InspiredResearch Winter 2013 Issue 4 Research News from the Department of Computer Science, CITIES OF SLIME Computational Biology Group models bacteria to boost understanding of biofilm – p4

Facebook Photos: The Hidden message Student’s tool for hiding secret messages in Facebook photos hits headlines – p16

Nature flies in with a solution Distributed computing problem solved by studying how flies’ cells develop – p8

Chips with confidence Collaboration between Oxford and Intel to improve chips – p6 InSpired NEWS Research… Oxford sweeps up Prominent Paper is a twice-yearly newsletter published by the Department BCS accolades Award for artificial of Computer Science at Oxford University. intelligence research If you would like to learn more Thomas Lukasiewicz and his co- about anything you read in these Dr Boris Motik authors have won the prestigious pages please get in touch: AIJ Prominent Paper Award 2013 for Department of Computer Science, the paper ‘Combining answer set University of Oxford, Samson Abramsky FRS Prof. programming with description logics Wolfson Building, for the Semantic Web’. Parks Road, Oxford, OX1 3QD Two academics from Oxford’s This paper proposes dl-programs, a [email protected] Computer Science Department have been recognised by BCS, The formalism that integrates description Chartered Institute for IT, for their logics with rule-based logic programs outstanding contribution to the field. under answer set semantics. It Editorial board provides not only detailed theoretical Suzanna Marsh (editor) Dr Boris Motik has been named as the recipient of the BCS Roger analyses of these programs in Helen Wilcox (freelance editor) terms of their expressive power and Suvarna Designs (designer) Needham Award while Professor Samson Abramsky FRS has received computational complexities, but also Wendy Adams the BCS Lovelace Medal. an implementation that illustrates the Bob Coecke usefulness of the proposed formalism Ivan Flechais Their prizes include the opportunity in the Semantic Web. Jeremy Gibbons to deliver a public lecture about Leslie Ann Goldberg their research. Dr Motik will present This work highlights many difficult Fred Hoffman the 2013 BCS Needham lecture in issues in the problem of adding rules Shoshannah Holdom November, and Professor Abramsky and default rules into description Alexander Horn will deliver the Lovelace lecture in 2014. logics, and has been very influential in Peter Jeavons subsequent work in this area. Thomas Lukasiewicz Boris, whose work has had an impact Kelly Ryan both inside and outside academia, Professorship links Maureen York has made major contributions to the design and standardisation of the industry and academia OWL2 ontology language, which is The Royal Society has for the Contributors widely used in industrial research and first time awarded a Research Samson Abramsky applications. His research is around Professorship to an industry scientist, Phil Armstrong the development of techniques for which will enable him to embark on Nycole Cain intelligent management of large academic research while retaining Jassim Happa amounts of data. his position in industry. The award Sophie Kay has been made to Dr Luca Cardelli, Elias Koutsoupias Samson is pre-eminent in setting the a top computer scientist at Microsoft Marta Kwiatkowska modern agenda in the foundations Research, to take up an honorary Sharon Lloyd of computer science, an area where position at Oxford’s Department of Thomas Lukasiewicz he has made immense contributions Computer Science. Ines Marusic since the 1980s. His contributions in Peter Millican each of the past three decades had He will use his professorship to Gary Mirams a major impact on the field, notably: work at the interface of biology, Boris Motik Domain Theory in Logical Form, nanotechnology and computing, as Blanca Rodriguez Game Semantics and Categorical he believes that the convergence of Kelly Ryan Quantum Mechanics. His work over these scientific disciplines will bring William Smith the past decade has shown that about the greatest future changes methods and concepts developed in healthcare and technology. He in theoretical computer science can has strong interests in investigating be applied very directly in quantum computational structures in biology Printed on recycled paper information, and the foundations of and in engineering computational quantum mechanics itself. structures from biologic materials.

2 InSpired Research: Research news from the Department of Computer Science, University of Oxford NEWS

Fellowships galore new foundations for quantum logic. the Northeast of the United States The prize is awarded once every two no longer occur. Stefan joined the Oxford computer scientists have years during the award ceremony Department of Computer Science as received a lot of recognition for held at the bi-annual conference a postdoctoral research assistant in their research over the past few of the International Quantum November 2009. months, receiving fellowships from Structures Association. the EPSRC, the Royal Society, Stanislav has returned to take up a the ERC and the Wellcome Trust, Phil was awarded the EPSRC post at Oxford this October where he plus an Honorary Fellowship from fellowship for his project entitled will work on his project ‘Optimisation ESCMSET, and the Birkhoff – von ‘Bayesian Models of Grammar of separable functions’. He obtained Neumann prize. Induction and Translation’. His his in Computer research programme aims to Science at Oxford in 2009. Since Dr Chris Heunen and Dr Phil develop large-scale and language- then he has worked for Microsoft Blunsom have been successful in independent to allow Research Cambridge, the University gaining highly sought after five- for syntactic analyses of real world of Oxford, and was most recently at year EPSRC Fellowships. Chris of language data, without the need the University of Warwick when he the Quantum Group has received for traditional hand annotation. The applied for the Fellowship. funding for his project ‘Combining development of such a model could Viewpoints in Quantum Theory’, increase our understanding of how Dr Blanca Rodriguez has been which intends to use computer children learn languages and could awarded a five-year Wellcome science, physics and mathematics to lead to the development of advanced Trust Senior Research Fellowship in progress our understanding of and language technologies for processing Biomedicial Sciences, and Dr Gary capabilities in quantum computing. online data. Mirams the five-year Henry Dale These advancements could greatly Fellowship, which will support their ease the future development of Additionally, prestigious Royal Society work in the field of Computational protocols for quantum hardware. University Research Fellowships have Medicine. See p13 for more details of Chris has held a Junior Research been awarded to Dr Stefan Kiefer and Blanca and Gary’s work. Fellowship since joining the Dr Stanislav Živný, which will fund Department in 2010. their research for the next five years. Professor Kevin Burrage has been awarded an Honorary Fellowship Chris has also been awarded the Stefan’s project ‘Quantitative Analysis by the European Society of 2012 Birkhoff – von Neumann prize of Infinite-State Systems’ centres on Computational Methods in Sciences, for his research, which includes computer-aided formal verification Engineering and Technology the analysis of quantum logic from to ensure that dynamic, infinite state (ESCMSET), its highest distinction, the perspective of categorical logic systems behave as they are intended. for his outstanding contribution in the and the study of how algebraic Improved computer-aided verification fields of Computational Mathematics quantum mechanics can be related could, in future, ensure that incidents and Numerical Analysis. to topos theory so as to construct such as the 2003 power blackout in

ERC Professor Leslie Ann Goldberg of computational counting has been awarded a five-year problems, determining which advanced European Research Council problems are tractable, and which Advanced Grant for her project are intractable; and to discover grant ‘Mapping the Complexity of complexity characterisations awarded Counting’, to start in March which elucidate the features that 2014. The overall objectives make counting problems tractable are: to map out the landscape or intractable. NEWS FLASH £1.26 Million Platform Grant for Information Systems The Information Systems Group has just been awarded a highly sought after Platform Grant from EPSRC. Platform Grants provide a base of flexible funding to support the retention of key staff, feasibility studies, longer term research and international networking. Congratulations to all involved in making this application a success. We will bring you details of the research in future editions.

www.cs.ox.ac.uk Issue 4, Winter 2013 3 Cities of slime

Most bacteria live together in quasi-social colonies, which are known for exhibiting fascinating behaviour. The way that these biofilms grow is currently being modelled by The Oxford Computational Biology Group. In this article, Will Smith explains why slimy layers of bacteria are so important, and describes some of the group’s current research.

What do you imagine when you hear computational modelling. For Recent work performed in the the word ‘bacteria’? Perhaps some example, biofilms can form intricate Computational Biology Group little green blobs swimming about, structures during growth; tower- has begun to direct the power no doubt plotting to infect some like edifices, internal nutrient of the Chaste (Cancer, Heart unattended kitchen surface and supply channels and fractal-like And Soft Tissue Environment) cause domestic havoc. This is the growth patterns are all common platform towards the modelling of picture often painted by, for instance, examples of the amazing emergent biofilm biology. An exciting new disinfectant advertisements – but it configurations observed. collaboration between the Foster neglects to tell the full and awesome group (Oxford Zoology), the Toulouse story of the bacterial lifestyle. They can also display remarkably Institute of Fluid Mechanics, and sophisticated sociobiology: film the Oxford Computational Biology Now, imagine a complex, dynamic bacteria can cooperate to achieve Group has been using Chaste to community where countless species common goals, coordinating create new computational models of of bacteria live and die together – chemical counter-attacks on biofilm growth. billions of organisms competing, assailants and producing communal sharing and interacting within materials for the benefit of the So far, this work has focused on microscopic architectures built of colony. A good example of this is the development of new modelling cells and slime. Sounds fantastic? the slime (termed ‘Extra-cellular frameworks, designed to examine Welcome to the amazing world of Polymeric Substance’ or EPS) the role that cell shape plays the biofilm. that holds the biofilm together: in biofilm growth and structure the contributions of many bacteria formation. Could cell shape affect The vast majority of bacteria on the combine to form a viscous the evolutionary strategies adopted planet live – like us – together in protective blanket, anchoring the by bacteria in competing for space quasi-social colonies, grouped under colony to surfaces and shielding and resources? We aim to find out. the heading of biofilms. These dense, it from chemical attacks – such as slimy layers of bacteria can form on disinfectants. Boosting human understanding virtually any surface, and can be a of biofilm growth is crucial for great nuisance if allowed to grow However, it’s not all peace, predicting and manipulating the unchecked – blocking pipes, fouling love and understanding. Whilst behaviour of these fascinating ships’ hulls, and contaminating water cooperation between film systems, and is providing us supplies. Biofilms are also notorious inhabitants is sometimes observed, with stunning insights into the pathogens, accounting for some vicious competition is usually fundamentals of evolutionary biology. 80% of all chronic infections, and are the rule of thumb, with rival The computational modelling of well known for their robust resistance populations of bacteria constantly biofilms has much to teach us about to antibiotic treatments. Dental contending for coveted space the microorganisms with which we plaque, associated with tooth decay and resources. Again, slime plays share our daily lives, and could prove and gum disease, is a well-known a critical role here: like Roman to be a key resource for unlocking instance of a bacterial biofilm. soldiers in a tortoise formation, the secrets of the cities of slime. subgroups of bacteria can use EPS But on top of their industrial and as a barrier to eject and exclude You can find out more about the medical infamy, bacterial biofilms other microbes, allowing them to Chaste Biofilm project at exhibit a great deal of fascinating progressively dominate the biofilm www.cs.ox.ac.uk/chaste biological behaviour, which has territory (see background photo). or by contacting Will Smith made them popular targets for ([email protected]).

4 InSpired Research: Research news from the Department of Computer Science, University of Oxford [background photo] Slime as a weapon: by producing extra EPS, a biofilm subpopulation (stained green) is able to Volunteer power burst through a dense mat of bacteria and expand into the space of their competitors. By engaging members of the BOINC is managed as a community- public and their computers in a developed tool out of Berkeley, climate modelling project, Oxford and Oxford’s contribution is University has helped establish a acknowledged by the now head of software platform for scientists to this group. BOINC is now widely use in creating secure volunteer used by scientific communities computing projects. across the world. According to www. boincstats.com 2,599,338 people Climate modelling research at Oxford have installed the BOINC software has underpinned the development on their machines and there are of the current version of Berkeley currently 272,459 active users. The Open Infrastructure for Network global reach of the CPDN project Computing (BOINC), a technology to using BOINC is significant. enable secure volunteer computing. This was done as part of the Of the 82 BOINC projects, in climateprediction.net project which May 2012 climateprediction.net is currently managed as CPDN was the fourth most popular by through the Oxford e-Research work-units in progress. Over 129 centre supporting international million simulation-years have been climate modelling. CPDN models performed since the project’s climate change using donated cycles inception and registered users are on users’ computers, with almost located in 221 countries. Since 2008, 700,000 users registered by 2013. 40,702 distinct individual users have successfully completed one or more Significant work to develop the model simulations. The computing BOINC technology in the CPDN time required for all the model has enabled scientists to embrace simulations run successfully since volunteer computing to solve 2008 is equivalent to a 32,220 core scientific modelling challenges. machine running full time for one BOINC has become recognised as year and producing 100% successful the key open-source resource for results. An estimate of the value volunteer computing, supporting of this CPU time is $22.5M, based significant international scientific on the rate of the Amazon Elastic endeavours. Compute Cloud Standard Spot instance ($0.08/hour default). The work on BOINC by the Oxford team enabled the uptake of the technology to grow enormously. It meant community users were confident of its ability to harvest compute cycles without compromising the security of their PCs, as well as modellers being able to develop more complex codes to run out in the community and return timely results. It enabled the public to engage in science in a way which had not been achieved before Acknowledgments: Many thanks to with thousands of users observing James Osborne, Joe Pitt-Francis, a changing globe graphic on their Yohan Davit, and Kevin Foster for machines showing the results of their their help with the project, and own models running on behalf of the to IMFT and the ESPRC for their climate scientists. CPDN was, and funding. Images kindly provided by still is, producing climate modelling Wook Kim and Katharine Z. Coyte, results which are used by the Met Kevin R. Foster, and William M. Office. Durham. www.cs.ox.ac.uk Issue 4, Winter 2013 5 Chips with confidence

Collaboration between the University of Oxford and Intel Corporation has developed new methods to check that electronic chips do what they’re meant to do, before they are manufactured.

Integrated electronic chips, such as such technique has been patented the processor in a laptop, contain by Intel and Tom. Twenty-five many billions of interconnected years ago these advanced formal transistors, all working together verification techniques were thought to run programs. The engineering unachievable; today they are in design of a new chip is extremely routine use by Intel and other challenging, and ensuring that the companies worldwide. finished chip works correctly is vitally important. Almost half of the Tom’s collaboration with Intel is several years spent creating a new a prime example of knowledge chip goes on testing it for potential exchange between academia and errors. industry. Intel, led by experts such as Senior Principal Engineer Dr Carl Fabricating a prototype chip to test Seger, has pioneered the use of a design is prohibitively expensive, formal verification on the hardest so computer simulations are industrial chip design problems. daily struggle to get the next design widely used to validate designs. Tom has worked closely with Intel out the door, has been invaluable. But simulation of every possible engineers for over a decade, and Some of this joint work provided internal set of connections in every Intel researchers have spent time at the foundation for methods that are possible operating condition would the University of Oxford – including today used at half a dozen design take many millions of years to test Carl as a Visiting Fellow of Balliol centres on three continents. In a chip exhaustively, so is clearly not College during 2006-7. addition, I believe the benefits have feasible. been mutual in that we have also The ability to rapidly identify design provided Professor Melham with a Tom Melham, Professor of errors in a chip is cost-effectively wealth of interesting, challenging, Computer Science, has been driving forward new designs that and relevant research problems.’ working with Intel Corporation since use less power and are more the late 1990s to develop and apply environmentally friendly. The This research has been funded a mathematical validation technique technique also has applications by Intel Corporation and the known as formal verification. This in safety-critical systems, such Engineering and Physical Sciences entails building a mathematical as aeroplane, automotive, or rail Research Council. description of the chip design and control, where confidence in the then analysing its correctness chips is vital. This article first appeared as part of by rigorous mathematical proof. The Oxford Impacts series. To find The proofs are very large, so a Carl commented: ‘Having Professor more articles in the series visit: simplification technique called Melham working with us and helping http://partnership.ox.ac.uk/ abstraction is used to pick out us articulate and evaluate the “big category/impact/ salient features for testing; one picture”, which often gets lost in the

talking about their career path and Women in CS Society launched experiences – could become role models and inspirations. The Oxford Women in Computer It exists for all women – students, Science Society (OxWoCS) was faculty, and staff. Other events include a welcome started in June 2013 with the goal of event for freshers, trips to lectures supporting and promoting women OxWoCS organises a variety of and conferences, most notably the in computer science. OxWoCS is a activities and events, including London Hopper Colloquium, as society within Oxford’s Department weekly coffee meetings, and a well as some joint events with the of Computer Science and aims to Distinguished Speaker Seminar Cambridge women@CL Society. provide networking opportunities Series featuring accomplished and a support network comprising female speakers from either More information: http://www.cs.ox. role models, mentors, and peers. academia or industry who – through ac.uk/societies/women/

6 InSpired Research: Research news from the Department of Computer Science, University of Oxford Expanding research

The new algorithms group in the Department of Computer Science was inaugurated in October 2012 with an international workshop on algorithms. The group, headed by Leslie Ann Goldberg, has brought together existing Oxford expertise in algorithms (including Michael Benedikt, Georg Gottlob, Peter Jeavons, Thomas Lukasiewicz and Joel Ouaknine) under one theme, and has expanded upon it with the appointment of three more experts to the department: Professors Elias Koutsoupias, Leslie Ann Goldberg and Paul Goldberg. Algorithms with The launch of the new theme was marked by a two-day meeting of world-class the right incentives researchers in the field, held Research into algorithmic game The price of anarchy attempts to jointly between the Department theory under the leadership of capture the loss of efficiency resulting of Computer Science and St Professor Elias Koutsoupias from the from competing selfish individuals John’s College. The speakers Department of Computer Science is or companies. For example, average included the winners of the being funded for the next five years. traffic delays on streets could be Turing Award, the Gödel Prize reduced if drivers were following a and the Knuth Prize. The project ‘Algorithms, Games, centralised plan instead of choosing Mechanisms, and the Price of their own best route. Leslie Ann and Paul moved Anarchy (ALGAME)’, which aims to to Oxford this summer from investigate fundamental questions The explosive growth of the web the University of Liverpool. about algorithms, has received and the internet has radically Paul was the founding an advanced grant funded by the changed the economy and society head of the Economics and European Research Council (ERC) to and shifted the focus of many Computation (ECCO) research run from 2013 to 2018. scientific fields, and has especially group at Liverpool. Leslie Ann transformed computer science. specialises in computational Elias’ objective is to bring together a It used to be about software and complexity, where the aim is to local team of young researchers who hardware systems designed, built, discover which computational will work closely with international and operated by a single team, but problems are feasible, which collaborators to advance the state- now it is more about systems that are inherently infeasible, of-the-art of algorithmic game theory are created and operated by many and why. Elias joined the and open new avenues of research different entities, usually competitors. team from the University of at the interface of computer science, Athens last year, bringing with game theory, and economics. The With this dramatic shift in the him extensive expertise in project consists mainly of three foundational assumptions of algorithmic game theory, its intertwined research strands: computer systems, we have now applications to the internet, algorithmic mechanism design, to focus on algorithms that are the web, and the economy, the price of anarchy, and online not simply efficient but which also online algorithms, and, more algorithms. provide the right incentives to the generally, decision-making computing agents involved. under uncertainty. www.cs.ox.ac.uk Issue 4, Winter 2013 7 Nature flies in with a solution

By studying how a fly’s cells develop, computer scientists have solved a distributed computing problem. A team from Oxford – Peter Jeavons, Alex Scott, and Lei Xu – have used the way that the fly selects special cells to develop a new algorithm to choose leaders in a network.

During a fly’s development, certain One new idea about how to tackle to the formal requirements in the cells specialise into an unusual this problem comes from looking at maximal independent set selection state, which then go on to become nature. The MIS selection problem problem. cells attached to bristles on the has some similarity with the ‘fine- back of the fly. The choice of grained’ pattern formation among However the method used by the which cells specialise in this way groups of neighbouring cells that fly to select these cells appears resembles a fundamental problem takes place in many living organisms. to be very different from any in distributed computing known In particular, Afek et al. recently of the algorithms designed by as maximal independent set (MIS) pointed out in a paper in Science mathematicians and computer selection. that MIS selection is similar to the scientists for choosing an MIS. All selection of certain cells during the of these previous algorithms rely In MIS selection, a large network development of the nervous system on precise numerical calculations, of identical agents need to choose of the fruit fly Drosophila. and generally require explicit a small set of leaders. Every agent information about the number of should be connected to at least one During development, certain cells of active neighbours that each node leader, but the leaders should not the fly specialise to become sensory in the network currently has. They be directly connected to each other. organ precursor (SOP) cells, which also generally rely on exchanging a The need for this sort of selection later develop into cells attached complex set of messages. process arises in many different to small bristles (microchaetes) on kinds of computer networks. the back of the fly that are used By contrast, the cells of the fly to sense the environment (see appear to solve the problem using The challenge is to compute Figure 2). During the first stage of only simple local interactions. These such a set of leaders efficiently this developmental process each local interactions involve proteins on in a distributed way where each cell either becomes an SOP or the surface of the cells that allow the agent makes its own independent a neighbour of an SOP, and no cells to switch between two mutually decisions and there is no central two SOPs are neighbours. These exclusive states. control. observed conditions are identical continued on next page

8 InSpired Research: Research news from the Department of Computer Science, University of Oxford from previous page In one state the cells display high Studying the way that the fly proposed – but is much simpler levels of a protein called Delta on selects special cells leads to a to implement. Unlike previous their surface, and low levels of a new distributed algorithm for MIS algorithms it requires no knowledge protein called Notch. In the other selection: each node signals that it of the overall graph, uses very simple state they display high levels of wishes to join the MIS with a certain messages, and is extremely robust. Notch and low levels of Delta. probability. If none of its neighbours By a careful mathematical analysis These two proteins affect the signals at the same time, then it we showed that in any network with behaviour of neighbouring cells, succeeds and joins the MIS. If there n nodes the expected number of by a process of negative feedback, is a clash, where two neighbours rounds needed to select an MIS in so that cells that choose the first both wish to join the MIS at the same this way is O(log n), which is known state tend to encourage their time, then they both have to wait, to be the best possible performance neighbours to go into the other and they both lower their probability. that is achievable using single-bit state. At the multicellular level, If neither a cell nor its neighbours messages. this lateral inhibition mechanism signal in some round, then that cell can break the symmetry among raises its probability of signalling in Our description of the algorithm, cells and amplify small differences the next round. with some simulations and a between neighbouring cells, detailed mathematical analysis, was giving rise to patterns, such as the We have shown that this simple presented at the ACM Symposium pattern of bristles on the back of algorithm is just as fast as the on Principles of Distributed the fly. most efficient algorithms previously Computing in July 2013.

Figure 1: Some examples of Maximal Independent Sets. cities are less than (A) The red nodes form an MIS in this grid 100 km graph. Every black node is adjacent to at apart least one red node but no two red nodes are adjacent to each other. A (B) The five red nodes form an MIS in this random graph with 20 nodes.

(C) The 13 red nodes form an MIS in this network of UK cities. The nodes of the network correspond to 73 major cities in the UK, and two nodes are adjacent if the corresponding B C cities are less than 100km apart.

Figure 2: Pattern formation in the fly.

high Delta/low Notch A B C low Delta/high Notch (A) During development, certain (B) The choice of which cells (C) The cells of the fly use simple cells specialise into an unusual specialise in this way (indicated by local interactions between the state. These cells then develop darker colour) resembles the MIS transmembrane proteins Notch and into cells that are attached to small selection problem. Delta to generate mutually exclusive bristles on the back of the fly that signalling states. are used to sense the environment.

www.cs.ox.ac.uk Issue 4, Winter 2013 9 Underground tracking to become a commercial reality

It should soon be possible ‘Most technologies are only Having successfully used the to track people in mines or checking the magnitude of the basic technology in wildlife underground emergencies signal – the signal strength from tracking, the researchers are now using a commercial application each transmitter – to work out aiming to incorporate it into smart that is being created by Oxford distance,’ Andrew told Mark mobile devices: Andrew and Niki researchers from technology that Piesing of Wired.co.uk. The new are developing a demonstrator on they originally developed to study technology measures ‘vectors, an Android platform and, once the badgers. which give you the magnitude technology is perfected, versions and direction… Our technology suitable for other popular smart When Dr Andrew Markham can work out your position in phones, such as the iPhone, and Dr Niki Trigoni from the three dimensions from a single shouldn’t be far behind. Department of Computer Science transmitter.’ needed to work out the position They have started working with of animals underground, they This contrasts with other Isis Innovation to commercialise came up with the idea of using approaches such as GPS or WiFi their research and are currently technology that generated very which are based on triangulation raising money for a spinout firm. low frequency fields. These can and typically require signals from The team has proven the basic penetrate obstacles, enabling at least four transmitters. As algorithms and software and are positioning and communication well as being used underground, working on more sophisticated even through thick layers of the very low frequency tracking techniques to increase rock, soil and concrete, which could also be used for indoor performance and accuracy. conventional technology, such as applications, for instance in a GPS, cannot do. shopping centre or airport.

Oxford plays publically accessible in October Wikimedia Deutschland has 2012. All international Wikipedia developed and maintained Wikidata part in creating editions were connected to the since 2012. The team of eight data by March 2013 – the new developers is led by Dr Denny database of world’s system most notably serves the Vrandečić at Wikimedia Deutschland. knowledge links to other languages, shown on He and Markus are co-founders of the bottom left of every Wikipedia the Semantic MediaWiki project, A quiet revolution in the way page. As of May 2013, Wikidata which has pursued the goals of Wikipedia offers access to, and became the most frequently Wikidata for the last few years. manages its data, has taken place edited Wikimedia project with with the recent launch of Wikidata. around 15 million contributions The initial funding from the Allen By creating new ways for Wikipedia per month. Large amounts of data Institute of Artificial Intelligence, to manage its data on a global scale, are continuing to be entered by a Google and the Gordon and Betty Wikidata allows users direct access growing community. Moore Foundation, has been to its data. Dr Markus Krötzsch from extended by a donation from Russian the Department of Computer Science The common-source principle search engine provider Yandex. is one of the original architects of behind Wikidata is expected to It will help fund the development the project, and continues to be a lead to a higher consistency and of outstanding features, such as consultant to the development team quality within Wikipedia articles, support for ranking statements on technical questions. as well as increased availability of as preferred or deprecated, and information in the smaller language adding more major datatypes, The site, which aims to provide a editions. Wikidata should also such as numbers and URLs. More collaboratively edited database of reduce the maintenance effort for information about the project can be the world’s knowledge, became Wikipedia’s volunteers. found at www.wikidata.org

10 InSpired Research: Research news from the Department of Computer Science, University of Oxford Big expansion in cyber security portfolio

Cyber security activities at the skills to contribute research-derived Each dimension has two co-chairs, University of Oxford have been expertise to business or government. drawn from Oxford and other leading expanding with an array of exciting The training is focusing on emerging research bodies. They are working new research projects, education technology themes such as the with a wide range of global partners, and training. They all sit under the security of ‘big data’, cyber-physical including governments, international umbrella of the Cyber Security security, effective systems verification organisations and the private sector. Centre, which was set up in March and assurance, and real-time security. 2012 and unites experts in the field Another cyber research project and other interested bodies. The Oxford centre expects to produce got under way in February looking over 40 DPhil graduates, spread over into the risk from insider attacks to This year, the Cyber Security Centre three intakes, in the next seven years. organisations and how to combat has added to its portfolio the recently A similar centre has been established them. The Corporate Insider Threat established Global Centre for Cyber at Royal Holloway. Funding for the Detection research project, a joint Security Capacity-Building, the Centre two centres together is £7.5 million. venture between the Universities of for Doctoral Training in Cyber Security, Oxford, Leicester and Cardiff, aims and the Corporate Insider Threat The new Global Centre for Cyber to examine how to reduce risks to an Detection research project. Security Capacity-Building was also organisation from disgruntled, corrupt Various departments are involved in set up this year. It aims to understand or just poorly-trained employees, the Cyber Security Centre, and the how to deliver effective cyber security deliberately or accidentally harming Centre for Doctoral Training. The main both within the UK and internationally. crucial data or digital infrastructure. ones are: the Department of Computer The research, funded initially for two Science; The Oxford Internet Institute; years by the UK Government, is The project has been commissioned Saïd Business School; the Blavatnik divided into five dimensions: devising by the Centre for the Protection of School of Government; and Oxford cyber policy and cyber defence; National Infrastructure (CPNI), and eResearch Centre. encouraging responsible cyber culture will develop a conceptual model, within society; building cyber skills as well as a prototype monitoring The Centre for Doctoral Training in into the workforce and leadership; software, designed to detect cyber Cyber Security began PhD training creating effective legal and regulatory insider threats and help identify this autumn. Doctoral training will last frameworks; and controlling risks hazards to businesses before the four years and provide graduates with through technology and processes. threat is realised.

opensource project, ran the day, News in brief and gave presentations and advice to representatives from more than • Nature Scientific Reports has 25 companies. published a paper that uses PRISM to study cell cycle switch as a • The 29th British National computing device. PRISM is a Conference on Databases probabilistic model checker being (BNCOD) was held in St Anne’s developed at the Universities of College in Oxford in July. The Oxford and Birmingham. theme this year was ‘Big Data’, More PRISM information: addressing the growing need www.prismmodelchecker.org. to manage data that is too big, too fast, or too hard for existing • A team of computer science technology. Robotics and Systems (TAROS) doctoral students – William – was held in Oxford in August. Zeng, Brendan Fong and Miriam • The Department has recently taken over the Robert Hooke The highlight was a public Backens – was one of 21 winners demonstration of driverless car in the Summer of Innovation building, just a few minutes walk from the main site. The newly technology being developed at competition for their idea WikiNets: Oxford University by Engineering a collaborative, open source, refurbished area is now home to the Centre for Doctoral Training expert Professor Paul Newman and network building tool to share and his team. Other topics included organise notes and research. in Cyber Security, as well as the Department’s cyber security theme, swarms of robots, robot vision, • The Department of Computer plus teaching and social spaces. aerial robots and robots inspired by Science hosted the ‘Internet of nature. The conference was chaired Things mash-up day’ in September. • Britain’s leading conference on by Reader in Computing Science The Webinos Foundation, an robotics – Towards Autonomous Dr Stephen Cameron.

www.cs.ox.ac.uk Issue 4, Winter 2013 11 Optimal rhythm to improve life

Professor Marta Kwiatkowska has of cardiac pacemakers, battery- methods to derive optimal been awarded a grant for the project, powered medical devices which pacing rates for a given patient. VERIPACE, which aims to lengthen stimulate the heart to beat It aims to exploit the model- the battery life of pacemakers and appropriately and need to be based framework for quantitative improve the patient’s quality of life. replaced every five to six years. verification of pacemaker software If successful, it will also mean that recently developed within the the patient needs fewer replacement In the UK alone, there are European Research Council (ERC) surgeries, significantly reducing around 25,000 pacemaker Advanced Grant, VERIWARE (www. healthcare costs. implants per year, each costing veriware.org). approximately £20,000. Timing Cardiac arrhythmias – irregularities faults in the software embedded The ERC Proof of Concept grant in the heart rhythm – are common in a pacemaker device can lead to awarded to VERIPACE was diseases that are expected to discomfort, or even patient death. introduced in March 2011 to increase with the aging population. establish the innovation potential The typical treatment is by The main idea of the VERIPACE of ideas from ERC-funded frontier expensive surgical implantation project is to develop novel research projects.

Faster radiotherapy (STFC), through its Innovations Department of Computer Science Partnership Scheme, with the have experience in the handling planning support of Siemens Healthcare. of ‘smart’ data systems – using metadata elements to allow data to A collaborative project between Once the research is completed, be searched and processed in more physicists, oncologists and computer free software tools will be available intuitive ways. The team includes scientists at Oxford and Cambridge to radiotherapy treatment centres. Dr Neil Burnet from the University Universities is developing new These tools will increase patient of Cambridge and Professor Andy software to plan radiotherapy access to high precision radiotherapy Parker and his team at the High treatment. Accel-RT will help by reducing the bottlenecks in the Energy Physics group in Cambridge. overcome the time constraints that clinical workflow. The system will currently limit the use of complex operate as a ‘virtual oncologist’, ‘In essence, Accel-RT is helping to treatment by developing improved observing what the oncologist is identify tumours and surrounding software tools and processes for treating and using novel search organs during the planning and the planning of high precision algorithms to recall similar cases delivery of radiotherapy treatment,’ radiotherapy. from a clinical archive. Models of said Andy, Principal Investigator tissue structures will be used to help for Accel-RT. ‘Tracking the change While modern radiotherapy machines outline normal tissue automatically, in position and volume of these can now deliver highly targeted as well as to track the movement of structures is a complex problem. treatment, the use of high precision these structures during the course of To perform these calculations techniques is extremely demanding radiotherapy treatment. in real time for a single patient in terms of hours spent. Over three would require up to 16 Teraflops of years the team is aiming to develop The key players in the project are processing power – tools to speed up the process. established leaders in their fields. approximately 100 times the power Accel-RT was launched in December At Oxford University, Professor of a standard PC workstation.’ 2011, and is funded by the Science Jim Davies and his team from the More details: www.accelrt.org. and Technologies Facilities Council

12 InSpired Research: Research news from the Department of Computer Science, University of Oxford Experts advise on Department of Computer Science at Impact Acceleration Award, to support the University of Oxford to present work done with various members of simulations for drug their work and inform them of the Department, including Dr Alfonso new technologies available for the Bueno-Orovio, John Walmsley, safety testing evaluation of drug-induced effects on Oliver Britton, Dr Ana Mincholé and Two Oxford computer scientists the heart using computer simulations. Professor Kevin Burrage. were among just six experts invited The aim of inviting experts to present to advise the US on replacing the their research was to start the process Blanca has also been invited to way it evaluates medicine to include of shaping the details of the in silico present their work, in the context computer simulations. assays that the FDA will request from of the FDA changes, at the Annual pharmaceutical companies to test for Meeting of the Safety Pharmacology Before being released to the drug cardiotoxicity. Society in September in Rotterdam market, medicines are evaluated and at a joint Safety Pharmacology by pharmaceutical companies to The work in this area in Oxford was and British Toxicological Pathology rule out the possibility of potentially initiated by Prof Denis Noble and the Societies meeting organised in the lethal, adverse side-effects on award of the preDiCT project funded headquarters of the pharmaceutical the heart. Regulatory agencies by the European Commission from company AstraZeneca in November. such as the USA Food and Drug 2008-2011, also led by Prof David Administration (FDA) assess whether Gavaghan and Blanca. After that, The importance of the world- the results for cardiotoxicity provided Gary’s research was supported by leading research conducted in by the companies are convincing funding from industry (GlaxoSmithKline) the Department in this area of or not before authorising the and a grant from the National Council Computational Medicine has also commercialisation of the drug. for the Replacement, Refinement and been recognised by the Wellcome Reduction of Animal Experiments. Trust through the award of a Senior In July, the FDA announced a big Blanca was awarded a Medical Research Fellowship in Biomedical change in the way medicines are Research Council Industry Partnership Sciences to Blanca and a Henry Dale evaluated before being released to Award, research grants by Janssen Fellowship to Gary to support their market: they want to replace one of Pharmaceuticals and an EPSRC research for the next five years. the studies conducted in humans (the thorough QT study) by a combined in silico and in vitro assay using computer simulations and human stem cell derived cardiomyocytes. The move is to be implemented by 2015, a big shake-up for the pharmaceutical industry.

The FDA invited Dr Gary Mirams and Dr Blanca Rodriguez from the

Panton Fellowship and open working techniques. A The fellowship involved a significant pilot scheme was run at Oxford’s public aspect, including presentations sees advances in Doctoral Training Centres for at the Open Knowledge Festival in open science Systems Biology, the Life Sciences Helsinki, an international conference Interface, and the Industrial in open technologies, policy and Sophie Kay (née Kershaw) of the Doctorate, in January 2013 and academia, and participation in Computational Biology group has looks set to appear in a network panel debates at OKFest and Digital recently completed a one-year Panton of institutions across Europe, the Research. Sophie also showcased Fellowship in association with the US and Commonwealth over the OSTI at several major institutions in Open Knowledge Foundation. coming year. California, including Stanford and Berkeley. As part of her fellowship work, Sophie’s paper addressing the Sophie founded the Open Science benefits of OSTI’s novel education OSTI enjoyed success at the Training Initiative (OSTI), an pattern for developing robust scientific University of Oxford’s OxTalent educational scheme for pre-doctoral research practices was also included awards in June 2013, winning its and early-career researchers. in the European Commission’s report category for Open Educational OSTI aims to address the issue on Higher Education as part of their Resources. Sophie has been of reproducibility in scientific vision for Open Education 2030. invited to deliver a workshop research by driving students’ For further information: at #solo13, a conference of the engagement with digital practices www.opensciencetraining.com. Nature Publication Group.

www.cs.ox.ac.uk Issue 4, Winter 2013 13 Floating Points in Dragon Boat challenge

A team of staff and students – The team achieved seventh place in Floating Points @ CS – took part in the heats, with their quickest time the annual Abingdon Dragon Boat over the course a very respectable Race this September. 1 minute, 18.9 seconds. Although this wasn’t enough to take the The team were raising money for team into the finals, it was less SeaSaw (offering grief support to than 1.5 seconds behind the best young people), the Thames Valley & time posted by the competition’s Chiltern Air Ambulance, and Daybreak ultimate winners, the ‘Wittenham (providing day clubs for dementia- Wannabees’. sufferers in Oxford).

Doctoral student Martin Lester, is Earlier in the year, he was in an Other exploits ranked the best Riichi Mahjong Oxford team that won a bronze player in the UK, having taken silver medal in the British Universities Our students and academics are of at the Oranda Sai-kou tournament in Team Time Trial Championships, course very accomplished computer the Netherlands. and finished seventh overall in the scientists. But they’ve got some British Universities 25 mile Individual rather surprising other talents. Here Karen Barnes from the Admin & Time Trial Championships, leading are a few of their non-subject-related Support team has been raising Oxford to a bronze medal in the team achievements in the last year: money for local charity NEETS (for classification. young people not in employment Doctoral student Adrian Duncan or education) by undertaking four At this year’s Oxford-Cambridge won a gold medal in Archery and daring challenges, including stopping Boat Race, Oxford jumped to a bronze in the Table Tennis at the an in-flight arrow with the hollow of an immediate lead and held it British Transplant Games. This adds her neck, and doing a fire walk. throughout to win the 159th Boat to his silver in Table Tennis from last Race, by a length and a half. MSc year’s games. In August, doctoral student Aistis student Paul Bennett was in the No. Šimaitis won third place in the 5 seat. Oxford completed a clean Bob Coecke – aka Professor Bob – Chlumec International Triathlon sweep of Cambridge, as the Isis has been using music to understand (involving a 400m swim, 36km bike crew (featuring DPhil student William his chosen field of quantum ride, 5km run and 3 pints of beer) Zeng, who was in the Boat Race last mechanics for years. He’s recently after leading the race on finishing the year) had beaten Goldie by one-third been gigging in Beijing. bike ride. of a length earlier in the day. Students present at Eurographics UK The winners of a student project, were a collection of both original was accepted and presented in early which they designed as part of their and well-established approaches September 2013. undergraduate degree at Oxford, developed in a modular fashion, have presented their research to the allowing for new visualisations to be ‘We are extremely pleased to have Eurographics UK conference. appended to the core framework. worked with undergraduate students who have been both keen and able The Group Design Practicals are ‘After positive feedback from industry to deliver this high level of quality a new element to the Computer visitors during the departmental work, and hope to see more of it in Science degrees, and give second- demonstration, we – in the Cyber future projects.’ year students the opportunity to work Security Group – encouraged the on a development project from a list students to submit their work as a of design briefs. The IBM prize for research paper to the Eurographics Best Group Project was awarded UK conference, a venue for graphics to Team Four for NetVis: a tool research,’ said Dr Jassim Happa, the assisting users to detect potential departmental mentor for the winning network attacks by visualising traffic team. ‘We assisted in the writing The members of the winning group captures in a variety of perspectives phases, helping the paper conform were: James Nicholls, Dominik that complement each other. The to conference guidelines and general Peters, Albert Slawinski, Thomas techniques implemented in NetVis paper-writing practices. The paper Spoor and Sergiu Vicol.

14 InSpired Research: Research news from the Department of Computer Science, University of Oxford The following have joined the Department in the last year (2013) [previous role and organisation in grey]: Dr Cas Cremers – University Lecturer in Computer Science (Software and Systems Security) [Senior Scientist: Institute of Information Security, ETH Zurich] Dr Dmitrii Pasechnik – Senior Research Fellow [Assistant Professor: Nanyang Technological University] Dr Edith Elkind – University Lecturer in Computer Science (Computational Game Theory) [Assistant Professor (NRF Fellow): Nanyang Technological University] Dr Egor Kostylev – Departmental Lecturer in Computer Science (Information Systems) [Research Fellow/Associate: The School of Informatics at the ] Dr Kasper Rasmussen – Departmental Lecturer in Computer Science [Visiting Assistant Project Scientist: University of California, Irvine] Professor Leslie Ann Goldberg – Professor of Computer Science [Professor: University of Liverpool] Livia Predoiu – Marie Curie Fellow [Computer International league Scientist: State Archive of Saxony Anhalt] Professor Luca Cardelli FRS – Royal Society Research Professor. [retains his position at Microsoft Research Cambridge] table success Professor Nando De Freitas – Professor of Computer Science [Professor: University of British Columbia] Computer science at Oxford has universities are in the global top 200 Professor Paul Goldberg – Professor of recently topped a number of for at least one subject. According to Computer Science [Professor: University of important international league tables. the BBC, overall, Cambridge was in Liverpool] the top 10 for 27 subjects, Oxford for Dr Stanislav Živný re-joined – Research Lecturer and Royal Society Research Fellow. The Academic Ranking of World 15 subjects, and Imperial for 10. [Senior Research Fellow in Advances in Universities named Oxford in August Discrete Mathematics: University of Warwick] as best in Europe (and best in the The Department’s academics have world outside North America) in made it into various top tables too. Staff who have changed role internally: the 2013 Computer Science league Both Ian Horrocks and Michael Dr Chris Heunen – Research Lecturer table. Up two places on last year’s Wooldridge currently rank in Microsoft Dr Evgeny Kharlamov – Senior Research Fellow position, Oxford was the only British Academic Search’s top ten authors Dr James Vicary – Senior Research Fellow university to appear in the top 20 in the field of artificial intelligence. Ian Dr Markus Krötzsch – Departmental Lecturer for Computer Science in this year’s Horrocks is also recognised as one Dr Stefan Kiefer – Research Lecturer and rankings. The Academic Ranking of the top authors in the World Wide Royal Society Research Fellow [all Research Assistants] of World Universities (ARWU) – Web research domain. Dr Andrew Markham – University Lecturer sometimes known as the Shanghai in Computer Science (Software Engineering). Rankings – is conducted by This year also sees an increased [EPSRC Postdoctoral Research Fellow] researchers at the Center for World- number of students starting with the Dr Blanca Rodriguez – University Lectureship Class Universities of Shanghai Jiao Department of Computer Science in Computational Medicine, and Wellcome Tong University (CWCU). on taught courses. In October, we Trust Senior Research Fellowship [Medical Research Council Career Development welcomed over 60 students across the Fellowship] In May, the QS World University three undergraduate computer science Dr Gary Mirams – Wellcome Trust / Royal Rankings placed Oxford third courses. In addition, over 60 new Society Henry Dale Fellowship [College globally, and top in Europe, for students started on the full-time MSc Lecturer] Computer Science & Information programme. In excess of 30 doctoral Dr Vojtĕch Forejt – University Lecturer in Systems, up from sixth place last students have begun their studies Computer Science (Software Engineering. year. The table, produced annually with us, alongside more than 15 [Researcher] by Quacquarelli Symonds (QS), is students in the newly opened Doctoral Academic staff appointed: based on a global survey of opinions Training Centre in Cyber Security. Professor Michael Wooldridge, Professor of academics and employers. More than 80 students have joined the of Computer Science as Deputy Head of Some 110 UK universities appear in part-time MSc software engineering Department. these subject rankings, which look programmes in the last year. Professor Jeremy Gibbons as interim Director at 30 disciplines. Of these, 65 UK of the Software Engineering Programme. www.cs.ox.ac.uk Issue 4, Winter 2013 15 when processed by Facebook. MAKING HEADLINES SecretBook also combines error correction (where the errors cannot be known in advanced) with avoiding Facebook photos: the the unalterable parts of the image (which are known in advance). The hidden photo message combination is achieved using a nested code, so that even if parts of Third year student Owen Campbell- Written in Javascript, Secretbook the data are corrupted, the message Moore made headlines around the utilises a technique known as JPEG is still decipherable. world last April with ‘Secretbook’, steganography to make many a research project creating an app visually imperceptible changes to The goal of Owen’s project was to allowing users to embed hidden encode the data. This technique isn’t demonstrate a proof of concept messages in Facebook images. new, but has always required that of performing steganography on a images are transmitted unaltered. social network, not to provide total Dr Andrew Ker had set the challenge: This is the first time software, security. Since the images contain a to develop a steganography which allows the JPEGs to be large number of changes, it would be app, which allows messages to recompressed without damaging the relatively straightforward to write an be securely sent and received secret contents, has been publicly algorithm to identify ones that have inside pictures, using Facebook; available. This solves the problem been manipulated. and to demonstrate that JPEG of social networks altering files steganography can be performed on when uploaded, which disrupts the Andrew commented: ‘Tools to social media where it has previously intricate arrangement of hidden data, maintain privacy are increasingly been impossible. Owen, under the and makes the message unreadable. important, given recent revelations guidance of Andrew, took up the about total surveillance of the internet gauntlet and produced a Chrome The message in Secretbook is hidden by government agencies… future Extension, ‘Secretbook’. in the digital makeup of the picture, research could allow longer messages not its pixels, so it’s comparable to to be hidden with higher security.’ Secretbook allows users to embed digital invisible ink. Owen replicated up to 140 characters of data into Facebook’s recompression algorithm, Owen’s research was in headlines any image, which is then transmitted so that whilst embedding the worldwide, including the Daily Mail, using Facebook. Any of the user’s message, the extension automatically The Times of India, NBC News, and friends provided with the pre-shared compresses the image. It therefore Wired. More about media coverage password can then decode the minimises the amount of change the and Secretbook’s creator is at: http:// message using the same extension. file, and the message, will undergo www.owencampbellmoore.com/.

The Unmasking Peter. She later ‘confessed’ that was President Barack Obama was ghost- of J K Rowling indeed the case. written by a former terrorist, Bill Ayers. Signature can be used to analyse More recently, Peter has been heavily Professor Peter Millican hit the ‘literary fingerprints’: word length involved in setting up Oxford’s new headlines in July when he helped and punctuation, sentence and undergraduate degree in Computer unmask JK Rowling’s secret paragraph length, frequency and Science and Philosophy. He has also identity as ‘debut’ crime writer patterns of usage of particular developed his ‘Turtle’ software to Robert Galbraith, author of The words and phrases, etc. It then encourage computer programming Cuckoo’s Calling. statistically processes and plots in schools and help make it the results of these analyses on more attractive to students in the A Sunday Times journalist the various texts, indicating how humanities. approached Peter with the far they are apart and whether they Further information is at: hypothesis, following a tip-off that ‘cluster’. Even very common words, www.philocomp.net. turned out to have originated from such as ‘the’, ‘to’, or ‘in’, can help Rowling’s lawyer. Peter used his reveal authorship, because patterns ‘Signature’ software to compare The amongst these, along with their Cuckoo’s Calling and other Rowling frequency, tend to be unconscious books against works of several well- to the author and often quite known crime writers. consistent between their texts.

‘The analysis corroborated quite Peter previously hit the headlines strongly the hypothesis that had in 2008 with Signature, when he been put to me that JK Rowling found that it was unlikely that the had written Cuckoo’s Calling,’ said autobiography of United States

16 InSpired Research: Research news from the Department of Computer Science, University of Oxford