Grid technology for collaborative ontology development

In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on stand-alone editors running on users’ desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and Protégé) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be made of the storage, versioning and visualisation techniques being developed by the database and e- Science communities. BioSphere is an online ontology editor supporting multiple users and is underpinned by a server that stores versions (in OWL-XML) and provides a discussion portal

Differentiation theory : intersensory substitution and the use of the sonicguide

This thesis investigates the possibilities and parameters of intersensory substitution - the provision through one sense of information normally provided through another sense. An artificial ultrasonic echo-location device, providing, through sound, information usually provided through sight, was used. A series of interlinked cross-sectional and longitudinal studies was run, using both blind and simulated blind subjects of a range of ages. Infants, pre-school children, school-age children and adults were tested. Although some subjects in all age groups were shown to be able to make some use of the device, by adopting strict criteria for testing the effectiveness of this use, both qualitative and quantitative age differences in use were demonstrated to exist. The implications of these results for conflicting theories of development, in particular perceptual development, are considered. A differentiation theory in which development is seen as proceeding from abstract to specific, while not consistent with all the results, is shown with modification, to have the greatest explanatory value

Renter Residential Search: An Empirical Investigation In Cognition And Behaviour

It is believed that search constitutes an important cognitive process. Substantial research has enhanced our elemental understanding of this area of enquiry. This notwithstanding, the process of search remains little understood.;This thesis investigates the residential search behaviour of a sample of individuals who were in the process of relocating within the rental housing sector. The purpose of the study is severalfold. Firstly, it explores the distinctiveness of renter search behaviour. Secondly, it is an investigation into the links between cognition and overt behaviour. Thirdly, it describes groupings of like-minded individuals within the renter sector. Finally, it reveals how renters construe housing submarkets and, accordingly, it demonstrates the spatial effect of this construed structure on renter search.;Individuals form mental schemata to order and give meaning to their environment. Based on this assumption, a model is adopted which emphasises three aspects of cognitive behaviour: the process of housing search, the orientation and flexibility of mental schemata as revealed through personal constructs, and overt spatial behaviour. The model provides a conceptual framework for the empirical design of the thesis.;It is revealed that renters\u27 search processes comprise at least two separate behaviours: passive and active search. The analyses support the contention that individuals utilise a set of fairly general, discriminatory constructs when they are required to evaluate vacancies off-site during passive search. These constructs determine a region of potential residential occupancy, and effect limited search. Active search constitutes a functionally discrete behaviour. At this stage, the individual uses a set of specific constructs in order to evaluate differences among housing opportunities and to select between alternatives. It is at this stage that the distinctiveness of rental housing search becomes apparent.;Groupings of like-minded individuals are differentiated on the basis of the housing attributes that they use to evaluate housing vacancies. This analysis is only partially successful. Intra-group commonalities are obscured by the rich individualistic, and idiosyncratic, data. However, by focusing on some very general hypothesised spatial patterns, several distinctive renter groups are identified. Some support is forwarded for an association between choice of housing and life-style. Furthermore, some evidence is garnered for the existence of substantial links between movers\u27 spatial schemata, their overt search behaviour, and the structure of an housing submarket

New Models for Expert System Design

This thesis presents new work on the analysis of human lung sound. Experimental studies investigated the relationship between the condition of the lungs and the power spectrum of lung sound detected at the chest wall. The conclusion drawn from two clinical studies was that the median frequency of the lung sound power spectrum increases with a decrease in airway calibre. The technique for the analysis of lung sound presented in this thesis is a non-invasive method which may be capable of assessing differences in airway calibre between different lobes of the lung. An expert system for the analysis of lung sound data and pulmonary function data was designed. The expert knowledge was expressed in a belief logic, a system of logic which is more expressive than first order logic. New automated theorem proving methods were developed for the belief logic. The new methods were implemented to form the 'inference engine' of the expert system. The new expert system compared favourably with systems which perform a similar task. The use of belief logic allows introspective reasoning to be carried out. Plausible reasoning, a type of introspective reasoning which allows conclusions to be drawn when the database is incomplete, was proposed and tested. The author concludes that the use of a belief logic in expert system design has significant advantages over conventional approaches. The experimental results of the lung sound research were incorporated into the expert system rule base: the medical and expert system research were complementary

Feature selection and classification for microarray data analysis: Evolutionary methods for identifying predictive genes

BACKGROUND: In the clinical context, samples assayed by microarray are often classified by cell line or tumour type and it is of interest to discover a set of genes that can be used as class predictors. The leukemia dataset of Golub et al. [1] and the NCI60 dataset of Ross et al. [2] present multiclass classification problems where three tumour types and nine cell lines respectively must be identified. We apply an evolutionary algorithm to identify the near-optimal set of predictive genes that classify the data. We also examine the initial gene selection step whereby the most informative genes are selected from the genes assayed. RESULTS: In the absence of feature selection, classification accuracy on the training data is typically good, but not replicated on the testing data. Gene selection using the RankGene software [3] is shown to significantly improve performance on the testing data. Further, we show that the choice of feature selection criteria can have a significant effect on accuracy. The evolutionary algorithm is shown to perform stably across the space of possible parameter settings – indicating the robustness of the approach. We assess performance using a low variance estimation technique, and present an analysis of the genes most often selected as predictors. CONCLUSION: The computational methods we have developed perform robustly and accurately, and yield results in accord with clinical knowledge: A Z-score analysis of the genes most frequently selected identifies genes known to discriminate AML and Pre-T ALL leukemia. This study also confirms that significantly different sets of genes are found to be most discriminatory as the sample classes are refined

Using ant colony optimisation in learning Bayesian network equivalence classes

Bayesian networks are a useful tool in the representation of uncertain knowledge. This paper proposes a new algorithm to learn the structure of a Bayesian network. It does this by conducting a search through the space of equivalence classes of Bayesian networks using Ant Colony Optimization (ACO). To this end, two novel extensions of traditional ACO techniques are proposed and implemented. Firstly, multiple types of moves are allowed on the ACO construction graph. Secondly, moves can be given in terms of arbitrary identifiers. The algorithm is implemented and tested. The results show that ACO performs better than a greedy search whilst searching in the space of equivalence classes