http://www.dspace.cam.ac.uk:80/handle/1810/219481 Thu, 23 May 2013 04:27:06 GMT 2013-05-23T04:27:06Z http://www.dspace.cam.ac.uk:80/handle/1810/244568 Title: Colour videos with depth : acquisition, processing and evaluation Authors: Richardt, Christian Abstract: The human visual system lets us perceive the world around us in three dimensions by integrating evidence from depth cues into a coherent visual model of the world. The equivalent in computer vision and computer graphics are geometric models, which provide a wealth of information about represented objects, such as depth and surface normals. Videos do not contain this information, but only provide per-pixel colour information. In this dissertation, I hence investigate a combination of videos and geometric models: videos with per-pixel depth (also known as RGBZ videos). I consider the full life cycle of these videos: from their acquisition, via filtering and processing, to stereoscopic display. I propose two approaches to capture videos with depth. The first is a spatiotemporal stereo matching approach based on the dual-cross-bilateral grid – a novel real-time technique derived by accelerating a reformulation of an existing stereo matching approach. This is the basis for an extension which incorporates temporal evidence in real time, resulting in increased temporal coherence of disparity maps – particularly in the presence of image noise. The second acquisition approach is a sensor fusion system which combines data from a noisy, low-resolution time-of-flight camera and a high-resolution colour video camera into a coherent, noise-free video with depth. The system consists of a three-step pipeline that aligns the video streams, efficiently removes and fills invalid and noisy geometry, and finally uses a spatiotemporal filter to increase the spatial resolution of the depth data and strongly reduce depth measurement noise. I show that these videos with depth empower a range of video processing effects that are not achievable using colour video alone. These effects critically rely on the geometric information, like a proposed video relighting technique which requires high-quality surface normals to produce plausible results. In addition, I demonstrate enhanced non-photorealistic rendering techniques and the ability to synthesise stereoscopic videos, which allows these effects to be applied stereoscopically. These stereoscopic renderings inspired me to study stereoscopic viewing discomfort. The result of this is a surprisingly simple computational model that predicts the visual comfort of stereoscopic images. I validated this model using a perceptual study, which showed that it correlates strongly with human comfort ratings. This makes it ideal for automatic comfort assessment, without the need for costly and lengthy perceptual studies. Tue, 06 Mar 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244568 2012-03-06T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244239 Title: Privacy engineering for social networks Authors: Anderson, Jonathan Abstract: In this dissertation, I enumerate several privacy problems in online social networks (OSNs) and describe a system called Footlights that addresses them. Footlights is a platform for distributed social applications that allows users to control the sharing of private information. It is designed to compete with the performance of today's centralised OSNs, but it does not trust centralised infrastructure to enforce security properties. Based on several socio-technical scenarios, I extract concrete technical problems to be solved and show how the existing research literature does not solve them. Addressing these problems fully would fundamentally change users' interactions with OSNs, providing real control over online sharing. I also demonstrate that today's OSNs do not provide this control: both user data and the social graph are vulnerable to practical privacy attacks. Footlights' storage substrate provides private, scalable, sharable storage using untrusted servers. Under realistic assumptions, the direct cost of operating this storage system is less than one US dollar per user-year. It is the foundation for a practical shared filesystem, a perfectly unobservable communications channel and a distributed application platform. The Footlights application platform allows third-party developers to write social applications without direct access to users' private data. Applications run in a confined environment with a private-by-default security model: applications can only access user information with explicit user consent. I demonstrate that practical applications can be written on this platform. The security of Footlights user data is based on public-key cryptography, but users are able to log in to the system without carrying a private key on a hardware token. Instead, users authenticate to a set of authentication agents using a weak secret such as a user-chosen password or randomly-assigned 4-digit number. The protocol is designed to be secure even in the face of malicious authentication agents. Tue, 08 Jan 2013 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244239 2013-01-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244102 Title: Modelling energy efficiency for computation Authors: Reams, Charles Abstract: In the last decade, efficient use of energy has become a topic of global significance, touching almost every area of modern life, including computing. From mobile to desktop to server, energy efficiency concerns are now ubiquitous. However, approaches to the energy problem are often piecemeal and focus on only one area for improvement. I argue that the strands of the energy problem are inextricably entangled and cannot be solved in isolation. I offer a high-level view of the problem and, building from it, explore a selection of subproblems within the field. I approach these with various levels of formality, and demonstrate techniques to make improvements on all levels. Tue, 13 Nov 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244102 2012-11-13T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/244047 Title: Supporting virtuosity and flow in computer music Authors: Nash, Chris Abstract: As we begin to realise the sonic and expressive potential of the computer, HCI researchers face the challenge of designing rewarding and accessible user experiences that enable individuals to explore complex creative domains such as music. In performance-based music systems such as sequencers, a disjunction exists between the musician’s specialist skill with performance hardware and the generic usability techniques applied in the design of the software. The creative process is not only fragmented across multiple physical (and virtual) devices, but divided across creativity and productivity phases separated by the act of recording. Integrating psychologies of expertise and intrinsic motivation, this thesis proposes a design shift from usability to virtuosity, using theories of “flow” (Csikszentmihalyi, 1996) and feedback “liveness” (Tanimoto, 1990) to identify factors that facilitate learning and creativity in digital notations and interfaces, leading to a set of design heuristics to support virtuosity in notation use. Using the cognitive dimensions of notations framework (Green, 1996), models of the creative user experience are developed, working towards a theoretical framework for HCI in music systems, and specifically computer-aided composition. Extensive analytical methods are used to look at corollaries of virtuosity and flow in real-world computer music interaction, notably in soundtracking, a software-based composing environment offering a rapid edit-audition feedback cycle, enabled by the user’s skill in manipulating the text-based notation (and program) through the computer keyboard. The interaction and development of more than 1,000 sequencer and tracker users was recorded over a period of 2 years, to investigate the nature and development of skill and technique, look for evidence of flow experiences, and establish the use and role of both visual and musical feedback in music software. Quantitative analyses of interaction data are supplemented with a detailed video study of a professional tracker composer, and a user survey that draws on psychometric methods to evaluate flow experiences in the use of digital music notations, such as sequencers and trackers. Empirical findings broadly support the proposed design heuristics, and enable the development of further models of liveness and flow in notation use. Implications for UI design are discussed in the context of existing music systems, and supporting digitally-mediated creativity in other domains based on notation use. Mon, 08 Oct 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/244047 2012-10-08T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243444 Title: Guessing human-chosen secrets Authors: Bonneau, Joseph Abstract: Authenticating humans to computers remains a notable weak point in computer security despite decades of effort. Although the security research community has explored dozens of proposals for replacing or strengthening passwords, they appear likely to remain entrenched as the standard mechanism of human-computer authentication on the Internet for years to come. Even in the optimistic scenario of eliminating passwords from most of today's authentication protocols using trusted hardware devices or trusted servers to perform federated authentication, passwords will persist as a means of "last-mile" authentication between humans and these trusted single sign-on deputies. This dissertation studies the difficulty of guessing human-chosen secrets, introducing a sound mathematical framework modeling human choice as a skewed probability distribution. We introduce a new metric, alpha-guesswork, which can accurately models the resistance of a distribution against all possible guessing attacks. We also study the statistical challenges of estimating this metric using empirical data sets which can be modeled as a large random sample from the underlying probability distribution. This framework is then used to evaluate several representative data sets from the most important categories of human-chosen secrets to provide reliable estimates of security against guessing attacks. This includes collecting the largest-ever corpus of user-chosen passwords, with nearly 70 million, the largest list of human names ever assembled for research, the largest data sets of real answers to personal knowledge questions and the first data published about human choice of banking PINs. This data provides reliable numbers for designing security systems and highlights universal limitations of human-chosen secrets. Mon, 11 Jun 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243444 2012-06-11T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243442 Title: Towards a worldwide storage infrastructure Authors: Quintard, Julien Abstract: Peer-to-peer systems have recently gained a lot of attention in the academic community especially through the design of KBR (Key-Based Routing) algorithms and DHT (Distributed Hash Table)s. On top of these constructs were built promising applications such as video streaming applications but also storage infrastructures benefiting from the availability and resilience of such scalable network protocols. Unfortunately, rare are the storage systems designed to be scalable and fault-tolerant to Byzantine behaviour, conditions required for such systems to be deployed in an environment such as the Internet. Furthermore, although some means of access control are often provided, such file systems fail to offer the end-users the flexibility required in order to easily manage the permissions granted to potentially hundreds or thousands of end-users. In addition, as for centralised file systems which rely on a special user, referred to as root on Unices, distributed file systems equally require some tasks to operate at the system level. The decentralised nature of these systems renders impossible the use of a single authoritative entity for performing such tasks since implicitly granting her superprivileges, unacceptable configuration for such decentralised systems. This thesis addresses both issues by providing the file system objects a completely decentralised access control and administration scheme enabling users to express access control rules in a flexible way but also to request administrative tasks without the need for a superuser. A prototype has been developed and evaluated, proving feasible the deployment of such a decentralised file system in large-scale and untrustworthy environments. Mon, 11 Jun 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243442 2012-06-11T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243406 Title: Biomedical event extraction from abstracts and full papers using search-based structured prediction Authors: Vlachos, Andreas; Craven, Mark Abstract: Abstract Background Biomedical event extraction has attracted substantial attention as it can assist researchers in understanding the plethora of interactions among genes that are described in publications in molecular biology. While most recent work has focused on abstracts, the BioNLP 2011 shared task evaluated the submitted systems on both abstracts and full papers. In this article, we describe our submission to the shared task which decomposes event extraction into a set of classification tasks that can be learned either independently or jointly using the search-based structured prediction framework. Our intention is to explore how these two learning paradigms compare in the context of the shared task. Results We report that models learned using search-based structured prediction exceed the accuracy of independently learned classifiers by 8.3 points in F-score, with the gains being more pronounced on the more complex Regulation events (13.23 points). Furthermore, we show how the trade-off between recall and precision can be adjusted in both learning paradigms and that search-based structured prediction achieves better recall at all precision points. Finally, we report on experiments with a simple domain-adaptation method, resulting in the second-best performance achieved by a single system. Conclusions We demonstrate that joint inference using the search-based structured prediction framework can achieve better performance than independently learned classifiers, thus demonstrating the potential of this learning paradigm for event extraction and other similarly complex information-extraction tasks. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Mon, 25 Jun 2012 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243406 2012-06-25T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/243359 Title: Examples of plotter output, screenshots, and photographs of usage from Ivan Sutherland's Sketchpad program on the TX2 computer. Authors: Sutherland, Ivan Tue, 01 Jan 1963 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/243359 1963-01-01T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241494 Title: Abstracting information on body area networks Authors: Brandão, Pedro Abstract: Healthcare is changing, correction...healthcare is in need of change. The population ageing, the increase in chronic and heart diseases and just the increase in population size will overwhelm the current hospital-centric healthcare. There is a growing interest by individuals to monitor their own physiology. Not only for sport activities, but also to control their own diseases. They are changing from the passive healthcare receiver to a proactive self-healthcare taker. The focus is shifting from hospital centred treatment to a patient-centric healthcare monitoring. Continuous, everyday, wearable monitoring and actuating is part of this change. In this setting, sensors that monitor the heart, blood pressure, movement, brain activity, dopamine levels, and actuators that pump insulin, “pump” the heart, deliver drugs to specific organs, stimulate the brain are needed as pervasive components in and on the body. They will tend for people’s need of self-monitoring and facilitate healthcare delivery. These components around a human body that communicate to sense and act in a coordinated fashion make a Body Area Network (BAN). In most cases, and in our view, a central, more powerful component will act as the coordinator of this network. These networks aim to augment the power to monitor the human body and react to problems discovered with this observation. One key advantage of this system is their overarching view of the whole network. That is, the central component can have an understanding of all the monitored signals and correlate them to better evaluate and react to problems. This is the focus of our thesis. In this document we argue that this multi-parameter correlation of the heterogeneous sensed information is not being handled in BANs. The current view depends exclusively on the applica- tion that is using the network and its understanding of the parameters. This means that every application will oversee the BAN’s heterogeneous resources managing them directly without taking into consideration other applications, their needs and knowledge. There are several physiological correlations already known by the medical field. Correlating blood pressure and cross sectional area of blood vessels to calculate blood velocity, estimating oxygen delivery from cardiac output and oxygen saturation, are such examples. This knowledge should be available in a BAN and shared by the several applications that make use of the network. This architecture implies a central component that manages the knowledge and the resources. And this is, in our view, missing in BANs. Our proposal is a middleware layer that abstracts the underlying BAN’s resources to the applica- tion, providing instead an information model to be queried. The model describes the correlations for producing new information that the middleware knows about. Naturally, the raw sensed data is also part of the model. The middleware hides the specificities of the nodes that constitute the BAN, by making available their sensed production. Applications are able to query for information attaching requirements to these requests. The middleware is then responsible for satisfying the requests while optimising the resource usage of the BAN. Our architecture proposal is divided in two corresponding layers, one that abstracts the nodes’ hardware (hiding node’s particularities) and the information layer that describes information available and how it is correlated. A prototype implementation of the architecture was done to illustrate the concept. Tue, 10 Jan 2012 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241494 2012-01-10T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241109 Title: Distributed virtual environment scalability and security Authors: Miller, John Abstract: Distributed virtual environments (DVEs) have been an active area of research and engineering for more than 20 years. The most widely deployed DVEs are network games such as Quake, Halo, and World of Warcraft (WoW), with millions of users and billions of dollars in annual revenue. Deployed DVEs remain expensive centralized implementations despite significant research outlining ways to distribute DVE workloads. This dissertation shows previous DVE research evaluations are inconsistent with deployed DVE needs. Assumptions about avatar movement and proximity - fundamental scale factors - do not match WoW’s workload, and likely the workload of other deployed DVEs. Alternate workload models are explored and preliminary conclusions presented. Using realistic workloads it is shown that a fully decentralized DVE cannot be deployed to today’s consumers, regardless of its overhead. Residential broadband speeds are improving, and this limitation will eventually disappear. When it does, appropriate security mechanisms will be a fundamental requirement for technology adoption. A trusted auditing system (“Carbon”) is presented which has good security, scalability, and resource characteristics for decentralized DVEs. When performing exhaustive auditing, Carbon adds 27% network overhead to a decentralized DVE with a WoW-like workload. This resource consumption can be reduced significantly, depending upon the DVE’s risk tolerance. Finally, the Pairwise Random Protocol (PRP) is described. PRP enables adversaries to fairly resolve probabilistic activities, an ability missing from most decentralized DVE security proposals. Thus, this dissertations contribution is to address two of the obstacles for deploying research on decentralized DVE architectures. First, lack of evidence that research results apply to existing DVEs. Second, the lack of security systems combining appropriate security guarantees with acceptable overhead. Tue, 08 Nov 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241109 2011-11-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241042 Title: Proximity coherence for chip-multiprocessors Authors: Barrow-Williams, Nick Abstract: Many-core architectures provide an efficient way of harnessing the growing numbers of transistors available in modern fabrication processes; however, the parallel programs run on these platforms are increasingly limited by the energy and latency costs of communication. Existing designs provide a functional communication layer but do not necessarily implement the most efficient solution for chip-multiprocessors, placing limits on the performance of these complex systems. In an era of increasingly power limited silicon design, efficiency is now a primary concern that motivates designers to look again at the challenge of cache coherence. The first step in the design process is to analyse the communication behaviour of parallel benchmark suites such as Parsec and SPLASH-2. This thesis presents work detailing the sharing patterns observed when running the full benchmarks on a simulated 32-core x86 machine. The results reveal considerable locality of shared data accesses between threads with consecutive operating system assigned thread IDs. This pattern, although of little consequence in a multi-node system, corresponds to strong physical locality of shared data between adjacent cores on a chip-multiprocessor platform. Traditional cache coherence protocols, although often used in chip-multiprocessor designs, have been developed in the context of older multi-node systems. By redesign- ing coherence protocols to exploit new patterns such as the physical locality of shared data, improving the efficiency of communication, specifically in chip-multiprocessors, is possible. This thesis explores such a design – Proximity Coherence – a novel scheme in which L1 load misses are optimistically forwarded to nearby caches via new dedicated links rather than always being indirected via a directory structure. Tue, 08 Nov 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241042 2011-11-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/241035 Title: Second-order algebraic theories Authors: Mahmoud, Ola Abstract: Second-order universal algebra and second-order equational logic respectively provide a model theory and a formal deductive system for languages with variable binding and parameterised metavariables. This work completes the foundations of the subject from the viewpoint of categorical algebra. Specifically, this thesis introduces the notion of second-order algebraic theory and develops its basic theory. Two categorical equivalences are established: at the syntactic level, that of second-order equational presentations and second-order algebraic theories; at the semantic level, that of second-order algebras and second-order functorial models. The development includes a mathematical definition of syntactic translation between second-order equational presentations. This gives the first formalisation of notions such as encodings and transforms in the context of languages with variable binding. Tue, 08 Nov 2011 00:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/241035 2011-11-08T00:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240741 Title: Trends in modeling Biomedical Complex Systems Abstract: Abstract In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 14 Oct 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240741 2009-10-14T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240631 Title: Social network support for data delivery infrastructures Authors: Sastry, Nishanth Ramakrishna Abstract: Network infrastructures often need to stage content so that it is accessible to consumers. The standard solution, deploying the content on a centralised server, can be inadequate in several situations. Our thesis is that information encoded in social networks can be used to tailor content staging decisions to the user base and thereby build better data delivery infrastructures. This claim is supported by two case studies, which apply social information in challenging situations where traditional content staging is infeasible. Our approach works by examining empirical traces to identify relevant social properties, and then exploits them. The first study looks at cost-effectively serving the ``Long Tail'' of rich-media user-generated content, which need to be staged close to viewers to control latency and jitter. Our traces show that a preference for the unpopular tail items often spreads virally and is localised to some part of the social network. Exploiting this, we propose Buzztraq, which decreases replication costs by selectively copying items to locations favoured by viral spread. We also design SpinThrift, which separates popular and unpopular content based on the relative proportion of viral accesses, and opportunistically spins down disks containing unpopular content, thereby saving energy. The second study examines whether human face-to-face contacts can efficiently create paths over time between arbitrary users. Here, content is staged by spreading it through intermediate users until the destination is reached. Flooding every node minimises delivery times but is not scalable. We show that the human contact network is resilient to individual path failures, and for unicast paths, can efficiently approximate flooding in delivery time distribution simply by randomly sampling a handful of paths found by it. Multicast by contained flooding within a community is also efficient. However, connectivity relies on rare contacts and frequent contacts are often not useful for data delivery. Also, periods of similar duration could achieve different levels of connectivity; we devise a test to identify good periods. We finish by discussing how these properties influence routing algorithms. Mon, 10 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240631 2011-10-10T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240612 Title: A model personal energy meter Authors: Hay, Simon Abstract: Every day each of us consumes a significant amount of energy, both directly through transport, heating and use of appliances, and indirectly from our needs for the production of food, manufacture of goods and provision of services. This dissertation investigates a personal energy meter which can record and apportion an individual's energy usage in order to supply baseline information and incentives for reducing our environmental impact. If the energy costs of large shared resources are split evenly without regard for individual consumption each person minimises his own losses by taking advantage of others. Context awareness offers the potential to change this balance and apportion energy costs to those who cause them to be incurred. This dissertation explores how sensor systems installed in many buildings today can be used to apportion energy consumption between users, including an evaluation of a range of strategies in a case study and elaboration of the overriding principles that are generally applicable. It also shows how second-order estimators combined with location data can provide a proxy for fine-grained sensing. A key ingredient for apportionment mechanisms is data on energy usage. This may come from metering devices or buildings directly, or from profiling devices and using secondary indicators to infer their power state. A mechanism for profiling devices to determine the energy costs of specific activities, particularly applicable to shared programmable devices is presented which can make this process simpler and more accurate. By combining crowdsourced building-inventory information and a simple building energy model it is possible to estimate an individual's energy use disaggregated by device class with very little direct sensing. Contextual information provides crucial cues for apportioning the use and energy costs of resources, and one of the most valuable sources from which to infer context is location. A key ingredient for a personal energy meter is a low cost, low infrastructure location system that can be deployed on a truly global scale. This dissertation presents a description and evaluation of the new concept of inquiry-free Bluetooth tracking that has the potential to offer indoor location information with significantly less infrastructure and calibration than other systems. Finally, a suitable architecture for a personal energy meter on a global scale is demonstrated using a mobile phone application to aggregate energy feeds based on the case studies and technologies developed. Mon, 10 Oct 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240612 2011-10-10T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/240491 Title: Minimizing Detection Probability Routing in Ad Hoc Networks Using Directional Antennas Abstract: In a hostile environment, it is important for a transmitter to make its wireless transmission invisible to adversaries because an adversary can detect the transmitter if the received power at its antennas is strong enough. This paper defines a detection probability model to compute the level of a transmitter being detected by a detection system at arbitrary location around the transmitter. Our study proves that the probability of detecting a directional antenna is much lower than that of detecting an omnidirectional antenna if both the directional and omnidirectional antennas provide the same Effective Isotropic Radiated Power (EIRP) in the direction of the receiver. We propose a Minimizing Detection Probability (MinDP) routing algorithm to find a secure routing path in ad hoc networks where nodes employ directional antennas to transmit data to decrease the probability of being detected by adversaries. Our study shows that the MinDP routing algorithm can reduce the total detection probability of deliveries from the source to the destination by over 74%. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Sun, 07 Jun 2009 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/240491 2009-06-07T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/239410 Title: Software lock elision for x86 machine code Authors: Roy, Amitabha Abstract: More than a decade after becoming a topic of intense research there is no transactional memory hardware nor any examples of software transactional memory use outside the research community. Using software transactional memory in large pieces of software needs copious source code annotations and often means that standard compilers and debuggers can no longer be used. At the same time, overheads associated with software transactional memory fail to motivate programmers to expend the needed effort to use software transactional memory. The only way around the overheads in the case of general unmanaged code is the anticipated availability of hardware support. On the other hand, architects are unwilling to devote power and area budgets in mainstream microprocessors to hardware transactional memory, pointing to transactional memory being a "niche" programming construct. A deadlock has thus ensued that is blocking transactional memory use and experimentation in the mainstream. This dissertation covers the design and construction of a software transactional memory runtime system called SLE_x86 that can potentially break this deadlock by decoupling transactional memory from programs using it. Unlike most other STM designs, the core design principle is transparency rather than performance. SLE_x86 operates at the level of x86 machine code, thereby becoming immediately applicable to binaries for the popular x86 architecture. The only requirement is that the binary synchronise using known locking constructs or calls such as those in Pthreads or OpenMP libraries. SLE_x86 provides speculative lock elision (SLE) entirely in software, executing critical sections in the binary using transactional memory. Optionally, the critical sections can also be executed without using transactions by acquiring the protecting lock. The dissertation makes a careful analysis of the impact on performance due to the demands of the x86 memory consistency model and the need to transparently instrument x86 machine code. It shows that both of these problems can be overcome to reach a reasonable level of performance, where transparent software transactional memory can perform better than a lock. SLE_x86 can ensure that programs are ready for transactional memory in any form, without being explicitly written for it. Mon, 11 Jul 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/239410 2011-07-11T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238287 Title: Exploring subdomain variation in biomedical language Authors: Lippincott, Thomas; Ó Séaghdha, Diarmuid; Korhonen, Anna Abstract: AbstractApplications of Natural Language Processing (NLP) technology to biomedical texts have generated significant interest in recent years. In this paper we identify and investigate the phenomenon of linguistic subdomain variation within the biomedical domain, i.e., the extent to which different subject areas of biomedicine are characterised by different linguistic behaviour. While variation at a coarser domain level such as between newswire and biomedical text is well-studied and known to affect the portability of NLP systems, we are the first to conduct an extensive investigation into more fine-grained levels of variation. Using the large OpenPMC text corpus, which spans the many subdomains of biomedicine, we investigate variation across a number of lexical, syntactic, semantic and discourse-related dimensions. These dimensions are chosen for their relevance to the performance of NLP systems. We use clustering techniques to analyse commonalities and distinctions among the subdomains. We find that while patterns of inter-subdomain variation differ somewhat from one feature set to another, robust clusters can be identified that correspond to intuitive distinctions such as that between clinical and laboratory subjects. In particular, subdomains relating to genetics and molecular biology, which are the most common sources of material for training and evaluating biomedical NLP tools, are not representative of all biomedical subdomains. We conclude that an awareness of subdomain variation is important when considering the practical use of language processing applications by biomedical researchers. Thu, 26 May 2011 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238287 2011-05-26T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238020 Title: The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case Abstract: Abstract Background Histidine biosynthesis is one of the best characterized anabolic pathways. There is a large body of genetic and biochemical information available, including operon structure, gene expression, and increasingly larger sequence databases. For over forty years this pathway has been the subject of extensive studies, mainly in Escherichia coli and Salmonella enterica, in both of which details of histidine biosynthesis appear to be identical. In these two enterobacteria the pathway is unbranched, includes a number of unusual reactions, and consists of nine intermediates; his genes are arranged in a compact operon (hisGDC [NB]HAF [IE]), with three of them (hisNB, hisD and hisIE) coding for bifunctional enzymes. We performed a detailed analysis of his gene fusions in available genomes to understand the role of gene fusions in shaping this pathway. Results The analysis of HisA structures revealed that several gene elongation events are at the root of this protein family: internal duplication have been identified by structural superposition of the modules composing the TIM-barrel protein. Several his gene fusions happened in distinct taxonomic lineages; hisNB originated within γ-proteobacteria and after its appearance it was transferred to Campylobacter species (ε-proteobacteria) and to some Bacteria belonging to the CFB group. The transfer involved the entire his operon. The hisIE gene fusion was found in several taxonomic lineages and our results suggest that it probably happened several times in distinct lineages. Gene fusions involving hisIE and hisD genes (HIS4) and hisH and hisF genes (HIS7) took place in the Eukarya domain; the latter has been transferred to some δ-proteobacteria. Conclusion Gene duplication is the most widely known mechanism responsible for the origin and evolution of metabolic pathways; however, several other mechanisms might concur in the process of pathway assembly and gene fusion appeared to be one of the most important and common. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 15 Aug 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238020 2007-08-15T23:00:00Z http://www.dspace.cam.ac.uk:80/handle/1810/238019 Title: Modeling HIV quasispecies evolutionary dynamics Abstract: Abstract Background During the HIV infection several quasispecies of the virus arise, which are able to use different coreceptors, in particular the CCR5 and CXCR4 coreceptors (R5 and X4 phenotypes, respectively). The switch in coreceptor usage has been correlated with a faster progression of the disease to the AIDS phase. As several pharmaceutical companies are starting large phase III trials for R5 and X4 drugs, models are needed to predict the co-evolutionary and competitive dynamics of virus strains. Results We present a model of HIV early infection which describes the dynamics of R5 quasispecies and a model of HIV late infection which describes the R5 to X4 switch. We report the following findings: after superinfection (multiple infections at different times) or coinfection (simultaneous infection by different strains), quasispecies dynamics has time scales of several months and becomes even slower at low number of CD4+ T cells. Phylogenetic inference of chemokine receptors suggests that viral mutational pathway may generate a large variety of R5 variants able to interact with chemokine receptors different from CXCR4. The decrease of CD4+ T cells, during AIDS late stage, can be described taking into account the X4-related Tumor Necrosis Factor dynamics. Conclusion The results of this study bridge the gap between the within-patient and the inter-patients (i.e. world-wide) evolutionary processes during HIV infection and may represent a framework relevant for modeling vaccination and therapy. Description: RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are. Wed, 15 Aug 2007 23:00:00 GMT http://www.dspace.cam.ac.uk:80/handle/1810/238019 2007-08-15T23:00:00Z