available to it to assess whether that level of spending is appropriate. The report also doesn’t appear to contain any proposals for new agency or federal government-wide initiatives in information technology. Both were key aspects of the 1999 PITAC report — recommendations that helped propel the growth of the NITRD program and led to the creation the National Science Foundation’s Information Technology Research program, a program that ultimately helped more than double the budget of the NSF Computer and Information Science and Engineering directorate over 5 years.
    But otherwise, the report appears to be pretty solid. The committee discussion after the presentation was very positive, with much of the conversation focused on strengthening the recommendations with the addition of some sort of metrics. Identifying exactly what those metrics might be will likely prove challenging, though. One example given by Scalise was again in the area of semiconductors — the metric for the FOCUS Center program is essentially “are we keeping pace with Moore’s law?” PCAST Co-chair Floyd Kvamme asked if it was conceivable that one could envision a “moore’s law” type of metric for each component area, or each strategic area — something that might force the agencies to agree that the key to area “A” is challenge “X.” Scalise responded that he thought that methodology could address “90 percent of the problem.”
    One other interesting area of discussion centered around the workforce issue. PCAST member Norm Augustine (former Lockheed Martin CEO and Chair of the National Academies Rising Above the Gathering Storm report) asked the committee to “suppose we produce more high-quality IT professionals — and so do other countries. Why then, under the pressures of the marketplace, won’t industry continue to shift work abroad?” Scalise answered that he thought the rate of change of salaries worldwide meant that salaries and costs are going to equalize. So he thought it was a problem, but not an overwhelming one. He said he was convinced that if we decided to compete with China in the semiconductor world — and we could equalize the one area where there’s a substantial imbalance…namely tax policy — then you could build a fab plant in China and one here in the U.S. and the one in the U.S. would compete favorably. Stratton Sclavos, CEO of Verisign, added another data point in support of the “salaries will equalize” argument by noting that his company’s “R&D salaries” in the U.S. are rising at 6 – 8 percent per year; but in India, the rate is closer to 30 to 40 percent a year. Verisign expects the offshore salaries to equalize within 10 years.
    In the end, the committee reached consensus on all the recommendations as presented. The report now goes back to the PCAST IT subcommittee for “final” drafting in preparation for its release this summer.
    Update: (4/26/07) — Dan Reed has posted his take on the meeting over at his blog.
    Update 2:: (5/2/2007) — Dan’s slides are now up on the OSTP website.

  • Previously on PCAST.
  • Please use the Category and Archive Filters below, to find older posts. Or you may also use the search bar.

    Categories

    Archives