Testing native speakers of German and Portuguese on the understanding of topological operators-line-region relations in gvSIG

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

A qualitive reasoning approach for improving query results for sketch based queries by topological analysis of spatial aggregation

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

Cognitive assessment of topological movement Patterns and direction turns: An influence of scale

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

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.

Multi-region routing

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Exploratory geospatial data analysis using self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Ciência e Sistemas de Informação Geográfica

Engenharia de tráfego leve ao nível do inter-domínio

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Using an LED as a sensor and visible light communication device in a smart illumination system

The need for more efficient illumination systems has led to the proliferation of Solid-State Lighting (SSL) systems, which offer optimized power consumption. SSL systems are comprised of LED devices which are intrinsically fast devices and permit very fast light modulation. This, along with the congestion of the radio frequency spectrum has paved the path for the emergence of Visible Light Communication (VLC) systems. VLC uses free space to convey information by using light modulation. Notwithstanding, as VLC systems proliferate and cost competitiveness ensues, there are two important aspects to be considered. State-of-the-art VLC implementations use power demanding PAs, and thus it is important to investigate if regular, existent Switched-Mode Power Supply (SMPS) circuits can be adapted for VLC use. A 28 W buck regulator was implemented using a off-the-shelf LED Driver integrated circuit, using both series and parallel dimming techniques. Results show that optical clock frequencies up to 500 kHz are achievable without any major modification besides adequate component sizing. The use of an LED as a sensor was investigated, in a short-range, low-data-rate perspective. Results show successful communication in an LED-to-LED configuration, with enhanced range when using LED strings as sensors. Besides, LEDs present spectral selective sensitivity, which makes them good contenders for a multi-colour LED-to-LED system, such as in the use of RGB displays and lamps. Ultimately, the present work shows evidence that LEDs can be used as a dual-purpose device, enabling not only illumination, but also bi-directional data communication.

Análise configuracional dos grandes conjuntos urbanos na Região de Lisboa (1945-1974) : contributos da sintaxe espacial para a história de arte como história da cidade

A presente investigação debruça-se sobre o estudo dos grandes conjuntos urbanos, tendo como referência a área de Lisboa no período entre 1945 e 1974. O seu objetivo principal é compreender o padrão espacial e respetivas variantes destas formas urbanas relativamente recentes bem como avaliar o seu impato na estrutura global da cidade e da sociedade. Tomando como ponto de partida a história de arte como história da cidade, a tese toma como objeto o grande conjunto urbano e aponta a hipótese do estudo da relação forma-fundo como meio de obter informações relevantes que relacionem o uso e função com respeito ao desenho do espaço aberto. Como diferentes arranjos entre espaços abertos e fechados implicam tipos espaciais distintos (Medeiros 2013), o estudo da relação entre a forma (cheio) e o fundo (vazio) dos grandes conjuntos urbanos e respetivas variações, pode fornecer-nos informação espacial relevante, que nos permitem compreender melhor estas formas urbanas recentes. Usando a abordagem própria da teoria da sintaxe espacial (Hillier e Hanson 1984), do tipo configuracional, determinam-se as relações entre os vários elementos constituintes dos sistemas espaciais formados nestas urbanizações. Essas relações são depois analisadas através de medidas e variáveis topológicas que nos permitem identificar qualidades e valores espaciais para a sociedade. Os resultados obtidos a partir dessas variáveis e medidas permitem-nos, depois, avaliar os graus de ‘formalidade’ e ‘urbanidade’ em cada sistema (Holanda 2002). Consequentemente, a avaliação qualitativa das características espaciais que se pretendem obter nesta investigação, tem como base a avaliação quantitativa, permitindo assim comparar mais facilmente os diversos casos de estudo. De entre o conjunto de casos analisados, o estudo revela uma série de características comuns, que nos permitem identificar um padrão específico de urbanismo modernista que reflete claramente um conjunto de ideologias associadas a uma visão reformista da sociedade através do espaço. Mas por outro lado, existem também um conjunto de características particulares de cada caso, que reportam para a estrutura morfológica da cidade tradicional. No que reporta à hipótese de estudo levantada nesta investigação sobre a relação forma-fundo, verifica-se através da amostra que esta relação aparece invertida. Esta diferenciação deve-se ao abandono dos tradicionais sistemas de rua e de quarteirão, ainda presentes nas urbanizações de Alvalade e do Areeiro e a sua substituição pelo bloco livre em espaço aberto como nos casos de Alfragide, Portela e Olivais. Tal facto, como prova a teoria da Sintaxe Espacial ou Lógica Social do Espaço, traduziu-se necessariamente em diferentes modos de vida pública e privada e consequentemente de vida espacial e social. Assim concluímos, através da análise dos casos de estudo apresentados, que embora fazendo parte duma mesma ideologia urbana com características comuns (genótipo modernista), os mesmos apresentam resultados espaciais totalmente diferenciados o que justifica a dificuldade da sua análise comparativa.