Hierarchical Bayesian modelling of early detection surveillance for plant pest invasions

Early detection surveillance programs aim to find invasions of exotic plant pests and diseases before they are too widespread to eradicate. However, the value of these programs can be difficult to justify when no positive detections are made. To demonstrate the value of pest absence information provided by these programs, we use a hierarchical Bayesian framework to model estimates of incursion extent with and without surveillance. A model for the latent invasion process provides the baseline against which surveillance data are assessed. Ecological knowledge and pest management criteria are introduced into the model using informative priors for invasion parameters. Observation models assimilate information from spatio-temporal presence/absence data to accommodate imperfect detection and generate posterior estimates of pest extent. When applied to an early detection program operating in Queensland, Australia, the framework demonstrates that this typical surveillance regime provides a modest reduction in the estimate that a surveyed district is infested. More importantly, the model suggests that early detection surveillance programs can provide a dramatic reduction in the putative area of incursion and therefore offer a substantial benefit to incursion management. By mapping spatial estimates of the point probability of infestation, the model identifies where future surveillance resources can be most effectively deployed.

Bayesian methodology for genetics of complex diseases

Genetic research of complex diseases is a challenging, but exciting, area of research. The early development of the research was limited, however, until the completion of the Human Genome and HapMap projects, along with the reduction in the cost of genotyping, which paves the way for understanding the genetic composition of complex diseases. In this thesis, we focus on the statistical methods for two aspects of genetic research: phenotype definition for diseases with complex etiology and methods for identifying potentially associated Single Nucleotide Polymorphisms (SNPs) and SNP-SNP interactions. With regard to phenotype definition for diseases with complex etiology, we firstly investigated the effects of different statistical phenotyping approaches on the subsequent analysis. In light of the findings, and the difficulties in validating the estimated phenotype, we proposed two different methods for reconciling phenotypes of different models using Bayesian model averaging as a coherent mechanism for accounting for model uncertainty. In the second part of the thesis, the focus is turned to the methods for identifying associated SNPs and SNP interactions. We review the use of Bayesian logistic regression with variable selection for SNP identification and extended the model for detecting the interaction effects for population based case-control studies. In this part of study, we also develop a machine learning algorithm to cope with the large scale data analysis, namely modified Logic Regression with Genetic Program (MLR-GEP), which is then compared with the Bayesian model, Random Forests and other variants of logic regression.

A Python package for Bayesian estimation using Markov Chain Monte Carlo

Markov chain Monte Carlo (MCMC) estimation provides a solution to the complex integration problems that are faced in the Bayesian analysis of statistical problems. The implementation of MCMC algorithms is, however, code intensive and time consuming. We have developed a Python package, which is called PyMCMC, that aids in the construction of MCMC samplers and helps to substantially reduce the likelihood of coding error, as well as aid in the minimisation of repetitive code. PyMCMC contains classes for Gibbs, Metropolis Hastings, independent Metropolis Hastings, random walk Metropolis Hastings, orientational bias Monte Carlo and slice samplers as well as specific modules for common models such as a module for Bayesian regression analysis. PyMCMC is straightforward to optimise, taking advantage of the Python libraries Numpy and Scipy, as well as being readily extensible with C or Fortran.

Single-layer decoupling networks for circulant symmetric arrays

Reduced element spacing in antenna arrays gives rise to strong mutual coupling between array elements and may cause significant performance degradation. These effects can be alleviated by introducing a decoupling network consisting of interconnected reactive elements. The existing design approach for the synthesis of a decoupling network for circulant symmetric arrays allows calculation of element values using closed-form expressions, but the resulting circuit configuration requires multilayer technology for implementation. In this paper, a new structure for the decoupling of circulant symmetric arrays of more than four elements is presented. Element values are no longer obtained in closed form, but the resulting circuit is much simpler and can be implemented on a single layer.

Dual-frequency decoupling networks for compact antenna arrays

Decoupling networks can alleviate the effects of mutual coupling in antenna arrays. Conventional decoupling networks can provide decoupled and matched ports at a single frequency. This paper describes dual-frequency decoupling which is achieved by using a network of series or parallel resonant circuits instead of single reactive elements.

An efficient public key management system : an application in vehicular ad hoc networks

The major purpose of Vehicular Ad Hoc Networks (VANETs) is to provide safety-related message access for motorists to react or make a life-critical decision for road safety enhancement. Accessing safety-related information through the use of VANET communications, therefore, must be protected, as motorists may make critical decisions in response to emergency situations in VANETs. If introducing security services into VANETs causes considerable transmission latency or processing delays, this would defeat the purpose of using VANETs to improve road safety. Current research in secure messaging for VANETs appears to focus on employing certificate-based Public Key Cryptosystem (PKC) to support security. The security overhead of such a scheme, however, creates a transmission delay and introduces a time-consuming verification process to VANET communications. This paper proposes an efficient public key management system for VANETs: the Public Key Registry (PKR) system. Not only does this paper demonstrate that the proposed PKR system can maintain security, but it also asserts that it can improve overall performance and scalability at a lower cost, compared to the certificate-based PKC scheme. It is believed that the proposed PKR system will create a new dimension to the key management and verification services for VANETs.

Protection of distributed generation interfaced networks

With the rapid increase in electrical energy demand, power generation in the form of distributed generation is becoming more important. However, the connections of distributed generators (DGs) to a distribution network or a microgrid can create several protection issues. The protection of these networks using protective devices based only on current is a challenging task due to the change in fault current levels and fault current direction. The isolation of a faulted segment from such networks will be difficult if converter interfaced DGs are connected as these DGs limit their output currents during the fault. Furthermore, if DG sources are intermittent, the current sensing protective relays are difficult to set since fault current changes with time depending on the availability of DG sources. The system restoration after a fault occurs is also a challenging protection issue in a converter interfaced DG connected distribution network or a microgrid. Usually, all the DGs will be disconnected immediately after a fault in the network. The safety of personnel and equipment of the distribution network, reclosing with DGs and arc extinction are the major reasons for these DG disconnections. In this thesis, an inverse time admittance (ITA) relay is proposed to protect a distribution network or a microgrid which has several converter interfaced DG connections. The ITA relay is capable of detecting faults and isolating a faulted segment from the network, allowing unfaulted segments to operate either in grid connected or islanded mode operations. The relay does not make the tripping decision based on only the fault current. It also uses the voltage at the relay location. Therefore, the ITA relay can be used effectively in a DG connected network in which fault current level is low or fault current level changes with time. Different case studies are considered to evaluate the performance of the ITA relays in comparison to some of the existing protection schemes. The relay performance is evaluated in different types of distribution networks: radial, the IEEE 34 node test feeder and a mesh network. The results are validated through PSCAD simulations and MATLAB calculations. Several experimental tests are carried out to validate the numerical results in a laboratory test feeder by implementing the ITA relay in LabVIEW. Furthermore, a novel control strategy based on fold back current control is proposed for a converter interfaced DG to overcome the problems associated with the system restoration. The control strategy enables the self extinction of arc if the fault is a temporary arc fault. This also helps in self system restoration if DG capacity is sufficient to supply the load. The coordination with reclosers without disconnecting the DGs from the network is discussed. This results in increased reliability in the network by reduction of customer outages.

Urban maze : A typological investigation in porous morphology and dynamic pedestrian networks

Mixed use typologies and pedestrian networks are two strategies commonly applied in design of the contemporary city. These approaches, aimed towards the creation of a more sustainalble urban environment, have their roots in the traditional, pre-industrial towns; they characterize urban form, articulating the tension between privaate and public realms through a series of typological variations as well as stimulating commercial activity in the city centre. Arcades, loggias and verandas are just some of the elements which can mediate this tension. Historically they have defined physical and social spaces with particular character; in the contemporary city these features are applied to deform the urban form and create a porous, dynamic morphology. This paper, comparing case studies from Italy, Japan and Australia, investigates how the design of the transition zone can define hybrid pedestrian networks, where a clear distinction between the public and private realms is no longer applicable. Pedestrians use the city in a dynamic way, combining trajectories on the public street with ones on the fringe or inside of the private built environment. In some cases, cities offer different pedestrian network possibilities at different times, as the commercial precints are subject to variations in accessibility across various timeframes. These walkable systems have an impact on the urban form and identity of places, redefining typologies and requiring an in depth analysis through plan, section and elevation diagrams.

Multicast traffic filtering for sampled value process bus networks

Ethernet is a key component of the standards used for digital process buses in transmission substations, namely IEC 61850 and IEEE Std 1588-2008 (PTPv2). These standards use multicast Ethernet frames that can be processed by more than one device. This presents some significant engineering challenges when implementing a sampled value process bus due to the large amount of network traffic. A system of network traffic segregation using a combination of Virtual LAN (VLAN) and multicast address filtering using managed Ethernet switches is presented. This includes VLAN prioritisation of traffic classes such as the IEC 61850 protocols GOOSE, MMS and sampled values (SV), and other protocols like PTPv2. Multicast address filtering is used to limit SV/GOOSE traffic to defined subsets of subscribers. A method to map substation plant reference designations to multicast address ranges is proposed that enables engineers to determine the type of traffic and location of the source by inspecting the destination address. This method and the proposed filtering strategy simplifies future changes to the prioritisation of network traffic, and is applicable to both process bus and station bus applications.

The sample complexity of pattern classification with neural networks: the size of the weights is more important than the size of the network

Sample complexity results from computational learning theory, when applied to neural network learning for pattern classification problems, suggest that for good generalization performance the number of training examples should grow at least linearly with the number of adjustable parameters in the network. Results in this paper show that if a large neural network is used for a pattern classification problem and the learning algorithm finds a network with small weights that has small squared error on the training patterns, then the generalization performance depends on the size of the weights rather than the number of weights. For example, consider a two-layer feedforward network of sigmoid units, in which the sum of the magnitudes of the weights associated with each unit is bounded by A and the input dimension is n. We show that the misclassification probability is no more than a certain error estimate (that is related to squared error on the training set) plus A3 √((log n)/m) (ignoring log A and log m factors), where m is the number of training patterns. This may explain the generalization performance of neural networks, particularly when the number of training examples is considerably smaller than the number of weights. It also supports heuristics (such as weight decay and early stopping) that attempt to keep the weights small during training. The proof techniques appear to be useful for the analysis of other pattern classifiers: when the input domain is a totally bounded metric space, we use the same approach to give upper bounds on misclassification probability for classifiers with decision boundaries that are far from the training examples.

Exponentiated gradient algorithms for conditional random fields and max-margin Markov Networks

Log-linear and maximum-margin models are two commonly-used methods in supervised machine learning, and are frequently used in structured prediction problems. Efficient learning of parameters in these models is therefore an important problem, and becomes a key factor when learning from very large data sets. This paper describes exponentiated gradient (EG) algorithms for training such models, where EG updates are applied to the convex dual of either the log-linear or max-margin objective function; the dual in both the log-linear and max-margin cases corresponds to minimizing a convex function with simplex constraints. We study both batch and online variants of the algorithm, and provide rates of convergence for both cases. In the max-margin case, O(1/ε) EG updates are required to reach a given accuracy ε in the dual; in contrast, for log-linear models only O(log(1/ε)) updates are required. For both the max-margin and log-linear cases, our bounds suggest that the online EG algorithm requires a factor of n less computation to reach a desired accuracy than the batch EG algorithm, where n is the number of training examples. Our experiments confirm that the online algorithms are much faster than the batch algorithms in practice. We describe how the EG updates factor in a convenient way for structured prediction problems, allowing the algorithms to be efficiently applied to problems such as sequence learning or natural language parsing. We perform extensive evaluation of the algorithms, comparing them to L-BFGS and stochastic gradient descent for log-linear models, and to SVM-Struct for max-margin models. The algorithms are applied to a multi-class problem as well as to a more complex large-scale parsing task. In all these settings, the EG algorithms presented here outperform the other methods.

Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.