May

16

The Computing Community Consortium At Three – A Quick Self-Assessment

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The Computing Community Consortium was launched three years ago –- in the Spring of 2007. The “long version” of what we’ve been up to is detailed in a formal self-assessment submitted to NSF in the Summer of 2009. The “PowerPoint version” is contained in an overview slideset. Here, I’m going to focus on just a few specific activities, to argue the benefits of having our act together as a field.

Broad agenda-setting

During the transition period to the Obama administration, we had the opportunity to feed a number of “white papers” into the transition team’s planning process.  Thanks to the receptiveness of the incoming administration, these white papers had impact far beyond what we had dared to imagine.

Our approach was to focus on the fact that fundamental advances in computer science and computer engineering are essential to meeting the nation’s challenges and achieving the nation’s priorities.  America’s energy future, from transportation to the smart grid, depends essentially on fundamental advances in computer science and computer engineering.  Ditto for the transformation of health care.  Ditto for the future of education.  Ditto for 21st century data-driven discovery — “eScience” — which will be transformational, ubiquitous, and driven by fundamental advances in computer science and computer engineering.

This approach does not position our field a “tool” of other fields, because it is not about applying today’s technology.  Rather, it focuses on the fundamental advances in computer science and computer engineering that will be necessary to meet the nation’s challenges and achieve the nation’s priorities.

This work was done pro bono by a small number of people.  (Committees produce consensus; leaders produce visions.)  And it was carried out as what computer architects would call “speculative execution” — effort devoted in the belief that it might prove to be useful.  (If you wait until someone asks you for something, it’s too late — you need to have it ready!)

Focused agenda-setting

The CCC funds workshops initiated by members of sub-fields who want to chart a future direction.  Some of these have been hugely influential.

A great example is a robotics effort led by Henrik Christensen (Georgia Tech), Vijay Kumar (Penn), Matt Mason (CMU), and others.  This broad community effort, carried out over a period of 18 months, yielded a coherent direction for fundamental research in robotics, a set of “research roadmaps” for the field, and a white paper that is likely to result in a significant federal research initiative during the next fiscal year.

Computing Innovation Fellows

During the 2008-09 academic year it became clear that, due to the economic downturn, many extremely strong Ph.D. graduates would “exit the research game” due to lack of employment opportunities at universities and industrial research labs — sacrificing the nation’s investment in their education, and jeopardizing the nation’s future competitiveness.

Computer science had never had a broad-based coordinated postdoc program, but the Computing Community Consortium, working closely with NSF, was able to establish the Computing Innovation Fellows Project in remarkably short order — from concept to awards in less than six months.  It was NSF’s confidence in CCC as a “proxy” for the computing research community that made this possible.

The CIFellows Project had several unique aspects that we expect to have broad impact.  The first was the “max 2 rule” — at most two awardees were allowed to come from, or go to, any one institution.  (The goal was to establish persistent interactions between diverse institutions.)  The second was an ordering of the holistic quality assessment of candidates:  at each iteration (as the field was reduced from 500+ proposals to 60 awards), members of under-represented groups (women, minorities, particular research areas, etc.) were discussed first.  When the dust had settled, 42% of CIFellows awardees were women!  (To be clear:  gender only influenced the order of discussion!)

Summary

There’s lots more to say, but this is getting long for a blog post.  The bottom line is that a group of community-oriented research leaders can have a profound effect, given the endorsement (confidence and good will) of the research community, and the right environment in Washington.

There are many, many ways in which you can participate.  See the CCC web page for ideas!

Nov

6

Metagenomics and the Computing Challenges of Microbial Communities

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Why should you care about microbial communities?
Except for viruses, they are the most abundant life on Earth and have an
overwhelming effect on our environment and our lives. Consider that about
half the carbon dioxide on Earth is processed through microbes that live in
the oceans. Then consider that the most modern climate models of ocean life
include just five organisms. This is despite recent findings that point to
thousands of oceanic species, which do many different things and presumably
influence our climate.

Metagenomics is a relatively new field that seeks to understand the
structure and function of the shockingly large number of microorganisms on
our planet.  New technologies permit us to now sequence samples taken from
their environment rather than only those that are cultivated in the lab. For
example, Craig Ventner’s Global Ocean Sampling Expedition has collected water throughout the world’s oceans, captured organisms, and sequenced their DNA. In the initial pilot study alone, nearly 150 new bacteria were discovered through this process.

The science and computing challenges are huge. A single gram of soil
contains approximately one trillion base pairs of DNA. Scientists at the National Institutes of Health recently compared over 100,000 bacterial gene sequences on the human skin and discovered a far larger number of different bacteria living on human skin than had been previously known (Science, May 28, 2009). Sequencing and making sense of these data introduces new computational problems, not merely slight extensions of existing ones.

The potential impacts of understanding these data are huge as well. In the
case of soil, microbial communities have an impact on carbon sequestration
and understanding them may help us with cleaning toxic waste. In our bodies,
microbial cells are estimated to outnumber our human cells by a factor of
ten to one and are important in protecting our skin, digestion, and much
more. Understanding these large microbial communities is therefore likely to
have a positive impact on human health. The NIH has launched the Human
Microbiome Project to support work in this field.

Complete DNA sequences of thousands of organisms are piling up in databases
because of the efficiency of DNA sequencing technologies. Most of this
remains unanalyzed for several reasons. We don’t yet know the right
biological questions to ask. We don’t have all the clever programs that
would actually ask these questions of the computer. And there is now so much
data that many questions totally overwhelm even existing high performance
computers.

Among the computational challenges in this field are the design of new
algorithms and cloud computing technologies. In the National Academies of
Science publication “The New Science of Metagenomics: Revealing the Secrets
of our Microbial Planet”, the authors conclude “What then, will metagenomics
have become, in 20 years? We believe that it too will be a concept-driven
computational science… We can expect, in 20 years, enormous advances on
three fronts – technical, computational, and biological – as well as a host
of specific applications.”

We encourage our community to explore and engage in this and other emerging
fields at the crossroads of biology and computation. This is one of the
exciting areas for 21st century computing.

Contributed by Bill Feiereisen with assistance from Ran Libeskind-Hadas

Sep

25

Inducing Innovation with Prizes

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The awarding of the $1 million Netflix Prize this week reopens an interesting bigger question:  Are prizes a viable mechanism for encouraging research in the computing fields?  From Netflix’s perspective, the answer is almost certainly yes.  Netflix CEO Reed Hastings is quoted telling the New York Times (probably tongue-in-cheek) “You’re getting Ph.D.’s for a dollar an hour.”

Could prizes be useful to the broader computing community in advancing research?  The Clay Mathematics Institute established the Millenium Prizes in 2000, offering $1 million for the solutions to each of seven famous open problems, including the question of whether P=NP.  It’s hard to imagine that many researchers have decided to shape their research agendas based on the existence of this prize.  On the other hand, Wolfram Research sponsored a $25,000 prize, with a blue ribbon prize committee, to determine if a specific small (2 states and 3 symbols) Turing Machine is universal. The problem was solved (in the affirmative) in 2007 by a 20-year-old from Birmingham, England.

There is a rich history of prizes for technical innovation.  In the early 18th century, the British Parliament offered the Longitude Prize for a practical method of precisely determining a ship’s longitude, with different monetary amounts depending on the accuracy of the instrument.  The rules were changed during the course of the competition and the prize was never awarded.

More recently, there have been numerous technical prizes such as the $10 million Ansari X PRIZE for carrying three people to 100 kilometers above the earth’s surface.  Following on the success of the Ansari Prize, The X PRIZE Foundation has established several other major prizes for specific achievements that have “the potential to benefit humanity”.

Are there some major problems in computer science that could be incentivized by prizes – financial or otherwise?  What are the potential benefits and risks of this approach?  We’re eager to hear your thoughts.

Some good additional readings include the following:

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