InspiredResearch Winter 2015 Issue 7 News from the Department of Computer Science, University of Oxford Resistance is Futile New computational model helps find innovative ways to tackle antibiotic resistance in bacteria – p8

Let’s get physical: embedded systems Royal Society Fellowship to study security issues around the interface between the physical world and embedded systems – p4 Railworker safety: the TrackSafe project Developing magneto-inductive positioning to protect lives on the railways – p16

Organic ‘computers’ made of DNA Processing data inside our bodies – p18

CompSciOxford DepartmentOfComputerScienceUniversityOfOxford Inspired Research is a twice-yearly newsletter published Letter from the by the Department of Computer Science at the University of Oxford. Head of Department If you would like to learn more As I scan through the articles to appear in this edition of Inspired about anything you read in these Research, I find myself struggling with an embarrassment of riches. pages, please get in touch: [email protected] In this issue, you will read about how our research is helping to keep To subscribe to future issues, workers safe on railways, and how it helps to deal with the problem e-mail: [email protected] of bacterial resistance to antibiotics; you will read about how our To download previous issues, visit researchers are helping to build safer buildings, by embedding www.cs.ox.ac.uk/inspiredresearch sensors into structures to monitor them for bending or twisting; you will read about how our security researchers are helping governments to construct IT systems that are safe against malicious attacks, and Editorial board how social media can be managed to prevent digital wildfires… Suzanna Marsh (Editor) What I find remarkable about all this is, apart from the sheer diversity, Kiri Walden (Sub-Editor) how clearly it demonstrates the ever-increasing role that computing Suvarna Designs (Designer) plays in our lives. As these examples clearly show, Oxford remains at the heart of the ongoing digital revolution, and I have no doubt that Jeremy Gibbons we will continue to be surprised and delighted by the innovations of Shoshannah Holdom Oxford’s computer scientists. Peter Jeavons Thomas Lukasiewicz We have just welcomed a new cohort of undergraduates, eager to drink their fill at Oxford’s fountain of knowledge – or possibly at the Martha Lewis Kings Arms. Everyone who gains a place to study at Oxford does so Daniel Marsden against fierce competition, but this year’s intake of Computer Science Benjamin Neal undergraduates has a special distinction: the programmes on which Daniel Neville they will study are now amongst the most competitive and sought after in Oxford, and indeed in the UK. Jason Nurse Dima Pasechnik We now receive 10 applicants for every undergraduate place we Kelly Ryan are able to offer. Most applications we receive are very strong, Helena Webb and the upshot of this is that we end up having to turn away large Frances Wheare numbers of outstanding candidates, simply because we don’t have enough places to offer. I would dearly like us to be able to offer more Maureen York undergraduate places, and this means expanding the number of tutorial fellows in our colleges. Contributors There are very promising signs that more colleges are interested Katherine Fletcher in offering Computer Science, or expanding their student numbers Tim Furche in our subject. I am particularly pleased to be able to welcome David Gavaghan new tutorial fellows at St Catherine’s College (Shimon Whiteson), St Anne’s College (Alex Rogers), and Magdalen College (Rahul David Hobbs Santhanam). It has been many years since our department welcomed Laura Jones three new tutorial fellows in the same year – I very much hope that Marta Kwiatkowska we will welcome more new tutorial fellows in the years to come. Andrew Markham Ursula Martin We hope you enjoy reading this edition of Inspired Research. As ever, we’d be delighted Daniel Nichol to hear from you if there’s anything of Bill Roscoe particular interest that you’d like to explore Julie Sheppard further; do get in touch via Michael Wooldridge [email protected]

Professor Michael Wooldridge October 2015

2 Inspired Research: News from the Department of Computer Science, University of Oxford NEWS Not only are we rated highly by the News in brief academic community and industry, but by the student community too. Royal Society Research Professor, In University league tables produced Luca Cardelli has been awarded by The Guardian, for Computer the Programming Languages Science and Information Systems Achievement Award by ACM Oxford was awarded 100/100 for SIGPLAN. The award recognises student satisfaction and scored very individuals who have made a A league of our own well across all other categories. significant and lasting contribution In 2015 Oxford has been recognised to the field of programming as the best UK University for Oxford University is also the top languages. Computer Science. choice for anyone who wants to graduate and continue into a career Blanca Rodriguez and the The latest subject-specific tables in Computer Science or related Computational Cardiovascular produced by higher education data industries. Tech commentator Science Research Group have specialists QS rank Oxford as the website Business Insider has said been nominated for the Lush top University in Europe. In the Oxford is the best University in both Prize, for their work that supports Academic Reputation and Employer the UK and Europe to attend if you the replacement and reduction Reputation categories we surpass want a great job in tech. It identifies of animal testing. The Prize is a any other University in the world for investment from Google as just one collaboration between Lush, the Computer Science. reason for our success. well-known manufacturer and retailer of handmade cosmetics, of such models under different and Ethical Consumer, a research, Assessing models: experimental conditions: both to publishing and campaigning co- Web Lab characterise a model’s behaviours, operative. In September the department hosted and to compare hypotheses by the Cardiac Electrophysiology Web seeing how different models react Lab Workshop. The Web Lab (https:// under the same protocol. chaste.cs.ox.ac.uk/WebLab) is a https://goo.gl/AXjc1a new online system developed in the Computational Biology Group, that supports easy definition of simulated experimental protocols, and allows any heart cell model to be tested under these protocols. This enables examination of the behaviours

Fellowship develop techniques to analyse linear dynamical systems for the awarded for purposes of automated verification.

Dr Andrew Ker, a University verification of EPSRC Established Career Lecturer in the Department of linear dynamical Fellowships are awarded Computer Science, received an to academics who have an MPLS teaching award in June systems research outstanding track record of 2015. This followed Andrew ’s research, impact delivery, nomination for Most Acclaimed Professor James Worrell has been leadership and innovation. Lecturer in the 2015 Oxford awarded an EPSRC Established Fellowship holders at this level University Student Union (OUSU) Career Fellowship for a research are recognised internationally Teaching Awards. Professor project called Verification of Linear and are known for pushing the Andrew Martin, Director of the Dynamical Systems. Current boundaries of enquiry within their Centre for Doctoral Training in computer-aided design tools field. In addition to their strong Cyber Security, was the second allow engineers to create models academic profile, they show an member of the department and test them, but not to verify on-going commitment to inspire to receive a nomination, for them, ie, to conclusively prove and maximise the potential of future Outstanding Supervisor. that they meet their specification. research leaders. The goal of this project is to

www.cs.ox.ac.uk Issue 7 Winter 2015 3 Let’s get physical: embedded systems Kasper Rasmussen has been awarded the Royal Society University Research Fellowship (URF) for 2015. Kasper joined University of Oxford in 2013 as a Lecturer in the Computer Science Department. Before coming to Oxford Kasper completed his PhD at the Department of Computer Science at ETH Zurich, and then worked as a post-doc at University of California, Irvine. Below he discusses the background to his research.

The small computers that are The interfaces with embedded Initial experiments have shown automating more and more aspects systems that have most often that it is possible, indeed quite of our lives are collectively called been considered in the past are easy, to induce a current in the ‘embedded systems’ or sometimes radio interfaces, or components wires connecting a microphone cyber-physical systems. An that allow interaction with people, to an embedded system using embedded system consists of a eg buttons, keypads, etc. The an electromagnetic signal. This micro controller, ie a small chip interface that this project aims to means that such an embedded capable of performing calculations, explore is the interface between the system could be fooled into and some form of interaction with embedded system and the sensors believing that sound was present the physical world. Such systems and actuators that are attached to at the microphone, while in permeate every aspect of modern the system. fact the audio signal was being life: they are used in anything from induced using (inaudible) radio modern cars where embedded Any embedded system that wishes waves from (potentially) far away. systems manage braking, power to control or measure something, Due to that lack of authentication steering, engine performance, etc; must have a sensor or an actuator the micro controller has no way to factory control systems where attached as a peripheral element. of differentiating between a such systems control sensors and Sensors come in many different signal generated by the attached actuators as well as the flow of varieties but most are ‘dumb’ microphone and one induced diagnostic information. devices that convert the quantity by adversarial electromagnetic they are supposed to sense into interference (EMI). The fact that this A lot of research has been devoted an analog electrical signal that can be done from far away, only to how embedded systems can can be processed by a micro makes the problem more serious be made more robust against controller. As an example consider and potentially more damaging, deliberate attacks from an a microphone measuring sound. since an attacker can have a large adversary. This includes research A condenser microphone consists circle of influence. in different mobility and adversarial of a diaphragm which acts as one models, as well as secure plate of a capacitor (an electrical There has been surprisingly little communication and tamper-evident component consisting of two research on this topic so far. Some hardware, ie hardware that is parallel plates that never touch), work has been done in the area difficult to alter without leaving an and the sound vibrations affect this of electromagnetic interference, obvious trace. For many embedded diaphragm to produce changes in in the context of fault tolerance systems, wireless security is also the distance between the plates. and reliability. Notably, NASA has a crucial area; countless protocols The voltage maintained across the done several experiments on the have been proposed for use capacitor plates thus changes with behaviour of electronic circuits in between embedded systems, to the vibrations in the air. Given this outer space. This work is mainly solve everything from key exchange construction there is no way for the concerned with the impact of bit to routing. microphone itself to authenticate the flips (changing a 0 to a 1 or vice signal coming out of it. The signal versa), caused by cosmic radiation; There is one aspect of embedded is simply the result of a physical how to shield wires from radiation systems that has so far received process. This means that the micro and so on. very little attention, namely the controller has no choice but to interface between the physical consider whatever comes from the world and the embedded system. microphone as authentic. continued on next page

4 Inspired Research: News from the Department of Computer Science, University of Oxford from previous page Another application where arbitrarily thick shielding cannot easily be Shielding is certainly going applied is the aviation industry. to help reduce the impact of In aviation ‘fly-by-wire’ is seeing EMI, however no shielding more and more use in civilian method can completely block airliners. Fly-by-wire refers to an an electromagnetic signal. RF aircraft where the control surfaces (Radio Frequency) signals are only are moved, not by steel cables as attenuated by shielding and thus was the case in the past, but by it becomes a race between the electronic commands, sent through adversary who can buy bigger and wires to embedded devices located more powerful equipment, and the near the control surface. These defender who can put on a thicker, devices will then interpret the heavier, more durable shield. It is commands and move the control analog device. If an adversary can not feasible in all scenarios to just surface accordingly. Fly-by-wire inject signals into the electric motor increase the amount of shielding. enables much more fine grained (wires) directly, they will be able Consider for example the field control and easier integration of to influence the control surfaces. of implantable medical devices computerised flight control systems, Perhaps ultimately be able to (IMDs), where embedded systems such as auto pilots and auto landing control the plane remotely. are packaged in sealed containers systems, which in turn gives better and implanted into the human body flight characteristics. However, it These vulnerabilities do not only to control things like pacemakers, also means that the control surfaces apply to control surfaces of planes insulin pumps and so on. In IMDs of the plane are ultimately driven by but also to more subtle functions form factor and size, and to some electric motors. A plane’s internal in a wide variety of vehicles and degree weight, play a huge role in communication bus can employ other areas. For example fuel the functional characteristics of the shielding and digital signal coding injection in an engine is controlled device. It is not possible to simply to make sure interference cannot by a valve that is opened and add more lead shielding, even if inadvertently create unintended closed by a solenoid connected that is desirable from an EMI point commands, even if the interference to an embedded micro controller. of view. is malicious in nature. The same If the solenoid can be opened or cannot be said for the final analog closed directly, bypassing the micro interface between the controlling controller, an adversary would be device and the electric motor. able to stop or accelerate a running The embedded device receiving car. For similar reasons the brakes commands from the flight computer could be influenced by an adversary will ultimately translate those to either brake, or prevent braking commands into analog signals of a moving car. driving a stepper motor. The analog motor interface cannot be By focussing on the interface protected by the same encryption between the physical world and the and signal coding mechanisms as embedded system it is hoped that are used on the communication this research will improve security bus, because the motor is a ‘dumb’ across a range of different industries.

www.cs.ox.ac.uk Issue 7, Winter 2015 5 Computer Science granted Alan Turing Bronze Athena Swan Award Institute announces The department’s work in advancing But even in the 1950s – comfortably gender equality has been recognised within living memory – an initiative with an Athena SWAN Bronze like Athena Swan would have been Director departmental award. The award unimaginable. Since then, the recognises commitment and working environment for women In the summer of 2015, The success in developing practices to in science has surely improved University of Oxford became a support the careers of women in immeasurably. But this is not the end founding partner in the newly formed science, technology, engineering, of the story: there is still a lot more Alan Turing Institute, the UK’s maths and medicine (STEMM) in work to do, and we will see many national institute for data science. academia and research. more changes in the years to come. This is fantastic news, and testament This collaboration between EPSRC Professor Michael Wooldridge, Head to the incredible amount of work that (Engineering and Physical Sciences of Department commented ‘I’m went into the submission.’ Research Council), The British tremendously proud of this award, Library, Oxford University, Cambridge recognising our firm commitment An awards ceremony was held on University, University College London, to support women in Computer 15 June 2015 at the University of Warwick University and Edinburgh Science. The department is a recent Greenwich. The award was collected University will be headed up by development for Oxford University by Professor Marina Jirotka and Professor Andrew Blake, who will be – we trace our origins to the 1950s, Department Administrator Sharon the first Institute Director. Andrew is which is nothing when set against Lloyd on behalf of the department. currently a Microsoft Distinguished the university’s eight century history. Scientist and Laboratory Director of The University of Oxford was a Microsoft Research. founder member of the Athena Charter and has held an institutional The institute is headquartered at Bronze award since 2006. More The British Library, at the heart of information: ecu.ac.uk/equality- London’s knowledge quarter, and will charter-marks/athena-swan/ bring together leaders in advanced mathematics and Computer Science Computing in Cardiology (CinC) from the five founding universities News in brief Conference in Nice, France. and other partners. It marked its Aurore’s work is part of her DPhil first few days of operations with Professor Ursula Martin, Associate in computational medicine at the the confirmation of £10 million of Professor Edith Elkind and interface of Computer Science research funding from Lloyd’s Register Senior Research Fellow Dmitrii and medicine. It focuses on the Foundation, a research partnership Pasechnik are involved in an open analysis of the electrocardiogram with GCHQ, a collaboration with source software project to extend to identify potentially lethal Cray Inc. and EPSRC. The institute the capacity of computational abnormalities in cardiac function will commence research work this mathematics and interactive in patients with hypertrophic autumn. computing environments. cardiomyopathy using signal OpenDreamKit is a €7.6 million processing and machine learning The institute’s mission is to: undertake project funded by the European techniques. data science research at the Union’s Framework 2020 project, intersection of Computer Science, and brings together 15 academic mathematics, statistics and systems and industry partners from France, engineering; provide technically Germany, Norway, Poland, informed advice to policy makers on Switzerland and the United the wider implications of algorithms; Kingdom. The resulting code, enable researchers from industry together with associated data and and academia to work together to research publications, will be made undertake research with practical available as open source software. applications; and act as a magnet opendreamkit.org/ for leaders in academia and industry from around the world to engage Aurore Lyon [pictured right] with the UK in data science and its has been awarded the Young applications. Further information: Investigator Award at the 2015 turing.ac.uk/

6 Inspired Research: News from the Department of Computer Science, University of Oxford Rewiring News in brief The 12th International Workshop perceptions on Quantum Physics and Logic (QPL) took place at the – Creating a department in July 2015. QPL is a workshop that brings together researchers working generational on mathematical foundations of quantum physics, quantum gender shift computing, spatio-temporal causal structures, and related areas such as computational linguistics. The Computer Science is a subject ‘girls will be able to make informed prize for best student paper was notorious for harbouring decisions about careers in science, won by Oxford DPhil student Amar preconceived perceptions about technology, engineering and maths, Hadzihasanovic for his paper: ‘A those who study, and work in the so that eventually women can be diagrammatic axiomatisation of the sector. The department is taking a proportionally represented in the GHZ and W quantum states’. leading role among higher education field’. More information can be institutions to try and break down found at www.stemettes.org Professor Peter Millican spoke those perceptions. In April this at the Sunday Times Festival of year, Anne-Marie Imafidon [pictured Anne-Marie’s keynote lecture was Education in Berkshire in June. below] was invited to give a keynote just one in a diverse programme His session was titled ‘Coding address at the department’s annual of lectures and talks given at the and Computer Science in the Women in Computer Science event. Facebook led a session on Classroom (KS2-5)’ event. This full-day life as an Engineer at the company conference held at and many female members of the ACM A.M. Turing award winner the department saw department talked about their own Shafi Goldwasser gave the Oxford up to 60 secondary- areas of research, including game Women in Computer Science school students attend theory, quantum computing and Society (OxWoCS) Distinguished lectures given by cyber security. Speaker Lecture in April. She various speakers about spoke on ‘Modern Cryptography Computer Science. Women in Computer Science is in the Age of Cloud Computing’. among many other events that the Anne-Marie was accepted to read Department of Computer Science Pirates, philosophy, cyberwar for a degree in Mathematics and organises throughout the year to help and censorship – lots of inspiring Computer Science at Oxford when break down barriers and perceptions topics were covered in the she was just 15. After graduating held by young people about research showcase held at the with a Master’s at age 19, she went Computer Science, and the University Centre for Doctoral Training in on to set up STEMettes, with a of Oxford. Further information: Cyber Security on 1 October. vision of creating a world where www.cs.ox.ac.uk/opendays Media wall Our pick of the latest • Cyberspace Governance • Howard Bentham podcasts and vodcasts that – Sadie Creese – Ashutosh Natraj feature Computer Science ‘Cyberspace is the new nervous Ashutosh Natraj appeared research at Oxford. system for the world,’ says at BBC Oxford on Howarth Professor of Cyber Security Sadie Bentham’s morning talk show, • Oxford in your Day Creese, ‘We are all interdependent discussing UAVs (Unmanned Work from the University of and interconnected.’ The video Aerial Vehicles) safety, and how Oxford appears in your daily explores some of the challenges intelligent software can ensure life more than you might think... of governing and protecting this safe use of UAVs. http://goo.gl/ http://goo.gl/5PP1qL collective space. http://goo.gl/ fmM0Lg KPzdl4

www.cs.ox.ac.uk Issue 7 Winter 2015 7 Resistance is futile

A new computational model helps to find innovative ways to tackle the dangerous problem of antibiotic resistance in bacteria. Doctoral student Dan Nichol [pictured below] explains his research.

antibiotics; instead we must find which encodes the population new uses for existing drugs in dynamics of an evolving bacterial treating highly-resistant disease. population as a Markov chain, Daniel Nichol and Jacob Scott have Traditional medical wisdom is that built a tool capable of predicting to effectively treat infections we sequential adaptive therapies for should prescribe the most effective E. coli which reduce, and in many drugs, at the highest tolerable cases entirely prevent, the risk of dose, for as long as is needed highly resistant disease emerging. to clear the infection. However a new paradigm, known as adaptive To design these adaptive therapies therapy, which has emerged from it is first necessary to predict how mathematical modelling of the a population of bacteria will evolve. treatment of bacterial infections, Recently published empirical viruses and cancer suggests measures of the fitness landscapes Antibiotic-resistant strains of that this strategy may be driving of E. coli under fifteen different bacteria are currently causing resistance. antibiotics have made these an annual worldwide death toll predictions possible. A fitness totalling hundreds of thousands By considering disease from the landscape is a mapping which of lives. A recent report from the Darwinian perspective, where assigns to each possible bacterial Review of Antimicrobial Resistance, treatment imposes selective genotype an associated level of commissioned by the government, pressure and drives the evolution of resistance, or fitness, to a given suggests that this number could resistance, mathematical modelling drug. The landscape metaphor, reach 10 million by the year 2050. (coupled with biological experiments first introduced by Sewell Wright This rapid increase in the rate of and clinical observation) suggests in the 1930s, is a visualisation of antibiotic resistance has been that the optimal treatment strategy this mapping as a surface on which coupled with a drastic slowdown may be to prescribe multiple drugs, an evolving population ‘climbs’ in the discovery of novel antibiotic in sequence or in combination, to uphill. By considering the relevant compounds. It is becoming ever pre-empt or exploit evolution. bacterial genotypes as the vertices clearer that this crisis cannot be solved simply by discovering novel Using a simple computational model continued on next page

8 Inspired Research: News from the Department of Computer Science, University of Oxford from previous page of a weighted directed graph, By checking all possible sequences where the edge weights encode of two, three or four antibiotics for the probability of a change in the which empirical landscapes are population genotype, this ‘uphill known, the research reveals that climb’ in the fitness landscape can the majority, over 70%, of drug be reduced to a biased random sequences increase the likelihood walk on a graph. By encoding this of resistance emerging to the final random walk formally as a Markov drug (when compared to giving that chain, the complex process of drug alone). evolution within a population of bacteria exposed to an antibiotic In particular, giving is reduced to a single matrix Piperacillin+Tazobactam, an multiplication. The immediate antibiotic often used after others consequence of this model is fail, as the final drug in a sequence that, as matrix multiplication is of two or three antibiotics increases non-commutative, the order in the likelihood of resistance arising which drugs are given will have a in over 90% of cases. By giving significant impact on the final state drugs in arbitrary orders we may after evolution. This observation be inadvertently encouraging the leads to a natural question: are emergence of antibiotic resistance some orderings better than others? just as giving drugs with incorrect doses can do so. In their work, published this month in PLOS Computational Biology, Daniel To move their theoretical findings and Jacob show that the answer is towards the clinic, Daniel and ‘yes’. Using the recently published Jacob have partnered with landscapes for E. coli, the research microbiologists at the Louis Stokes demonstrates that it is possible Department of Veterans Affairs http://goo.gl/WcdxmC to prime the disease population Hospital in Cleveland to perform using sequences of one to three empirical tests of evolutionary antibiotics such that resistance to a steering. They are also working Project contributors: final antibiotic cannot emerge. This with Dr Alexander Anderson and Daniel Nichol – 1 & 5 finding suggests a new treatment Dr Robert Gatenby at the Moffitt Peter Jeavons – 1 strategy in fighting antibiotic Cancer Research Center, to adapt Alexander G. Fletcher – 2 disease: adaptive therapies which their model to predicting the Robert A. Bonomo – 3 use sequences of drugs to steer, effectiveness of cancer therapies. Philip K. Maini – 2 in an evolutionary sense, a disease Jerome L. Paul – 4 population to a configuration from A major impediment to designing Robert A. Gatenby – 5 which it is both readily treatable adaptive therapies using their Alexander R.A. Anderson – 5 but also from which resistance method is that measuring fitness Jacob G. Scott – 2 & 5 cannot emerge. landscapes is a complex problem Eric Haura – 5 where the number of strains that Chris Bryant – 6 As well as demonstrating the need to be synthesised grows possibility of adaptive, sequential exponentially with the number 1 – Department of Computer therapy for treating highly-resistant of mutations of interest. Despite Science, University of Oxford bacterial infections, Daniel and this difficulty, empirical fitness 2 – Wolfson Centre for Mathematical Jacob also provide a cautionary landscape research, aided by Biology, Mathematical Institute, warning regarding current clinical machine learning techniques which University of Oxford practice. When antibiotics are help to reduce the number of 3 – Department of Medicine, Louis prescribed in sequence, as is strains that need to be synthesised, Stokes Department of Veterans often the case in treatment of H has grown rapidly in recent Affairs Hospital, Cleveland, USA 4 – School of Computing Sciences pylori, Hepatitis B or the transition years. As this trend continues the and Informatics, University of from broad to narrow spectrum potential for therapies exploiting Cincinnati, Cincinnati, USA antibiotics, no guidelines presently evolutionary steering, and with it 5 – Department of Integrated exist to specify the order in which the role of computational models in Mathematical Oncology, drugs should be given. Instead this designing treatment, will continue H. Lee Moffitt Cancer Center and decision is left to the clinician’s to grow - hopefully enabling better Research Institute, Tampa, USA personal preference. treatment for a variety of deadly 6 – Department of Medicine, Case diseases in the future. Western Reserve University, USA.

www.cs.ox.ac.uk Issue 7 Winter 2015 9 OxCEPT spin- out finalist at the Mobile Innovations Awards

Oxford spin-out OxCEPT, the technology company behind the development of one of the world’s most secure protocols for transmitting data, has reached the finals in the ‘Best Management of Mobile Security’ category of the Mobile Innovations Awards.

OxCEPT is focused on the Perfecting the folds: improving development and commercialisation of authentication security techniques in DNA Origami technologies and products. The A group of researchers from the However, while DNA origami is spinout developed Scrambl, a Departments of Physics and a reliable technique for simple smartphone communications app Computer Science at Oxford have structures, it begins to fail when designed to keep its users safe from published a paper in Nature about applied to more complicated hackers and thieves. It is based on their investigation into how DNA structures. Current research is the proprietary HCBK authentication origami folds. Computer Science devoted to designing a system protocol originally invented to protect DPhil student Frits Dannenberg, so we can better understand the military communications of the who is supervised by Professors the mechanism that makes UK Department of Defence. Marta Kwiatkowska and Andrew DNA origami fold in the way Turberfield, developed the folding that it does. The paper reports Bill Roscoe, Professor of Computing model that was successfully used on findings that demonstrate and OxCept Director of IP, said ‘It’s to predict the outcome of their the existence of efficient folding wonderful that our new user-centred experiments. pathways – analogous to the model of security has caught the folding landscape of proteins. imagination of the panel like this. I Nearly ten years ago, researchers am looking forward to the imminent first described a technique to fold Read more on the University’s release of Scrambl and its take-up by a long single strand of DNA into Science Blog: www.ox.ac.uk/ a number of organisations that have various two- and three-dimensional news/science-blog/origami- agreed to use it’. shapes. DNA origami has the life The full report can be read potential to be developed as the in Nature and is co-authored Annich McIntosh, Director of the basis for designing and mass- by Katherine Dunn, Jon Bath, Awards said ‘This year there was producing nano-sized objects that Andrew Turberfield, Tom a 100% increase in entries, which can interact with molecules and Ouldridge, Frits Dannenberg and demonstrates the level of creativity human cells. Such objects would Marta Kwiatkowska. and ingenuity transforming the way have many important medical we lead our mobile lives.’ applications. http://goo.gl/qfXlWq Further Information: www.oxcept.com © Jonathan Bath and K. Dunn

10 Inspired Research: News from the Department of Computer Science, University of Oxford Digital Wildfires

(Mis)information flows, propagation scientists from the Universities of map” that will assist stakeholders and responsible governance are Oxford, Warwick, Cardiff and De to navigate through current policy the key themes of new research Montfort are analysing social media and make informed decisions about around social media, being datasets to assess how digital appropriate behaviours on social conducted by Professor Marina wildfires emerge and unfold. They are media. We will also develop materials Jirotka and Dr Helena Webb. identifying forms of ‘self-governance’ that aim to promote digital maturity through which social media users amongst potentially vulnerable social Social media platforms such as manage their own and others’ online media users, such as children and Facebook, Instagram, Snapchat behaviours and will examine how teenagers. We are holding a range of and Twitter are a popular feature of these practices may be consolidated project events, including a one-day modern life which enable users to to limit the damage caused by digital workshop in London in January 2016. share content with others around the wildfires. They are also identifying We will present some of our project world. The increasing popularity of and drawing on the perspectives of findings and invite other researchers social media brings many benefits but social media companies, legislators, to discuss their work on social media, also risks such as ‘digital wildfires’ in the police, civil liberties groups, provocative content and responsible which provocative content spreads anti-harassment organisations, and governance.’ The workshop will also rapidly and can cause serious harm. educators. Through these activities include a youth panel in which young This provocative content may take the the researchers will explore potential people will discuss their concerns form of a rumour, false information, regulatory tools and mechanisms on about social media and Baroness hate speech, or a malicious campaign social media. Beeban Kidron, founder of the iRights against others. When it spreads campaign for young people, will rapidly it can damage the reputation It is anticipated that the project will deliver a keynote address. and well-being of individuals, groups advance the responsible governance or entire communities. The prevalence of social media in relation to the Further information: www. of digital wildfires in modern life has risks of digital wildfires. Research digitalwildfire.org, contact helena. led to questions over the appropriate Associate Helena Webb explains: [email protected] or on Twitter @ regulation of social media. Should ‘We will produce an “ethical security EthicsWildfire. the police and legal system take more interest in what is posted on social media or should social media This research complements the work of Dr Jason Nurse, a Research companies do more to limit the Associate within the department’s Cyber Security group, who has spread of provocative content? What should individuals do to ensure they focused on innovative ways to use social media for good. Amongst post responsibly? What about rights other things, his work has involved the creation of novel tools to to freedom of speech? assist users in assessing the confidence they should place in social media content when making decisions, and also the development of The Digital Wildfires project seeks systems to extract real value from hundreds of thousands of social to address some of these important media posts, to support activities such as tourists planning holiday questions. A collaborative group of computer scientists and social trips or companies gathering market intelligence.

www.cs.ox.ac.uk Issue 7 Winter 2015 11 ALUMNI ROUND-UP

A letter from… the Development and Alumni From AI to Manager Snowden: Alumni Weekend 2015 The long vacation has whizzed by here in Oxford, and we find ourselves once again at the start of a new academic year. In the spirit This year, the Department of of new beginnings, I’m delighted to let you know that we have recently Computer Science was involved in relaunched the Department of Computer Science Alumni Network three events during the 2015 Meeting website. The new website allows you to update your personal details, Minds: Alumni Weekend in Oxford. interests and communications preferences, as well as featuring news from the department, forthcoming events, and more. We will be writing We started at the Saïd Business to you all with information about how to log into the new website, so School, the main venue for the do check your emails. weekend’s events, where Head of Department Michael Wooldridge We hope that you like the new website and welcome your comments joined Professors Nando de Freitas on how we might improve it in future. and Stephen Pulman in a panel discussion chaired by Dr Cecilia Alumni Weekend Events Tilli, Academic Project Manager at It was lovely to see so many of you at the recent Alumni Weekend. the Future of Humanity Institute. Computer Science was well represented across the weekend ‘The quest for artificial intelligence’ considered recent advances in programme, with members of the department participating in ae lively panel discussion on Artificial Intelligence and the Softwar machine learning and assessed the Engineering Programme’s annual lecture, delivered by Alan Rusbridger. ethical, philosophical and practical consequences of such technological advancement, provoking lively Survey discussion from members of Thank you to all those of you who responded to our recent survey. the audience. The results made for extremely interesting reading and we look forward to working more closely with all those of you who were Over at the Robert Hooke Building, keen to become more involved. As ever, if you have any thoughts, Software Engineering Programme comments or suggestions, please do email [email protected]. and Computer Science alumni caught up with members of the Changes to the Alumni Office department over tea and cakes. Finally, I wanted to let you know that after a fantastic 18 months, I will be leaving the Department of Computer Science to take up Shortly afterwards, guests arrived a new role within the university. I will take this opportunity to say at the Museum of Natural History how much I’ve enjoyed getting to know you over the past year and for the Software Engineering a half, and to thank you all for your support in getting the alumni Programme Annual Lecture, given network up and running. by Alan Rusbridger, former Editor- in-Chief of The Guardian and The department remains committed to developing and growing its incoming Principal of Lady Margaret alumni activities and we have a number of exciting plans that will Hall. Entitled ‘The 21st century be announced over the coming months. So surveillance state: implications of the do keep in touch – follow us on Twitter, like Snowden revelations’, the lecture us on Facebook, and register with our new covered privacy, security, press website so that we can keep you up to date freedom and public interest, and with our plans. ended with a simple call to action: ‘My appeal is to try and get software engineers to help inform this debate. Frances Wheare, There are an immense number of Development and complex and interrelated issues and Alumni Manager we need to find a way of talking about them.’

12 Inspired Research: News from the Department of Computer Science, University of Oxford Alumni Profile Dr Pia-Ramona Wojtinnek (Somerville, 2008) Dr Pia-Ramona Wojtinnek joined the University of Oxford from Bonn University and the University of Cologne in Germany, with a background in Medieval German Language and Literature as well as Mathematics and Computer Science. Here, she talks about her experience as a DPhil student in Oxford. She currently works for investment management company GSA Capital as Senior Strategist.

Before starting your DPhil in a different balance between social life go. My advice would be not to get too Computer Science, you studied within and outside of the university. stressed, and to follow the questions languages and linguistics. What that sound interesting. To get some attracted you to Computer What did you enjoy most about ideas for jobs outside of academia, Science, and was it a difficult your time at Oxford? job fairs can be helpful such as the transition to make? I really enjoyed my time at the one organised by the department I read for both Mathematics with Department of Computer Science, or the startup-focused Silicon Computer Science (at the University because there was a very friendly Milkroundabout in London, as well as of Cologne) and Medieval German atmosphere amongst students, talking to people. Language and Literature (at Bonn academics and other staff. University) during my undergraduate The academics were always News in brief studies and then proceeded to a approachable, which makes for Master’s in General Linguistics. a welcoming study and research This year, the University of Oxford Doing a DPhil in Computer Science, environment. I also rowed for marks the 200th anniversary of in particular in Computational Somerville and was part of the Oxford Ada Lovelace with a series of Linguistics, allowed me to work on University Salsa Team, which were events celebrating her life and the intersection of these fields. When I both great experiences. work. As part of this series, the started my DPhil, I needed to expand Department of Computer Science my programming skills, but I found the How do you think doing a DPhil will hold the inaugural Lovelace fact that I had a background in both has helped you? Lecture, the first in an annual series fields to be very valuable. The DPhil showed me that I enjoyed of lectures to be delivered by an doing applied research and coding up eminent female computer scientist. What made you decide to focus large projects. I wanted to continue The first lecture will be given by on Computer Science? working quantitatively, while learning Professor Barbara Liskov, Ford I was attracted to Computer Science something completely new and Professor of Engineering at MIT as a general field because of its seeing a very direct impact of my and winner of the 2008 ACM A.M. applicability to a variety of areas: research. Quant trading was a great Turing Award for Computing. The during my time as an undergraduate choice as it allowed me to apply lecture is generously supported I did research on applying graph some of the techniques I knew to by Facebook. Alumni welcome. theory to sociopolitical networks, a very different field. At the same For further information on all Ada my DPhil concerned computational time, there is a growing interest Lovelace events and details on how representation of lexical semantics, in exploiting textual news and to book, visit: blogs.bodleian.ox.ac. now I work in quantitative trading sentiment for trading so there is a lot uk/adalovelace/events/ of equities. of scope for using my background in Computational Linguistics. A symposium, celebrating Ada How did student life in Oxford Lovelace’s 200th birthday is compare to your time at the What advice would you give to being held on 10 December university in Germany? someone who’s unsure about 2015 in Oxford. It is aimed at Oxford has a campus-like feel to where their degree might take those interested in the history it, with the university forming an them? and culture of mathematics and Computer Science, presenting essential part of the city and the Computer Science is a very versatile current scholarship on Lovelace’s college providing a particular social degree, so there are a lot of directions life and work, and linking her structure for the students. Student you can go into afterwards. The ideas to contemporary thinking life at Cologne and Bonn, both large question of what comes next can be about computing and artificial city universities was more loosely daunting and often the reality is that intelligence. blogs.bodleian.ox.ac. organised, such as being connected you don’t know whether something uk/adalovelace/symposium/ through tutorial groups, so there was is right for you until you just give it a

www.cs.ox.ac.uk Issue 7 Winter 2015 13 Cyber Security update Cyber Security Technical Papers available During their first year, Centre for number of objects become linked Doctoral Training (CDT) students via networks. As we enter into a Early-careers embark upon their own research new technological age and as digital projects that deal with the real- networking has become integral researchers world issues and implications of to our daily lives the security of cyber security, as well as theories these networks is paramount and symposium for and foundations, exploring the topic we expect our CDT students to cyber security for the long term. These projects be at the forefront of providing promise to provide a fascinating and researching the solutions to research in Oxford look into how cyber security affects problems seen today and anticipated our everyday lives and where its tomorrow. On 30 September the inaugural weaknesses and strengths lie. The Early-Careers Researchers research areas covered range from The CDT’s Technical Paper series Symposium for cyber security the domestic application of cyber allows our students to disseminate research was held in Oxford. security in the household to the their work via the Oxford Research Organised by the Cyber national and multinational level. For Archive to a wide audience, Security Oxford network, the example, recently students have demonstrating the high quality multidisciplinary event drew been exploring how on a national research being undertaken. together researchers and doctoral level we deal with a cyber-crisis and students working in the field comparing this with other EU states. For more information on our from across the university. The Other students have been looking students’ research, please see diverse range of talks making up into the security implications of www.cybersecurity.ox.ac.uk/ the day included ‘The evolution cyber-physical systems such as air techincal-papers of computer misuse legislation’, traffic control. ‘Exposing insider threats using eye movement biometrics’ and All of the research projects aim ‘States’ use of proxies in the to both provide insights into the cyber domain’. The event was strengths and shortcomings of cyber hosted by the Computer Science security in the current day, and also Department with support from what needs to happen in the future Ocado Technology. to remain secure as an increasing

and set priorities for capacity from the Dutch Government to Uganda & Kosovo: development. enhance the online Cybersecurity going global with Capacity Portal, which lead to the The last few months have been appointment of Carolin Weisser as cyber security extremely busy, with research teams a new portal manager. The centre visiting a wide range of countries to continues to attract international capacity development apply the model, most recently to recognition and was pleased to be Uganda, with further assessments awarded additional funding from the The Global Cyber Security Capacity taking place shortly in the UK and Norwegian Government. Two new Centre (GCSCC) is a leading in Indonesia (in cooperation with researchers, Lilly Muller and Eva international centre for research on the Oxford Internet Institute). June Ignatuschtschenko, joined the team effective security capacity-building. saw the successful launch of the in September. It has created a new kind of model first assessment report in Kosovo, in to measure cyber security capacity collaboration with the World Bank. Further information: www. maturity, which aims to enable oxfordmartin.ox.ac.uk/ nations to self-assess, benchmark, The centre attended the Global cybersecurity/ www.sbs.ox.ac.uk/ better plan investments and Conference on CyberSpace 2015 cybersecurity-capacity national cyber security strategies, in the Hague. It secured funding

14 Inspired Research: News from the Department of Computer Science, University of Oxford News in brief

Jassim Happa has been invited to give a course in cyber security, on the topic of cyber situational awareness at the Centro de Investigación en Computación del Instituto Politécnico Nacional in Mexico City, in November.

DPhil student Ines Marusic won an Anita Borg Memorial scholarship. The Scholarship is given annually by Google to encourage women to excel in computing and technology at university, and encourages network authorisation or rejection women to become active role London for potentially suspicious models and leaders within transactions, particularly focused their field. on supporting the elderly or vulnerable people who aren’t DPhil student Elizabeth CyberHack tech-savvy or smart phone users. Phillips received a student travel grant to attend the We asked Linda Geaves about IEEE Symposium on Security success her experience participating in and Privacy (S&P) and the the Hackathon: ‘The Hackathon Women in Cybersecurity was a great experience, especially Oxford students won (WiCyS) conferences. She working in collaboration with the will also attend a two-week two of the four available guys from CS, of whom I cannot summer exchange with the prizes at the London speak highly enough. US Embassy for Future Cyber Leaders. CyberHack for Financial I saw the Hackathon publicised Security, organised in on the Oxford Entrepreneurs Elizabeth Phillips also won a July by The Accelerator Network, and, having taught scholarship to attend the 2015 Network, NatWest, and the myself to code for over a decade Grace Hopper Celebration, and then worked alone on a Department for Business, along with fellow DPhil student Computer Science based DPhil Ines Marusic. Grace Hopper is Innovation and Skills (BIS). project in Oxford’s Environmental the largest gathering of women Change Institute, I really wanted technologists, organised by The challenge was to help to get some idea of where my the Anita Borg Institute and NatWest better identify and skills were in comparison to other the ACM (the Association for authenticate their customers, computer scientists. Computing Machinery). providing a seamless experience without compromising security So, taking part in the Hackathon, – and ideally improving it. The having such a great, welcoming Oxford team, made up of Katriel and open-minded team, and then Cohn-Gordon, Max Whitby winning has meant an awful lot and Martin Dehnel-Wild from to me, as I know all the years the Department of Computer I’ve put in to learning bits and Science, and Linda Geaves from bobs in Computer Science hasn’t the School of Geography and been in vain! Plus, it was great the Environment, won both ‘Best to combine the theories and Design and User Experience’ issues learned in geography to and ‘The NatWest Challenge’ those in cyber security, as there categories, scooping £2,000 in are many overlapping subjects, prize money. Their project, based and, I believe, many areas for on developing friend-based collaboration.’

www.cs.ox.ac.uk Issue 7 Winter 2015 15 Increasing railworker safety: the TrackSafe project

Developing magneto-inductive positioning to protect lives on the railways

be used in any trackside environment and is robust and reliable. Restricted areas (geofences) can be created by the site controller, which alert both workers and controllers if they stray into dangerous areas. These areas dynamically change as a train approaches, guiding workers to a pre-designated place of safety.

Magneto-inductive positioning is an innovative, patent-pending approach to determining the location of moving people and objects by sensing the changes in the magnetic vector Every day, over 70,000 workers the workers 45 seconds to clear the field generated by a transmitter. access railway lines across the UK to track. As such, they only had three Modulated magnetic fields penetrate maintain, repair and construct tracks seconds to clear the track as the train most materials without loss. Ferrous and equipment. Working alongside came around a bend. materials however do distort the railway lines is extremely dangerous magnetic fields and one of the major and strict safety regulations, are in This incident highlights the need challenges of this work is to maintain place to reduce the frequency of for an automated trackside safety accurate positioning even in the accidents. Despite these regulations system - the key factor is the ability vicinity of large metallic objects such in the UK alone four workers were to know, in real-time, the location of as rail-lines and trains. killed in the last three years from every track worker and whether or being struck by trains, with many not they are in a danger (‘red’) zone. This proposal aims to significantly more injured. This is particularly However, track workers often operate reduce the risk and danger faced by relevant for workers close to in environments where conventional track workers everyday, by providing operational lines (known as red- positioning techniques like GPS fail, an automated system that warns zones), where trains can approach such as within tunnels, under bridges of hazards and oncoming trains. It at over 100mph, giving very little or next to embankments. also seeks to improve efficiency, by warning of arrival. As trains become providing seamless location capability automated (driverless) the need for TrackSafe is a £1m Innovate UK underground and outdoors. As such it a technology-driven safety system funded project between a leading has immediate impact on the lives of becomes more and more critical. navigation company, Guidance workers, drivers and rail companies, Automation, and the University of by potentially reducing the number Safe working practice is frequently Oxford to address the need for safe of fatalities and injuries. Key is the complicated by dark and confined trackside working. The research ability to position and communicate operating conditions and the use component is led by Dr Andrew with workers who can be working of noisy equipment. As a particular Markham and Professor Niki Trigoni in dangerous areas such as within example of a near miss, in May 2014 and revolves around the use of low tunnels and under bridges. As there a train travelling at 100mph almost frequency magneto-inductive fields is simply no other system that can struck nine track workers. A lookout for positioning through obstacles operate through-the-earth, it is likely positioned two miles up the track such as tunnels, soil and concrete. that this work will have significant failed to give a warning over the The aim of the project is to develop a impact not only in the UK, but radio system that would have given GPS-like positioning system that can globally as well.

16 Inspired Research: News from the Department of Computer Science, University of Oxford Distortions of magnetic fields caused by reinforced steel bars (circles) within a concrete structure. These deviations degrade positioning accuracy.

mi6sense: Smart sensors for smarter structures

Catastrophic failure of large civil measured. The time-consuming extend to form a larger, merged structures like bridges, dams, and costly installation of fibre-optic communication system. embankments and buildings can sensors within foundations and result in human fatalities as well as surrounding soil/rock limits their use The sensors can measure their other costly and environmentally to high risk projects. precise position and orientation detrimental consequences. Structural within the structure and how this collapse during construction poses mi6sense is an ambitious two-year changes over time. With a number a high risk to people working on project led by Dr Andrew Markham of these sensors the actual shape of construction sites and failures and postdoc Dr Orfeas Kypris. the structural element and how it is can also occur in the surrounding This was one of only four projects bending or twisting with loads can groundwork, for example landslides funded across the UK by EPSRC be sensed. A key advantage of low and subsidence (sinkholes). There in the Civil Engineering Big Pitch frequency magnetic vector fields is is a strong need for a sensing challenge, targeting blue-sky ideas. that they have both magnitude and technology that is able to measure This project seeks to develop a low- direction in 3-D. This is currently the performance of a structure cost, wireless, embeddable sensing impossible to achieve using any over its entire lifetime, as well as technology (small enough to add to other distributed sensing technology. its associated foundations and the the concrete mix or be injected into surrounding soil and rock supporting rock) that can measure structural The mi6sense project has the the structure. This will help to provide deformations in 3-D from deep within potential to make buildings and large early warning of impending failure, a structure, its foundations and structures truly smart, using low which apart from saving lives will surrounding groundwork. Not only cost, easy to deploy sensors that inform repair operations and optimise can each sensor measure changes can operate from within the structure building methods. in its position, it can also measure and the surrounding groundwork. changes in orientation, yielding a full Real-time monitoring of key The current gold-standard for six degrees of freedom sensor. indicators of potential failure over the monitoring structural stress and lifetime of the structure will provide failure are distributed fibre-optic When mixed into the concrete pour early warning of impending disaster, sensors. These use the change in the these cm-scale, low cost sensors with potentially life-saving results. properties of a thin fibre-optic cable instantly form a self-organizing and to measure aspects such as strain. healing communication network. Further information: mi6sense.org However, because fibre-optic sensors These devices start monitoring from are essentially wired into the structure the moment the element (eg a pillar they require deployment effort and or a beam) is poured, providing View of MI provide a point of ingress, weakening information over the entire lifetime sensors (spheres) obtaining 3-D the integrity of the structure. More of a particular structural element, measurements importantly though, fibre-optic from the concrete curing process of position and sensors can only measure strain to loading, to monitoring cracks orientation along the fibre axis, meaning that the and corrosion. When structural from within a reinforced three-dimensional shape deformation elements are placed next to each concrete beam of the structure cannot be directly other, the network will automatically

www.cs.ox.ac.uk Issue 7 Winter 2015 17 Organic ‘computers’ made of DNA could process data inside our bodies

We invariably imagine electronic Boolean logic, arithmetical formulas, arranged into logical decision trees devices to be made from silicon and neural network computation. on a DNA tile, with enzymes used to chips, with which computers store Called molecular programming, this control the decision branching along and process information as binary approach applies concepts and the tree, causing the walker to take digits (zeros and ones) represented designs customary to computing to one track or another. by tiny electrical charges. But it nano-scale approaches appropriate need not be this way: among the for working with DNA. DNA walkers can also carry molecular alternatives to silicon are organic cargo, and so could be used to mediums such as DNA. In this sense ‘programming’ is really deliver drugs inside the body. biochemistry. The ‘programs’ created DNA computing was first are in fact methods of selecting Why DNA computing? demonstrated in 1994 by Leonard molecules that interact in a way that DNA molecules many appealing Adleman, who encoded and solved achieves a specific result through the features include their size (2nm the travelling salesman problem, process of DNA self-assembly, where width), programmability and high a maths problem to find the most disordered collections of molecules storage capacity – much greater efficient route for a salesman to take will spontaneously interact to form than their silicon counterparts. DNA between hypothetical cities, entirely the desired arrangement of strands is also versatile, cheap and easy in DNA. of DNA. to synthesise, and computing with DNA requires much less energy than Deoxyribonucleaic acid, DNA, can DNA ‘robots’ electric powered silicon processors. store vast amounts of information DNA can also be used to control DNA’s drawback is speed: it encoded as sequences of the motion, allowing for DNA-based currently takes several hours to molecules, known as nucleotides, nano-mechanical devices. This compute the square root of a cytosine (C), guanine (G), was first achieved by Bernard four digit number, something that adenine (A), or thymine (T). The Yurke and colleagues in 2000, who a conventional computer could complexity and enormous variance created from DNA strands a pair of compute in a fraction of a second. of different species’ genetic tweezers that opened and pinched. Another drawback is that DNA codes demonstrates how much Later experiments such as those by circuits are single-use, and need information can be stored within Shelley Wickham and colleagues in to be recreated to run the same DNA encoded using CGAT, and 2011 and at Andrew Turberfield’s computation again. this capacity can be put to use in lab at Oxford demonstrated nano- computing. DNA molecules can molecular walking machines made Perhaps the greatest advantage of be used to process information, entirely from DNA that could DNA over electronic circuits is that using a bonding process between traverse set routes. it can interact with its biochemical DNA pairs known as hybridisation. environment. Computing with This takes single strands of DNA One possible application is that molecules involves recognising as input and produces subsequent such a nano-robot DNA walker the presence or absence of certain strands of DNA through could progress along tracks making molecules, and so a natural transformation as output. decisions and signal when reaching application of DNA computing is to the end of the track, indicating bring such programmability into the Since Adleman’s experiment, computation has finished. Just as realm of environmental biosensing, many DNA-based ‘circuits’ have electronic circuits are printed onto or delivering medicines and therapies been proposed that implement circuit boards, DNA molecules inside living organisms. computational methods such as could be used to print similar tracks continued on next page

18 Inspired Research: News from the Department of Computer Science, University of Oxford News in brief

Following a visual-refresh the new Department of Computer Science website went live in October 2015. The URL remains www.cs.ox.ac.uk

It’s a proud moment when one of your colleagues receives a cheque for 1 hexadecimal dollar! Computer Science Tutor Mike Spivey spotted an error in Knuth’s Concrete Mathematics.

Computer Science and Philosophy undergraduate Nick D’Aloisio was named as number 3 in the FT’s ‘Top 10 European Tech Entrepreneurs under 30’. Before coming to Oxford, Nick founded Summly, an app that algorithmically summarises the news for the smartphone generation, which was bought by Yahoo! from previous page great speed, delivering point-of-care diagnostics and proof-of-concept Undergraduate Computer DNA programs have already been smart drugs – those that can make Science and Philosophy put to medical uses, such as diagnostic decisions about the type student Miraan Tabrez has diagnosing tuberculosis. Another of therapy to deliver. been hitting the headlines proposed use is a nano-biological with his app Tripr. He and two ‘program’ by Ehud Shapiro of the There are many challenges, of other Oxford students have Weizmann Institute of Science in course, that need to be addressed developed a tool that connects Israel, termed the “doctor in the so that the technology can move people travelling to the same cell” that targets cancer molecules. forward from the proof-of-concept place at the same time. Other DNA programs for medical to real smart drugs: the reliability of applications target lymphocytes (a the DNA walkers, the robustness of Oxford’s Lambros Petrou type of white blood cell), which are DNA self-assembly, and improving was in a team of three MSc defined by the presence or absence drug delivery. But a century of students who reached the final of certain cell markers and so can traditional Computer Science of the ACM SIGMOD 2015 be naturally detected with true/ research is well placed to contribute programming contest. This false Boolean logic. However, more to developing DNA computing year’s challenge was to build effort is required before we can through new programming a system to efficiently support inject smart drugs directly into living languages, abstractions, and formal thousands of queries over a organisms. verification techniques – techniques relational database under heavy that have already revolutionised transactional updates. Future of DNA computing silicon circuit design, and can help Taken broadly, DNA computation launch organic computing down the Thinking about applying for has enormous future potential. same path. one of our full-time graduate Its huge storage capacity, low courses? Please visit the energy cost, ease of manufacturing Department of Computer that exploits the power of self- Marta Kwiatkowska is Professor Science on 31 October 2015 for assembly and its easy affinity with of Computing Systems at the the Graduate Open Day, where the natural world are an entry to University of Oxford. This article you can find out more about nanoscale computing, possibly was originally published in The DPhils, the full-time MSc, or through designs that incorporate Conversation. Read the original studying at one of our Centres both molecular and electronic article at http://goo.gl/YcWeSS It is for Doctoral Training. components. Since its inception, republished here under a creative http://goo.gl/4LYN2d the technology has progressed at commons licence.

www.cs.ox.ac.uk Issue 7 Winter 2015 19 established in the late 1990s) open Computer to all students and staff within the department and associated Centres for Doctoral Training. Science The Conference is organised by students for students. Academic Student staff are also involved, either giving the keynote speech or helping to Conference judge the talks and posters. 2015 Congratulations go to six DPhil students who won awards. The This year the Computer Science standard of the presentations was Student Conference took place on so high that it was impossible to trustworthy remote entity’ and to 12 June and included an impressive pick an overall winner and so there Daniel Nichol. You can read more 11 talks and 10 posters, with were two winners in each of the about Daniel’s research on antibiotic representation from a variety of three categories. Prizes for the best resistance on pages 8 and 9 of research groups. The conference talks were given to Andrew Paverd this edition of Inspired Research. is an annual event (originally for his work on ‘Applications of a Prizes for the best posters were given to Varduhi Yeghiazaryan for ‘Comparison of evaluation methods for medical image segmentation’ and to Gonzalo Diaz for his work on ‘The exact complexity of the first- order logic definability problem’. Prizes for the best abstracts went to Simon Eberz for ‘Looks like Eve: exposing insider threats using eye movement biometrics’ and Ciaran Lee’s ‘Computation in generalised probabilistic theories.’

Members of the department have some rather surprising talents outside of Computer The World outside Science. Below are a few non-subject-related achievements from the last year:

Elizabeth Polgreen, from the team who made their way to the rowed for Oxford in this year’s administration team, won the European Quidditch finals in July. varsity match with the reserve lightweight title and silver medal in The Brits came second only to crew that beat Cambridge on 11 the women’s quads at the British France, losing to a score of 90*-50. April, by three lengths. Rowing Championship, with Wallingford Rowing club. Katie Dicks, finance manager, took Julie Sheppard and Claire part in her tenth consecutive Race Hawtin, both members of the Jan Mikolajczak [pictured For Life which supports Cancer administration team, strolled the below], who reads Mathematics Research. Katie promised her mother, streets of Oxford for 10.6 miles and Computer Science, was a who battled cancer for 16 years but raising £205 for Sobell House. member of the British Quidditch passed away three years ago, that she would take part in the run for ten Kiri Walden, the department’s consecutive years, raising at least new PR Assistant, took part £100 per race. Katie Dicks: ‘Since I in the 70th anniversary of VE have worked here [7 years] I’ve raised Day. Kiri was part of an all- between £500-£1000 each race, so female WW2 Searchlight crew everyone has been really supportive who lit up St Paul’s Cathedral and generous’ She was supported by with their 1939 searchlight and Sharon Lloyd, Jo Leggett, Jo Smith generator as part of the national and Jennie Charlton. anniversary celebrations. Kiri regularly attends events and James Mountain, who is studying anniversaries as an ATS (WW2

© Emily Hayes Emily © for a doctorate in Systems Biology, women’s army) reenactor.

20 Inspired Research: News from the Department of Computer Science, University of Oxford End-of-year examination prizes Congratulations to all the students who were awarded prizes for their performance in end-of-year examinations in 2015. Fourth year (Part C) Dominik Peters – Mathematics and Computer Science, St John’s College The G-Research Prize for best Computer Industry involved in practicals Science project in Mathematics and Computer Science 2015 Industry representatives once again the intention of using the data Matej Balog – Mathematics and formed part of the judging panel that for regional marketing. The team Computer Science, Merton College chose the winners in the second year consisted of Christopher Kew, Michal The Hoare Prize for the best overall students’ group design practicals. Bock, Blagovest Gospodinov, Miraan performance 2015 (Part C) Teams of four to six undergraduates Tabrez and Lukas Halgas, and Xavier Wilders – Computer Science, presented and demonstrated were co-supervised by Dr Ioannis St Anne’s College (joint winner) their projects at an event in May, Agrafiotis, a Research Assistant in Sergiu Vicol – Computer Science, having chosen a topic to work on the department, and Dr Jason Nurse. Oriel College (joint winner) in January, from eleven possible The Hoare Prize for the best overall project topics that were presented as Team 6 were tasked with predicting performance in Computer Science outline design briefs. The practicals stock movements using information 2015 (Part C) allow students to develop and apply from news headlines. They were given Kay Douglass – Computer Science, theory learnt on the course. Part of a prize from WorldQuant, for careful Worcester College (joint winner) the work was to undertake a proper assessment of multiple learning Yuchen Cai – Computer Science, St requirements analysis, working models. Professor Alessandro Abate John’s (joint winner) with the project mentor. Some supervised the team, which consisted The Microsoft Prize for best challenges were set or sponsored of Tomas Vaskevicius, Matthew Computer Science project 2015 by the industry partners, which this Gripton, Ying Zhu, Robert Carlan and Third year (Part B) year included G-Research, Winton Zichuan Huang. Andrew Mowll – Mathematics and Capital, Palantir and WorldQuant. Computer Science, Worcester College Team 7 produced a car racing game, The British Telecom Research and driven by an artificial intelligence, Technology Prize for Mathematics and were awarded a prize by and Computer Science 2015 for best Metaswitch for their impressive overall performance, with special demonstration. The team were regard for Computer Science papers Mateusz Dombrowksi, Ozan – Mathematics and Sevsevil, Matthew Boughen, Xin Sun Pritesh Patel Computer Science, Merton College and Mengying Xue, and their mentor was lecturer Dr Peter Minary. The Junior Mathematics Prize for Mathematics and Computer Science Team 3 were awarded the Ensoft Finally, team 11 were awarded a 2015 for outstanding performance in Prize for a well-designed user prize by Bloomberg for their faultless the mathematical papers in Part B interface. They used information presentation. Again supervised by Dr Benjamin Dawes – Computer Science gathered from Twitter to display Jason Nurse, their challenge was to and Philosophy, Hertford College users’ languages on a map of produce an augmented reality map The Gibbs Prize for Computer Europe. The team was supervised of Oxford. The team were: Richard Science and Philosophy 2015 for by Dr Jason Nurse, a researcher Appleby, Sonal Vedi, Lawrence Parts A and B, paying particular in the Cyber Security Centre, and Okoth-Odida, Joshua Warwick, regard to Computer Science papers consisted of Dan-Andrei Gheorghe, Charlotte Smyth and Paul Logan. Ashok Menon – Computer Science, Toby Cathcart Burn, Alexander Oriel College Bridgeland, Paul-Stefan Herman and Each industry-sponsored prize was The Hoare Prize for the best overall Mariya Lazarova. worth £400. Companies interested performance in Computer Science 2015 in suggesting project ideas or Joe Fowler – Computer Science, Team 4 were awarded a prize from sponsoring prizes should please Keble College Palantir for an engaging pitch. Their contact: The G-Research Prize for best project gathered and analysed the [email protected] project in Computer Science 2015. sentiment of Twitter users with

www.cs.ox.ac.uk Issue 7 Winter 2015 21 Science, has set out to design News in brief Wrapidity offers a system for fully automatic, affordable, and self-maintaining Sentiment analysis spinout easier access to data extraction. Wrapidity builds on company TheySay has been DIADEM, a 5-year ERC (European grabbing headlines. Analysis of big data Research Council) advanced the worldwide Twitter reaction to investigator grant awarded to the launch of Apple Music and Want to know the location and hours Professor Georg Gottlob. Donald Trump’s performance of all the restaurants or gigs in the in the first republican debate US or the prices of all the houses or This year Georg, Dr Tim Furche have featured in news outlets headphones on sale in the UK? (CTO), Dr Giovanni Grasso (head worldwide. Professor Stephen of data extraction), and Dr Giorgio Pulman appeared on the Radio 4 Accurate databases covering entire Orsi (head of entities), all from programme Fry’s English Delights verticals – such as places, products, Oxford, joined with businessman alongside host Stephen Fry, flights, rentals, or events – promise Leon Shpilsky to commercialise and John ‘Jonny Rotten’ Lydon to be the gold of the ‘big data DIADEM’s success in Wrapidity. In in August. age’. Maintaining those databases the six months since its founding, has unfortunately often required Wrapidity has already extracted

Jeremy Corbyn - Mentions on Twitter 15000 hundreds of people dedicated to millions of products, businesses,

11250 7500 their collection and curation. places, and other entities from 3750

0 11:00 11:15 11:30 11:45 12:00 12:15 SAMPLE DATA | THEYSAY LTD 2015 hundreds of thousands of sources

Jeremy Corbyn - Happiness and Sadness on Twitter 4000 Wrapidity, an Oxford spin-off for companies ranging from social 3000 2000 founded by a team of researchers networks and travel search engines 1000

0 11:00 11:15 11:30 11:45 12:00 12:15 SAMPLE DATA | THEYSAY LTD 2015 from the Department of Computer to data markets.

NQIT (pronounced ‘N-kit’) Dr Max Van Kleek has been stands for Networked Quantum Staff appointed as the Senior Research Information Technologies. The Fellow on SOCIAM – see p 24 of this NQIT Hub, part of the UK National appointments edition of Inspired Research for more Quantum Technology Programme, information. is led by the University of Oxford and changes and involves 29 globally leading Professor Sir Nigel Shadbolt has quantum centres and major Since the last edition of Inspired joined us as a Senior Research companies, all working together to Research, there have been some Fellow, and Principal of Jesus realise an entirely new technology changes: College. sector. The Hub’s focus is on systems that can connect Professor Alex Rogers arrives Shimon Whiteson has been together to form flexible, scalable as Associate Professor in Cyber appointed Associate Professor in solutions for diverse applications. Physical Systems, and Tutorial Machine Learning and Tutorial Fellow Three members of the department Fellow at St Anne’s College. at St Catherine’s College. are involved: Professor Marina Jirotka working on responsible Ms Eva Ignatuschtschenko and Ms The Recognition of Distinction innovation, Professor Samson Lilly Pijnenburg Muller join us as exercise 2015 awarded Bernardo Abramsky on hybrid classical/ new Global Cybersecuriy Capacity Cuenca Grau, Cas Cremers and quantum computing and Dr Centre Research Fellows. Niki Trigoni with Full Professor title. Jonathan Barrett on secure communications and verification. Further information: nqit.ox.ac.uk/ Calling Computer Science

MSc (part-time) in researchers on a career break

Software Are you a scientist, technologist, engineer or mathematician who has had Engineering a career break of two or more years for family, caring or health reasons and and wishes to return to research? A Daphne Jackson Fellowship offers Software and STEM professionals wishing to return to a research career after a break, the opportunity to balance an individually tailored retraining programme with a Systems Security challenging research project in a suitably supportive environment. Fellows flexible, professional education normally carry out their research part-time over two years. Anyone interested in joining the Department of Computer Science under the scheme should www.softeng.ox.ac.uk contact: Laura Jones, HR manager, or [email protected]

22 Inspired Research: News from the Department of Computer Science, University of Oxford Software Engineering allied with archaeology through ALIGNED

Research project ALIGNED develops new ways to curate archaeology big data © Mark Byzewski

The rapid growth of web data (Software Engineering Group) leads house in Chaco Canyon, creates demand for software the research on semantics-driven New Mexico. engineering methods which can software engineering. The School build and maintain applications that of Anthropology and Museum Seshat systematically collects what extract, process and publish web Ethnography leads the work on is currently known about the social data. However, converting big data provision of an expert-curated and political organisation of human sources into high-quality, structured databank, Seshat, which offers a societies and how civilizations have knowledge for use in business platform to study the past through evolved over time. This massive processes is a challenging endeavour. well-established scientific techniques. collection of historical information Seshat is also one of the four allows a large international and The University of Oxford is one of the significant use cases for ALIGNED. interdisciplinary team from fields key partners in an exciting research as diverse as evolutionary biology, project: ALIGNED, which is focussed Our collective knowledge about psychology, and archaeology to on quality-centric, software and past societies is almost entirely in rigorously test different hypotheses data engineering. Funded by H2020 a form inaccessible to scientific about the rise and fall of large-scale (an EU framework programme for analysis, stored in historians’ brains societies across the globe and research and innovation) ALIGNED or scattered over heterogeneous human history. will develop new ways to build and notes and publications. The huge maintain IT systems that use big potential of this knowledge for Seshat extracts the data from data on the web, using models, testing theories about political a combination of databases, methods and tools for engineering and economic development Linked Data, websites, academic information systems based on co- has been largely untapped. The publications and human experts. evolving software and web data. The Seshat: Global History Databank ALIGNED will develop new ALIGNED project will develop data- brings together the most current techniques for data curation intensive tools to support combined and comprehensive body of that build on data quality metric data and software engineering. An knowledge about human history frameworks for data integrity ALIGNED system specification will in one place. A typical example of assurance, runtime quality analytics be based on a specialisation of a such historical knowledge, would to automate and prioritise data domain-specific model. be data on population size and curation tasks and curation density, interlinked with background workflows that link together data The ALIGNED project brings information such as levels of harvesters, domain experts and data together research tools developed by social complexity for a particular consumers to improve data quality. computer scientists in Trinity College archaeological excavation site, such Dublin, University of Leipzig and as Pueblo Bonito, the largest great Further information: aligned-project.eu University of Oxford and a semantic platform developed by the Semantic Another noteworthy use for ALIGNED is provided by JURION, an Web Company to support four use innovative legal information platform developed by Wolters Kluwer cases which cut across industrial, Germany. JURION merges and interlinks over one million documents of not-for profit and academic sectors. content and data from diverse sources such as national and European legislation and court judgements, extensive internally authored content Two departments of University of and local customer data, as well as social media and web data (eg Oxford are involved in ALIGNED. The from DBpedia). ALIGNED will enable JURION to address more complex Department of Computer Science business requirements that rely on tighter coupling of software and data.

www.cs.ox.ac.uk Issue 7 Winter 2015 23 The social machine of mathematics Photo © Balint Hirling Anzenberger Agency Photo © Balint Hirling Anzenberger

In the summer of 2014 the ‘Social Machine of Mathematics’ and strategic decisions along the mathematician Tom Hales [pictured project is to try and understand how way – provides a unique insight into above] of the University of Pittsburgh human mathematicians do what how mathematics is done. announced his proof of the 400 they do, and how to best harness year old Kepler conjecture, a result the combination of human skill and Ursula is pulling together a team that says, essentially, that the most computer power to improve the around the world with expertise efficient way of packing cannon balls process of producing mathematics, in mathematics, social science, (or oranges) into a box is the obvious with people doing what people do philosophy, computer proof and the one. What was remarkable about best, and the computers taking care science of the internet. The first Hales’ proof was that every step of checking all the details. steps involve working with social had been written in formal logic and scientists to understand what is checked line by line by a computer This kind of combination of people going on when mathematicians – using HOL and Isabelle – systems and machines was dubbed a ‘social collaborate in the polymath project more usually used to prove the machine’ by internet pioneer Tim – what motivates them to take part, correctness of complex algorithms Berners Lee, and research on social and how do they understand and in safety critical applications. Hales machines is being led in Oxford by trust each other? The polymath had previously announced a proof Sir Nigel Shadbolt and David De archives provide a wonderful source in 1998, but his paper had been Roure (Oxford e-Research Centre) as for empirical research – for example, rejected by a top journal because the part of an EPSRC Programme Grant, how do creative ideas emerge? Or referees did not feel able to trust the SOCIAM. what is involved in a mathematical complex calculations involved. explanation? To get a handle on To get started on understanding everything that is going on we need The Oxford mathematician Andrew this social machine of mathematics to find a suitable way of representing Wiles, who proved Fermat’s Last Professor Ursula Martin is looking such mathematical conversations – Theorem, famously described at another recent innovation – not just the logic of proofs, but the mathematical research as being crowdsourced proofs in a format logic of guesses, dead ends and like ‘stumbling around in the dark’ – called `polymath’. What happens back tracking – and that involves eventually the light comes on, and when a group of experts use a experts in analyzing discourse. you see the way forward, only to blog to collaborate to prove a Finally to build software to support move on to the next problem, and mathematical result? As well as collaborative mathematical proofs, more stumbling around in the dark. new mathematical successes, with we need to integrate our ideas the open format allowing people from these new domains with the Yet mathematicians like Wiles, and from a range of mathematical rigorous discipline of computer Hales, do solve immensely hard backgrounds to contribute, the proof, informed by the ideas of our problems, ones where computers resulting document – not just the colleagues who are developing the would even now be able to make proof but also all the conjectures, science of the internet. very little progress. The purpose of mistakes, false starts, red herrings

24 Inspired Research: News from the Department of Computer Science, University of Oxford