This paper explores how known machine learning techniques can be applied in unique ways to simplify software and therefore dramatically increase its usability. As software has increased in popularity, its complexity has increased in lockstep, to a point where it has become burdensome. By shifting the focus from the software to the user, great advances can be achieved by way of simplification. The example problem used in this report is well known: suggest local dining choices tailored to a specific person based on known habits and those of similar people. By analyzing past choices and applying likely probabilities, assumptions can be made to reduce user interaction, allowing the user to realize the benefits of the software faster and more frequently. This is accomplished with Java Servlets, Apache Mahout machine learning libraries, and various third party resources to gather dimensions on each recommendation. / text

Phenotypes and diseases may be related by seemingly dissimilar phenotypes in other species by means of the orthology of underlying genes. Such "orthologous phenotypes," or "phenologs," are examples of deep homology, and one member of the orthology relationship may be used to predict candidate genes for its counterpart. (There exists evidence of "paralogous phenotypes" as well, but validation is non-trivial.) In Chapter 2, I demonstrate the utility of including plant phenotypes in our database, and provide as an example the prediction of mammalian neural crest defects from an Arabidopsis thaliana phenotype, negative gravitropism defective. In the third chapter, I describe the incorporation of additional phenotypes into our database (including chicken, zebrafish, E. coli, and new C. elegans datasets). I present a method, developed in coordination with Martin Singh-Blom, for ranking predicted candidate genes by way of a k nearest neighbors naïve Bayes classifier drawing phenolog information from a variety of species. The fourth chapter relates to a computational method and application for identifying shared and overlapping pathways which contribute to phenotypes. I describe a method for rapidly querying a database of phenotype--gene associations for Boolean combinations of phenotypes which yields improved predictions. This method offers insight into the divergence of orthologous pathways in evolution. I demonstrate connections between breast cancer and zebrafish methylmercury response (through oxidative stress and apoptosis); human myopathy and plant red light response genes, minus those involved in water deprivation response (via autophagy); and holoprosencephaly and an array of zebrafish phenotypes. In the first appendix, I present the SciRuby Project, which I co-founded in order to bring scientific libraries to the Ruby programming language. I describe the motivation behind SciRuby and my role in its creation. Finally in Appendix B, I discuss the first beta release of NMatrix, a dense and sparse matrix library for the Ruby language, which I developed in part to facilitate and validate rapid phenolog searches. In this work, I describe the concept of phenologs as well as the development of the necessary computational tools for discovering phenotype orthology relationships, for predicting associated genes, and for statistically validating the discovered relationships and predicted associations. / text

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Aggregated data appears in many areas such as econimics, sociology, geography, etc. This motivates an importance of studying the (dis)aggregation problem. One of the most important reasons why the contemporaneous aggregation become an object of research is the possibility of obtaining the long memory phenomena in processes. The aggregation provides an explanation of the long-memory effect in time series and a simulation method of such series as well. Accumulation of short-memory non-ergodic random processes can lead to the long memory ergodic process, that can be used for the forecasts of the macro and micro variables. We explore the aggregation scheme of AR(1) processes and nearest-neighbour random fields with infinite variance. We provide results on the existence of limit aggregated processes, and find conditions under which it has long memory properties in certain sense. For the random fields on Z^2, we introduce the notion of (an)isotropic long memory based on the behavior of partial sums. In L_2 case, the known aggregation of independent AR(1) processes leads to the Gaussian limit. While we describe a new model of aggregation based on independent triangular arrays. This scheme gives the limit aggregated process with finite variance which is not necessary Gaussian. We study a discrete time risk insurance model with stationary claims, modeled by the aggregated heavy-tailed process. We establish the asymptotic properties of the ruin probability and the dependence structure... [to full text] / Agreguoti duomenys naudojami daugelyje mokslo sričių tokių kaip ekonomika, sociologija, geografija ir kt. Tai motyvuoja tirti (de)agregavimo uždavinį. Viena iš pagrindinių priežasčių kodėl vienalaikis agregavimas tapo tyrimų objektu yra galimybė gauti ilgos atminties procesus. Agregavimas paaiškina ilgos atminties atsiradima procesuose ir yra vienas iš būdų tokius procesus generuoti. Agreguodami trumpos atminties neergodiškus atsitiktinius procesus, galime gauti ilgos atminties ergodišką procesą, kuris gali būti naudojamas mikro ir makro kintamųjų prognozavimui. Disertacijoje nagrinėjama AR(1) procesų bei artimiausio kaimyno atsitiktinių laukų, turinčių begalinę dispersiją, agregavimo schema, randamos sąlygos, kurioms esant ribinis agreguotas procesas egzistuoja, ir turi ilgąją atmintį tam tikra prasme. Atsitiktinių laukų atveju, įvedamas anizotropinės/izotropinės ilgos atminties apibrėžimas, kuris yra paremtas dalinių sumų elgesiu. Baigtinės dispersijos atveju yra gerai žinoma nepriklausomų AR(1) procesų schema, kuri rezultate duoda Gauso ribinį agreguotą procesą. Disertacijoje aprašoma trikampio masyvo agregavimo modelis, kuris baigtinės dispersijos atveju duoda nebūtinai Gauso ribinį agreguotą procesą. Taip pat disertacijoje nagrinėjama bankroto tikimybės asimptotika, kai žalos yra aprašomos sunkiauodegiu agreguotu procesu, nusakoma priklausomybė tarp žalų, apibūdinama žalų ilga atmintis.

Agreguoti duomenys naudojami daugelyje mokslo sričių tokių kaip ekonomika, sociologija, geografija ir kt. Tai motyvuoja tirti (de)agregavimo uždavinį. Viena iš pagrindinių priežasčių kodėl vienalaikis agregavimas tapo tyrimų objektu yra galimybė gauti ilgos atminties procesus. Agregavimas paaiškina ilgos atminties atsiradima procesuose ir yra vienas iš būdų tokius procesus generuoti. Agreguodami trumpos atminties neergodiškus atsitiktinius procesus, galime gauti ilgos atminties ergodišką procesą, kuris gali būti naudojamas mikro ir makro kintamųjų prognozavimui. Disertacijoje nagrinėjama AR(1) procesų bei artimiausio kaimyno atsitiktinių laukų, turinčių begalinę dispersiją, agregavimo schema, randamos sąlygos, kurioms esant ribinis agreguotas procesas egzistuoja, ir turi ilgąją atmintį tam tikra prasme. Atsitiktinių laukų atveju, įvedamas anizotropinės/izotropinės ilgos atminties apibrėžimas, kuris yra paremtas dalinių sumų elgesiu. Baigtinės dispersijos atveju yra gerai žinoma nepriklausomų AR(1) procesų schema, kuri rezultate duoda Gauso ribinį agreguotą procesą. Disertacijoje aprašoma trikampio masyvo agregavimo modelis, kuris baigtinės dispersijos atveju duoda nebūtinai Gauso ribinį agreguotą procesą. Taip pat disertacijoje nagrinėjama bankroto tikimybės asimptotika, kai žalos yra aprašomos sunkiauodegiu agreguotu procesu, nusakoma priklausomybė tarp žalų, apibūdinama žalų ilga atmintis. / Aggregated data appears in many areas such as econimics, sociology, geography, etc. This motivates an importance of studying the (dis)aggregation problem. One of the most important reasons why the contemporaneous aggregation become an object of research is the possibility of obtaining the long memory phenomena in processes. The aggregation provides an explanation of the long-memory effect in time series and a simulation method of such series as well. Accumulation of short-memory non-ergodic random processes can lead to the long memory ergodic process, that can be used for the forecasts of the macro and micro variables. We explore the aggregation scheme of AR(1) processes and nearest-neighbour random fields with infinite variance. We provide results on the existence of limit aggregated processes, and find conditions under which it has long memory properties in certain sense. For the random fields on Z^2, we introduce the notion of (an)isotropic long memory based on the behavior of partial sums. In L_2 case, the known aggregation of independent AR(1) processes leads to the Gaussian limit. While we describe a new model of aggregation based on independent triangular arrays. This scheme gives the limit aggregated process with finite variance which is not necessary Gaussian. We study a discrete time risk insurance model with stationary claims, modeled by the aggregated heavy-tailed process. We establish the asymptotic properties of the ruin probability and the dependence structure... [to full text]

Spacecraft design is inherently difficult due to the nonlinearity of the systems involved as well as the expense of testing hardware in a realistic environment. The number and cost of flight tests can be reduced by performing extensive simulation and analysis work to understand vehicle operating limits and identify circumstances that lead to mission failure. A Monte Carlo simulation approach that varies a wide range of physical parameters is typically used to generate thousands of test cases. Currently, the data analysis process for a fully integrated spacecraft is mostly performed manually on a case-by-case basis, often requiring several analysts to write additional scripts in order to sort through the large data sets. There is no single method that can be used to identify these complex variable interactions in a reliable and timely manner as well as be applied to a wide range of flight dynamics problems. This dissertation investigates the feasibility of a unified, general approach to the process of analyzing flight dynamics Monte Carlo data. The main contribution of this work is the development of a systematic approach to finding and ranking the most influential variables and combinations of variables for a given system failure. Specifically, a practical and interactive analysis tool that uses tractable pattern recognition methods to automate the analysis process has been developed. The analysis tool has two main parts: the analysis of individual influential variables and the analysis of influential combinations of variables. This dissertation describes in detail the two main algorithms used: kernel density estimation and nearest neighbors. Both are non-parametric density estimation methods that are used to analyze hundreds of variables and combinations thereof to provide an analyst with insightful information about the potential cause for a specific system failure. Examples of dynamical systems analysis tasks using the tool are provided.

In order to obtain perspectives of Canadian dentists on the quality of the undergraduate education received in orthodontics and the extent of orthodontic services provided, a descriptive survey was constructed. Methods An anonymous, web-based survey was created using Survey Monkey® (Palo Alto, USA), and distributed to registered dentists in Canada via links in newsletters and mass emails. Results There were 427 respondents. Results showed that 71% of dentists provide some orthodontic treatment, and 33% of them offered only space maintainers. A total of 23% treated most of their patients requiring interceptive treatment, compared to 15% for those requiring comprehensive treatment. A driving time greater than 1 hour to the closest orthodontist resulted in a 16% increase in the provision of orthodontic treatment by the general dentists. The undergraduate orthodontic education was deemed above average by 21.4% to 50.5% of the respondents. Conclusions The percentage of dentists currently providing orthodontic services to their patients is similar to previous reports. A driving time of more than 1 hour is an influencing factor on the provision of orthodontic treatment by Canadian general dentists. The quality of undergraduate orthodontic education provided has improved over the last 25 years, although some amelioration may be beneficial.

Age related macular degeneration (AMD) is a public health concern in an aging society. The retinal pigment epithelium (RPE) layer of the eye is a principal site of pathogenesis for AMD. Morphological characteristics of the cells in the RPE layer can be used to discriminate age and disease status of individuals. In this thesis three genotypes of mice of various ages are used to study the predictive abilities of these characteristics. The disease state is represented by two mutant genotypes and the healthy state by the wild-type. Classification analysis is applied to the RPE morphology from the different spatial regions of the RPE layer. Variable reduction is accomplished by principal component analysis (PCA) and classification analysis by the k-nearest neighbor (k-NN) algorithm. In this way the differential ability of the spatial regions to predict age and disease status by cellular variables is explored.

The two-stage data mining technique for classifications in tourism recommendation system is necessary to connect user perception, decision criteria and decision purpose. In existed literature, hybrid data mining method combining Decision Tree and K-nearest neighbour approaches (DTKNN) were proposed. It has a high precision rate of approximately 80% in K-nearest Neighbour (KNN) but a much lower rate in the first stage using Decision Tree (Fu & Tu, 2011). It included two potential improvements on two-stage technique. To improve the first stage of DTKNN in precision rate and the efficiency, the amount of questions is decreased when users search for the desired recommendation on the system. In this paper, the researcher investigates the way to improve the first stage of DTKNN for full questionnaires and also determines the suitability of dynamic questionnaire based on its precision rate in future tourism recommendation system. Firstly, this study compared and chose the highest precision rate among Decision Tree, Multi-staged Binary Tree and Back Propagation of Error Neural Network (BPNN). The chosen method is then combined with KNN to propose a new methodology. Secondly, the study compared and deter¬mined the suitability of dynamic questionnaires for all three classification methods by decreasing the number of attributes. The suitable dynamic questionnaire is based on the least amount of attributes used with an appropriate precision rate. Tourism recommendation system is selected as the target to apply and analyse the usefulness of the algorithm as tourism selection is a two-stage example. Tourism selection is to determine expected goal and experience before going on a tour at the first stage and to choose the tour that best matches stage one. The result indicates that Multi-staged Bi¬nary Tree has the highest precision rate of 74.167% comparing to Decision Tree with 73.33% then BPNN with 65.47% for full questionnaire. This new approach will improve the effectiveness of the system by improving the precision rate of first stage under the current DTKNN method. For dynamic questionnaire, the result has shown that Decision Tree is the most suitable method given that it resulted in the least difference of 1.33% in precision rate comparing to full questionnaire, as opposed to 1.48% for BPNN and 4% for Multi-staged Binary Tree. Thus, dynamic questionnaire will also improve the efficiency by decreasing the amount of questions which users are required to fill in when searching for the desired recommendation on the system. It provides users with the option to not answer some questions. It also increases the practicality of non-dynamic questionnaire and, therefore, affects the ultimate precision rate.

This thesis deals with a series of quantum computer implementation issues from the Kane 31P in 28Si architecture to Shor’s integer factoring algorithm and beyond. The discussion begins with simulations of the adiabatic Kane CNOT and readout gates, followed by linear nearest neighbor implementations of 5-qubit quantum error correction with and without fast measurement. A linear nearest neighbor circuit implementing Shor’s algorithm is presented, then modified to remove the need for exponentially small rotation gates. Finally, a method of constructing optimal approximations of arbitrary single-qubit fault-tolerant gates is described and applied to the specific case of the remaining rotation gates required by Shor’s algorithm.