A Non-MCMC Procedure for Fitting Dirichlet Process Mixture Models

Cluster analysis is concerned with partitioning cases into clusters such that the cases in a cluster are similar in terms of a set of variables. The K-Means Clustering Algorithm is a popular clustering method. It finds k clusters by choosing k data points as initial cluster centroids. Each data point is then assigned to the cluster with center that is closest to that point. In K-Means, the number of clusters has to be supplied in advance, which may be difficult in practice. A new method, the X-Means Clustering Algorithm, was proposed to solve this problem, which starts with an initial partition, then recursively runs a local K-Means in each cluster to split it until a lower Bayesian Information Criterion (BIC) value is reached compared with the previous larger cluster. However, this method would introduce a more severe local mode problem, that is, the previous inappropriate partition of cases cannot be corrected in the following local splitting. In this work, we develop a new algorithm that is based on Bayesian Dirichlet process mixture models, called the Non-MCMC DPM clustering algorithm. In the new clustering algorithm, we run the EM algorithm with all the cases to find a tentative partition, and then decide whether to accept the new partion with a criterion called DPC. We have tested our new clustering algorithm based on several simulated data sets, and found that it performs better than X-Means. We have also applied the algorithm to a real micorarray sample data set for predicting the class label (cancer or normal) based on the clustering results found by our new algorithm, and found that the prediction performance is comparable to state-of-the-art methods

A mixture of variational canonical correlation analysis for nonlinear and quality-relevant process monitoring

Proper monitoring of quality-related variables in industrial processes is nowadays one of the main worldwide challenges with significant safety and efficiency implications.Variational Bayesian mixture of canonical correlation analysis (VBMCCA)-based process monitoring method was proposed in this paper to predict and diagnose these hard-to-measure quality-related variables simultaneously. Use of Student's t-distribution, rather than Gaussian distribution, in the VBMCCA model makes the proposed process monitoring scheme insensitive to disturbances, measurement noises, and model discrepancies. A sequential perturbation (SP) method together with derived parameter distribution of VBMCCA is employed to approach the uncertainty levels, which is able to provide a confidence interval around the predicted values and give additional control line, rather than just a certain absolute control limit, for process monitoring. The proposed process monitoring framework has been validated in a wastewater treatment plant (WWTP) simulated by benchmark simulation model with abrupt changes imposing on a sensor and a real WWTP with filamentous sludge bulking. The results show that the proposed methodology is capable of detecting sensor faults and process faults with satisfactory accuracy

Complexity-based classification of software modules

Software plays a major role in many organizations. Organizational success depends partially on the quality of software used. In recent years, many researchers have recognized that statistical classification techniques are well-suited to develop software quality prediction models. Different statistical software quality models, using complexity metrics as early indicators of software quality, have been proposed in the past. At a high-level the problem of software categorization is to classify software modules into fault prone and non-fault prone. The focus of this thesis is two-fold. One is to study some selected classification techniques including unsupervised and supervised learning algorithms widely used for software categorization. The second emphasis is to explore a new unsupervised learning model, employing Bayesian and deterministic approaches. Besides, we evaluate and compare experimentally these approaches using a real data set. Our experimental results show that different algorithms lead to different statistically significant results

Sistemática e evolução do gênero de morcegos neotropical Lophostoma d'Orbigny, 1836 (Chiroptera: Phyllostomidae)

Morcegos Lophostoma d'Orbigny, 1836 (Chiroptera: Phyllostomidae) estão distribuídos desde o sul do México até o sudoeste do Paraguai e sudeste do Brasil. Este gênero inclui sete espécies de morcegos insetívoros, conhecidos como morcegos-de-orelhas-redondas. A sistemática e taxonomia do grupo têm sido objeto de diversos estudos, que utilizando dados morfológicos e moleculares revelaram uma enorme diversidade fenotípica e genotípica, indicando a possível existência de espécies crípticas, principalmente em Lophostoma brasiliense Peters, 1866 e Lophostoma silvicola d'Orbigny, 1836. O principal objetivo do presente estudo foi analisar a diversidade críptica de Lophostoma ao longo de sua distribuição geográfica, integrando análises moleculares, morfológicas e morfométricas para esclarecer os limites taxonômicos, distribuição e relações evolutivas das suas espécies. No primeiro capítulo, apresento uma avaliação taxonômica de L. brasiliense. Foram utilizados métodos de delimitação fenotípica e molecular das espécies com base no marcador mitocondrial Citocromo c oxidase subunidade 1 (COI), dados morfológicos, morfométricos lineares e geométricos. Os resultados reconheceram L. brasiliense como duas linhagens distintas com distribuições alopátricas. Uma corresponde à L. brasiliense sensu stricto, com distribuição cis-andina; outra corresponde à L. nicaraguae (Goodwin, 1942), atualmente sinônimo de L. brasiliense, com distribuição transandina. O status de espécie válida é proposto para L. nicaraguae considerando as evidências apresentadas. No segundo capítulo, faço uma avaliação taxonômica de L. silvicola baseada em dois genes mitocondriais (COI, Cyt-b) e múltiplas evidências fenotípicas (morfologia qualitativa e quantitativa). As análises suportam a validação de duas entidades taxonômicas adicionais à L. silvicola: L. laephotis (Thomas, 1910) e L. amblyotis Peters, 1867. Por fim, apresento informações sobre a distribuição de cada uma das espécies aqui reconhecidas, bem como hipóteses sobre a sua diversificação, e discuto as possíveis implicações das barreiras geográficas na origem destas espécies.Bats of genus Lophostoma d'Orbigny, 1836 (Chiroptera: Phyllostomidae) are distributed from southern Mexico to southwestern Paraguay and southwestern Brazil. This genus includes seven species of insectivorous bats, which are known as round-eared bats. Systematics and taxonomy of the group have been the subject of several studies, which using morphological and molecular data revealed an enormous phenotypic and genetic diversity, indicating the possible existence of cryptic species, mainly in Lophostoma brasiliense Peters, 1866 and Lophostoma silvicola d'Orbigny, 1836. The main objective of the present study was to analyze the cryptic diversity of Lophostoma throughout its geographic distribution, integrating molecular, morphological and morphometric analyzes to clarify the taxonomic limits, distribution and evolutionary relationships of its species. In the first chapter, I present a taxonomic assessment of L. brasiliense. Phenotypic and molecular species delimitation methods were used based on the mitochondrial marker Cytochrome c oxidase subunit I (COI), morphological, linear and geometric morphometric data. The results recognized L. brasiliense as two distinct lineages with allopatric distributions. One corresponds to L. brasiliense sensu stricto, with a cis-Andean distribution; another corresponds to L. nicaraguae (Goodwin, 1942), currently synonymous with L. brasiliense, with trans-Andean distribution. Valid species status is proposed for L. nicaraguae considering the evidence presented. In the second chapter, I perform a taxonomic assessment of L. silvicola based on two mitochondrial genes (COI, Cyt-b) and multiple phenotypic evidences (qualitative and quantitative morphology). The analyzes supported the validation of two additional taxonomic entities to L. silvicola: L. laephotis (Thomas, 1910) and L. amblyotis Peters, 1867. Finally, I present information on the distribution of each of the species recognized here, as well as hypotheses about their diversification, and discuss the possible implications of geographic barriers in the origin of these species

puma: a Bioconductor package for propagating uncertainty in microarray analysis

BACKGROUND: Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has been shown that we can improve results of differential expression detection, principal component analysis and clustering. Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of differential expression detection, have been limited in the experimental designs to which they can be applied. RESULTS: puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data. puma extends the differential expression detection methods of previous work from the 2-class case to the multi-factorial case. puma can be used to automatically create design and contrast matrices for typical experimental designs, which can be used both within the package itself but also in other Bioconductor packages. The implementation of differential expression detection methods has been parallelised leading to significant decreases in processing time on a range of computer architectures. puma incorporates the first R implementation of an uncertainty propagation version of principal component analysis, and an implementation of a clustering method based on uncertainty propagation. All of these techniques are brought together in a single, easy-to-use package with clear, task-based documentation. CONCLUSION: For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. These methods can be used to improve results from more traditional analyses of microarray data. puma also offers improvements in terms of scope and speed of execution over previously available methods. puma is recommended for anyone working with the Affymetrix GeneChip platform for gene expression analysis and can also be applied more generally

Multi-sensor data fusion in mobile devices for the identification of Activities of Daily Living

Following the recent advances in technology and the growing use of mobile devices such as smartphones, several solutions may be developed to improve the quality of life of users in the context of Ambient Assisted Living (AAL). Mobile devices have different available sensors, e.g., accelerometer, gyroscope, magnetometer, microphone and Global Positioning System (GPS) receiver, which allow the acquisition of physical and physiological parameters for the recognition of different Activities of Daily Living (ADL) and the environments in which they are performed. The definition of ADL includes a well-known set of tasks, which include basic selfcare tasks, based on the types of skills that people usually learn in early childhood, including feeding, bathing, dressing, grooming, walking, running, jumping, climbing stairs, sleeping, watching TV, working, listening to music, cooking, eating and others. On the context of AAL, some individuals (henceforth called user or users) need particular assistance, either because the user has some sort of impairment, or because the user is old, or simply because users need/want to monitor their lifestyle. The research and development of systems that provide a particular assistance to people is increasing in many areas of application. In particular, in the future, the recognition of ADL will be an important element for the development of a personal digital life coach, providing assistance to different types of users. To support the recognition of ADL, the surrounding environments should be also recognized to increase the reliability of these systems. The main focus of this Thesis is the research on methods for the fusion and classification of the data acquired by the sensors available in off-the-shelf mobile devices in order to recognize ADL in almost real-time, taking into account the large diversity of the capabilities and characteristics of the mobile devices available in the market. In order to achieve this objective, this Thesis started with the review of the existing methods and technologies to define the architecture and modules of the method for the identification of ADL. With this review and based on the knowledge acquired about the sensors available in off-the-shelf mobile devices, a set of tasks that may be reliably identified was defined as a basis for the remaining research and development to be carried out in this Thesis. This review also identified the main stages for the development of a new method for the identification of the ADL using the sensors available in off-the-shelf mobile devices; these stages are data acquisition, data processing, data cleaning, data imputation, feature extraction, data fusion and artificial intelligence. One of the challenges is related to the different types of data acquired from the different sensors, but other challenges were found, including the presence of environmental noise, the positioning of the mobile device during the daily activities, the limited capabilities of the mobile devices and others. Based on the acquired data, the processing was performed, implementing data cleaning and feature extraction methods, in order to define a new framework for the recognition of ADL. The data imputation methods were not applied, because at this stage of the research their implementation does not have influence in the results of the identification of the ADL and environments, as the features are extracted from a set of data acquired during a defined time interval and there are no missing values during this stage. The joint selection of the set of usable sensors and the identifiable set of tasks will then allow the development of a framework that, considering multi-sensor data fusion technologies and context awareness, in coordination with other information available from the user context, such as his/her agenda and the time of the day, will allow to establish a profile of the tasks that the user performs in a regular activity day. The classification method and the algorithm for the fusion of the features for the recognition of ADL and its environments needs to be deployed in a machine with some computational power, while the mobile device that will use the created framework, can perform the identification of the ADL using a much less computational power. Based on the results reported in the literature, the method chosen for the recognition of the ADL is composed by three variants of Artificial Neural Networks (ANN), including simple Multilayer Perceptron (MLP) networks, Feedforward Neural Networks (FNN) with Backpropagation, and Deep Neural Networks (DNN). Data acquisition can be performed with standard methods. After the acquisition, the data must be processed at the data processing stage, which includes data cleaning and feature extraction methods. The data cleaning method used for motion and magnetic sensors is the low pass filter, in order to reduce the noise acquired; but for the acoustic data, the Fast Fourier Transform (FFT) was applied to extract the different frequencies. When the data is clean, several features are then extracted based on the types of sensors used, including the mean, standard deviation, variance, maximum value, minimum value and median of raw data acquired from the motion and magnetic sensors; the mean, standard deviation, variance and median of the maximum peaks calculated with the raw data acquired from the motion and magnetic sensors; the five greatest distances between the maximum peaks calculated with the raw data acquired from the motion and magnetic sensors; the mean, standard deviation, variance, median and 26 Mel- Frequency Cepstral Coefficients (MFCC) of the frequencies obtained with FFT based on the raw data acquired from the microphone data; and the distance travelled calculated with the data acquired from the GPS receiver. After the extraction of the features, these will be grouped in different datasets for the application of the ANN methods and to discover the method and dataset that reports better results. The classification stage was incrementally developed, starting with the identification of the most common ADL (i.e., walking, running, going upstairs, going downstairs and standing activities) with motion and magnetic sensors. Next, the environments were identified with acoustic data, i.e., bedroom, bar, classroom, gym, kitchen, living room, hall, street and library. After the environments are recognized, and based on the different sets of sensors commonly available in the mobile devices, the data acquired from the motion and magnetic sensors were combined with the recognized environment in order to differentiate some activities without motion, i.e., sleeping and watching TV. The number of recognized activities in this stage was increased with the use of the distance travelled, extracted from the GPS receiver data, allowing also to recognize the driving activity. After the implementation of the three classification methods with different numbers of iterations, datasets and remaining configurations in a machine with high processing capabilities, the reported results proved that the best method for the recognition of the most common ADL and activities without motion is the DNN method, but the best method for the recognition of environments is the FNN method with Backpropagation. Depending on the number of sensors used, this implementation reports a mean accuracy between 85.89% and 89.51% for the recognition of the most common ADL, equals to 86.50% for the recognition of environments, and equals to 100% for the recognition of activities without motion, reporting an overall accuracy between 85.89% and 92.00%. The last stage of this research work was the implementation of the structured framework for the mobile devices, verifying that the FNN method requires a high processing power for the recognition of environments and the results reported with the mobile application are lower than the results reported with the machine with high processing capabilities used. Thus, the DNN method was also implemented for the recognition of the environments with the mobile devices. Finally, the results reported with the mobile devices show an accuracy between 86.39% and 89.15% for the recognition of the most common ADL, equal to 45.68% for the recognition of environments, and equal to 100% for the recognition of activities without motion, reporting an overall accuracy between 58.02% and 89.15%. Compared with the literature, the results returned by the implemented framework show only a residual improvement. However, the results reported in this research work comprehend the identification of more ADL than the ones described in other studies. The improvement in the recognition of ADL based on the mean of the accuracies is equal to 2.93%, but the maximum number of ADL and environments previously recognized was 13, while the number of ADL and environments recognized with the framework resulting from this research is 16. In conclusion, the framework developed has a mean improvement of 2.93% in the accuracy of the recognition for a larger number of ADL and environments than previously reported. In the future, the achievements reported by this PhD research may be considered as a start point of the development of a personal digital life coach, but the number of ADL and environments recognized by the framework should be increased and the experiments should be performed with different types of devices (i.e., smartphones and smartwatches), and the data imputation and other machine learning methods should be explored in order to attempt to increase the reliability of the framework for the recognition of ADL and its environments.Após os recentes avanços tecnológicos e o crescente uso dos dispositivos móveis, como por exemplo os smartphones, várias soluções podem ser desenvolvidas para melhorar a qualidade de vida dos utilizadores no contexto de Ambientes de Vida Assistida (AVA) ou Ambient Assisted Living (AAL). Os dispositivos móveis integram vários sensores, tais como acelerómetro, giroscópio, magnetómetro, microfone e recetor de Sistema de Posicionamento Global (GPS), que permitem a aquisição de vários parâmetros físicos e fisiológicos para o reconhecimento de diferentes Atividades da Vida Diária (AVD) e os seus ambientes. A definição de AVD inclui um conjunto bem conhecido de tarefas que são tarefas básicas de autocuidado, baseadas nos tipos de habilidades que as pessoas geralmente aprendem na infância. Essas tarefas incluem alimentar-se, tomar banho, vestir-se, fazer os cuidados pessoais, caminhar, correr, pular, subir escadas, dormir, ver televisão, trabalhar, ouvir música, cozinhar, comer, entre outras. No contexto de AVA, alguns indivíduos (comumente chamados de utilizadores) precisam de assistência particular, seja porque o utilizador tem algum tipo de deficiência, seja porque é idoso, ou simplesmente porque o utilizador precisa/quer monitorizar e treinar o seu estilo de vida. A investigação e desenvolvimento de sistemas que fornecem algum tipo de assistência particular está em crescente em muitas áreas de aplicação. Em particular, no futuro, o reconhecimento das AVD é uma parte importante para o desenvolvimento de um assistente pessoal digital, fornecendo uma assistência pessoal de baixo custo aos diferentes tipos de pessoas. pessoas. Para ajudar no reconhecimento das AVD, os ambientes em que estas se desenrolam devem ser reconhecidos para aumentar a fiabilidade destes sistemas. O foco principal desta Tese é o desenvolvimento de métodos para a fusão e classificação dos dados adquiridos a partir dos sensores disponíveis nos dispositivos móveis, para o reconhecimento quase em tempo real das AVD, tendo em consideração a grande diversidade das características dos dispositivos móveis disponíveis no mercado. Para atingir este objetivo, esta Tese iniciou-se com a revisão dos métodos e tecnologias existentes para definir a arquitetura e os módulos do novo método de identificação das AVD. Com esta revisão da literatura e com base no conhecimento adquirido sobre os sensores disponíveis nos dispositivos móveis disponíveis no mercado, um conjunto de tarefas que podem ser identificadas foi definido para as pesquisas e desenvolvimentos desta Tese. Esta revisão também identifica os principais conceitos para o desenvolvimento do novo método de identificação das AVD, utilizando os sensores, são eles: aquisição de dados, processamento de dados, correção de dados, imputação de dados, extração de características, fusão de dados e extração de resultados recorrendo a métodos de inteligência artificial. Um dos desafios está relacionado aos diferentes tipos de dados adquiridos pelos diferentes sensores, mas outros desafios foram encontrados, sendo os mais relevantes o ruído ambiental, o posicionamento do dispositivo durante a realização das atividades diárias, as capacidades limitadas dos dispositivos móveis. As diferentes características das pessoas podem igualmente influenciar a criação dos métodos, escolhendo pessoas com diferentes estilos de vida e características físicas para a aquisição e identificação dos dados adquiridos a partir de sensores. Com base nos dados adquiridos, realizou-se o processamento dos dados, implementando-se métodos de correção dos dados e a extração de características, para iniciar a criação do novo método para o reconhecimento das AVD. Os métodos de imputação de dados foram excluídos da implementação, pois não iriam influenciar os resultados da identificação das AVD e dos ambientes, na medida em que são utilizadas as características extraídas de um conjunto de dados adquiridos durante um intervalo de tempo definido. A seleção dos sensores utilizáveis, bem como das AVD identificáveis, permitirá o desenvolvimento de um método que, considerando o uso de tecnologias para a fusão de dados adquiridos com múltiplos sensores em coordenação com outras informações relativas ao contexto do utilizador, tais como a agenda do utilizador, permitindo estabelecer um perfil de tarefas que o utilizador realiza diariamente. Com base nos resultados obtidos na literatura, o método escolhido para o reconhecimento das AVD são as diferentes variantes das Redes Neuronais Artificiais (RNA), incluindo Multilayer Perceptron (MLP), Feedforward Neural Networks (FNN) with Backpropagation and Deep Neural Networks (DNN). No final, após a criação dos métodos para cada fase do método para o reconhecimento das AVD e ambientes, a implementação sequencial dos diferentes métodos foi realizada num dispositivo móvel para testes adicionais. Após a definição da estrutura do método para o reconhecimento de AVD e ambientes usando dispositivos móveis, verificou-se que a aquisição de dados pode ser realizada com os métodos comuns. Após a aquisição de dados, os mesmos devem ser processados no módulo de processamento de dados, que inclui os métodos de correção de dados e de extração de características. O método de correção de dados utilizado para sensores de movimento e magnéticos é o filtro passa-baixo de modo a reduzir o ruído, mas para os dados acústicos, a Transformada Rápida de Fourier (FFT) foi aplicada para extrair as diferentes frequências. Após a correção dos dados, as diferentes características foram extraídas com base nos tipos de sensores usados, sendo a média, desvio padrão, variância, valor máximo, valor mínimo e mediana de dados adquiridos pelos sensores magnéticos e de movimento, a média, desvio padrão, variância e mediana dos picos máximos calculados com base nos dados adquiridos pelos sensores magnéticos e de movimento, as cinco maiores distâncias entre os picos máximos calculados com os dados adquiridos dos sensores de movimento e magnéticos, a média, desvio padrão, variância e 26 Mel-Frequency Cepstral Coefficients (MFCC) das frequências obtidas com FFT com base nos dados obtidos a partir do microfone, e a distância calculada com os dados adquiridos pelo recetor de GPS. Após a extração das características, as mesmas são agrupadas em diferentes conjuntos de dados para a aplicação dos métodos de RNA de modo a descobrir o método e o conjunto de características que reporta melhores resultados. O módulo de classificação de dados foi incrementalmente desenvolvido, começando com a identificação das AVD comuns com sensores magnéticos e de movimento, i.e., andar, correr, subir escadas, descer escadas e parado. Em seguida, os ambientes são identificados com dados de sensores acústicos, i.e., quarto, bar, sala de aula, ginásio, cozinha, sala de estar, hall, rua e biblioteca. Com base nos ambientes reconhecidos e os restantes sensores disponíveis nos dispositivos móveis, os dados adquiridos dos sensores magnéticos e de movimento foram combinados com o ambiente reconhecido para diferenciar algumas atividades sem movimento (i.e., dormir e ver televisão), onde o número de atividades reconhecidas nesta fase aumenta com a fusão da distância percorrida, extraída a partir dos dados do recetor GPS, permitindo também reconhecer a atividade de conduzir. Após a implementação dos três métodos de classificação com diferentes números de iterações, conjuntos de dados e configurações numa máquina com alta capacidade de processamento, os resultados relatados provaram que o melhor método para o reconhecimento das atividades comuns de AVD e atividades sem movimento é o método DNN, mas o melhor método para o reconhecimento de ambientes é o método FNN with Backpropagation. Dependendo do número de sensores utilizados, esta implementação reporta uma exatidão média entre 85,89% e 89,51% para o reconhecimento das AVD comuns, igual a 86,50% para o reconhecimento de ambientes, e igual a 100% para o reconhecimento de atividades sem movimento, reportando uma exatidão global entre 85,89% e 92,00%. A última etapa desta Tese foi a implementação do método nos dispositivos móveis, verificando que o método FNN requer um alto poder de processamento para o reconhecimento de ambientes e os resultados reportados com estes dispositivos são inferiores aos resultados reportados com a máquina com alta capacidade de processamento utilizada no desenvolvimento do método. Assim, o método DNN foi igualmente implementado para o reconhecimento dos ambientes com os dispositivos móveis. Finalmente, os resultados relatados com os dispositivos móveis reportam uma exatidão entre 86,39% e 89,15% para o reconhecimento das AVD comuns, igual a 45,68% para o reconhecimento de ambientes, e igual a 100% para o reconhecimento de atividades sem movimento, reportando uma exatidão geral entre 58,02% e 89,15%. Com base nos resultados relatados na literatura, os resultados do método desenvolvido mostram uma melhoria residual, mas os resultados desta Tese identificam mais AVD que os demais estudos disponíveis na literatura. A melhoria no reconhecimento das AVD com base na média das exatidões é igual a 2,93%, mas o número máximo de AVD e ambientes reconhecidos pelos estudos disponíveis na literatura é 13, enquanto o número de AVD e ambientes reconhecidos com o método implementado é 16. Assim, o método desenvolvido tem uma melhoria de 2,93% na exatidão do reconhecimento num maior número de AVD e ambientes. Como trabalho futuro, os resultados reportados nesta Tese podem ser considerados um ponto de partida para o desenvolvimento de um assistente digital pessoal, mas o número de ADL e ambientes reconhecidos pelo método deve ser aumentado e as experiências devem ser repetidas com diferentes tipos de dispositivos móveis (i.e., smartphones e smartwatches), e os métodos de imputação e outros métodos de classificação de dados devem ser explorados de modo a tentar aumentar a confiabilidade do método para o reconhecimento das AVD e ambientes

VI Workshop on Computational Data Analysis and Numerical Methods: Book of Abstracts

The VI Workshop on Computational Data Analysis and Numerical Methods (WCDANM) is going to be held on June 27-29, 2019, in the Department of Mathematics of the University of Beira Interior (UBI), Covilhã, Portugal and it is a unique opportunity to disseminate scientific research related to the areas of Mathematics in general, with particular relevance to the areas of Computational Data Analysis and Numerical Methods in theoretical and/or practical field, using new techniques, giving especial emphasis to applications in Medicine, Biology, Biotechnology, Engineering, Industry, Environmental Sciences, Finance, Insurance, Management and Administration. The meeting will provide a forum for discussion and debate of ideas with interest to the scientific community in general. With this meeting new scientific collaborations among colleagues, namely new collaborations in Masters and PhD projects are expected. The event is open to the entire scientific community (with or without communication/poster)

Analytical fusion of multimodal magnetic resonance imaging to identify pathological states in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats

[EN] Alcohol abuse is one of the most alarming issues for the health authorities. It is estimated that at least 23 million of European citizens are affected by alcoholism causing a cost around 270 million euros. Excessive alcohol consumption is related with physical harm and, although it damages the most of body organs, liver, pancreas, and brain are more severally affected. Not only physical harm is associated to alcohol-related disorders, but also other psychiatric disorders such as depression are often comorbiding. As well, alcohol is present in many of violent behaviors and traffic injures. Altogether reflects the high complexity of alcohol-related disorders suggesting the involvement of multiple brain systems. With the emergence of non-invasive diagnosis techniques such as neuroimaging or EEG, many neurobiological factors have been evidenced to be fundamental in the acquisition and maintenance of addictive behaviors, relapsing risk, and validity of available treatment alternatives. Alterations in brain structure and function reflected in non-invasive imaging studies have been repeatedly investigated. However, the extent to which imaging measures may precisely characterize and differentiate pathological stages of the disease often accompanied by other pathologies is not clear. The use of animal models has elucidated the role of neurobiological mechanisms paralleling alcohol misuses. Thus, combining animal research with non-invasive neuroimaging studies is a key tool in the advance of the disorder understanding. As the volume of data from very diverse nature available in clinical and research settings increases, an integration of data sets and methodologies is required to explore multidimensional aspects of psychiatric disorders. Complementing conventional mass-variate statistics, interests in predictive power of statistical machine learning to neuroimaging data is currently growing among scientific community. This doctoral thesis has covered most of the aspects mentioned above. Starting from a well-established animal model in alcohol research, Marchigian Sardinian rats, we have performed multimodal neuroimaging studies at several stages of alcohol-experimental design including the etiological mechanisms modulating high alcohol consumption (in comparison to Wistar control rats), alcohol consumption, and treatment with the opioid antagonist Naltrexone, a well-established drug in clinics but with heterogeneous response. Multimodal magnetic resonance imaging acquisition included Diffusion Tensor Imaging, structural imaging, and the calculation of magnetic-derived relaxometry maps. We have designed an analytical framework based on widely used algorithms in neuroimaging field, Random Forest and Support Vector Machine, combined in a wrapping fashion. Designed approach was applied on the same dataset with two different aims: exploring the validity of the approach to discriminate experimental stages running at subject-level and establishing predictive models at voxel-level to identify key anatomical regions modified during the experiment course. As expected, combination of multiple magnetic resonance imaging modalities resulted in an enhanced predictive power (between 3 and 16%) with heterogeneous modality contribution. Surprisingly, we have identified some inborn alterations correlating high alcohol preference and thalamic neuroadaptations related to Naltrexone efficacy. As well, reproducible contribution of DTI and relaxometry -related biomarkers has been repeatedly identified guiding further studies in alcohol research. In summary, along this research we demonstrate the feasibility of incorporating multimodal neuroimaging, machine learning algorithms, and animal research in the advance of the understanding alcohol-related disorders.[ES] El abuso de alcohol es una de las mayores preocupaciones de las autoridades sanitarias en la Unión Europea. El consumo de alcohol en exceso afecta en mayor o menor medida la totalidad del organismo siendo el páncreas e hígado los más severamente afectados. Además de estos, el sistema nervioso central sufre deterioros relacionados con el alcohol y con frecuencia se presenta en paralelo con otras patologías psiquiátricas como la depresión u otras adicciones como la ludopatía. La presencia de estas comorbidades demuestra la complejidad de la patología en la que multitud de sistemas neuronales interaccionan entre sí. El uso imágenes de resonancia magnética (RM) han ayudado en el estudio de enfermedades psiquiátricas facilitando el descubrimiento de mecanismos neurológicos fundamentales en el desarrollo y mantenimiento de la adicción al alcohol, recaídas y el efecto de los tratamientos disponibles. A pesar de los avances, todavía se necesita investigar más para identificar las bases biológicas que contribuyen a la enfermedad. En este sentido, los modelos animales sirven, por lo tanto, a discriminar aquellos factores únicamente relacionados con el alcohol controlando otros factores que facilitan el desarrollo del alcoholismo. Estudios de resonancia magnética en animales de laboratorio y su posterior evaluación en humanos juegan un papel fundamental en el entendimiento de las patologías psiquatricas como la addicción al alcohol. La imagen por resonancia magnética se ha integrado en entornos clínicos como prueba diagnósticas no invasivas. A medida que el volumen de datos se va incrementando, se necesitan herramientas y metodologías capaces de fusionar información de muy distinta naturaleza y así establecer criterios diagnósticos cada vez más exactos. El poder predictivo de herramientas derivadas de la inteligencia artificial como el aprendizaje automático sirven de complemento a tradicionales métodos estadísticos. En este trabajo se han abordado la mayoría de estos aspectos. Se han obtenido datos multimodales de resonancia magnética de un modelo validado en la investigación de patologías derivadas del consumo del alcohol, las ratas Marchigian-Sardinian desarrolladas en la Universidad de Camerino (Italia) y con consumos de alcohol comparables a los humanos. Para cada animal se han adquirido datos antes y después del consumo de alcohol y bajo dos condiciones de abstinencia (con y sin tratamiento de Naltrexona, una medicaciones anti-recaídas usada como farmacoterapia en el alcoholismo). Los datos de resonancia magnética multimodal consistentes en imágenes de difusión, de relaxometría y estructurales se han fusionado en un esquema analítico multivariable incorporando dos herramientas generalmente usadas en datos derivados de neuroimagen, Random Forest y Support Vector Machine. Nuestro esquema fue aplicado con dos objetivos diferenciados. Por un lado, determinar en qué fase experimental se encuentra el sujeto a partir de biomarcadores y por el otro, identificar sistemas cerebrales susceptibles de alterarse debido a una importante ingesta de alcohol y su evolución durante la abstinencia. Nuestros resultados demostraron que cuando biomarcadores derivados de múltiples modalidades de neuroimagen se fusionan en un único análisis producen diagnósticos más exactos que los derivados de una única modalidad (hasta un 16% de mejora). Biomarcadores derivados de imágenes de difusión y relaxometría discriminan estados experimentales. También se han identificado algunos aspectos innatos que están relacionados con posteriores comportamientos con el consumo de alcohol o la relación entre la respuesta al tratamiento y los datos de resonancia magnética. Resumiendo, a lo largo de esta tesis, se demuestra que el uso de datos de resonancia magnética multimodales en modelos animales combinados en esquemas analíticos multivariados es una herramienta válida en el entendimiento de patologías[CAT] L'abús de alcohol es una de les majors preocupacions per part de les autoritats sanitàries de la Unió Europea. Malgrat la dificultat de establir xifres exactes, se estima que uns 23 milions de europeus actualment sofreixen de malalties derivades del alcoholisme amb un cost que supera els 150.000 milions de euros per a la societat. Un consum de alcohol en excés afecta en major o menor mesura el cos humà sent el pàncreas i el fetge el més afectats. A més, el cervell sofreix de deterioraments produïts per l'alcohol i amb freqüència coexisteixen amb altres patologies com depressió o altres addiccions com la ludopatia. Tot aquest demostra la complexitat de la malaltia en la que múltiple sistemes neuronals interactuen entre si. Tècniques no invasives com el encefalograma (EEG) o imatges de ressonància magnètica (RM) han ajudat en l'estudi de malalties psiquiàtriques facilitant el descobriment de mecanismes neurològics fonamentals en el desenvolupament i manteniment de la addició, recaiguda i la efectivitat dels tractaments disponibles. Tot i els avanços, encara es necessiten més investigacions per identificar les bases biològiques que contribueixen a la malaltia. En aquesta direcció, el models animals serveixen per a identificar únicament dependents del abús del alcohol. Estudis de ressonància magnètica en animals de laboratori i posterior avaluació en humans jugarien un paper fonamental en l' enteniment de l'ús del alcohol. L'ús de probes diagnostiques no invasives en entorns clínics has sigut integrades. A mesura que el volum de dades es incrementa, eines i metodologies per a la fusió d' informació de molt distinta natura i per tant, establir criteris diagnòstics cada vegada més exactes. La predictibilitat de eines desenvolupades en el camp de la intel·ligència artificial com la aprenentatge automàtic serveixen de complement a mètodes estadístics tradicionals. En aquesta investigació se han abordat tots aquestes aspectes. Dades multimodals de ressonància magnètica se han obtingut de un model animal validat en l'estudi de patologies relacionades amb el consum d'alcohol, les rates Marchigian-Sardinian desenvolupades en la Universitat de Camerino (Italià) i amb consums d'alcohol comparables als humans. Per a cada animal es van adquirir dades previs i després al consum de alcohol i dos condicions diferents de abstinència (amb i sense tractament anti-recaiguda). Dades de ressonància magnètica multimodal constituides per imatges de difusió, de relaxometria magnètica i estructurals van ser fusionades en esquemes analítics multivariats incorporant dues metodologies validades en el camp de neuroimatge, Random Forest i Support Vector Machine. Nostre esquema ha sigut aplicat amb dos objectius diferenciats. El primer objectiu es determinar en quina fase experimental es troba el subjecte a partir de biomarcadors obtinguts per neuroimatge. Per l'altra banda, el segon objectiu es identificar el sistemes cerebrals susceptibles de ser alterats durant una important ingesta de alcohol i la seua evolució durant la fase del tractament. El nostres resultats demostraren que l'ús de biomarcadors derivats de varies modalitats de neuroimatge fusionades en un anàlisis multivariat produeixen diagnòstics més exactes que els derivats de una única modalitat (fins un 16% de millora). Biomarcadors derivats de imatges de difusió i relaxometria van contribuir de distints estats experimentals. També s'han identificat aspectes innats que estan relacionades amb posterior preferències d'alcohol o la relació entre la resposta al tractament anti-recaiguda i les dades de ressonància magnètica. En resum, al llarg de aquest treball, es demostra que l'ús de dades de ressonància magnètica multimodal en models animals combinats en esquemes analítics multivariats són una eina molt valida en l'enteniment i avanç de patologies psiquiàtriques com l'alcoholisme.Cosa Liñán, A. (2017). Analytical fusion of multimodal magnetic resonance imaging to identify pathological states in genetically selected Marchigian Sardinian alcohol-preferring (msP) rats [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/90523TESI