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.

Contributo da análise ergonómica do trabalho na avaliação do risco de lesões músculoesqueléticas ligadas ao trabalho

Mestrado em Segurança e Higiene no Trabalho

Inherently chiral calix[4]arenes with planar chirality: two new entries to the family

The synthesis of two new inherently chiral calix[4]arenes (ICCs, 1 and 2), endowed with electron-rich concave surfaces, has been achieved through the desymmetrization of a lower rim distal-bridged oxacyclophane (OCP) macrocycle. The new highly emissive ICCs were resolved by chiral HPLC, and the enantiomeric nature of the isolated antipodes proved by electronic circular dichroism (CD). Using time-dependent density functional calculations of CD spectra, their absolute configurations were established. NMR studies with (S)-Pirkle's alcohol unequivocally showed that the host-guest interactions occur in the chiral pocket comprehending the calix-OCP exo cavities and the carbazole moieties.

A inclusão de uma criança com nee – papel do adulto e dos pares na sua participação ativa no jardim de infância

Relatório da Prática Profissional Supervisionada Mestrado em Educação Pré-Escolar

Caracterização do desempenho das redes rodoviárias com base em modelos de afetação de tráfego: aplicação à Rede Rodoviária Nacional

Relatório de estágio para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização em Vias de Comunicação e Transportes

O impacto do ambiente e das energias renováveis no projeto de instalações de frio industrial num matadouro

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecãnica

Aplicação de métodos estocásticos na gestão de custos de construção de condutas de saneamento

O trabalho apresentado centra-se na determinação dos custos de construção de condutas de pequenos e médios diâmetros em Polietileno de Alta Densidade (PEAD) para saneamento básico, tendo como base a metodologia descrita no livro Custos de Construção e Exploração – Volume 9 da série Gestão de Sistemas de Saneamento Básico, de Lencastre et al. (1994). Esta metodologia descrita no livro já referenciado, nos procedimentos de gestão de obra, e para tal foram estimados custos unitários de diversos conjuntos de trabalhos. Conforme Lencastre et al (1994), “esses conjuntos são referentes a movimentos de terras, tubagens, acessórios e respetivos órgãos de manobra, pavimentações e estaleiro, estando englobado na parte do estaleiro trabalhos acessórios correspondentes à obra.” Os custos foram obtidos analisando vários orçamentos de obras de saneamento, resultantes de concursos públicos de empreitadas recentemente realizados. Com vista a tornar a utilização desta metodologia numa ferramenta eficaz, foram organizadas folhas de cálculo que possibilitam obter estimativas realistas dos custos de execução de determinada obra em fases anteriores ao desenvolvimento do projeto, designadamente numa fase de preparação do plano diretor de um sistema ou numa fase de elaboração de estudos de viabilidade económico-financeiros, isto é, mesmo antes de existir qualquer pré-dimensionamento dos elementos do sistema. Outra técnica implementada para avaliar os dados de entrada foi a “Análise Robusta de Dados”, Pestana (1992). Esta metodologia permitiu analisar os dados mais detalhadamente antes de se formularem hipóteses para desenvolverem a análise de risco. A ideia principal é o exame bastante flexível dos dados, frequentemente antes mesmo de os comparar a um modelo probabilístico. Assim, e para um largo conjunto de dados, esta técnica possibilitou analisar a disparidade dos valores encontrados para os diversos trabalhos referenciados anteriormente. Com os dados recolhidos, e após o seu tratamento, passou-se à aplicação de uma metodologia de Análise de Risco, através da Simulação de Monte Carlo. Esta análise de risco é feita com recurso a uma ferramenta informática da Palisade, o @Risk, disponível no Departamento de Engenharia Civil. Esta técnica de análise quantitativa de risco permite traduzir a incerteza dos dados de entrada, representada através de distribuições probabilísticas que o software disponibiliza. Assim, para por em prática esta metodologia, recorreu-se às folhas de cálculo que foram realizadas seguindo a abordagem proposta em Lencastre et al (1994). A elaboração e a análise dessas estimativas poderão conduzir à tomada de decisões sobre a viabilidade da ou das obras a realizar, nomeadamente no que diz respeito aos aspetos económicos, permitindo uma análise de decisão fundamentada quanto à realização dos investimentos.

Sobrevivência das redes de transporte da nova geração

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia de Electrónica e Telecomunicações

Solving Conflicting Beliefs with a Distributed Belief Revision Approach

The ability to solve conflicting beliefs is crucial for multi- agent systems where the information is dynamic, incomplete and dis- tributed over a group of autonomous agents. The proposed distributed belief revision approach consists of a distributed truth maintenance sy- stem and a set of autonomous belief revision methodologies. The agents have partial views and, frequently, hold disparate beliefs which are au- tomatically detected by system’s reason maintenance mechanism. The nature of these conflicts is dynamic and requires adequate methodolo- gies for conflict resolution. The two types of conflicting beliefs addressed in this paper are Context Dependent and Context Independent Conflicts which result, in the first case, from the assignment, by different agents, of opposite belief statuses to the same belief, and, in the latter case, from holding contradictory distinct beliefs. The belief revision methodology for solving Context Independent Con- flicts is, basically, a selection process based on the assessment of the cre- dibility of the opposing belief statuses. The belief revision methodology for solving Context Dependent Conflicts is, essentially, a search process for a consensual alternative based on a “next best” relaxation strategy.

LSP communication in a digital age: the outcomes of teaching and learning in tertiary education

This paper discusses the changes brought by the communication revolution in teaching and learning in the scope of LSP. Its aim is to provide an insight on how teaching which was bi-dimensional, turned into a multidimensional system, gathering other complementary resources that have transformed, in a incredibly short time, the ways we receive share and store information, for instance as professionals, and keep in touch with our peers. The increasing rise of electronic publications, the incredible boom of social and professional networks, search engines, blogs, list servs, forums, e-mail blasts, Facebook pages, YouTube contents, Tweets and Apps, have twisted the way information is conveyed. Classes ceased to be predictable and have been empowered by digital platforms, innumerous and different data repositories (TILDE, IATE, LINGUEE, and so many other terminological data banks) that have definitely transformed the academic world in general and tertiary education in particular. There is a bulk of information to be digested by students, who are no longer passive but instead responsible and active for their academic outcomes. The question is whether they possess the tools to select only what is accurate and important for a certain subject or assignment, due to that overflow? Due to the reduction of the number of course years in most degrees, after the implementation of Bologna and the shrinking of the curricula contents, have students the possibility of developing critical thinking? Both teaching and learning rely on digital resources to improve the speed of the spreading of knowledge. But have those changes been effective to promote really communication? Furthermore, with the increasing Apps that have already been developed and will continue to appear for learning foreign languages, for translation among others, will the students feel the need of learning them once they have those Apps. These are some the questions we would like to discuss in our paper.

No limite a alma: ensaio sobre um objecto artístico/instalação: trabalho de projecto

Trabalho de Projeto submetido à Escola Superior de Teatro e Cinema para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Teatro - especialização em Design de Cena.

Unified overhead-aware schedulability analysis for slot-based task-splitting

Hard real- time multiprocessor scheduling has seen, in recent years, the flourishing of semi-partitioned scheduling algorithms. This category of scheduling schemes combines elements of partitioned and global scheduling for the purposes of achieving efficient utilization of the system’s processing resources with strong schedulability guarantees and with low dispatching overheads. The sub-class of slot-based “task-splitting” scheduling algorithms, in particular, offers very good trade-offs between schedulability guarantees (in the form of high utilization bounds) and the number of preemptions/migrations involved. However, so far there did not exist unified scheduling theory for such algorithms; each one was formulated in its own accompanying analysis. This article changes this fragmented landscape by formulating a more unified schedulability theory covering the two state-of-the-art slot-based semi-partitioned algorithms, S-EKG and NPS-F (both fixed job-priority based). This new theory is based on exact schedulability tests, thus also overcoming many sources of pessimism in existing analysis. In turn, since schedulability testing guides the task assignment under the schemes in consideration, we also formulate an improved task assignment procedure. As the other main contribution of this article, and as a response to the fact that many unrealistic assumptions, present in the original theory, tend to undermine the theoretical potential of such scheduling schemes, we identified and modelled into the new analysis all overheads incurred by the algorithms in consideration. The outcome is a new overhead-aware schedulability analysis that permits increased efficiency and reliability. The merits of this new theory are evaluated by an extensive set of experiments.

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

The influence of pre-departure training on expatriate adjustment: an empirical investigation with portuguese international assignees

This chapter examines the cross-cultural influence of training on the adjustment of international assignees. We focus on the pre-departure training (PDT) before an international assignment. It is an important topic because in the globalized world of today more and more expatriations are needed. The absence of PDT may generate the failure of the expatriation experience. Companies may neglect PDT due to cost reduction practices and ignorance of the need for it. Data were collected through semi-structured interviews to 42 Portuguese international assignees and 18 organizational representatives from nine Portuguese companies. The results suggest that companies should develop PDT programs, particularly when the cultural distance to the host country is bigger and when there is no previous experience of expatriation to that country in the company. The study is original because it details in depth the methods of PDT, its problems, and consequences. Some limitations linked to the research design and detailed in the conclusion should be overcome in future studies.

Otimização da produção de biogás com recurso a redes neuronais artificiais

Numa Estação de Tratamento de Águas Residuais (ETAR), são elevados os custos não só de tratamento das águas residuais como também de manutenção dos equipamentos lá existentes, nesse sentido procura-se utilizar processos capazes de transformar os resíduos em produtos úteis. A Digestão Anaeróbia (DA) é um processo atualmente disponível capaz de contribuir para a redução da poluição ambiental e ao mesmo tempo de valorizar os subprodutos gerados. Durante o processo de DA é produzido um gás, o biogás, que pode ser utilizado como fonte de energia, reduzindo assim a dependência energética da ETAR e a emissão de gases com efeito de estufa para a atmosfera. A otimização do processo de DA das lamas é essencial para o aumento da produção de biogás, mas a complexidade do processo constitui um obstáculo à sua otimização. Neste trabalho, aplicaram-se Redes Neuronais Artificiais (RNA) ao processo de DA de lamas de ETAR. RNA são modelos simplificados inspirados no funcionamento das células neuronais humanas e que adquirem conhecimento através da experiência. Quando a RNA é criada e treinada, produz valores de output aproximadamente corretos para os inputs fornecidos. Foi esse o motivo para recorrer a RNA na otimização da produção de biogás no digestor I da ETAR Norte da SIMRIA, usando o programa NeuralToolsTM da PalisadeTM para desenvolvimento das RNA. Para tal, efetuou-se uma análise e tratamento de dados referentes aos últimos quatro anos de funcionamento do digestor. Os resultados obtidos permitiram concluir que as RNA modeladas apresentam boa capacidade de generalização do processo de DA. Considera-se que este caso de estudo é promissor, fornecendo uma boa base para o desenvolvimento de modelos eventualmente mais gerais de RNA que, aplicado conjuntamente com as características de funcionamento de um digestor e o processo de DA, permitirá otimizar a produção de biogás em ETAR.