Aplicação de técnicas de aprendizado de máquina no reconhecimento de classes estruturais de proteínas

Nowadays, classifying proteins in structural classes, which concerns the inference of patterns in their 3D conformation, is one of the most important open problems in Molecular Biology. The main reason for this is that the function of a protein is intrinsically related to its spatial conformation. However, such conformations are very difficult to be obtained experimentally in laboratory. Thus, this problem has drawn the attention of many researchers in Bioinformatics. Considering the great difference between the number of protein sequences already known and the number of three-dimensional structures determined experimentally, the demand of automated techniques for structural classification of proteins is very high. In this context, computational tools, especially Machine Learning (ML) techniques, have become essential to deal with this problem. In this work, ML techniques are used in the recognition of protein structural classes: Decision Trees, k-Nearest Neighbor, Naive Bayes, Support Vector Machine and Neural Networks. These methods have been chosen because they represent different paradigms of learning and have been widely used in the Bioinfornmatics literature. Aiming to obtain an improvment in the performance of these techniques (individual classifiers), homogeneous (Bagging and Boosting) and heterogeneous (Voting, Stacking and StackingC) multiclassification systems are used. Moreover, since the protein database used in this work presents the problem of imbalanced classes, artificial techniques for class balance (Undersampling Random, Tomek Links, CNN, NCL and OSS) are used to minimize such a problem. In order to evaluate the ML methods, a cross-validation procedure is applied, where the accuracy of the classifiers is measured using the mean of classification error rate, on independent test sets. These means are compared, two by two, by the hypothesis test aiming to evaluate if there is, statistically, a significant difference between them. With respect to the results obtained with the individual classifiers, Support Vector Machine presented the best accuracy. In terms of the multi-classification systems (homogeneous and heterogeneous), they showed, in general, a superior or similar performance when compared to the one achieved by the individual classifiers used - especially Boosting with Decision Tree and the StackingC with Linear Regression as meta classifier. The Voting method, despite of its simplicity, has shown to be adequate for solving the problem presented in this work. The techniques for class balance, on the other hand, have not produced a significant improvement in the global classification error. Nevertheless, the use of such techniques did improve the classification error for the minority class. In this context, the NCL technique has shown to be more appropriated

Uma Análise de métodos de distriubuição de atributos em comitês de classificadores

The objective of the researches in artificial intelligence is to qualify the computer to execute functions that are performed by humans using knowledge and reasoning. This work was developed in the area of machine learning, that it s the study branch of artificial intelligence, being related to the project and development of algorithms and techniques capable to allow the computational learning. The objective of this work is analyzing a feature selection method for ensemble systems. The proposed method is inserted into the filter approach of feature selection method, it s using the variance and Spearman correlation to rank the feature and using the reward and punishment strategies to measure the feature importance for the identification of the classes. For each ensemble, several different configuration were used, which varied from hybrid (homogeneous) to non-hybrid (heterogeneous) structures of ensemble. They were submitted to five combining methods (voting, sum, sum weight, multiLayer Perceptron and naïve Bayes) which were applied in six distinct database (real and artificial). The classifiers applied during the experiments were k- nearest neighbor, multiLayer Perceptron, naïve Bayes and decision tree. Finally, the performance of ensemble was analyzed comparatively, using none feature selection method, using a filter approach (original) feature selection method and the proposed method. To do this comparison, a statistical test was applied, which demonstrate that there was a significant improvement in the precision of the ensembles

Sviluppo di un approccio congiunto fuzzy-Bayesiano per l'analisi e la modellizzazione degli ecosistemi: applicazione ad ecosistemi marini costieri.

Nell’attuale contesto di aumento degli impatti antropici e di “Global Climate Change” emerge la necessità di comprenderne i possibili effetti di questi sugli ecosistemi inquadrati come fruitori di servizi e funzioni imprescindibili sui quali si basano intere tessiture economiche e sociali. Lo studio previsionale degli ecosistemi si scontra con l’elevata complessità di questi ultimi in luogo di una altrettanto elevata scarsità di osservazioni integrate. L’approccio modellistico appare il più adatto all’analisi delle dinamiche complesse degli ecosistemi ed alla contestualizzazione complessa di risultati sperimentali ed osservazioni empiriche. L’approccio riduzionista-deterministico solitamente utilizzato nell’implementazione di modelli non si è però sin qui dimostrato in grado di raggiungere i livelli di complessità più elevati all’interno della struttura eco sistemica. La componente che meglio descrive la complessità ecosistemica è quella biotica in virtù dell’elevata dipendenza dalle altre componenti e dalle loro interazioni. In questo lavoro di tesi viene proposto un approccio modellistico stocastico basato sull’utilizzo di un compilatore naive Bayes operante in ambiente fuzzy. L’utilizzo congiunto di logica fuzzy e approccio naive Bayes è utile al processa mento del livello di complessità e conseguentemente incertezza insito negli ecosistemi. I modelli generativi ottenuti, chiamati Fuzzy Bayesian Ecological Model(FBEM) appaiono in grado di modellizare gli stati eco sistemici in funzione dell’ elevato numero di interazioni che entrano in gioco nella determinazione degli stati degli ecosistemi. Modelli FBEM sono stati utilizzati per comprendere il rischio ambientale per habitat intertidale di spiagge sabbiose in caso di eventi di flooding costiero previsti nell’arco di tempo 2010-2100. L’applicazione è stata effettuata all’interno del progetto EU “Theseus” per il quale i modelli FBEM sono stati utilizzati anche per una simulazione a lungo termine e per il calcolo dei tipping point specifici dell’habitat secondo eventi di flooding di diversa intensità.

Regularization for sparsity in statistical analysis and machine learning

Pragmatism is the leading motivation of regularization. We can understand regularization as a modification of the maximum-likelihood estimator so that a reasonable answer could be given in an unstable or ill-posed situation. To mention some typical examples, this happens when fitting parametric or non-parametric models with more parameters than data or when estimating large covariance matrices. Regularization is usually used, in addition, to improve the bias-variance tradeoff of an estimation. Then, the definition of regularization is quite general, and, although the introduction of a penalty is probably the most popular type, it is just one out of multiple forms of regularization. In this dissertation, we focus on the applications of regularization for obtaining sparse or parsimonious representations, where only a subset of the inputs is used. A particular form of regularization, L1-regularization, plays a key role for reaching sparsity. Most of the contributions presented here revolve around L1-regularization, although other forms of regularization are explored (also pursuing sparsity in some sense). In addition to present a compact review of L1-regularization and its applications in statistical and machine learning, we devise methodology for regression, supervised classification and structure induction of graphical models. Within the regression paradigm, we focus on kernel smoothing learning, proposing techniques for kernel design that are suitable for high dimensional settings and sparse regression functions. We also present an application of regularized regression techniques for modeling the response of biological neurons. Supervised classification advances deal, on the one hand, with the application of regularization for obtaining a na¨ıve Bayes classifier and, on the other hand, with a novel algorithm for brain-computer interface design that uses group regularization in an efficient manner. Finally, we present a heuristic for inducing structures of Gaussian Bayesian networks using L1-regularization as a filter. El pragmatismo es la principal motivación de la regularización. Podemos entender la regularización como una modificación del estimador de máxima verosimilitud, de tal manera que se pueda dar una respuesta cuando la configuración del problema es inestable. A modo de ejemplo, podemos mencionar el ajuste de modelos paramétricos o no paramétricos cuando hay más parámetros que casos en el conjunto de datos, o la estimación de grandes matrices de covarianzas. Se suele recurrir a la regularización, además, para mejorar el compromiso sesgo-varianza en una estimación. Por tanto, la definición de regularización es muy general y, aunque la introducción de una función de penalización es probablemente el método más popular, éste es sólo uno de entre varias posibilidades. En esta tesis se ha trabajado en aplicaciones de regularización para obtener representaciones dispersas, donde sólo se usa un subconjunto de las entradas. En particular, la regularización L1 juega un papel clave en la búsqueda de dicha dispersión. La mayor parte de las contribuciones presentadas en la tesis giran alrededor de la regularización L1, aunque también se exploran otras formas de regularización (que igualmente persiguen un modelo disperso). Además de presentar una revisión de la regularización L1 y sus aplicaciones en estadística y aprendizaje de máquina, se ha desarrollado metodología para regresión, clasificación supervisada y aprendizaje de estructura en modelos gráficos. Dentro de la regresión, se ha trabajado principalmente en métodos de regresión local, proponiendo técnicas de diseño del kernel que sean adecuadas a configuraciones de alta dimensionalidad y funciones de regresión dispersas. También se presenta una aplicación de las técnicas de regresión regularizada para modelar la respuesta de neuronas reales. Los avances en clasificación supervisada tratan, por una parte, con el uso de regularización para obtener un clasificador naive Bayes y, por otra parte, con el desarrollo de un algoritmo que usa regularización por grupos de una manera eficiente y que se ha aplicado al diseño de interfaces cerebromáquina. Finalmente, se presenta una heurística para inducir la estructura de redes Bayesianas Gaussianas usando regularización L1 a modo de filtro.

Contributions to Bayesian network learning with applications to neuroscience

Neuronal morphology is a key feature in the study of brain circuits, as it is highly related to information processing and functional identification. Neuronal morphology affects the process of integration of inputs from other neurons and determines the neurons which receive the output of the neurons. Different parts of the neurons can operate semi-independently according to the spatial location of the synaptic connections. As a result, there is considerable interest in the analysis of the microanatomy of nervous cells since it constitutes an excellent tool for better understanding cortical function. However, the morphologies, molecular features and electrophysiological properties of neuronal cells are extremely variable. Except for some special cases, this variability makes it hard to find a set of features that unambiguously define a neuronal type. In addition, there are distinct types of neurons in particular regions of the brain. This morphological variability makes the analysis and modeling of neuronal morphology a challenge. Uncertainty is a key feature in many complex real-world problems. Probability theory provides a framework for modeling and reasoning with uncertainty. Probabilistic graphical models combine statistical theory and graph theory to provide a tool for managing domains with uncertainty. In particular, we focus on Bayesian networks, the most commonly used probabilistic graphical model. In this dissertation, we design new methods for learning Bayesian networks and apply them to the problem of modeling and analyzing morphological data from neurons. The morphology of a neuron can be quantified using a number of measurements, e.g., the length of the dendrites and the axon, the number of bifurcations, the direction of the dendrites and the axon, etc. These measurements can be modeled as discrete or continuous data. The continuous data can be linear (e.g., the length or the width of a dendrite) or directional (e.g., the direction of the axon). These data may follow complex probability distributions and may not fit any known parametric distribution. Modeling this kind of problems using hybrid Bayesian networks with discrete, linear and directional variables poses a number of challenges regarding learning from data, inference, etc. In this dissertation, we propose a method for modeling and simulating basal dendritic trees from pyramidal neurons using Bayesian networks to capture the interactions between the variables in the problem domain. A complete set of variables is measured from the dendrites, and a learning algorithm is applied to find the structure and estimate the parameters of the probability distributions included in the Bayesian networks. Then, a simulation algorithm is used to build the virtual dendrites by sampling values from the Bayesian networks, and a thorough evaluation is performed to show the model’s ability to generate realistic dendrites. In this first approach, the variables are discretized so that discrete Bayesian networks can be learned and simulated. Then, we address the problem of learning hybrid Bayesian networks with different kinds of variables. Mixtures of polynomials have been proposed as a way of representing probability densities in hybrid Bayesian networks. We present a method for learning mixtures of polynomials approximations of one-dimensional, multidimensional and conditional probability densities from data. The method is based on basis spline interpolation, where a density is approximated as a linear combination of basis splines. The proposed algorithms are evaluated using artificial datasets. We also use the proposed methods as a non-parametric density estimation technique in Bayesian network classifiers. Next, we address the problem of including directional data in Bayesian networks. These data have some special properties that rule out the use of classical statistics. Therefore, different distributions and statistics, such as the univariate von Mises and the multivariate von Mises–Fisher distributions, should be used to deal with this kind of information. In particular, we extend the naive Bayes classifier to the case where the conditional probability distributions of the predictive variables given the class follow either of these distributions. We consider the simple scenario, where only directional predictive variables are used, and the hybrid case, where discrete, Gaussian and directional distributions are mixed. The classifier decision functions and their decision surfaces are studied at length. Artificial examples are used to illustrate the behavior of the classifiers. The proposed classifiers are empirically evaluated over real datasets. We also study the problem of interneuron classification. An extensive group of experts is asked to classify a set of neurons according to their most prominent anatomical features. A web application is developed to retrieve the experts’ classifications. We compute agreement measures to analyze the consensus between the experts when classifying the neurons. Using Bayesian networks and clustering algorithms on the resulting data, we investigate the suitability of the anatomical terms and neuron types commonly used in the literature. Additionally, we apply supervised learning approaches to automatically classify interneurons using the values of their morphological measurements. Then, a methodology for building a model which captures the opinions of all the experts is presented. First, one Bayesian network is learned for each expert, and we propose an algorithm for clustering Bayesian networks corresponding to experts with similar behaviors. Then, a Bayesian network which represents the opinions of each group of experts is induced. Finally, a consensus Bayesian multinet which models the opinions of the whole group of experts is built. A thorough analysis of the consensus model identifies different behaviors between the experts when classifying the interneurons in the experiment. A set of characterizing morphological traits for the neuronal types can be defined by performing inference in the Bayesian multinet. These findings are used to validate the model and to gain some insights into neuron morphology. Finally, we study a classification problem where the true class label of the training instances is not known. Instead, a set of class labels is available for each instance. This is inspired by the neuron classification problem, where a group of experts is asked to individually provide a class label for each instance. We propose a novel approach for learning Bayesian networks using count vectors which represent the number of experts who selected each class label for each instance. These Bayesian networks are evaluated using artificial datasets from supervised learning problems. Resumen La morfología neuronal es una característica clave en el estudio de los circuitos cerebrales, ya que está altamente relacionada con el procesado de información y con los roles funcionales. La morfología neuronal afecta al proceso de integración de las señales de entrada y determina las neuronas que reciben las salidas de otras neuronas. Las diferentes partes de la neurona pueden operar de forma semi-independiente de acuerdo a la localización espacial de las conexiones sinápticas. Por tanto, existe un interés considerable en el análisis de la microanatomía de las células nerviosas, ya que constituye una excelente herramienta para comprender mejor el funcionamiento de la corteza cerebral. Sin embargo, las propiedades morfológicas, moleculares y electrofisiológicas de las células neuronales son extremadamente variables. Excepto en algunos casos especiales, esta variabilidad morfológica dificulta la definición de un conjunto de características que distingan claramente un tipo neuronal. Además, existen diferentes tipos de neuronas en regiones particulares del cerebro. La variabilidad neuronal hace que el análisis y el modelado de la morfología neuronal sean un importante reto científico. La incertidumbre es una propiedad clave en muchos problemas reales. La teoría de la probabilidad proporciona un marco para modelar y razonar bajo incertidumbre. Los modelos gráficos probabilísticos combinan la teoría estadística y la teoría de grafos con el objetivo de proporcionar una herramienta con la que trabajar bajo incertidumbre. En particular, nos centraremos en las redes bayesianas, el modelo más utilizado dentro de los modelos gráficos probabilísticos. En esta tesis hemos diseñado nuevos métodos para aprender redes bayesianas, inspirados por y aplicados al problema del modelado y análisis de datos morfológicos de neuronas. La morfología de una neurona puede ser cuantificada usando una serie de medidas, por ejemplo, la longitud de las dendritas y el axón, el número de bifurcaciones, la dirección de las dendritas y el axón, etc. Estas medidas pueden ser modeladas como datos continuos o discretos. A su vez, los datos continuos pueden ser lineales (por ejemplo, la longitud o la anchura de una dendrita) o direccionales (por ejemplo, la dirección del axón). Estos datos pueden llegar a seguir distribuciones de probabilidad muy complejas y pueden no ajustarse a ninguna distribución paramétrica conocida. El modelado de este tipo de problemas con redes bayesianas híbridas incluyendo variables discretas, lineales y direccionales presenta una serie de retos en relación al aprendizaje a partir de datos, la inferencia, etc. En esta tesis se propone un método para modelar y simular árboles dendríticos basales de neuronas piramidales usando redes bayesianas para capturar las interacciones entre las variables del problema. Para ello, se mide un amplio conjunto de variables de las dendritas y se aplica un algoritmo de aprendizaje con el que se aprende la estructura y se estiman los parámetros de las distribuciones de probabilidad que constituyen las redes bayesianas. Después, se usa un algoritmo de simulación para construir dendritas virtuales mediante el muestreo de valores de las redes bayesianas. Finalmente, se lleva a cabo una profunda evaluaci ón para verificar la capacidad del modelo a la hora de generar dendritas realistas. En esta primera aproximación, las variables fueron discretizadas para poder aprender y muestrear las redes bayesianas. A continuación, se aborda el problema del aprendizaje de redes bayesianas con diferentes tipos de variables. Las mixturas de polinomios constituyen un método para representar densidades de probabilidad en redes bayesianas híbridas. Presentamos un método para aprender aproximaciones de densidades unidimensionales, multidimensionales y condicionales a partir de datos utilizando mixturas de polinomios. El método se basa en interpolación con splines, que aproxima una densidad como una combinación lineal de splines. Los algoritmos propuestos se evalúan utilizando bases de datos artificiales. Además, las mixturas de polinomios son utilizadas como un método no paramétrico de estimación de densidades para clasificadores basados en redes bayesianas. Después, se estudia el problema de incluir información direccional en redes bayesianas. Este tipo de datos presenta una serie de características especiales que impiden el uso de las técnicas estadísticas clásicas. Por ello, para manejar este tipo de información se deben usar estadísticos y distribuciones de probabilidad específicos, como la distribución univariante von Mises y la distribución multivariante von Mises–Fisher. En concreto, en esta tesis extendemos el clasificador naive Bayes al caso en el que las distribuciones de probabilidad condicionada de las variables predictoras dada la clase siguen alguna de estas distribuciones. Se estudia el caso base, en el que sólo se utilizan variables direccionales, y el caso híbrido, en el que variables discretas, lineales y direccionales aparecen mezcladas. También se estudian los clasificadores desde un punto de vista teórico, derivando sus funciones de decisión y las superficies de decisión asociadas. El comportamiento de los clasificadores se ilustra utilizando bases de datos artificiales. Además, los clasificadores son evaluados empíricamente utilizando bases de datos reales. También se estudia el problema de la clasificación de interneuronas. Desarrollamos una aplicación web que permite a un grupo de expertos clasificar un conjunto de neuronas de acuerdo a sus características morfológicas más destacadas. Se utilizan medidas de concordancia para analizar el consenso entre los expertos a la hora de clasificar las neuronas. Se investiga la idoneidad de los términos anatómicos y de los tipos neuronales utilizados frecuentemente en la literatura a través del análisis de redes bayesianas y la aplicación de algoritmos de clustering. Además, se aplican técnicas de aprendizaje supervisado con el objetivo de clasificar de forma automática las interneuronas a partir de sus valores morfológicos. A continuación, se presenta una metodología para construir un modelo que captura las opiniones de todos los expertos. Primero, se genera una red bayesiana para cada experto y se propone un algoritmo para agrupar las redes bayesianas que se corresponden con expertos con comportamientos similares. Después, se induce una red bayesiana que modela la opinión de cada grupo de expertos. Por último, se construye una multired bayesiana que modela las opiniones del conjunto completo de expertos. El análisis del modelo consensuado permite identificar diferentes comportamientos entre los expertos a la hora de clasificar las neuronas. Además, permite extraer un conjunto de características morfológicas relevantes para cada uno de los tipos neuronales mediante inferencia con la multired bayesiana. Estos descubrimientos se utilizan para validar el modelo y constituyen información relevante acerca de la morfología neuronal. Por último, se estudia un problema de clasificación en el que la etiqueta de clase de los datos de entrenamiento es incierta. En cambio, disponemos de un conjunto de etiquetas para cada instancia. Este problema está inspirado en el problema de la clasificación de neuronas, en el que un grupo de expertos proporciona una etiqueta de clase para cada instancia de manera individual. Se propone un método para aprender redes bayesianas utilizando vectores de cuentas, que representan el número de expertos que seleccionan cada etiqueta de clase para cada instancia. Estas redes bayesianas se evalúan utilizando bases de datos artificiales de problemas de aprendizaje supervisado.

Aplicação de técnicas inteligentes com análise no domínio do tempo para reconhecimento de defeitos em motores de indução trifásicos

Os motores de indução trifásicos são os principais elementos de conversão de energia elétrica em mecânica motriz aplicados em vários setores produtivos. Identificar um defeito no motor em operação pode fornecer, antes que ele falhe, maior segurança no processo de tomada de decisão sobre a manutenção da máquina, redução de custos e aumento de disponibilidade. Nesta tese são apresentas inicialmente uma revisão bibliográfica e a metodologia geral para a reprodução dos defeitos nos motores e a aplicação da técnica de discretização dos sinais de correntes e tensões no domínio do tempo. É também desenvolvido um estudo comparativo entre métodos de classificação de padrões para a identificação de defeitos nestas máquinas, tais como: Naive Bayes, k-Nearest Neighbor, Support Vector Machine (Sequential Minimal Optimization), Rede Neural Artificial (Perceptron Multicamadas), Repeated Incremental Pruning to Produce Error Reduction e C4.5 Decision Tree. Também aplicou-se o conceito de Sistemas Multiagentes (SMA) para suportar a utilização de múltiplos métodos concorrentes de forma distribuída para reconhecimento de padrões de defeitos em rolamentos defeituosos, quebras nas barras da gaiola de esquilo do rotor e curto-circuito entre as bobinas do enrolamento do estator de motores de indução trifásicos. Complementarmente, algumas estratégias para a definição da severidade dos defeitos supracitados em motores foram exploradas, fazendo inclusive uma averiguação da influência do desequilíbrio de tensão na alimentação da máquina para a determinação destas anomalias. Os dados experimentais foram adquiridos por meio de uma bancada experimental em laboratório com motores de potência de 1 e 2 cv acionados diretamente na rede elétrica, operando em várias condições de desequilíbrio das tensões e variações da carga mecânica aplicada ao eixo do motor.

Requirement Risk Level Forecast Using Bayesian Networks Classifiers

Requirement engineering is a key issue in the development of a software project. Like any other development activity it is not without risks. This work is about the empirical study of risks of requirements by applying machine learning techniques, specifically Bayesian networks classifiers. We have defined several models to predict the risk level for a given requirement using three dataset that collect metrics taken from the requirement specifications of different projects. The classification accuracy of the Bayesian models obtained is evaluated and compared using several classification performance measures. The results of the experiments show that the Bayesians networks allow obtaining valid predictors. Specifically, a tree augmented network structure shows a competitive experimental performance in all datasets. Besides, the relations established between the variables collected to determine the level of risk in a requirement, match with those set by requirement engineers. We show that Bayesian networks are valid tools for the automation of risks assessment in requirement engineering.

Classifying And Predicting Software Security Vulnerabilities based on Reproducibility

Security defects are common in large software systems because of their size and complexity. Although efficient development processes, testing, and maintenance policies are applied to software systems, there are still a large number of vulnerabilities that can remain, despite these measures. Some vulnerabilities stay in a system from one release to the next one because they cannot be easily reproduced through testing. These vulnerabilities endanger the security of the systems. We propose vulnerability classification and prediction frameworks based on vulnerability reproducibility. The frameworks are effective to identify the types and locations of vulnerabilities in the earlier stage, and improve the security of software in the next versions (referred to as releases). We expand an existing concept of software bug classification to vulnerability classification (easily reproducible and hard to reproduce) to develop a classification framework for differentiating between these vulnerabilities based on code fixes and textual reports. We then investigate the potential correlations between the vulnerability categories and the classical software metrics and some other runtime environmental factors of reproducibility to develop a vulnerability prediction framework. The classification and prediction frameworks help developers adopt corresponding mitigation or elimination actions and develop appropriate test cases. Also, the vulnerability prediction framework is of great help for security experts focus their effort on the top-ranked vulnerability-prone files. As a result, the frameworks decrease the number of attacks that exploit security vulnerabilities in the next versions of the software. To build the classification and prediction frameworks, different machine learning techniques (C4.5 Decision Tree, Random Forest, Logistic Regression, and Naive Bayes) are employed. The effectiveness of the proposed frameworks is assessed based on collected software security defects of Mozilla Firefox.

Machine learning techniques to improve software quality

A significant proportion of the cost of software development is due to software testing and maintenance. This is in part the result of the inevitable imperfections due to human error, lack of quality during the design and coding of software, and the increasing need to reduce faults to improve customer satisfaction in a competitive marketplace. Given the cost and importance of removing errors improvements in fault detection and removal can be of significant benefit. The earlier in the development process faults can be found, the less it costs to correct them and the less likely other faults are to develop. This research aims to make the testing process more efficient and effective by identifying those software modules most likely to contain faults, allowing testing efforts to be carefully targeted. This is done with the use of machine learning algorithms which use examples of fault prone and not fault prone modules to develop predictive models of quality. In order to learn the numerical mapping between module and classification, a module is represented in terms of software metrics. A difficulty in this sort of problem is sourcing software engineering data of adequate quality. In this work, data is obtained from two sources, the NASA Metrics Data Program, and the open source Eclipse project. Feature selection before learning is applied, and in this area a number of different feature selection methods are applied to find which work best. Two machine learning algorithms are applied to the data - Naive Bayes and the Support Vector Machine - and predictive results are compared to those of previous efforts and found to be superior on selected data sets and comparable on others. In addition, a new classification method is proposed, Rank Sum, in which a ranking abstraction is laid over bin densities for each class, and a classification is determined based on the sum of ranks over features. A novel extension of this method is also described based on an observed polarising of points by class when rank sum is applied to training data to convert it into 2D rank sum space. SVM is applied to this transformed data to produce models the parameters of which can be set according to trade-off curves to obtain a particular performance trade-off.

STALKERBOT : learning to navigate dynamic human environments by following people

Service robots that operate in human environments will accomplish tasks most efficiently and least disruptively if they have the capability to mimic and understand the motion patterns of the people in their workspace. This work demonstrates how a robot can create a humancentric navigational map online, and that this map re ects changes in the environment that trigger altered motion patterns of people. An RGBD sensor mounted on the robot is used to detect and track people moving through the environment. The trajectories are clustered online and organised into a tree-like probabilistic data structure which can be used to detect anomalous trajectories. A costmap is reverse engineered from the clustered trajectories that can then inform the robot's onboard planning process. Results show that the resultant paths taken by the robot mimic expected human behaviour and can allow the robot to respond to altered human motion behaviours in the environment.

Automatic classification of free-text radiology reports to identify limb fractures using machine learning and the SNOMED CT ontology

Objective To develop and evaluate machine learning techniques that identify limb fractures and other abnormalities (e.g. dislocations) from radiology reports. Materials and Methods 99 free-text reports of limb radiology examinations were acquired from an Australian public hospital. Two clinicians were employed to identify fractures and abnormalities from the reports; a third senior clinician resolved disagreements. These assessors found that, of the 99 reports, 48 referred to fractures or abnormalities of limb structures. Automated methods were then used to extract features from these reports that could be useful for their automatic classification. The Naive Bayes classification algorithm and two implementations of the support vector machine algorithm were formally evaluated using cross-fold validation over the 99 reports. Result Results show that the Naive Bayes classifier accurately identifies fractures and other abnormalities from the radiology reports. These results were achieved when extracting stemmed token bigram and negation features, as well as using these features in combination with SNOMED CT concepts related to abnormalities and disorders. The latter feature has not been used in previous works that attempted classifying free-text radiology reports. Discussion Automated classification methods have proven effective at identifying fractures and other abnormalities from radiology reports (F-Measure up to 92.31%). Key to the success of these techniques are features such as stemmed token bigrams, negations, and SNOMED CT concepts associated with morphologic abnormalities and disorders. Conclusion This investigation shows early promising results and future work will further validate and strengthen the proposed approaches.

Injury narrative text classification using factorization model

Narrative text is a useful way of identifying injury circumstances from the routine emergency department data collections. Automatically classifying narratives based on machine learning techniques is a promising technique, which can consequently reduce the tedious manual classification process. Existing works focus on using Naive Bayes which does not always offer the best performance. This paper proposes the Matrix Factorization approaches along with a learning enhancement process for this task. The results are compared with the performance of various other classification approaches. The impact on the classification results from the parameters setting during the classification of a medical text dataset is discussed. With the selection of right dimension k, Non Negative Matrix Factorization-model method achieves 10 CV accuracy of 0.93.

Application of higher-order spectra for automated grading of diabetic maculopathy

Diabetic macular edema (DME) is one of the most common causes of visual loss among diabetes mellitus patients. Early detection and successive treatment may improve the visual acuity. DME is mainly graded into non-clinically significant macular edema (NCSME) and clinically significant macular edema according to the location of hard exudates in the macula region. DME can be identified by manual examination of fundus images. It is laborious and resource intensive. Hence, in this work, automated grading of DME is proposed using higher-order spectra (HOS) of Radon transform projections of the fundus images. We have used third-order cumulants and bispectrum magnitude, in this work, as features, and compared their performance. They can capture subtle changes in the fundus image. Spectral regression discriminant analysis (SRDA) reduces feature dimension, and minimum redundancy maximum relevance method is used to rank the significant SRDA components. Ranked features are fed to various supervised classifiers, viz. Naive Bayes, AdaBoost and support vector machine, to discriminate No DME, NCSME and clinically significant macular edema classes. The performance of our system is evaluated using the publicly available MESSIDOR dataset (300 images) and also verified with a local dataset (300 images). Our results show that HOS cumulants and bispectrum magnitude obtained an average accuracy of 95.56 and 94.39 % for MESSIDOR dataset and 95.93 and 93.33 % for local dataset, respectively.

Computing the Stochastic Complexity of Simple Probabilistic Graphical Models

Minimum Description Length (MDL) is an information-theoretic principle that can be used for model selection and other statistical inference tasks. There are various ways to use the principle in practice. One theoretically valid way is to use the normalized maximum likelihood (NML) criterion. Due to computational difficulties, this approach has not been used very often. This thesis presents efficient floating-point algorithms that make it possible to compute the NML for multinomial, Naive Bayes and Bayesian forest models. None of the presented algorithms rely on asymptotic analysis and with the first two model classes we also discuss how to compute exact rational number solutions.

A data fusion approach of multiple maintenance data sources for real-world reliability modelling

A central tenet in the theory of reliability modelling is the quantification of the probability of asset failure. In general, reliability depends on asset age and the maintenance policy applied. Usually, failure and maintenance times are the primary inputs to reliability models. However, for many organisations, different aspects of these data are often recorded in different databases (e.g. work order notifications, event logs, condition monitoring data, and process control data). These recorded data cannot be interpreted individually, since they typically do not have all the information necessary to ascertain failure and preventive maintenance times. This paper presents a methodology for the extraction of failure and preventive maintenance times using commonly-available, real-world data sources. A text-mining approach is employed to extract keywords indicative of the source of the maintenance event. Using these keywords, a Naïve Bayes classifier is then applied to attribute each machine stoppage to one of two classes: failure or preventive. The accuracy of the algorithm is assessed and the classified failure time data are then presented. The applicability of the methodology is demonstrated on a maintenance data set from an Australian electricity company.