Statistical mechanics of ontology based annotations

We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.Comment: 27 pages, 5 figure

Learning from the machine: interpreting machine learning algorithms for point- and extended- source classification

We investigate star-galaxy classification for astronomical surveys in the context of four methods enabling the interpretation of black-box machine learning systems. The first is outputting and exploring the decision boundaries as given by decision tree based methods, which enables the visualization of the classification categories. Secondly, we investigate how the Mutual Information based Transductive Feature Selection (MINT) algorithm can be used to perform feature pre-selection. If one would like to provide only a small number of input features to a machine learning classification algorithm, feature pre-selection provides a method to determine which of the many possible input properties should be selected. Third is the use of the tree-interpreter package to enable popular decision tree based ensemble methods to be opened, visualized, and understood. This is done by additional analysis of the tree based model, determining not only which features are important to the model, but how important a feature is for a particular classification given its value. Lastly, we use decision boundaries from the model to revise an already existing method of classification, essentially asking the tree based method where decision boundaries are best placed and defining a new classification method. We showcase these techniques by applying them to the problem of star-galaxy separation using data from the Sloan Digital Sky Survey (hereafter SDSS). We use the output of MINT and the ensemble methods to demonstrate how more complex decision boundaries improve star-galaxy classification accuracy over the standard SDSS frames approach (reducing misclassifications by up to $\approx33\%$). We then show how tree-interpreter can be used to explore how relevant each photometric feature is when making a classification on an object by object basis.Comment: 12 pages, 8 figures, 8 table

Constitutive modelling of branched polymer melts in non-linear response

This thesis is concerned with modelling long chain branched polymer melts using the McLeish and Larson Pompom constitutive equations. Usually the non-linear terms in this model are fitted to uniaxial extensional data due its sensitivity to levels of branching, but in this thesis I will study a number of other non-linear flows using this model. For each flow the results are compared to experiments on a set of polyethylene melts. The first flow types I examine are simple shear flows. In a shear step-strain flow the stress relaxation of branched polymers is observed to be time-strain separable, whereby the relaxation modulus can be separated into the product of separate functions of time and strain. I show that although the Pompom model is not time-strain separable in general, there exist subsets of parameter values for which time-strain separability is valid. For these sets a branched damping function is derived which is analogous to the Doi-Edwards damping function for linear polymer melts. The other simple shear flow examined is oscillatory shear. Commonly, oscillatory shear is probed at low strain amplitudes over a range of frequencies to measure the usual dynamic moduli of linear viscoelasticity. In this work the effect of strain amplitude is explored up to absolute strains of order unity. The non-linear stress response is analysed from the higher harmonics in the Fourier series. In particular it is shown that the third Fourier components are dependent on the Pompom non-linear stretch relaxation time and a low-strain asymptote is obtained. Subsequently, this thesis focuses on the stagnation point flow generated in a cross-slot geometry. The stress calculated from the Pompom constitutive model is compared to experimental flow induced birefringence images. It is shown for linear and lightly branched materials that the Pompom model predicts both the form of the birefringence pattern and stress values obtained from the stress-optical law. However, for more highly branched polymers the Pompom model fails to predict the change to birefringence patterns. Subsequent analysis shows that there could exist a transient overshoot in extension which the Pompom model cannot capture as it stands. In the final part of my thesis I suggest an empirical alteration to the Pompom constitutive model to capture this transient extensional overshoot, which is able to resolve the differences between experimental flow induced birefringence images and theoretical simulations

A conceptual and historical exploration of ideological influences on the development of state education within England and Wales

This dissertation is concerned with the relationship between a state and its public education system. It is based upon the premise that the system in England and WaIes is inherently rooted in its nineteenth century past and that recent educational policies have only served to strengthen this fact rather than reforming the system to give it more relevance for a society about to enter the twenty-first century. This orientation serves to perpetrate epistemological, sociological, economic and vocational perspectives which are more appropriate for the nineteenth century than for our own times. The dissertation makes the point that educational policymaking at the end of the twentieth century in England is based on outmoded thinking, outdated concepts of statehood, society, the relationship between citizen and state, knowledge and, therefore, education itself. The thesis concerns itself with a comparative overview of the development of 'statehood' and a consideration of the notion of 'ideology'. It examines the ideological sources and development of education in three historical settings. This is followed by a detailed examination of the sources of the national system of education in England. The current educational climate is considered in the light of developments since the enactment of the legislation of 1944. This is centred upon a close study of the parliamentary debates which preceded the Acts of 1944 and 1988 which clearly demonstrated that the educational agenda, in political terms, is still dominated by nineteenth century thinking, not the least important aspect of which is religion. The conclusion argues that, with the advent of postmodernism, a new relationship is needed between education and the state. Indeed, the whole structure and methodology of education will need to be re-worked to take advantage not only of new means of understanding available, but also of new understanding of knowledge itself

A Program Plan and Evaluation Plan for the Carolina Alzheimer's Network: A Focus on the State-of-the-Art Workshop

In July of 2008, two professors from the University of North Carolina at Chapel Hill School of Medicine began the Carolina Alzheimer's Network, a program for expanding resources for specialized dementia care throughout the state of North Carolina. The Duke Endowment provided initial funds for equipping and networking primary care practitioners. In April of 2009, demonstration grant funding from the Administration on Aging became available to further the goal of the program by linking the network to aging services providers through the Area Agencies on Aging. Together, these two grants provide an opportunity for developing activities and infrastructure for sustainable improvements in dementia care throughout the state. As a graduate student in the Public Health Leadership Program, I became involved as a volunteer with several program activities in November of 2008. Based on my involvement, I have tried to provide, in this paper, an update on the program plan and evaluation plan for the Carolina Alzheimer's Network. The program plan seeks to meet the growing public health issue of dementia care in North Carolina, with a focus on poor, minority, and rural counties. For the purpose of initially networking primary care practitioners and equipping them with state-of-the-art tools for dementia assessment and management, the program plan includes providing continuing medical education workshops throughout the state. These workshops are also serving as an initial linking opportunity to aging services providers, the objective of the Administration on Aging demonstration grant. Other activities in the program plan include direct health services, enabling services, population-based services, and infrastructure services. The evaluation plan provides a framework for the entire program evaluation, but with a focus on the workshop evaluation. The role of the evaluation is broad and includes improving program activities, writing progress reports and disseminating program findings, and even planning new program activities. Using the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) method, this evaluation plan seeks to fulfill the demonstration Administration on Aging grant purpose of developing knowledge which can be disseminated throughout the nation, while, at the same time, providing for program improvement and the development of a sustainable program for the citizens of North Carolina.Master of Public Healt

Biological data and model development for management of longfinned eels

Objectives: 1. Estimate population parameters required for a management model. These include survival, density, age structure, growth, age and size at maturity and at recruitment to the adult eel fishery. Estimate their variability among individuals in a range of habitats. 2. Develop a management population dynamics model and use it to investigate management options. 3. Establish baseline data and sustainability indicators for long-term monitoring. 4. Assess the applicability of the above techniques to other eel fisheries in Australia, in collaboration with NSW. Distribute developed tools via the Australia and New Zealand Eel Reference Group

Biological data and model development for management of longfinned eels

Objectives: 1. Estimate population parameters required for a management model. These include survival, density, age structure, growth, age and size at maturity and at recruitment to the adult eel fishery. Estimate their variability among individuals in a range of habitats. 2. Develop a management population dynamics model and use it to investigate management options. 3. Establish baseline data and sustainability indicators for long-term monitoring. 4. Assess the applicability of the above techniques to other eel fisheries in Australia, in collaboration with NSW. Distribute developed tools via the Australia and New Zealand Eel Reference Group