A Research Platform for Artificial Neural Networks with Applications in Pediatric Epilepsy

This dissertation established a state-of-the-art programming tool for designing and training artificial neural networks (ANNs) and showed its applicability to brain research. The developed tool, called NeuralStudio, allows users without programming skills to conduct studies based on ANNs in a powerful and very user friendly interface. A series of unique features has been implemented in NeuralStudio, such as ROC analysis, cross-validation, network averaging, topology optimization, and optimization of the activation function’s slopes. It also included a Support Vector Machines module for comparison purposes. Once the tool was fully developed, it was applied to two studies in brain research. In the first study, the goal was to create and train an ANN to detect epileptic seizures from subdural EEG. This analysis involved extracting features from the spectral power in the gamma frequencies. In the second application, a unique method was devised to link EEG recordings to epileptic and non-epileptic subjects. The contribution of this method consisted of developing a descriptor matrix that can be used to represent any EEG file regarding its duration and the number of electrodes. The first study showed that the inter-electrode mean of the spectral power in the gamma frequencies and its duration above a specific threshold performs better than the other frequencies in seizure detection, exhibiting an accuracy of 95.90%, a sensitivity of 92.59%, and a specificity of 96.84%. The second study yielded that Hjorth’s parameter activity is sufficient to accurately relate EEG to epileptic and non-epileptic subjects. After testing, accuracy, sensitivity and specificity of the classifier were all above 0.9667. Statistical tests measured the superiority of activity at over 99.99 % certainty. It was demonstrated that 1) the spectral power in the gamma frequencies is highly effective in locating seizures from EEG and 2) activity can be used to link EEG recordings to epileptic and non-epileptic subjects. These two studies required high computational load and could be addressed thanks to NeuralStudio. From a medical perspective, both methods proved the merits of NeuralStudio in brain research applications. For its outstanding features, NeuralStudio has been recently awarded a patent (US patent No. 7502763).

A Digital Signal Processing Approach for Affective Sensing of a Computer User through Pupil Diameter Monitoring

Recent research has indicated that the pupil diameter (PD) in humans varies with their affective states. However, this signal has not been fully investigated for affective sensing purposes in human-computer interaction systems. This may be due to the dominant separate effect of the pupillary light reflex (PLR), which shrinks the pupil when light intensity increases. In this dissertation, an adaptive interference canceller (AIC) system using the H∞ time-varying (HITV) adaptive algorithm was developed to minimize the impact of the PLR on the measured pupil diameter signal. The modified pupil diameter (MPD) signal, obtained from the AIC was expected to reflect primarily the pupillary affective responses (PAR) of the subject. Additional manipulations of the AIC output resulted in a processed MPD (PMPD) signal, from which a classification feature, PMPDmean, was extracted. This feature was used to train and test a support vector machine (SVM), for the identification of stress states in the subject from whom the pupil diameter signal was recorded, achieving an accuracy rate of 77.78%. The advantages of affective recognition through the PD signal were verified by comparatively investigating the classification of stress and relaxation states through features derived from the simultaneously recorded galvanic skin response (GSR) and blood volume pulse (BVP) signals, with and without the PD feature. The discriminating potential of each individual feature extracted from GSR, BVP and PD was studied by analysis of its receiver operating characteristic (ROC) curve. The ROC curve found for the PMPDmean feature encompassed the largest area (0.8546) of all the single-feature ROCs investigated. The encouraging results seen in affective sensing based on pupil diameter monitoring were obtained in spite of intermittent illumination increases purposely introduced during the experiments. Therefore, these results confirmed the benefits of using the AIC implementation with the HITV adaptive algorithm to isolate the PAR and the potential of using PD monitoring to sense the evolving affective states of a computer user.

LCD-OpenPACS: sistema integrado de telerradiologia com auxílio ao diagnóstico de nódulos pulmonares em exames de tomografia computadorizada

Lung cancer is one of the most common types of cancer and has the highest mortality rate. Patient survival is highly correlated with early detection. Computed Tomography technology services the early detection of lung cancer tremendously by offering aminimally invasive medical diagnostic tool. However, the large amount of data per examination makes the interpretation difficult. This leads to omission of nodules by human radiologist. This thesis presents a development of a computer-aided diagnosis system (CADe) tool for the detection of lung nodules in Computed Tomography study. The system, called LCD-OpenPACS (Lung Cancer Detection - OpenPACS) should be integrated into the OpenPACS system and have all the requirements for use in the workflow of health facilities belonging to the SUS (Brazilian health system). The LCD-OpenPACS made use of image processing techniques (Region Growing and Watershed), feature extraction (Histogram of Gradient Oriented), dimensionality reduction (Principal Component Analysis) and classifier (Support Vector Machine). System was tested on 220 cases, totaling 296 pulmonary nodules, with sensitivity of 94.4% and 7.04 false positives per case. The total time for processing was approximately 10 minutes per case. The system has detected pulmonary nodules (solitary, juxtavascular, ground-glass opacity and juxtapleural) between 3 mm and 30 mm.

Classificador máquina de suporte vetorial com análise de Fourier aplicada em dados de EEG e EMG

The classifier support vector machine is used in several problems in various areas of knowledge. Basically the method used in this classier is to end the hyperplane that maximizes the distance between the groups, to increase the generalization of the classifier. In this work, we treated some problems of binary classification of data obtained by electroencephalography (EEG) and electromyography (EMG) using Support Vector Machine with some complementary techniques, such as: Principal Component Analysis to identify the active regions of the brain, the periodogram method which is obtained by Fourier analysis to help discriminate between groups and Simple Moving Average to eliminate some of the existing noise in the data. It was developed two functions in the software R, for the realization of training tasks and classification. Also, it was proposed two weights systems and a summarized measure to help on deciding in classification of groups. The application of these techniques, weights and the summarized measure in the classier, showed quite satisfactory results, where the best results were an average rate of 95.31% to visual stimuli data, 100% of correct classification for epilepsy data and rates of 91.22% and 96.89% to object motion data for two subjects.

Sistema inteligente para o processamento de imagens digitais intrabucais oclusais

Several are the areas in which digital images are used in solving day-to-day problems. In medicine the use of computer systems have improved the diagnosis and medical interpretations. In dentistry it’s not different, increasingly procedures assisted by computers have support dentists in their tasks. Set in this context, an area of dentistry known as public oral health is responsible for diagnosis and oral health treatment of a population. To this end, oral visual inspections are held in order to obtain oral health status information of a given population. From this collection of information, also known as epidemiological survey, the dentist can plan and evaluate taken actions for the different problems identified. This procedure has limiting factors, such as a limited number of qualified professionals to perform these tasks, different diagnoses interpretations among other factors. Given this context came the ideia of using intelligent systems techniques in supporting carrying out these tasks. Thus, it was proposed in this paper the development of an intelligent system able to segment, count and classify teeth from occlusal intraoral digital photographic images. The proposed system makes combined use of machine learning techniques and digital image processing. We first carried out a color-based segmentation on regions of interest, teeth and non teeth, in the images through the use of Support Vector Machine. After identifying these regions were used techniques based on morphological operators such as erosion and transformed watershed for counting and detecting the boundaries of the teeth, respectively. With the border detection of teeth was possible to calculate the Fourier descriptors for their shape and the position descriptors. Then the teeth were classified according to their types through the use of the SVM from the method one-against-all used in multiclass problem. The multiclass classification problem has been approached in two different ways. In the first approach we have considered three class types: molar, premolar and non teeth, while the second approach were considered five class types: molar, premolar, canine, incisor and non teeth. The system presented a satisfactory performance in the segmenting, counting and classification of teeth present in the images.

Sistema inteligente para o processamento de imagens digitais intrabucais oclusais

Several are the areas in which digital images are used in solving day-to-day problems. In medicine the use of computer systems have improved the diagnosis and medical interpretations. In dentistry it’s not different, increasingly procedures assisted by computers have support dentists in their tasks. Set in this context, an area of dentistry known as public oral health is responsible for diagnosis and oral health treatment of a population. To this end, oral visual inspections are held in order to obtain oral health status information of a given population. From this collection of information, also known as epidemiological survey, the dentist can plan and evaluate taken actions for the different problems identified. This procedure has limiting factors, such as a limited number of qualified professionals to perform these tasks, different diagnoses interpretations among other factors. Given this context came the ideia of using intelligent systems techniques in supporting carrying out these tasks. Thus, it was proposed in this paper the development of an intelligent system able to segment, count and classify teeth from occlusal intraoral digital photographic images. The proposed system makes combined use of machine learning techniques and digital image processing. We first carried out a color-based segmentation on regions of interest, teeth and non teeth, in the images through the use of Support Vector Machine. After identifying these regions were used techniques based on morphological operators such as erosion and transformed watershed for counting and detecting the boundaries of the teeth, respectively. With the border detection of teeth was possible to calculate the Fourier descriptors for their shape and the position descriptors. Then the teeth were classified according to their types through the use of the SVM from the method one-against-all used in multiclass problem. The multiclass classification problem has been approached in two different ways. In the first approach we have considered three class types: molar, premolar and non teeth, while the second approach were considered five class types: molar, premolar, canine, incisor and non teeth. The system presented a satisfactory performance in the segmenting, counting and classification of teeth present in the images.

Classificação de atividade eletromiográfia facial de indivíduos saudáveis e com hanseníese por meio de máquina de vetores de suporte

A number of studies in the areas of Biomedical Engineering and Health Sciences have employed machine learning tools to develop methods capable of identifying patterns in different sets of data. Despite its extinction in many countries of the developed world, Hansen’s disease is still a disease that affects a huge part of the population in countries such as India and Brazil. In this context, this research proposes to develop a method that makes it possible to understand in the future how Hansen’s disease affects facial muscles. By using surface electromyography, a system was adapted so as to capture the signals from the largest possible number of facial muscles. We have first looked upon the literature to learn about the way researchers around the globe have been working with diseases that affect the peripheral neural system and how electromyography has acted to contribute to the understanding of these diseases. From these data, a protocol was proposed to collect facial surface electromyographic (sEMG) signals so that these signals presented a high signal to noise ratio. After collecting the signals, we looked for a method that would enable the visualization of this information in a way to make it possible to guarantee that the method used presented satisfactory results. After identifying the method's efficiency, we tried to understand which information could be extracted from the electromyographic signal representing the collected data. Once studies demonstrating which information could contribute to a better understanding of this pathology were not to be found in literature, parameters of amplitude, frequency and entropy were extracted from the signal and a feature selection was made in order to look for the features that better distinguish a healthy individual from a pathological one. After, we tried to identify the classifier that best discriminates distinct individuals from different groups, and also the set of parameters of this classifier that would bring the best outcome. It was identified that the protocol proposed in this study and the adaptation with disposable electrodes available in market proved their effectiveness and capability of being used in different studies whose intention is to collect data from facial electromyography. The feature selection algorithm also showed that not all of the features extracted from the signal are significant for data classification, with some more relevant than others. The classifier Support Vector Machine (SVM) proved itself efficient when the adequate Kernel function was used with the muscle from which information was to be extracted. Each investigated muscle presented different results when the classifier used linear, radial and polynomial kernel functions. Even though we have focused on Hansen’s disease, the method applied here can be used to study facial electromyography in other pathologies.

Classificação de atividade eletromiográfia facial de indivíduos saudáveis e com hanseníase por meio de máquina de vetores de suporte

A number of studies in the areas of Biomedical Engineering and Health Sciences have employed machine learning tools to develop methods capable of identifying patterns in different sets of data. Despite its extinction in many countries of the developed world, Hansen’s disease is still a disease that affects a huge part of the population in countries such as India and Brazil. In this context, this research proposes to develop a method that makes it possible to understand in the future how Hansen’s disease affects facial muscles. By using surface electromyography, a system was adapted so as to capture the signals from the largest possible number of facial muscles. We have first looked upon the literature to learn about the way researchers around the globe have been working with diseases that affect the peripheral neural system and how electromyography has acted to contribute to the understanding of these diseases. From these data, a protocol was proposed to collect facial surface electromyographic (sEMG) signals so that these signals presented a high signal to noise ratio. After collecting the signals, we looked for a method that would enable the visualization of this information in a way to make it possible to guarantee that the method used presented satisfactory results. After identifying the method's efficiency, we tried to understand which information could be extracted from the electromyographic signal representing the collected data. Once studies demonstrating which information could contribute to a better understanding of this pathology were not to be found in literature, parameters of amplitude, frequency and entropy were extracted from the signal and a feature selection was made in order to look for the features that better distinguish a healthy individual from a pathological one. After, we tried to identify the classifier that best discriminates distinct individuals from different groups, and also the set of parameters of this classifier that would bring the best outcome. It was identified that the protocol proposed in this study and the adaptation with disposable electrodes available in market proved their effectiveness and capability of being used in different studies whose intention is to collect data from facial electromyography. The feature selection algorithm also showed that not all of the features extracted from the signal are significant for data classification, with some more relevant than others. The classifier Support Vector Machine (SVM) proved itself efficient when the adequate Kernel function was used with the muscle from which information was to be extracted. Each investigated muscle presented different results when the classifier used linear, radial and polynomial kernel functions. Even though we have focused on Hansen’s disease, the method applied here can be used to study facial electromyography in other pathologies.

Identificación de imágenes por análisis de texturas utilizando aprendizaje estadístico

Este documento explica la creación, implementación y uso del proyecto de fin de grado, desarrollado dentro del grupo de investigación ISCAR (Ingeniería de Sistemas, Control, Automática y Robótica) de la Facultad de Informática de la Universidad Complutense. El proyecto consiste en la implementación de una aplicación capaz de clasificar texturas extraídas de distintas imágenes mediante técnicas de visión por computador. Dicha aplicación se divide en tres pilares fundamentales: interfaz gráfica de usuario, algoritmos de extracción de características texturales y aprendizaje supervisado mediante una máquina “SVM” (Support Vector Machine). Interfaz gráfica: proporciona al usuario una forma fácil de uso de la aplicación por medio de la visualización gráfica de una imagen con una serie de elementos de configuración para su posterior análisis. Una vez analizada, el usuario si así lo desea, podrá visualizar los resultados de manera intuitiva, así como guardar dichos resultados después de la ejecución de los algoritmos pertinentes. Algoritmos de análisis de texturas: Procede al cálculo de las configuraciones y las muestras provistas por el usuario en la interfaz gráfica como el cálculo de la matriz de co-ocurrencia y el cálculo de los vectores de características (homogeneidad, media, varianza, Entropía, etc…). SVM: Utiliza los vectores de características obtenidos en los cálculos estadísticos de texturas para realizar el proceso de aprendizaje de un clasificador SVM. La aplicación ha sido construida en JAVA haciendo uso de librerías como JNI_SVM-light-6.01, commons-math3-3.0 y WindowsBuilder, para la construcción de la ventana gráfica, cálculo de los métodos estadísticos y máquina de aprendizaje automático. Dicha aplicación se ha utilizado con el objetivo de identificar y clasificar el quiste de Baker mediante imágenes obtenidas por Resonancias Magnéticas de la rodilla.

The permafrost carbon inventory on the Tibetan Plateau : a new evaluation using deep sediment cores

Acknowledgements We are grateful for Dr. Jens Strauss and the other two anonymous reviewers for their insightful comments on an earlier version of this MS, and appreciate members of the IBCAS Sampling Campaign Teams for their assistance in field investigation. This work was supported by the National Basic Research Program of China on Global Change (2014CB954001 and 2015CB954201), National Natural Science Foundation of China (31322011 and 41371213), and the Thousand Young Talents Program.

Facial affect processing inbipolar disorder:a magnetoencephalography study

Background: Identifying biological markers to aid diagnosis of bipolar disorder (BD) is critically important. To be considered a possible biological marker, neural patterns in BD should be discriminant from those in healthy individuals (HI). We examined patterns of neuromagnetic responses revealed by magnetoencephalography (MEG) during implicit emotion-processing using emotional (happy, fearful, sad) and neutral facial expressions, in sixteen BD and sixteen age- and gender-matched healthy individuals. Methods: Neuromagnetic data were recorded using a 306-channel whole-head MEG ELEKTA Neuromag System, and preprocessed using Signal Space Separation as implemented in MaxFilter (ELEKTA). Custom Matlab programs removed EOG and ECG signals from filtered MEG data, and computed means of epoched data (0-250ms, 250-500ms, 500-750ms). A generalized linear model with three factors (individual, emotion intensity and time) compared BD and HI. A principal component analysis of normalized mean channel data in selected brain regions identified principal components that explained 95% of data variation. These components were used in a quadratic support vector machine (SVM) pattern classifier. SVM classifier performance was assessed using the leave-one-out approach. Results: BD and HI showed significantly different patterns of activation for 0-250ms within both left occipital and temporal regions, specifically for neutral facial expressions. PCA analysis revealed significant differences between BD and HI for mild fearful, happy, and sad facial expressions within 250-500ms. SVM quadratic classifier showed greatest accuracy (84%) and sensitivity (92%) for neutral faces, in left occipital regions within 500-750ms. Conclusions: MEG responses may be used in the search for disease specific neural markers.

Can a Broader Education Narrow the Gap? Evidence on Non-Academic Features of Schooling

Empirical studies of education programs and systems, by nature, rely upon use of student outcomes that are measurable. Often, these come in the form of test scores. However, in light of growing evidence about the long-run importance of other student skills and behaviors, the time has come for a broader approach to evaluating education. This dissertation undertakes experimental, quasi-experimental, and descriptive analyses to examine social, behavioral, and health-related mechanisms of the educational process. My overarching research question is simply, which inside- and outside-the-classroom features of schools and educational interventions are most beneficial to students in the long term? Furthermore, how can we apply this evidence toward informing policy that could effectively reduce stark social, educational, and economic inequalities?

The first study of three assesses mechanisms by which the Fast Track project, a randomized intervention in the early 1990s for high-risk children in four communities (Durham, NC; Nashville, TN; rural PA; and Seattle, WA), reduced delinquency, arrests, and health and mental health service utilization in adolescence through young adulthood (ages 12-20). A decomposition of treatment effects indicates that about a third of Fast Track’s impact on later crime outcomes can be accounted for by improvements in social and self-regulation skills during childhood (ages 6-11), such as prosocial behavior, emotion regulation and problem solving. These skills proved less valuable for the prevention of mental and physical health problems.

The second study contributes new evidence on how non-instructional investments – such as increased spending on school social workers, guidance counselors, and health services – affect multiple aspects of student performance and well-being. Merging several administrative data sources spanning the 1996-2013 school years in North Carolina, I use an instrumental variables approach to estimate the extent to which local expenditure shifts affect students’ academic and behavioral outcomes. My findings indicate that exogenous increases in spending on non-instructional services not only reduce student absenteeism and disciplinary problems (important predictors of long-term outcomes) but also significantly raise student achievement, in similar magnitude to corresponding increases in instructional spending. Furthermore, subgroup analyses suggest that investments in student support personnel such as social workers, health services, and guidance counselors, in schools with concentrated low-income student populations could go a long way toward closing socioeconomic achievement gaps.

The third study examines individual pathways that lead to high school graduation or dropout. It employs a variety of machine learning techniques, including decision trees, random forests with bagging and boosting, and support vector machines, to predict student dropout using longitudinal administrative data from North Carolina. I consider a large set of predictor measures from grades three through eight including academic achievement, behavioral indicators, and background characteristics. My findings indicate that the most important predictors include eighth grade absences, math scores, and age-for-grade as well as early reading scores. Support vector classification (with a high cost parameter and low gamma parameter) predicts high school dropout with the highest overall validity in the testing dataset at 90.1 percent followed by decision trees with boosting and interaction terms at 89.5 percent.

Statistical methods for polyhedral shape classification with incomplete data - application to cryo-electron tomographic images

A certain type of bacterial inclusion, known as a bacterial microcompartment, was recently identified and imaged through cryo-electron tomography. A reconstructed 3D object from single-axis limited angle tilt-series cryo-electron tomography contains missing regions and this problem is known as the missing wedge problem. Due to missing regions on the reconstructed images, analyzing their 3D structures is a challenging problem. The existing methods overcome this problem by aligning and averaging several similar shaped objects. These schemes work well if the objects are symmetric and several objects with almost similar shapes and sizes are available. Since the bacterial inclusions studied here are not symmetric, are deformed, and show a wide range of shapes and sizes, the existing approaches are not appropriate. This research develops new statistical methods for analyzing geometric properties, such as volume, symmetry, aspect ratio, polyhedral structures etc., of these bacterial inclusions in presence of missing data. These methods work with deformed and non-symmetric varied shaped objects and do not necessitate multiple objects for handling the missing wedge problem. The developed methods and contributions include: (a) an improved method for manual image segmentation, (b) a new approach to 'complete' the segmented and reconstructed incomplete 3D images, (c) a polyhedral structural distance model to predict the polyhedral shapes of these microstructures, (d) a new shape descriptor for polyhedral shapes, named as polyhedron profile statistic, and (e) the Bayes classifier, linear discriminant analysis and support vector machine based classifiers for supervised incomplete polyhedral shape classification. Finally, the predicted 3D shapes for these bacterial microstructures belong to the Johnson solids family, and these shapes along with their other geometric properties are important for better understanding of their chemical and biological characteristics.

Dynamic classifiers for neonatal brain monitoring

Brain injury due to lack of oxygen or impaired blood flow around the time of birth, may cause long term neurological dysfunction or death in severe cases. The treatments need to be initiated as soon as possible and tailored according to the nature of the injury to achieve best outcomes. The Electroencephalogram (EEG) currently provides the best insight into neurological activities. However, its interpretation presents formidable challenge for the neurophsiologists. Moreover, such expertise is not widely available particularly around the clock in a typical busy Neonatal Intensive Care Unit (NICU). Therefore, an automated computerized system for detecting and grading the severity of brain injuries could be of great help for medical staff to diagnose and then initiate on-time treatments. In this study, automated systems for detection of neonatal seizures and grading the severity of Hypoxic-Ischemic Encephalopathy (HIE) using EEG and Heart Rate (HR) signals are presented. It is well known that there is a lot of contextual and temporal information present in the EEG and HR signals if examined at longer time scale. The systems developed in the past, exploited this information either at very early stage of the system without any intelligent block or at very later stage where presence of such information is much reduced. This work has particularly focused on the development of a system that can incorporate the contextual information at the middle (classifier) level. This is achieved by using dynamic classifiers that are able to process the sequences of feature vectors rather than only one feature vector at a time.

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.