On fast-slow consensus networks with a dynamic weight

We study dynamic networks under an undirected consensus communication protocol and with one state-dependent weighted edge. We assume that the aforementioned dynamic edge can take values over the whole real numbers, and that its behaviour depends on the nodes it connects and on an extrinsic slow variable. We show that, under mild conditions on the weight, there exists a reduction such that the dynamics of the network are organized by a transcritical singularity. As such, we detail a slow passage through a transcritical singularity for a simple network, and we observe that an exchange between consensus and clustering of the nodes is possible. In contrast to the classical planar fast-slow transcritical singularity, the network structure of the system under consideration induces the presence of a maximal canard. Our main tool of analysis is the blow-up method. Thus, we also focus on tracking the effects of the blow-up transformation on the network's structure. We show that on each blow-up chart one recovers a particular dynamic network related to the original one. We further indicate a numerical issue produced by the slow passage through the transcritical singularity

Computational Approaches for Predicting Drug Targets

This thesis reports the development of several computational approaches to predict human disease proteins and to assess their value as drug targets, using in-house domain functional families (CATH FunFams). CATH-FunFams comprise evolutionary related protein domains with high structural and functional similarity. External resources were used to identify proteins associated with disease and their genetic variations. These were then mapped to the CATH-FunFams together with information on drugs bound to any relatives within the FunFam. A number of novel approaches were then used to predict the proteins likely to be driving disease and to assess whether drugs could be repurposed within the FunFams for targeting these putative driver proteins. The first work chapter of this thesis reports the mapping of drugs to CATHFunFams to identify druggable FunFams based on statistical overrepresentation of drug targets within the FunFam. 81 druggable CATH-FunFams were identified and the dispersion of their relatives on a human protein interaction network was analysed to assess their propensity to be associated with side effects. In the second work chapter, putative drug targets for bladder cancer were identified using a novel computational protocol that expands a set of known bladder cancer genes with genes highly expressed in bladder cancer and highly associated with known bladder cancer genes in a human protein interaction network. 35 new bladder cancer targets were identified in druggable FunFams, for some of which FDA approved drugs could be repurposed from other protein domains in the FunFam. In the final work chapter, protein kinases and kinase inhibitors were analysed. These are an important class of human drug targets. A novel classification protocol was applied to give a comprehensive classification of the kinases which was benchmarked and compared with other widely used kinase classifications. Druginformation from ChEMBL was mapped to the Kinase-FunFams and analyses of protein network characteristics of the kinase relatives in each FunFam used to identify those families likely to be associated with side effects

Networks and the epidemiology of infectious disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues

Autonomy and Intelligence in the Computing Continuum: Challenges, Enablers, and Future Directions for Orchestration

Future AI applications require performance, reliability and privacy that the existing, cloud-dependant system architectures cannot provide. In this article, we study orchestration in the device-edge-cloud continuum, and focus on AI for edge, that is, the AI methods used in resource orchestration. We claim that to support the constantly growing requirements of intelligent applications in the device-edge-cloud computing continuum, resource orchestration needs to embrace edge AI and emphasize local autonomy and intelligence. To justify the claim, we provide a general definition for continuum orchestration, and look at how current and emerging orchestration paradigms are suitable for the computing continuum. We describe certain major emerging research themes that may affect future orchestration, and provide an early vision of an orchestration paradigm that embraces those research themes. Finally, we survey current key edge AI methods and look at how they may contribute into fulfilling the vision of future continuum orchestration.Comment: 50 pages, 8 figures (Revised content in all sections, added figures and new section

Proceedings of the GIS Research UK 18th Annual Conference GISRUK 2010

This volume holds the papers from the 18th annual GIS Research UK (GISRUK). This year the conference, hosted at University College London (UCL), from Wednesday 14 to Friday 16 April 2010. The conference covered the areas of core geographic information science research as well as applications domains such as crime and health and technological developments in LBS and the geoweb. UCL’s research mission as a global university is based around a series of Grand Challenges that affect us all, and these were accommodated in GISRUK 2010. The overarching theme this year was “Global Challenges”, with specific focus on the following themes: * Crime and Place * Environmental Change * Intelligent Transport * Public Health and Epidemiology * Simulation and Modelling * London as a global city * The geoweb and neo-geography * Open GIS and Volunteered Geographic Information * Human-Computer Interaction and GIS Traditionally, GISRUK has provided a platform for early career researchers as well as those with a significant track record of achievement in the area. As such, the conference provides a welcome blend of innovative thinking and mature reflection. GISRUK is the premier academic GIS conference in the UK and we are keen to maintain its outstanding record of achievement in developing GIS in the UK and beyond

Incentive-driven QoS in peer-to-peer overlays

A well known problem in peer-to-peer overlays is that no single entity has control over the software, hardware and configuration of peers. Thus, each peer can selfishly adapt its behaviour to maximise its benefit from the overlay. This thesis is concerned with the modelling and design of incentive mechanisms for QoS-overlays: resource allocation protocols that provide strategic peers with participation incentives, while at the same time optimising the performance of the peer-to-peer distribution overlay. The contributions of this thesis are as follows. First, we present PledgeRoute, a novel contribution accounting system that can be used, along with a set of reciprocity policies, as an incentive mechanism to encourage peers to contribute resources even when users are not actively consuming overlay services. This mechanism uses a decentralised credit network, is resilient to sybil attacks, and allows peers to achieve time and space deferred contribution reciprocity. Then, we present a novel, QoS-aware resource allocation model based on Vickrey auctions that uses PledgeRoute as a substrate. It acts as an incentive mechanism by providing efficient overlay construction, while at the same time allocating increasing service quality to those peers that contribute more to the network. The model is then applied to lagsensitive chunk swarming, and some of its properties are explored for different peer delay distributions. When considering QoS overlays deployed over the best-effort Internet, the quality received by a client cannot be adjudicated completely to either its serving peer or the intervening network between them. By drawing parallels between this situation and well-known hidden action situations in microeconomics, we propose a novel scheme to ensure adherence to advertised QoS levels. We then apply it to delay-sensitive chunk distribution overlays and present the optimal contract payments required, along with a method for QoS contract enforcement through reciprocative strategies. We also present a probabilistic model for application-layer delay as a function of the prevailing network conditions. Finally, we address the incentives of managed overlays, and the prediction of their behaviour. We propose two novel models of multihoming managed overlay incentives in which overlays can freely allocate their traffic flows between different ISPs. One is obtained by optimising an overlay utility function with desired properties, while the other is designed for data-driven least-squares fitting of the cross elasticity of demand. This last model is then used to solve for ISP profit maximisation