Learning techniques for automatic email message tagging

A organização automática de mensagens de correio electrónico é um desafio actual na área da aprendizagem automática. O número excessivo de mensagens afecta cada vez mais utilizadores, especialmente os que usam o correio electrónico como ferramenta de comunicação e trabalho. Esta tese aborda o problema da organização automática de mensagens de correio electrónico propondo uma solução que tem como objectivo a etiquetagem automática de mensagens. A etiquetagem automática é feita com recurso às pastas de correio electrónico anteriormente criadas pelos utilizadores, tratando-as como etiquetas, e à sugestão de múltiplas etiquetas para cada mensagem (top-N). São estudadas várias técnicas de aprendizagem e os vários campos que compõe uma mensagem de correio electrónico são analisados de forma a determinar a sua adequação como elementos de classificação. O foco deste trabalho recai sobre os campos textuais (o assunto e o corpo das mensagens), estudando-se diferentes formas de representação, selecção de características e algoritmos de classificação. É ainda efectuada a avaliação dos campos de participantes através de algoritmos de classificação que os representam usando o modelo vectorial ou como um grafo. Os vários campos são combinados para classificação utilizando a técnica de combinação de classificadores Votação por Maioria. Os testes são efectuados com um subconjunto de mensagens de correio electrónico da Enron e um conjunto de dados privados disponibilizados pelo Institute for Systems and Technologies of Information, Control and Communication (INSTICC). Estes conjuntos são analisados de forma a perceber as características dos dados. A avaliação do sistema é realizada através da percentagem de acerto dos classificadores. Os resultados obtidos apresentam melhorias significativas em comparação com os trabalhos relacionados.

Classification and staging of chronic liver disease from multimodal data

Chronic liver disease (CLD) is most of the time an asymptomatic, progressive, and ultimately potentially fatal disease. In this study, an automatic hierarchical procedure to stage CLD using ultrasound images, laboratory tests, and clinical records are described. The first stage of the proposed method, called clinical based classifier (CBC), discriminates healthy from pathologic conditions. When nonhealthy conditions are detected, the method refines the results in three exclusive pathologies in a hierarchical basis: 1) chronic hepatitis; 2) compensated cirrhosis; and 3) decompensated cirrhosis. The features used as well as the classifiers (Bayes, Parzen, support vector machine, and k-nearest neighbor) are optimally selected for each stage. A large multimodal feature database was specifically built for this study containing 30 chronic hepatitis cases, 34 compensated cirrhosis cases, and 36 decompensated cirrhosis cases, all validated after histopathologic analysis by liver biopsy. The CBC classification scheme outperformed the nonhierachical one against all scheme, achieving an overall accuracy of 98.67% for the normal detector, 87.45% for the chronic hepatitis detector, and 95.71% for the cirrhosis detector.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Fatty liver automatic diagnosis from ultrasound images

In this paper an automatic classification algorithm is proposed for the diagnosis of the liver steatosis, also known as, fatty liver, from ultrasound images. The features, automatically extracted from the ultrasound images used by the classifier, are basically the ones used by the physicians in the diagnosis of the disease based on visual inspection of the ultrasound images. The main novelty of the method is the utilization of the speckle noise that corrupts the ultrasound images to compute textural features of the liver parenchyma relevant for the diagnosis. The algorithm uses the Bayesian framework to compute a noiseless image, containing anatomic and echogenic information of the liver and a second image containing only the speckle noise used to compute the textural features. The classification results, with the Bayes classifier using manually classified data as ground truth show that the automatic classifier reaches an accuracy of 95% and a 100% of sensitivity.

Assessment of data-driven modeling strategies for water delivery canals

Conferência: CONTROLO’2012 - 16-18 July 2012 - Funchal

The contribution of multitemporal information from multispectral satellite images for automatic land cover classification at the national scale

Thesis submitted to the Instituto Superior de Estatística e Gestão de Informação da Universidade Nova de Lisboa in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Information Management – Geographic Information Systems

An Approach To Publish a Data Warehouse Content as Linked Data

Mestrado em Engenharia Informática - Área de Especialização em Tecnologias do Conhecimento e Decisão

Vertex component analysis: a geometric-based approach to unmix hyperspectral data

Hyperspectral remote sensing exploits the electromagnetic scattering patterns of the different materials at specific wavelengths [2, 3]. Hyperspectral sensors have been developed to sample the scattered portion of the electromagnetic spectrum extending from the visible region through the near-infrared and mid-infrared, in hundreds of narrow contiguous bands [4, 5]. The number and variety of potential civilian and military applications of hyperspectral remote sensing is enormous [6, 7]. Very often, the resolution cell corresponding to a single pixel in an image contains several substances (endmembers) [4]. In this situation, the scattered energy is a mixing of the endmember spectra. A challenging task underlying many hyperspectral imagery applications is then decomposing a mixed pixel into a collection of reflectance spectra, called endmember signatures, and the corresponding abundance fractions [8–10]. Depending on the mixing scales at each pixel, the observed mixture is either linear or nonlinear [11, 12]. Linear mixing model holds approximately when the mixing scale is macroscopic [13] and there is negligible interaction among distinct endmembers [3, 14]. If, however, the mixing scale is microscopic (or intimate mixtures) [15, 16] and the incident solar radiation is scattered by the scene through multiple bounces involving several endmembers [17], the linear model is no longer accurate. Linear spectral unmixing has been intensively researched in the last years [9, 10, 12, 18–21]. It considers that a mixed pixel is a linear combination of endmember signatures weighted by the correspondent abundance fractions. Under this model, and assuming that the number of substances and their reflectance spectra are known, hyperspectral unmixing is a linear problem for which many solutions have been proposed (e.g., maximum likelihood estimation [8], spectral signature matching [22], spectral angle mapper [23], subspace projection methods [24,25], and constrained least squares [26]). In most cases, the number of substances and their reflectances are not known and, then, hyperspectral unmixing falls into the class of blind source separation problems [27]. Independent component analysis (ICA) has recently been proposed as a tool to blindly unmix hyperspectral data [28–31]. ICA is based on the assumption of mutually independent sources (abundance fractions), which is not the case of hyperspectral data, since the sum of abundance fractions is constant, implying statistical dependence among them. This dependence compromises ICA applicability to hyperspectral images as shown in Refs. [21, 32]. In fact, ICA finds the endmember signatures by multiplying the spectral vectors with an unmixing matrix, which minimizes the mutual information among sources. If sources are independent, ICA provides the correct unmixing, since the minimum of the mutual information is obtained only when sources are independent. This is no longer true for dependent abundance fractions. Nevertheless, some endmembers may be approximately unmixed. These aspects are addressed in Ref. [33]. Under the linear mixing model, the observations from a scene are in a simplex whose vertices correspond to the endmembers. Several approaches [34–36] have exploited this geometric feature of hyperspectral mixtures [35]. Minimum volume transform (MVT) algorithm [36] determines the simplex of minimum volume containing the data. The method presented in Ref. [37] is also of MVT type but, by introducing the notion of bundles, it takes into account the endmember variability usually present in hyperspectral mixtures. The MVT type approaches are complex from the computational point of view. Usually, these algorithms find in the first place the convex hull defined by the observed data and then fit a minimum volume simplex to it. For example, the gift wrapping algorithm [38] computes the convex hull of n data points in a d-dimensional space with a computational complexity of O(nbd=2cþ1), where bxc is the highest integer lower or equal than x and n is the number of samples. The complexity of the method presented in Ref. [37] is even higher, since the temperature of the simulated annealing algorithm used shall follow a log( ) law [39] to assure convergence (in probability) to the desired solution. Aiming at a lower computational complexity, some algorithms such as the pixel purity index (PPI) [35] and the N-FINDR [40] still find the minimum volume simplex containing the data cloud, but they assume the presence of at least one pure pixel of each endmember in the data. This is a strong requisite that may not hold in some data sets. In any case, these algorithms find the set of most pure pixels in the data. PPI algorithm uses the minimum noise fraction (MNF) [41] as a preprocessing step to reduce dimensionality and to improve the signal-to-noise ratio (SNR). The algorithm then projects every spectral vector onto skewers (large number of random vectors) [35, 42,43]. The points corresponding to extremes, for each skewer direction, are stored. A cumulative account records the number of times each pixel (i.e., a given spectral vector) is found to be an extreme. The pixels with the highest scores are the purest ones. N-FINDR algorithm [40] is based on the fact that in p spectral dimensions, the p-volume defined by a simplex formed by the purest pixels is larger than any other volume defined by any other combination of pixels. This algorithm finds the set of pixels defining the largest volume by inflating a simplex inside the data. ORA SIS [44, 45] is a hyperspectral framework developed by the U.S. Naval Research Laboratory consisting of several algorithms organized in six modules: exemplar selector, adaptative learner, demixer, knowledge base or spectral library, and spatial postrocessor. The first step consists in flat-fielding the spectra. Next, the exemplar selection module is used to select spectral vectors that best represent the smaller convex cone containing the data. The other pixels are rejected when the spectral angle distance (SAD) is less than a given thresh old. The procedure finds the basis for a subspace of a lower dimension using a modified Gram–Schmidt orthogonalizati on. The selected vectors are then projected onto this subspace and a simplex is found by an MV T pro cess. ORA SIS is oriented to real-time target detection from uncrewed air vehicles using hyperspectral data [46]. In this chapter we develop a new algorithm to unmix linear mixtures of endmember spectra. First, the algorithm determines the number of endmembers and the signal subspace using a newly developed concept [47, 48]. Second, the algorithm extracts the most pure pixels present in the data. Unlike other methods, this algorithm is completely automatic and unsupervised. To estimate the number of endmembers and the signal subspace in hyperspectral linear mixtures, the proposed scheme begins by estimating sign al and noise correlation matrices. The latter is based on multiple regression theory. The signal subspace is then identified by selectin g the set of signal eigenvalue s that best represents the data, in the least-square sense [48,49 ], we note, however, that VCA works with projected and with unprojected data. The extraction of the end members exploits two facts: (1) the endmembers are the vertices of a simplex and (2) the affine transformation of a simplex is also a simplex. As PPI and N-FIND R algorithms, VCA also assumes the presence of pure pixels in the data. The algorithm iteratively projects data on to a direction orthogonal to the subspace spanned by the endmembers already determined. The new end member signature corresponds to the extreme of the projection. The algorithm iterates until all end members are exhausted. VCA performs much better than PPI and better than or comparable to N-FI NDR; yet it has a computational complexity between on e and two orders of magnitude lower than N-FINDR. The chapter is structure d as follows. Section 19.2 describes the fundamentals of the proposed method. Section 19.3 and Section 19.4 evaluate the proposed algorithm using simulated and real data, respectively. Section 19.5 presents some concluding remarks.

A Data-mining-based Methodology to support MV Electricity Customers' Characterization

This paper presents an electricity medium voltage (MV) customer characterization framework supportedby knowledge discovery in database (KDD). The main idea is to identify typical load profiles (TLP) of MVconsumers and to develop a rule set for the automatic classification of new consumers. To achieve ourgoal a methodology is proposed consisting of several steps: data pre-processing; application of severalclustering algorithms to segment the daily load profiles; selection of the best partition, corresponding tothe best consumers’ segmentation, based on the assessments of several clustering validity indices; andfinally, a classification model is built based on the resulting clusters. To validate the proposed framework,a case study which includes a real database of MV consumers is performed.

Declarative approach to data extraction of web pages

Thesis submitted to Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa, in partial fulfilment of the requirements for the degree of Master in Computer Science

Automatic musical instrument recognition for multimedia indexing

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Deteção e extinção de incêndio em Data Center

O presente trabalho enquadra-se na temática de segurança contra incêndio em edifícios e consiste num estudo de caso de projeto de deteção e extinção de incêndio num Data Center. Os objetivos deste trabalho resumem-se à realização de um estudo sobre o estado da arte da extinção e deteção automática de incêndio, ao desenvolvimento de uma ferramenta de software de apoio a projetos de extinção por agentes gasosos, como também à realização de um estudo e uma análise da proteção contra incêndios em Data Centers. Por último foi efetuado um estudo de caso. São abordados os conceitos de fogo e de incêndio, em que um estudo teórico à temática foi desenvolvido, descrevendo de que forma pode o fogo ser originado e respetivas consequências. Os regulamentos nacionais relativos à Segurança Contra Incêndios em Edifícios (SCIE) são igualmente abordados, com especial foco nos Sistemas Automáticos de Deteção de Incêndio (SADI) e nos Sistemas Automáticos de Extinção de Incêndio (SAEI), as normas nacionais e internacionais relativas a esta temática também são mencionadas. Pelo facto de serem muito relevantes para o desenvolvimento deste trabalho, os sistemas de deteção de incêndio são exaustivamente abordados, mencionando características de equipamentos de deteção, técnicas mais utilizadas como também quais os aspetos a ter em consideração no dimensionamento de um SADI. Quanto aos meios de extinção de incêndio foram mencionados quais os mais utilizados atualmente, as suas vantagens e a que tipo de fogo se aplicam, com especial destaque para os SAEI com utilização de gases inertes, em que foi descrito como deve ser dimensionado um sistema deste tipo. Foi também efetuada a caracterização dos Data Centers para que seja possível entender quais as suas funcionalidades, a importância da sua existência e os aspetos gerais de uma proteção contra incêndio nestas instalações. Por último, um estudo de caso foi desenvolvido, um SADI foi projetado juntamente com um SAEI que utiliza azoto como gás de extinção. As escolhas e os sistemas escolhidos foram devidamente justificados, tendo em conta os regulamentos e normas em vigor.

Automatic syllabification for danish text-to-speech systems

In this paper, a rule-based automatic syllabifier for Danish is described using the Maximal Onset Principle. Prior success rates of rule-based methods applied to Portuguese and Catalan syllabification modules were on the basis of this work. The system was implemented and tested using a very small set of rules. The results gave rise to 96.9% and 98.7% of word accuracy rate, contrary to our initial expectations, being Danish a language with a complex syllabic structure and thus difficult to be rule-driven. Comparison with data-driven syllabification system using artificial neural networks showed a higher accuracy rate of the former system.

Stratigraphic interpretation of Well-Log data of the Athabasca Oil Sands of Alberta Canada through Pattern recognition and Artificial Intelligence

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Automatic Small Bowel Tumor Diagnosis by Using Multi-Scale Wavelet-Based Analysis in Wireless Capsule Endoscopy Images

BACKGROUND: Wireless capsule endoscopy has been introduced as an innovative, non-invasive diagnostic technique for evaluation of the gastrointestinal tract, reaching places where conventional endoscopy is unable to. However, the output of this technique is an 8 hours video, whose analysis by the expert physician is very time consuming. Thus, a computer assisted diagnosis tool to help the physicians to evaluate CE exams faster and more accurately is an important technical challenge and an excellent economical opportunity. METHOD: The set of features proposed in this paper to code textural information is based on statistical modeling of second order textural measures extracted from co-occurrence matrices. To cope with both joint and marginal non-Gaussianity of second order textural measures, higher order moments are used. These statistical moments are taken from the two-dimensional color-scale feature space, where two different scales are considered. Second and higher order moments of textural measures are computed from the co-occurrence matrices computed from images synthesized by the inverse wavelet transform of the wavelet transform containing only the selected scales for the three color channels. The dimensionality of the data is reduced by using Principal Component Analysis. RESULTS: The proposed textural features are then used as the input of a classifier based on artificial neural networks. Classification performances of 93.1% specificity and 93.9% sensitivity are achieved on real data. These promising results open the path towards a deeper study regarding the applicability of this algorithm in computer aided diagnosis systems to assist physicians in their clinical practice.