This week the UK's Engineering and Physical Sciences Research Council met with government, academics and experts at the Institute of Physics to discuss the future of quantum computing and consider the funding of around £50-£100m that may be needed to make progress developing that computing quantum grail.

In the same week, researchers at Fraunhofer Institute, Algorithms & Scientific Computing with the Julich Supercomputing Centre, Forschungszentrum Jülich, have used their grid structure for large scale annotation of biomedical and chemical texts and image in pharmaceutical patents.

It is something that would surely have won the approval of Dr Jim Gray, passionate database software pioneer and Microsoft researcher, lost at sea off the California coast in January 2007 and to whose perspective colleagues at Microsoft Reesearch laboratory have paid tribute, by publishing a collection of essays “The Fourth Paradigm: Data-Intensive Scientific Discovery."

These focus on research on the earth and environment, health and well-being, scientific infrastructure and the way in which computers and networks transform scholarly communication. Also chronicled are the new generation of scientific instruments, increasingly hybrid sensor/computer,  capable of producing and capturing vast floods of data.

Quantum untangling
Thanks to the EPSRC £10m grant, the the field of quantum information processing has come a long way in the past five years, with focused activity in this field. As the grant’s lifespan comes to an end, an Institute of Physics meeting highlighted the most recent advances and discussed what is now needed to make the most of the opportunities that quantum information processing gives the UK.

The current EU roadmap gives annual expenditure in quantum information as: USA €75m; Japan €25m; Canada €125m; Singapore €4m. Some of these figures are known underestimates. The Institute for Quantum Computing at Waterloo in Canada has a philanthropic endowment of €18m available for release as matching funds are awarded. The Singapore Government has made an investment of €75m over five years in QIP.

Dr Hermann Hauser, successful venture capitalist strongly associated with Cambridge’s Silicon Fen,argued ‘Disentangling a billion dollar opportunity.’  “We need to invest £50-£100m in something which can give the UK a truly global lead with big market opportunities.  I’m talking a £5-£10bn pound return, not just a billion.” 

Prior to Dr Hauser’s presentation, quantum optics theorist Professor Sir Peter Knight  (from Imperial College London, optical communications systems Professor John Rarity from the University of Bristol, and physics of computation theorist Dr Simon Benjamin (right)  from the University of Oxford, used the platform to describe the latest advances made by them and their quantum colleagues.

The market opportunities associated with advances in quantum information processing (QIP) have long excited government and big businesses researchers seeking security technology to advance communications and to enable computers to tackle problems that classical machines falter on.

The security promise lies in quantum cryptography which could transform secure communications on macro and micro levels; from re-keying satellites to secure links between bank customers and ATMs.  Entangled photons provide a means to distribute keys which encrypt and decrypt information.  It is a particularly promising method which uses quantum properties to make hacking of information futile. (Though it is puzzling that such properties could not be similarily deployed to disentangle encryptions without corruption?)

For computer processing, benefits stem from quantum systems’ ability to exist in mutually contradictory states at any one time so the computer can explore a much wider range of possibilities than a classical machine, invaluable for example, to engineers working on large-scale projects with a need to take into account all of the different environmental factors that might have an impact on construction.

The financial promise of the field is yet to be realised, but all speakers believed QIP could well be one of the key disruptive technologies needed to breathe life back into the UK economy.

Professor Rarity, (left) on the potentially mass appeal of quantum keys for secure banking, said, “People will become as comfortable carrying their own personal quantum key, using it to secure all transactions by encoding their PIN, as they are with lasers in their DVD players.”

“The promise of QIP emerges from the remarkable property of being able to manipulate information to be in two states at once. There is spectacular potential in the field of sensors, quantum cryptography and computing.

"The UK started the second quantum revolution with the exploitation of quantum coherence in 1990 and now we need to ensure that we maintain a lead," concluded (right) Professor Knight.

Philosophy and paradigms for QIP? 
But it appears no-one feels that QIP might help offer a hybrid advantage to the current grid developments. Perhaps being so different from 'classical' computing, it may not need or even fit a grid approach? But, the jury is still out on what exactly is going to be the preferred quantum computing physical approach.

NIST in Boulder, Colorado built their quantum computer capable of processing 2qb in a gold-patterned aluminium wafer containing a 200 micrometer electromagnetic trap into which four ions – two magnesium, two beryllium were placed. The magnesium ions act as "refrigerants" removing unwanted vibrations from the ion chain and so keeping the device stable. The processor worked as planned, but with only 79 % overall accuracy for a given operation.

Computing paradigms
Dr Jim Gray, writes John Markoff in his elegant  feature in the New York Times talked of the first three computing paradigms as experimental, theoretical and, more recently, computational science.

The shift to a “fourth paradigm,” he explained as an evolving era in which an “exaflood” of observational data was threatening to overwhelm scientists. The only way to cope with it, he argued, was a new generation of scientific computing tools to manage, visualise and analyse the data flood.

In computing circles, (right) Dr  Gray’s crusade was described as, “It’s the data,  stupid.”  A point of view that caused him to break ranks with supercomputing nobility, who for decades focused on building machines calculating at picosecond intervals.

Gray argued government should focus on supporting cheaper clusters of computers to manage and process data. Distributed computing, in which a nation full of personal computers can crunch pools of data involved in the search for extraterrestrial intelligence, or protein folding.

The goal, he insisted, was not to have the biggest, fastest single computer, but rather “to have a world in which all of the science literature is online, all of the science data is online, and they interoperate with each other.” He was instrumental in making this a reality, particularly for astronomy, where he helped build vast databases that wove much of the world’s data into interconnected repositories creating, in effect, a worldwide telescope.

The essays also chronicle the new generation of scientific instruments that are increasingly part sensor, part computer, and which are capable of producing and capturing vast floods of data. For example, the Australian Square Kilometre Array of radio telescopes, CERN’s Large Hadron Collider and the Pan-Starrs array of telescopes, each capable of generating several petabytes of digital information each day, although research plans call for the generation of much smaller amounts of data, for financial and technical reasons.

“The advent of inexpensive high-bandwidth sensors is transforming every field from data-poor to data-rich,” Edward Lazowska, (left) a computer scientist and director of the University of Washington eScience Institute, said.

The same applies to most sciences. The shift giving rise to a computer science perspective, is dubbed “computational thinking” by Jeannette M Wing, assistant director of the Computer and Information Science and Engineering Directorate at the National Science Foundation.

Dr. Wing (right) argues that ideas like recursion, parallelism and abstraction taken from computer science will redefine modern science. Implicit in the idea of a fourth paradigm is the ability, and the need, to share data. In sciences like physics and astronomy, the instruments are so expensive that data must be shared. Now the data explosion and falling costs of computing and communications are creating pressure to share all scientific data.

“You can’t just work on your own patch.” Daron Green, director of external research for Microsoft Research says: “I’ve got to do things I’ve never done before: I’ve got to share my data.”

That marries well with the emerging computing “cloud,” approach driven by Microsoft, Google and others that believe, fuelled by the Internet, the shift is toward centralisation of computing facilities. Both Microsoft and Google are hoping to entice scientists by offering cloud services tailored for scientific experimentation.

Digital instruments are emerging in other fields. In a chapter, “Toward a Computational Microscope for Neurobiology,” Eric Horvitz, (right) AI researcher for Microsoft and William Kristan, (left) a neurobiologist at the University of California, San Diego, charts development of a tool they say is intended to help understand the communications among neurons.

“We have access to too much data now to understand what’s going on,” Dr Horvitz said. “My goal now is to develop a new kind of telescope or microscope.”

The promise of the shift described in the fourth paradigm is a blossoming of science. Tony Hey, a veteran British computer scientist now at Microsoft, said it could solve a common problem of poor use of graduate students.  “In the U.K.,” (right)  Dr. Hey said, “I saw many generations of graduates students really sacrificed to doing the low-level IT.”

In his chapter, “I Have Seen the Paradigm Shift, and It Is Us,” John Wilbanks, (left) director of Science Commons, a nonprofit organisation promoting the sharing of scientific information, argues “Data is not sweeping away the old reality,” he writes. “Data is simply placing a set of burdens on the methods and the social habits we use to deal with and communicate our empiricism and our theory.”

European pharmaceutical patents: 0.5m processed 1.5m to go
Researchers at the Fraunhofer Institute for Algorithms and Scientific Computing (SCAI) and at the Jülich Supercomputing Centre (JSC) of Forschungszentrum have used their computing grid infrastructures for a new application in scientific computing: the large-scale annotation of biomedical and chemical texts and images in pharmaceutical patents.

This will allow patent searches of an unparalleled power. Now queries give interesting insights into intersections between biology and chemistry, and  analysis of chemistry is truly multi-modal in the sense that text- and image-based information can be analysed simultaneously.

More than 50,000 patents describing inventions in pharmaceutical chemistry have been processed on the large-scale computing grid infrastructures at SCAI and JSC. Automated “named entity recognition” services have now identified and annotated:
• biological entities in text (eg protein names; gene names; gene polymorphisms; cell types)
• medical entities in text (eg disease names; pathology terms; risk factor terminology)
• chemical information in text (eg drug names; expressions following the naming standards of the International Union of Pure and Applied Chemistry
• images (eg chemical structure depictions).

The grid middleware Uniform Interface to Computing Resources (Unicore)) was used to manage the annotation services in the grid infrastructure, to control the streams of input and output data from the patents database to the annotation services, and to monitor the overall progress.

“This large-scale experiment opens new perspectives in scientific computing,” says Prof. Dr. Martin Hofmann-Apitius (right) head of the Department of Bioinformatics at Fraunhofer SCAI. “This type of application goes way beyond the usual simulation applications that we are used to in the scientific computing community.”

So far, text mining applications have only been run on bibliographic databases of life sciences and biomedical information such as MEDLINE. But the extension towards a multimodal analysis including annotation of text- and image-based information in full text documents on grid infrastructures has never been done before.

“We are pleased to see that our institute, which has a strong record in numerical simulation, has contributed to a new field of applications for supercomputers: what we call knowledge computing is likely to become a new discipline on its own,” emphasised Prof Dr Ulrich Trottenberg, director of Fraunhofer SCAI.

“UNICORE made it possible to run this experiment at such a large scale in computing grid infrastructures at SCAI and JSC,” says Dr Achim Streit, (left) head of Distributed Systems and Grid Computing at JSC. “The powerful workflow and data management capabilities allowed annotating the patents in a seamless and automated way. A supercomputer connected by UNICORE to the infrastructure of the German Grid Initiative (D-Grid) was used to perform the knowledge extraction. This initial step of the experiment demonstrates what is possible today, showing potential for more complex production runs infuture, using HPC systems connected in grid infrastructures”.
 
“This is a very good example of how powerful supercomputers at JSC equipped with world-class grid technologies like UNICORE can generate synergies to enable new fields of research.” explains Prof. Dr. Dr. Thomas Lippert, director of JSC.

The team at SCAI, led by Dr. Marc Zimmermann for the image analysis annotators, and by Dr Juliane Fluck (left) and Dr Christoph Friedrich (right) for the text analytics part, is currently working on the in-depth analysis of the meta- information generated in the course of this large-scale in silico-experiment.

Their colleague on the side of JSC in Jülich, (left)  Mathilde Romberg, is happy that after weeks of intensive work, first “production runs” have been completed.

However, both teams know another 1.5m patents await them. As does the problem of the quantum paradigm and whether quantum computing will be as amenable to handling the information exaflood or playing among the grids?

Gail Purvis.