Applying Supervised Learning Algorithms and a New Feature Selection Method to Predict Coronary Artery Disease

From a fresh data science perspective, this thesis discusses the prediction of coronary artery disease based on genetic variations at the DNA base pair level, called Single-Nucleotide Polymorphisms (SNPs), collected from the Ontario Heart Genomics Study (OHGS). First, the thesis explains two commonly used supervised learning algorithms, the k-Nearest Neighbour (k-NN) and Random Forest classifiers, and includes a complete proof that the k-NN classifier is universally consistent in any finite dimensional normed vector space. Second, the thesis introduces two dimensionality reduction steps, Random Projections, a known feature extraction technique based on the Johnson-Lindenstrauss lemma, and a new method termed Mass Transportation Distance (MTD) Feature Selection for discrete domains. Then, this thesis compares the performance of Random Projections with the k-NN classifier against MTD Feature Selection and Random Forest, for predicting artery disease based on accuracy, the F-Measure, and area under the Receiver Operating Characteristic (ROC) curve. The comparative results demonstrate that MTD Feature Selection with Random Forest is vastly superior to Random Projections and k-NN. The Random Forest classifier is able to obtain an accuracy of 0.6660 and an area under the ROC curve of 0.8562 on the OHGS genetic dataset, when 3335 SNPs are selected by MTD Feature Selection for classification. This area is considerably better than the previous high score of 0.608 obtained by Davies et al. in 2010 on the same dataset.Comment: This is a Master of Science in Mathematics thesis under the supervision of Dr. Vladimir Pestov and Dr. George Wells submitted on January 31, 2014 at the University of Ottawa; 102 pages and 15 figure

Differential evolution technique on weighted voting stacking ensemble method for credit card fraud detection

Differential Evolution is an optimization technique of stochastic search for a population-based vector, which is powerful and efficient over a continuous space for solving differentiable and non-linear optimization problems. Weighted voting stacking ensemble method is an important technique that combines various classifier models. However, selecting the appropriate weights of classifier models for the correct classification of transactions is a problem. This research study is therefore aimed at exploring whether the Differential Evolution optimization method is a good approach for defining the weighting function. Manual and random selection of weights for voting credit card transactions has previously been carried out. However, a large number of fraudulent transactions were not detected by the classifier models. Which means that a technique to overcome the weaknesses of the classifier models is required. Thus, the problem of selecting the appropriate weights was viewed as the problem of weights optimization in this study. The dataset was downloaded from the Kaggle competition data repository. Various machine learning algorithms were used to weight vote a class of transaction. The differential evolution optimization techniques was used as a weighting function. In addition, the Synthetic Minority Oversampling Technique (SMOTE) and Safe Level Synthetic Minority Oversampling Technique (SL-SMOTE) oversampling algorithms were modified to preserve the definition of SMOTE while improving the performance. Result generated from this research study showed that the Differential Evolution Optimization method is a good weighting function, which can be adopted as a systematic weight function for weight voting stacking ensemble method of various classification methods.School of ComputingM. Sc. (Computing

Novel Computationally Intelligent Machine Learning Algorithms for Data Mining and Knowledge Discovery

This thesis addresses three major issues in data mining regarding feature subset selection in large dimensionality domains, plausible reconstruction of incomplete data in cross-sectional applications, and forecasting univariate time series. For the automated selection of an optimal subset of features in real time, we present an improved hybrid algorithm: SAGA. SAGA combines the ability to avoid being trapped in local minima of Simulated Annealing with the very high convergence rate of the crossover operator of Genetic Algorithms, the strong local search ability of greedy algorithms and the high computational efficiency of generalized regression neural networks (GRNN). For imputing missing values and forecasting univariate time series, we propose a homogeneous neural network ensemble. The proposed ensemble consists of a committee of Generalized Regression Neural Networks (GRNNs) trained on different subsets of features generated by SAGA and the predictions of base classifiers are combined by a fusion rule. This approach makes it possible to discover all important interrelations between the values of the target variable and the input features. The proposed ensemble scheme has two innovative features which make it stand out amongst ensemble learning algorithms: (1) the ensemble makeup is optimized automatically by SAGA; and (2) GRNN is used for both base classifiers and the top level combiner classifier. Because of GRNN, the proposed ensemble is a dynamic weighting scheme. This is in contrast to the existing ensemble approaches which belong to the simple voting and static weighting strategy. The basic idea of the dynamic weighting procedure is to give a higher reliability weight to those scenarios that are similar to the new ones. The simulation results demonstrate the validity of the proposed ensemble model

Phylogenetic Machine Learning Methods and Application to Mammal Dental Traits and Bioclimatic Variables

Standard machine learning procedures are based on assumption that training and testing data is sampled independently from identical distributions. Comparative data of traits in biological species breaks this assumption. Data instances are related by ancestry relationships, that is phylogeny. In this study, new machine learning procedures are presented that take into account phylogenetic information when fitting predictive models. Phylogenetic statistics for classification accuracy and error are proposed based on the concept of effective sample size. Versions of perceptron training and KNN classification are built on these metrics. Procedures for regularised PGLS regression, phylogenetic KNN regression, neural network regression and regression trees are presented. Properties of phylogenetic perceptron training and KNN regression are studied with synthetic data. Experiments demonstrate that phylogenetic perceptron training improves robustness when the phylogeny is unbalanced. Regularised PGLS and KNN regression are applied to mammal dental traits and environments to both test the algorithms and gain insights in the relationship of mammal teeth and the environment

Finding the online cry for help : automatic text classification for suicide prevention

Successful prevention of suicide, a serious public health concern worldwide, hinges on the adequate detection of suicide risk. While online platforms are increasingly used for expressing suicidal thoughts, manually monitoring for such signals of distress is practically infeasible, given the information overload suicide prevention workers are confronted with. In this thesis, the automatic detection of suicide-related messages is studied. It presents the first classification-based approach to online suicidality detection, and focuses on Dutch user-generated content. In order to evaluate the viability of such a machine learning approach, we developed a gold standard corpus, consisting of message board and blog posts. These were manually labeled according to a newly developed annotation scheme, grounded in suicide prevention practice. The scheme provides for the annotation of a post's relevance to suicide, and the subject and severity of a suicide threat, if any. This allowed us to derive two tasks: the detection of suicide-related posts, and of severe, high-risk content. In a series of experiments, we sought to determine how well these tasks can be carried out automatically, and which information sources and techniques contribute to classification performance. The experimental results show that both types of messages can be detected with high precision. Therefore, the amount of noise generated by the system is minimal, even on very large datasets, making it usable in a real-world prevention setting. Recall is high for the relevance task, but at around 60%, it is considerably lower for severity. This is mainly attributable to implicit references to suicide, which often go undetected. We found a variety of information sources to be informative for both tasks, including token and character ngram bags-of-words, features based on LSA topic models, polarity lexicons and named entity recognition, and suicide-related terms extracted from a background corpus. To improve classification performance, the models were optimized using feature selection, hyperparameter, or a combination of both. A distributed genetic algorithm approach proved successful in finding good solutions for this complex search problem, and resulted in more robust models. Experiments with cascaded classification of the severity task did not reveal performance benefits over direct classification (in terms of F1-score), but its structure allows the use of slower, memory-based learning algorithms that considerably improved recall. At the end of this thesis, we address a problem typical of user-generated content: noise in the form of misspellings, phonetic transcriptions and other deviations from the linguistic norm. We developed an automatic text normalization system, using a cascaded statistical machine translation approach, and applied it to normalize the data for the suicidality detection tasks. Subsequent experiments revealed that, compared to the original data, normalized data resulted in fewer and more informative features, and improved classification performance. This extrinsic evaluation demonstrates the utility of automatic normalization for suicidality detection, and more generally, text classification on user-generated content