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.

EDP InovCity pilot study proposal: A set-top box interface

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

EDP inovcity pilot study proposal: A set-top box interface

In this work I propose an additional test to be implemented in EDP’s residential electricity use feedback trials, under InovCity’s project scope. The proposed product to be tested consists of an interface between the smart meter and the television, through a set-top box. I provide a theoretical framework of the importance of feedback, an analysis of results from past studies involving smart metering, and a detailed description of my proposal. The results of a self-developed questionnaire related to the proposal and segmentation issues are also analyzed. Finally, general conclusions are drawn and potential future improvements and challenges are presented.

Evaluation of the potential of translocated common cockle for ecological risk assessment studies: bioaccumulation and biomarkers test

Thesis submitted to the Faculdade de Ciências e Tecnologia to obtain the Master’s degree in Environmental Engineering, profile in Ecological Engineering

Discovery and retrieval of Geographic data using Google

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

The intersection of people, technology and local space. PPGIS and Web in practice for participatory planning

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

Including context in a routing algorithm for the internet of things

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

Automated illustration of multimedia stories

Submitted in part fulfillment of the requirements for the degree of Master in Computer Science

Vigilância activa de eventos após vacinação

A vigilância de efeitos indesejáveis após a vacinação é complexa. Existem vários actores de confundimento que podem dar origem a associações espúrias, meramente temporais mas que podem provocar uma percepção do risco alterada e uma consequente desconfiança generalizada acerca do uso das vacinas. Com efeito as vacinas são medicamentos complexos com características únicas cuja vigilância necessita de abordagens metodológicas desenvolvidas para esse propósito. Do exposto se entende que, desde o desenvolvimento da farmacovigilância se tem procurado desenvolver novas metodologias que sejam concomitantes aos Sistemas de Notificação Espontânea que já existem. Neste trabalho propusemo-nos a desenvolver e testar um modelo de vigilância de reacções adversas a vacinas, baseado na auto-declaração pelo utente de eventos ocorridos após a vacinação e testar a capacidade de gerar sinais aplicando cálculos de desproporção a datamining. Para esse efeito foi constituída uma coorte não controlada de utentes vacinados em Centros de Saúde que foram seguidos durante quinze dias. A recolha de eventos adversos a vacinas foi efectuada pelos próprios utentes através de um diário de registo. Os dados recolhidos foram objecto de análise descritiva e análise de data-mining utilizando os cálculos Proportional Reporting Ratio e o Information Component. A metodologia utilizada permitiu gerar um corpo de evidência suficiente para a geração de sinais. Tendo sido gerados quatro sinais. No âmbito do data-mining a utilização do Information Component como método de geração de sinais parece aumentar a eficiência científica ao permitir reduzir o número de ocorrências até detecção de sinal. A informação reportada pelos utentes parece válida como indicador de sinais de reacções adversas não graves, o que permitiu o registo de eventos sem incluir o viés da avaliação da relação causal pelo notificador. Os principais eventos reportados foram eventos adversos locais (62,7%) e febre (31,4%).------------------------------------------ABSTRACT: The monitoring of undesirable effects following vaccination is complex. There are several confounding factors that can lead to merely temporal but spurious associations that can cause a change in the risk perception and a consequent generalized distrust about the safe use of vaccines. Indeed, vaccines are complex drugs with unique characteristics so that its monitoring requires specifically designed methodological approaches. From the above-cited it is understandable that since the development of Pharmacovigilance there has been a drive for the development of new methodologies that are concomitant with Spontaneous Reporting Systems already in place. We proposed to develop and test a new model for vaccine adverse reaction monitoring, based on self-report by users of events following vaccination and to test its capability to generate disproportionality signals applying quantitative methods of signal generation to data-mining. For that effect we set up an uncontrolled cohort of users vaccinated in Healthcare Centers,with a follow-up period of fifteen days. Adverse vaccine events we registered by the users themselves in a paper diary The data was analyzed using descriptive statistics and two quantitative methods of signal generation: Proportional Reporting Ratio and Information Component. themselves in a paper diary The data was analyzed using descriptive statistics and two quantitative methods of signal generation: Proportional Reporting Ratio and Information Component. The methodology we used allowed for the generation of a sufficient body of evidence for signal generation. Four signals were generated. Regarding the data-mining, the use of Information Component as a method for generating disproportionality signals seems to increase scientific efficiency by reducing the number of events needed to signal detection. The information reported by users seems valid as an indicator of non serious adverse vaccine reactions, allowing for the registry of events without the bias of the evaluation of the casual relation by the reporter. The main adverse events reported were injection site reactions (62,7%) and fever (31,4%).

A questão visual na oftalmologia pediátrica da região de Lisboa

RESUMO: Na parte inicial incluem-se algumas notas sucintas com base no panorama científico,histórico e cultural da visão considerada segundo três abordagens - o olho (o olho humano na especificidade da sua posição filogenética, elemento anátomo-funcional básico do sistema visual ao qual o cérebro pertence), os olhos (unidades gémeas essenciais do rosto na sua actividade consensual e conjugada da binocularidade), o olhar (carregado de expressão psicológica e o seu efeito sobre o observador, sinal para o comportamento e criador de sentimentos, sedimentado em obras de arte e em formas de superstição dos povos). Segue-se a apresentação de um estudo descritivo transversal, como contribuição para o conhecimento do estado de saúde visual da população infantil da região de Lisboa e determinar factores que o influenciam. Entre Outubro de 2005 e Agosto de 2006 examinaram-se 649 crianças com idade inferior a 10 anos da Consulta de Oftalmologia Pediátrica dos Serviços de Assistência Médico-Social do Sindicato dos Bancários do Sul e Ilhas (SAMS). Colheram-se dados respeitantes a mais de 250 variáveis primárias que cobriram a maior parte dos itens do exame oftalmológico habitual. Na análise dos dados teve-se especialmente em conta a idade, com um papel decisivo nas principais fases de desenvolvimento do sistema visual. No caso das crianças de 6 a 7 anos de idade põem-se lado a lado resultados dos SAMS e das Escolas. A profusão de dados numéricos ditou a necessidade da determinação frequente da significância estatística dos resultados de subgrupos. Alguns resultados do estudo, na sua maioria do grupo SAMS: Crianças de 6-7 anos, 71,1% (SAMS) e 91,5% (Escolas) não tinham sido examinadas com menos de 4 anos. Frequência global de alterações miópicas 9,4%, de alterações hipermetrópicas 25,3%, umas e outras com variações acentuadas com a idade. Estrabismo convergente 3,9%. Ambliopia 2,6% (13/491 crianças >=4 anos de idade), mais frequente no sexo feminino, naquelas que tiveram a sua 1ª observação depois dos 4 anos e em que os pais não aderiam à terapêutica prescrita. Objectivos específicos ocuparam-se da acuidade visual e da refracção ocular. O estudo comparativo da refractometria automática sem e com cicloplegia permitiu evidenciar que o teste da acuidade visual é insuficiente, por si só, para fazer o diagnóstico correcto. A análise dos antecedentes familiares oftalmológicos demonstrou a importância do seu conhecimento e pôs em evidência, entre outras, as seguintes relações: 10 pag1.qxp 27-11-2001 18:28 Page 10 Índice Geral 11 Crianças com antecedentes de alterações miópicas têm maior frequência de diagnóstico de alterações miópicas e de refracção negativa, uma taxa mais elevada de correspondência quantitativa diagnóstico/refracção nas alterações miópicas. Estas crianças também têm, em geral, características inversas no que diz respeito a alterações hipermetrópicas. Crianças com antecedentes de alterações hipermetrópicas têm maior frequência de diagnóstico de alterações hipermetrópicas. Crianças com antecedentes de estrabismo têm maior frequência de diagnóstico de estrabismo convergente manifesto e de esodesvios no seu todo. Crianças com antecedentes familiares de astigmatismo têm maior frequência de diagnóstico de astigmatismo. Traçam-se alguns perfis oftalmológicos infantis que permitem apreciar de forma sinóptica um conjunto de parâmetros da saúde da visão. Os dados colhidos sobre a aderência dos pais à terapêutica prescrita e sobre a atitude em relação ao uso de óculos assim como os dados sobre o comportamento da criança na sala de aula e dificuldades de aprendizagem foram em geral escassos para permitirem tirar conclusões, embora mostrem indícios a investigar futuramente. Paralelamente ortoptistas e enfermeiras efectuaram um rastreio escolar da acuidade visual <0,8 e de alterações da motilidade ocular extrínseca que abrangeu 520 alunos do 1º ano do 1º ciclo do ensino básico (2005/2006) das escolas públicas da cidade de Lisboa. 101 destas crianças foram observadas no consultório da autora, umas referidas a partir do rastreio, outras como controlo deste. Quanto à acuidade visual o valor preditivo do teste negativo foi de 91% mas o do teste positivo de apenas 67% (33% de falsos positivos, consequentemente uma alta taxa de sobrerreferenciação). A qualidade do rastreio efectuado por ortoptistas foi inferior à do efectuado por enfermeiras. O rastreio não teve qualidade aceitável. Foi feito um inquérito a médicos e enfermeiros de centros de saúde sobre conhecimentos, atitudes e práticas em relação com os cuidados de oftalmologia pediátrica. Discutem-se os resultados, tiram-se conclusões e fazem-se recomendações susceptíveis de contribuir para uma melhor saúde visual das crianças. ABSTRACT: Firstly some brief remarks are made based on the scientific, historical and cultural panorama of the human vision with regard to three approaches: the eye (the human eye in its specific filogenetic place, fundamental anatomofunctional element of the visual system in interaction with the brain), the eyes (essential twin units of the face with their consensual and conjugated binocular activity), the gaze (psychologicaly overloaded, a means to express oneself and to influence the observer, a guide to other persons' behaviour, consolidated in works of art and in people's traditional superstitious believes and ways of thinking). A report is made on a cross-sectional descriptive study whose goal is to contribute to the knowledge of the level of visual health of children in the Lisbon Region and to identify factors which determine it. Between October 2005 and August 2006 649 children under 10 years were observed at the pediatric ophthalmologic consultation in the SAMS (Serviços de Assistência Médico-Social do Sindicato dos Bancários do Sul e Ilhas). Data were collected concerning more than 250 primary variables covering most itens of the usual ophthalmological examination. Special attention was paid to children's age since it plays a crucial role in main stages of visual system development. In the case of children age 6 to 7 SAMS and school results are often put side by side. On account of the great number of numerical data it was often necessary to look at the degree of statistical significancy of differencies between subgroups. Some of the study's results (mostly SAMS): Children age 6 to 7 - 71,1% (SAMS) and 91,5% (Schools) had not an ophthalmologic examination before 4 years old. Total frequency of myopic disorders 9,4%, of hypermetropic disorders 25,3%, both showing great differences between age groups; convergent strabismus 3,9%; amblyopia 2,6% (13/491 children over 3 years old), more frequent among little girls, in those with 1st examination after 4 years old and in those whose parents didn´t complied to the therapy ordered for the child. Specific objectives dealt with visual acuity and ocular refraction. The comparison of automatic refractometry without and with cycloplegy showed that visual acuity testing is often not enough for a correct diagnosis. Eye disorders in the family history proved to be a very important information. Analysis of corresponding data disclosed a lot of relationships among others: 12 pag1.qxp 27-11-2001 18:28 Page 12 Índice Geral 13 Children with a family history of myopic disorders have more frequently a diagnosis of myopic disorders and a negative refraction, a higher rate of quantitative diagnosis/refraction matching concerning myopic disorders. Those children have in general inverse characteristics regarding hypermetropic disorders. Children with a family history of hypermetropic disorders have more frequently a diagnosis of hypermetropic disorders. Children with a family history of strabismus have more frequently a diagnosis of manifest convergent strabismus and all forms of esodeviations. Children with a family history of astigmatism have more frequently a diagnosis of astigmatism. Ophthalmologic profiles are drawn allowing to take into account in a synoptic way a set of visual health parameters. Data on parents' compliance with therapy ordered for the child, and attitudes regarding child's glass wearing, as well as data on child's behaviour in the classroom and learning difficulties were as a rule too few to allow conclusions but still need more studies in the future. Orthoptists and nurses performed in the same study period a screening of visual acuity <0,8 and of ocular motility disorders addressed to children of 1srt degree of public schools (term 2005/2006) in the town of Lisbon. 520 of such children were screened. 101 of them were examined by the author in her medical office; some were refered, the others taken as a control. Regarding visual acuity the predictive value of a negative test was 91% but the predictive value of a positive test was only 67% (33% of false positive results, consequently a too high rate of overreferal). Performed by orthoptists screening quality was inferior in comparison with screening done by nurses. On the whole this screening had not the required quality. A survey on physicians' and nurses' knowledge, attitudes and practices related to pediatric ophthalmologic care was carried out in health centers. Results are discussed, conclusions drawn. Some suggestions are made aiming at a better children's visual health.

Prognostic modelling of breast cancer patients: a benchmark of predictive models with external validation

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores – Sistemas Digitais e Percepcionais pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Study of a 9th century silver earrings set from Mikulčice: corrosion, conservation and maintenance

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Conservação e Restauro

Modern techniques for constraint solving the CASPER experience

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia Informática, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Biomarkers in Solea Senegalensis Kaup, 1858 exposed to contaminated estuarine sediments: a multi-level approach

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia for the degree of Doctor of Philosophy in Environmental Sciences

Automated image tagging through tag propagation

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