Robust and fast vowel recognition using optimum-path forest

The applications of Automatic Vowel Recognition (AVR), which is a sub-part of fundamental importance in most of the speech processing systems, vary from automatic interpretation of spoken language to biometrics. State-of-the-art systems for AVR are based on traditional machine learning models such as Artificial Neural Networks (ANNs) and Support Vector Machines (SVMs), however, such classifiers can not deal with efficiency and effectiveness at the same time, existing a gap to be explored when real-time processing is required. In this work, we present an algorithm for AVR based on the Optimum-Path Forest (OPF), which is an emergent pattern recognition technique recently introduced in literature. Adopting a supervised training procedure and using speech tags from two public datasets, we observed that OPF has outperformed ANNs, SVMs, plus other classifiers, in terms of training time and accuracy. ©2010 IEEE.

Computational Methods for Identifying Hypertrophic Cardiomyopathy using 12-lead ECG

Hypertrophic cardiomyopathy (HCM) is a cardiovascular disease where the heart muscle is partially thickened and blood flow is - potentially fatally - obstructed. It is one of the leading causes of sudden cardiac death in young people. Electrocardiography (ECG) and Echocardiography (Echo) are the standard tests for identifying HCM and other cardiac abnormalities. The American Heart Association has recommended using a pre-participation questionnaire for young athletes instead of ECG or Echo tests due to considerations of cost and time involved in interpreting the results of these tests by an expert cardiologist. Initially we set out to develop a classifier for automated prediction of young athletes’ heart conditions based on the answers to the questionnaire. Classification results and further in-depth analysis using computational and statistical methods indicated significant shortcomings of the questionnaire in predicting cardiac abnormalities. Automated methods for analyzing ECG signals can help reduce cost and save time in the pre-participation screening process by detecting HCM and other cardiac abnormalities. Therefore, the main goal of this dissertation work is to identify HCM through computational analysis of 12-lead ECG. ECG signals recorded on one or two leads have been analyzed in the past for classifying individual heartbeats into different types of arrhythmia as annotated primarily in the MIT-BIH database. In contrast, we classify complete sequences of 12-lead ECGs to assign patients into two groups: HCM vs. non-HCM. The challenges and issues we address include missing ECG waves in one or more leads and the dimensionality of a large feature-set. We address these by proposing imputation and feature-selection methods. We develop heartbeat-classifiers by employing Random Forests and Support Vector Machines, and propose a method to classify full 12-lead ECGs based on the proportion of heartbeats classified as HCM. The results from our experiments show that the classifiers developed using our methods perform well in identifying HCM. Thus the two contributions of this thesis are the utilization of computational and statistical methods for discovering shortcomings in a current screening procedure and the development of methods to identify HCM through computational analysis of 12-lead ECG signals.

Machine learning for matching astronomy catalogues

An emerging issue in the field of astronomy is the integration, management and utilization of databases from around the world to facilitate scientific discovery. In this paper, we investigate application of the machine learning techniques of support vector machines and neural networks to the problem of amalgamating catalogues of galaxies as objects from two disparate data sources: radio and optical. Formulating this as a classification problem presents several challenges, including dealing with a highly unbalanced data set. Unlike the conventional approach to the problem (which is based on a likelihood ratio) machine learning does not require density estimation and is shown here to provide a significant improvement in performance. We also report some experiments that explore the importance of the radio and optical data features for the matching problem.

On the annealed VC entropy for margin classifiers: A statistical mechanics study

Using techniques from Statistical Physics, the annealed VC entropy for hyperplanes in high dimensional spaces is calculated as a function of the margin for a spherical Gaussian distribution of inputs.

Advances in large margin classifiers

We apply methods of Statistical Mechanics to study the generalization performance of Support vector Machines in large data spaces.

The risk of re-intervention after endovascular aortic aneurysm repair

This thesis studies survival analysis techniques dealing with censoring to produce predictive tools that predict the risk of endovascular aortic aneurysm repair (EVAR) re-intervention. Censoring indicates that some patients do not continue follow up, so their outcome class is unknown. Methods dealing with censoring have drawbacks and cannot handle the high censoring of the two EVAR datasets collected. Therefore, this thesis presents a new solution to high censoring by modifying an approach that was incapable of differentiating between risks groups of aortic complications. Feature selection (FS) becomes complicated with censoring. Most survival FS methods depends on Cox's model, however machine learning classifiers (MLC) are preferred. Few methods adopted MLC to perform survival FS, but they cannot be used with high censoring. This thesis proposes two FS methods which use MLC to evaluate features. The two FS methods use the new solution to deal with censoring. They combine factor analysis with greedy stepwise FS search which allows eliminated features to enter the FS process. The first FS method searches for the best neural networks' configuration and subset of features. The second approach combines support vector machines, neural networks, and K nearest neighbor classifiers using simple and weighted majority voting to construct a multiple classifier system (MCS) for improving the performance of individual classifiers. It presents a new hybrid FS process by using MCS as a wrapper method and merging it with the iterated feature ranking filter method to further reduce the features. The proposed techniques outperformed FS methods based on Cox's model such as; Akaike and Bayesian information criteria, and least absolute shrinkage and selector operator in the log-rank test's p-values, sensitivity, and concordance. This proves that the proposed techniques are more powerful in correctly predicting the risk of re-intervention. Consequently, they enable doctors to set patients’ appropriate future observation plan.

Computational Methods for Identifying Hypertrophic Cardiomyopathy using 12-lead ECG

Hypertrophic cardiomyopathy (HCM) is a cardiovascular disease where the heart muscle is partially thickened and blood flow is - potentially fatally - obstructed. It is one of the leading causes of sudden cardiac death in young people. Electrocardiography (ECG) and Echocardiography (Echo) are the standard tests for identifying HCM and other cardiac abnormalities. The American Heart Association has recommended using a pre-participation questionnaire for young athletes instead of ECG or Echo tests due to considerations of cost and time involved in interpreting the results of these tests by an expert cardiologist. Initially we set out to develop a classifier for automated prediction of young athletes’ heart conditions based on the answers to the questionnaire. Classification results and further in-depth analysis using computational and statistical methods indicated significant shortcomings of the questionnaire in predicting cardiac abnormalities. Automated methods for analyzing ECG signals can help reduce cost and save time in the pre-participation screening process by detecting HCM and other cardiac abnormalities. Therefore, the main goal of this dissertation work is to identify HCM through computational analysis of 12-lead ECG. ECG signals recorded on one or two leads have been analyzed in the past for classifying individual heartbeats into different types of arrhythmia as annotated primarily in the MIT-BIH database. In contrast, we classify complete sequences of 12-lead ECGs to assign patients into two groups: HCM vs. non-HCM. The challenges and issues we address include missing ECG waves in one or more leads and the dimensionality of a large feature-set. We address these by proposing imputation and feature-selection methods. We develop heartbeat-classifiers by employing Random Forests and Support Vector Machines, and propose a method to classify full 12-lead ECGs based on the proportion of heartbeats classified as HCM. The results from our experiments show that the classifiers developed using our methods perform well in identifying HCM. Thus the two contributions of this thesis are the utilization of computational and statistical methods for discovering shortcomings in a current screening procedure and the development of methods to identify HCM through computational analysis of 12-lead ECG signals.

Machine Learning Unsupervised Methods in the Design of an On-board Health Monitoring System for Satellite Applications

The dissertation starts by providing a description of the phenomena related to the increasing importance recently acquired by satellite applications. The spread of such technology comes with implications, such as an increase in maintenance cost, from which derives the interest in developing advanced techniques that favor an augmented autonomy of spacecrafts in health monitoring. Machine learning techniques are widely employed to lay a foundation for effective systems specialized in fault detection by examining telemetry data. Telemetry consists of a considerable amount of information; therefore, the adopted algorithms must be able to handle multivariate data while facing the limitations imposed by on-board hardware features. In the framework of outlier detection, the dissertation addresses the topic of unsupervised machine learning methods. In the unsupervised scenario, lack of prior knowledge of the data behavior is assumed. In the specific, two models are brought to attention, namely Local Outlier Factor and One-Class Support Vector Machines. Their performances are compared in terms of both the achieved prediction accuracy and the equivalent computational cost. Both models are trained and tested upon the same sets of time series data in a variety of settings, finalized at gaining insights on the effect of the increase in dimensionality. The obtained results allow to claim that both models, combined with a proper tuning of their characteristic parameters, successfully comply with the role of outlier detectors in multivariate time series data. Nevertheless, under this specific context, Local Outlier Factor results to be outperforming One-Class SVM, in that it proves to be more stable over a wider range of input parameter values. This property is especially valuable in unsupervised learning since it suggests that the model is keen to adapting to unforeseen patterns.

Machine learning tools for protein annotation: the cases of transmembrane β-barrel and myristoylated proteins

Biology is now a “Big Data Science” thanks to technological advancements allowing the characterization of the whole macromolecular content of a cell or a collection of cells. This opens interesting perspectives, but only a small portion of this data may be experimentally characterized. From this derives the demand of accurate and efficient computational tools for automatic annotation of biological molecules. This is even more true when dealing with membrane proteins, on which my research project is focused leading to the development of two machine learning-based methods: BetAware-Deep and SVMyr. BetAware-Deep is a tool for the detection and topology prediction of transmembrane beta-barrel proteins found in Gram-negative bacteria. These proteins are involved in many biological processes and primary candidates as drug targets. BetAware-Deep exploits the combination of a deep learning framework (bidirectional long short-term memory) and a probabilistic graphical model (grammatical-restrained hidden conditional random field). Moreover, it introduced a modified formulation of the hydrophobic moment, designed to include the evolutionary information. BetAware-Deep outperformed all the available methods in topology prediction and reported high scores in the detection task. Glycine myristoylation in Eukaryotes is the binding of a myristic acid on an N-terminal glycine. SVMyr is a fast method based on support vector machines designed to predict this modification in dataset of proteomic scale. It uses as input octapeptides and exploits computational scores derived from experimental examples and mean physicochemical features. SVMyr outperformed all the available methods for co-translational myristoylation prediction. In addition, it allows (as a unique feature) the prediction of post-translational myristoylation. Both the tools here described are designed having in mind best practices for the development of machine learning-based tools outlined by the bioinformatics community. Moreover, they are made available via user-friendly web servers. All this make them valuable tools for filling the gap between sequential and annotated data.

Modelo de data mining para deteção de embolias pulmonares

Trabalho de Projeto para obtenção do grau de Mestre em Engenharia Informática e de Computadores

Enhancing Multimodal Silent Speech Interfaces With Feature Selection

In research on Silent Speech Interfaces (SSI), different sources of information (modalities) have been combined, aiming at obtaining better performance than the individual modalities. However, when combining these modalities, the dimensionality of the feature space rapidly increases, yielding the well-known "curse of dimensionality". As a consequence, in order to extract useful information from this data, one has to resort to feature selection (FS) techniques to lower the dimensionality of the learning space. In this paper, we assess the impact of FS techniques for silent speech data, in a dataset with 4 non-invasive and promising modalities, namely: video, depth, ultrasonic Doppler sensing, and surface electromyography. We consider two supervised (mutual information and Fisher's ratio) and two unsupervised (meanmedian and arithmetic mean geometric mean) FS filters. The evaluation was made by assessing the classification accuracy (word recognition error) of three well-known classifiers (knearest neighbors, support vector machines, and dynamic time warping). The key results of this study show that both unsupervised and supervised FS techniques improve on the classification accuracy on both individual and combined modalities. For instance, on the video component, we attain relative performance gains of 36.2% in error rates. FS is also useful as pre-processing for feature fusion. Copyright © 2014 ISCA.

Interface caligráfica de escrita no ar

Na atualidade, está a emergir um novo paradigma de interação, designado por Natural User Interface (NUI) para reconhecimento de gestos produzidos com o corpo do utilizador. O dispositivo de interação Microsoft Kinect foi inicialmente concebido para controlo de videojogos, para a consola Xbox360. Este dispositivo demonstra ser uma aposta viável para explorar outras áreas, como a do apoio ao processo de ensino e de aprendizagem para crianças do ensino básico. O protótipo desenvolvido visa definir um modo de interação baseado no desenho de letras no ar, e realizar a interpretação dos símbolos desenhados, usando os reconhecedores de padrões Kernel Discriminant Analysis (KDA), Support Vector Machines (SVM) e $N. O desenvolvimento deste projeto baseou-se no estudo dos diferentes dispositivos NUI disponíveis no mercado, bibliotecas de desenvolvimento NUI para este tipo de dispositivos e algoritmos de reconhecimento de padrões. Com base nos dois elementos iniciais, foi possível obter uma visão mais concreta de qual o hardware e software disponíveis indicados à persecução do objetivo pretendido. O reconhecimento de padrões constitui um tema bastante extenso e complexo, de modo que foi necessária a seleção de um conjunto limitado deste tipo de algoritmos, realizando os respetivos testes por forma a determinar qual o que melhor se adequava ao objetivo pretendido. Aplicando as mesmas condições aos três algoritmos de reconhecimento de padrões permitiu avaliar as suas capacidades e determinar o $N como o que apresentou maior eficácia no reconhecimento. Por último, tentou-se averiguar a viabilidade do protótipo desenvolvido, tendo sido testado num universo de elementos de duas faixas etárias para determinar a capacidade de adaptação e aprendizagem destes dois grupos. Neste estudo, constatou-se um melhor desempenho inicial ao modo de interação do grupo de idade mais avançada. Contudo, o grupo mais jovem foi revelando uma evolutiva capacidade de adaptação a este modo de interação melhorando progressivamente os resultados.

A Clinical Support System Based on Quality of Life Estimation

Quality of life is a concept influenced by social, economic, psychological, spiritual or medical state factors. More specifically, the perceived quality of an individual's daily life is an assessment of their well-being or lack of it. In this context, information technologies may help on the management of services for healthcare of chronic patients such as estimating the patient quality of life and helping the medical staff to take appropriate measures to increase each patient quality of life. This paper describes a Quality of Life estimation system developed using information technologies and the application of data mining algorithms to access the information of clinical data of patients with cancer from Otorhinolaryngology and Head and Neck services of an oncology institution. The system was evaluated with a sample composed of 3013 patients. The results achieved show that there are variables that may be significant predictors for the Quality of Life of the patient: years of smoking (p value 0.049) and size of the tumor (p value < 0.001). In order to assign the variables to the classification of the quality of life the best accuracy was obtained by applying the John Platt's sequential minimal optimization algorithm for training a support vector classifier. In conclusion data mining techniques allow having access to patients additional information helping the physicians to be able to know the quality of life and produce a well-informed clinical decision.

Classificação de tumores de cancro na mama através de radar de banda ultra-larga de microondas

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Active Learning of Very-High Resolution Optical Imagery with SVM: Entropy vs Margin Sampling

An active learning method is proposed for the semi-automatic selection of training sets in remote sensing image classification. The method adds iteratively to the current training set the unlabeled pixels for which the prediction of an ensemble of classifiers based on bagged training sets show maximum entropy. This way, the algorithm selects the pixels that are the most uncertain and that will improve the model if added in the training set. The user is asked to label such pixels at each iteration. Experiments using support vector machines (SVM) on an 8 classes QuickBird image show the excellent performances of the methods, that equals accuracies of both a model trained with ten times more pixels and a model whose training set has been built using a state-of-the-art SVM specific active learning method