This thesis consists of two projects in which various machine learning approaches and statistical analysis for the integration of biomedical data analysis were explored, developed and tested. Integration of different biomedical data sources allows us to get a better understating of human body from a bigger picture. If we can get a more complete view of the data, we not only get a more complete view of the molecule basis of phenotype, but also possibly can identify abnormality in diseases which were not found when using only one type of biomedical data. The objective of the first project is to find biological pathways which are related to Duechenne Muscular Dystrophy(DMD) and Lamin A/C(LMNA) using the integration of multi-omics data. We proposed a novel method which allows us to integrate proteins, mRNAs and miRNAs to find disease related pathways. The goal of the second project is to develop a personalized recommendation system which recommend cancer treatments to patients. Compared to the traditional way of using only users' rating to impute missing values, we proposed a method to incorporate users' profile to help enhance the accuracy of the prediction. / Master of Science / There are two existing major problems in the biomedical field. Previously, researchers only used one data type for analysis. However, one measurement does not fully capture the processes at work and can lead to inaccurate result with low sensitivity and specificity. Moreover, there are too many missing values in the biomedical data. This left us with many questions unanswered and can lead us to draw wrong conclusions from the data. To overcome these problems, we would like to integrate multiple data types which not only better captures the complex biological processes but also leads to a more comprehensive characterization. Moreover, utilizing the correlation among various data structures also help us impute missing values in the biomedical datasets. For my two research projects, we are interested in integrating multiple biological data to identify disease specific pathways and predict unknown treatment responses for cancer patients. In this thesis, we propose a novel approach for pathways identification using the integration of multi-omics data. Secondly, we also develop a recommendation system which combines different types of patients’ medical information for missing treatment responses’ prediction. Our goal is that we would find disease related pathways for the first project and enhance missing treatment response’s prediction for the second project with the methods we develop. The findings of my studies show that it is possible to find pathways related to muscular dystrophies using the integration of multi-omics data. Moreover, we also demonstrate that incorporating patient’s genetic profile can improve the prediction accuracy compared to using the treatment responses matrix alone for imputation.

La liste des domaines touchés par l’apprentissage machine s’allonge rapidement. Au fur et à mesure que la quantité de données disponibles augmente, le développement d’algorithmes d’apprentissage de plus en plus puissants est crucial. Ce mémoire est constitué de trois parties: d’abord un survol des concepts de bases de l’apprentissage automatique et les détails nécessaires pour l’entraînement de réseaux de neurones, modèles qui se livrent bien à des architectures profondes. Ensuite, le premier article présente une application de l’apprentissage machine aux jeux vidéos, puis une méthode de mesure performance pour ceux-ci en tant que politique de décision. Finalement, le deuxième article présente des résultats théoriques concernant l’entraînement d’architectures profondes nonsupervisées. Les jeux vidéos sont un domaine particulièrement fertile pour l’apprentissage automatique: il estf facile d’accumuler d’importantes quantités de données, et les applications ne manquent pas. La formation d’équipes selon un critère donné est une tˆache commune pour les jeux en lignes. Le premier article compare différents algorithmes d’apprentissage à des réseaux de neurones profonds appliqués à la prédiction de la balance d’un match. Ensuite nous présentons une méthode par simulation pour évaluer les modèles ainsi obtenus utilisés dans le cadre d’une politique de décision en ligne. Dans un deuxième temps nous présentons une nouvelleméthode pour entraîner des modèles génératifs. Des résultats théoriques nous indiquent qu’il est possible d’entraîner par rétropropagation des modèles non-supervisés pouvant générer des échantillons qui suivent la distribution des données. Ceci est un résultat pertinent dans le cadre de la récente littérature scientifique investiguant les propriétés des autoencodeurs comme modèles génératifs. Ces résultats sont supportés avec des expériences qualitatives préliminaires ainsi que quelques résultats quantitatifs. / The list of areas affected by machine learning is growing rapidly. As the amount of available training data increases, the development of more powerful learning algorithms is crucial. This thesis consists of three parts: first an overview of the basic concepts of machine learning and the details necessary for training neural networks, models that lend themselves well to deep architectures. The second part presents an application of machine learning to online video games, and a performance measurement method when using these models as decision policies. Finally, the third section presents theoretical results for unsupervised training of deep architectures. Video games are a particularly fertile area for machine learning: it is easy to accumulate large amounts of data, and many tasks are possible. Assembling teams of equal skill is a common machine learning application for online games. The first paper compares different learning algorithms against deep neural networks applied to the prediction of match balance in online games. We then present a simulation based method to evaluate the resulting models used as decision policies for online matchmaking. Following this we present a new method to train generative models. Theoretical results indicate that it is possible to train by backpropagation unsupervised models that can generate samples following the data’s true distribution. This is a relevant result in the context of the recent literature investigating the properties of autoencoders as generative models. These results are supported with preliminary quantitative results and some qualitative experiments.

Falling among older adults is a leading cause of concern due to the known impacts including physical injury, loss of independence, increased health care costs, and mortality. In efforts to decrease the numbers of falls experienced by older adults, healthcare providers assess individuals’ fall risks and provide corresponding fall prevention recommendations. The effectiveness however, of these recommendations, is only as strong as the level of adherence to those recommendations; which has proven low in recent research. Using the theoretical foundation of the Health Belief Model, this study quantified adherence to environmental fall prevention recommendations. Twenty-two community-dwelling older adults participated in this randomized control group study that took place across three home visits, scheduled approximately 30 days apart. Participants were interviewed regarding their recent falls and perceived susceptibility to future falls; then a home evaluation was conducted. Treatment group participants were provided personalized education explaining how and why environmental fall prevention recommendations were important to decrease their risk of falls while control group participants were provided general recommendations. A two-sample t-test for independent groups determined a statistically significant relationship: participants who received personalized education intervention were more likely to follow recommendations than those who received general education intervention. Multiple regressions were conducted to review relationships between an individual’s recent falls, and their perceived susceptibility to future falls, with their extent of adherence with fall prevention recommendations. No statistically significant relationship was found. This study suggests that providing personalized education for community-dwelling older adults regarding environmental fall prevention recommendations increases their extent of adherence with such recommendations.

Les systèmes de recommandation sont devenus une partie indispensable des services et des applications d’internet, en particulier dû à la surcharge de données provenant de nombreuses sources. Quel que soit le type, chaque système de recommandation a des défis fondamentaux à traiter. Dans ce travail, nous identifions trois défis communs, rencontrés par tous les types de systèmes de recommandation: les données, les modèles d'apprentissage et la protection de la vie privée. Nous élaborons différents problèmes qui peuvent être créés par des données inappropriées en mettant l'accent sur sa qualité et sa quantité. De plus, nous mettons en évidence l'importance des réseaux sociaux dans la mise à disposition publique de systèmes de recommandation contenant des données sur ses utilisateurs, afin d'améliorer la qualité des recommandations. Nous fournissons également les capacités d'inférence de données publiques liées à des données relatives aux utilisateurs. Dans notre travail, nous exploitons cette capacité à améliorer la qualité des recommandations, mais nous soutenons également qu'il en résulte des menaces d'atteinte à la vie privée des utilisateurs sur la base de leurs informations. Pour notre second défi, nous proposons une nouvelle version de la méthode des k plus proches voisins (knn, de l'anglais k-nearest neighbors), qui est une des méthodes d'apprentissage parmi les plus populaires pour les systèmes de recommandation. Notre solution, conçue pour exploiter la nature bipartie des ensembles de données utilisateur-élément, est évolutive, rapide et efficace pour la construction d'un graphe knn et tire sa motivation de la grande quantité de ressources utilisées par des calculs de similarité dans les calculs de knn. Notre algorithme KIFF utilise des expériences sur des jeux de données réelles provenant de divers domaines, pour démontrer sa rapidité et son efficacité lorsqu'il est comparé à des approches issues de l'état de l'art. Pour notre dernière contribution, nous fournissons un mécanisme permettant aux utilisateurs de dissimuler leur opinion sur des réseaux sociaux sans pour autant dissimuler leur identité. / Recommendation systems have gained tremendous popularity, both in academia and industry. They have evolved into many different varieties depending mostly on the techniques and ideas used in their implementation. This categorization also marks the boundary of their application domain. Regardless of the types of recommendation systems, they are complex and multi-disciplinary in nature, involving subjects like information retrieval, data cleansing and preprocessing, data mining etc. In our work, we identify three different challenges (among many possible) involved in the process of making recommendations and provide their solutions. We elaborate the challenges involved in obtaining user-demographic data, and processing it, to render it useful for making recommendations. The focus here is to make use of Online Social Networks to access publicly available user data, to help the recommendation systems. Using user-demographic data for the purpose of improving the personalized recommendations, has many other advantages, like dealing with the famous cold-start problem. It is also one of the founding pillars of hybrid recommendation systems. With the help of this work, we underline the importance of user’s publicly available information like tweets, posts, votes etc. to infer more private details about her. As the second challenge, we aim at improving the learning process of recommendation systems. Our goal is to provide a k-nearest neighbor method that deals with very large amount of datasets, surpassing billions of users. We propose a generic, fast and scalable k-NN graph construction algorithm that improves significantly the performance as compared to the state-of-the art approaches. Our idea is based on leveraging the bipartite nature of the underlying dataset, and use a preprocessing phase to reduce the number of similarity computations in later iterations. As a result, we gain a speed-up of 14 compared to other significant approaches from literature. Finally, we also consider the issue of privacy. Instead of directly viewing it under trivial recommendation systems, we analyze it on Online Social Networks. First, we reason how OSNs can be seen as a form of recommendation systems and how information dissemination is similar to broadcasting opinion/reviews in trivial recommendation systems. Following this parallelism, we identify privacy threat in information diffusion in OSNs and provide a privacy preserving algorithm for the same. Our algorithm Riposte quantifies the privacy in terms of differential privacy and with the help of experimental datasets, we demonstrate how Riposte maintains the desirable information diffusion properties of a network.

Cette thèse porte sur l'étude des Systèmes de Recommandation dans un cadre séquentiel, où les retours des utilisateurs sur des articles arrivent dans le système l'un après l'autre. Après chaque retour utilisateur, le système doit le prendre en compte afin d'améliorer les recommandations futures. De nombreuses techniques de recommandation ou méthodologies d'évaluation ont été proposées par le passé pour les problèmes de recommandation. Malgré cela, l'évaluation séquentielle, qui est pourtant plus réaliste et se rapproche davantage du cadre d'évaluation d'un vrai système de recommandation, a été laissée de côté. Le contexte séquentiel nécessite de prendre en considération différents aspects non visibles dans un contexte fixe. Le premier de ces aspects est le dilemme dit d'exploration vs. exploitation: le modèle effectuant les recommandations doit trouver le bon compromis entre recueillir de l'information sur les goûts des utilisateurs à travers des étapes d'exploration, et exploiter la connaissance qu'il a à l'heure actuelle pour maximiser le feedback reçu. L'importance de ce premier point est mise en avant à travers une première évaluation, et nous proposons une approche à la fois simple et efficace, basée sur la Factorisation de Matrice et un algorithme de Bandit Manchot, pour produire des recommandations appropriées. Le second aspect pouvant apparaître dans le cadre séquentiel surgit dans le cas où une liste ordonnée d'articles est recommandée au lieu d'un seul article. Dans cette situation, le feedback donné par l'utilisateur est multiple: la partie explicite concerne la note donnée par l'utilisateur concernant l'article choisi, tandis que la partie implicite concerne les articles cliqués (ou non cliqués) parmi les articles de la liste. En intégrant les deux parties du feedback dans un modèle d'apprentissage, nous proposons une approche basée sur la Factorisation de Matrice, qui peut recommander de meilleures listes ordonnées d'articles, et nous évaluons cette approche dans un contexte séquentiel particulier pour montrer son efficacité. / This thesis is dedicated to the study of Recommendation Systems under a sequential setting, where the feedback given by users on items arrive one after another in the system. After each feedback, the system has to integrate it and try to improve future recommendations. Many techniques or evaluation methods have already been proposed to study the recommendation problem. Despite that, such sequential setting, which is more realistic and represent a closer framework to a real Recommendation System evaluation, has surprisingly been left aside. Under a sequential context, recommendation techniques need to take into consideration several aspects which are not visible for a fixed setting. The first one is the exploration-exploitation dilemma: the model making recommendations needs to find a good balance between gathering information about users' tastes or items through exploratory recommendation steps, and exploiting its current knowledge of the users and items to try to maximize the feedback received. We highlight the importance of this point through the first evaluation study and propose a simple yet efficient approach to make effective recommendation, based on Matrix Factorization and Multi-Armed Bandit algorithms. The second aspect emphasized by the sequential context appears when a list of items is recommended to the user instead of a single item. In such a case, the feedback given by the user includes two parts: the explicit feedback as the rating, but also the implicit feedback given by clicking (or not clicking) on other items of the list. By integrating both feedback into a Matrix Factorization model, we propose an approach which can suggest better ranked list of items, and we evaluate it in a particular setting.

本研究提出一創新的旅遊推薦服務系統，以意象模型作為旅客意象(包含自我意象和情感需求)、景點意象、以及中小企業所提供服務之意象在系統裡的一致性表達。以上所提及之利益關係人的意象會經由數個系統模組進行建立與管理，並演化以反映出意象擁有者在真實世界的狀態。除此之外，本系統為動態運行，強調旅遊產業裡各個利益關係人角色之間的互動關係。每當互動發生，相關意象模型會進行混合，演繹出額外的意象屬性，以進行意象模型之調整。另外，基於顏色與情緒可相互對應的相關研究，我們將色彩理論運用於意象媒合與意象混合模組之中，藉此為旅客推薦符合其情感需求的旅遊景點或服務。本研究所提出一系列基於意象衍伸的系統化方法，可被應用於各種不同的領域。我們相信本研究可以為其它領域之實務應用與學術探討帶來顯著的貢獻。 / This research presents a recommendation service system that considers the image as a uniform representation of tourist images (include self-image and emotional needs), destinations, and local SMEs. Images carried by each stakeholder roles are modeled and managed by several system modules, and they also evolve to reflect the real time situations of each entity. In addition, the system is dynamic in terms of its emphasis on the relationships among these roles. When interactions occur, image mixing will be conducted to derive extra image attributes for the adjustments of the images. Besides, since colors can be mapped onto emotions, we use colors to operate the image matching and mixing process to find good matches of destinations for the recommendation. This image related approach we proposed is domain-independent. We believe our method could contribute to other areas of practical applications and academic studies.

Pervasive computing systems aim to improve human-computer interaction, using users situation variables that define context. The boom of Internet makes growing availables items to choose, giving cost in made decision process. Affective Computing has in its goals to identify user s affective/emotional state in a computing interaction, in order to respond to it automatically. Recommendation systems help made decision selecting and suggesting items in scenarios where there are huge information volume, using, traditionally, users prefferences data. This process could be enhanced using context information (as physical, environmental or social), rising the Context-Aware Recommendation Systems. Due to emotions importance in our lives, that could be treated with Affective Computing, this work uses affective context as context variable, in recommendation process, proposing the Affective-Recommender a recommendation system that uses user s affective state to select and to suggest items. The system s model has four components: (i) detector, that identifies affective-state, using the multidimesional Pleasure, Arousal and Dominance model, and Self-Assessment Maniking instrument, that asks user to inform how he/she feels; (ii) recommender, that selects and suggests items, using a collaborative-filtering based approache, in which user s prefference to an item is his/her affective reaction to it as the affective state detected after access; (iii) application, which interacts with user, shows probable most interesting items defined by recommender, and requests affect identification when it is necessarly; and (iv) data base, that stores available items and users prefferences. As a use case, Affective-Recommender is used in a e-learning scenario, due to personalization obtained with recommendation and emotion importances in learning process. The system was implemented over Moodle LMS. To exposes its operation, a use scenario was organized, simulating recommendation process. In order to check system applicability, with students opinion about to inform how he/she feels and to receive suggestions, it was applied in three UFSM graduation courses classes, and then it were analyzed data access and the answers to a sent questionnaire. As results, it was perceived that students were able to inform how they feel, and that occured changes in their affecive state, based on accessed item, although they don t see improvements with the recommendation, due to small data available to process and showr time of application. / Sistemas de Computação Pervasiva buscam melhorar a interação humano-computador através do uso de variáveis da situação do usuário que definem o contexto. A explosão da Internet e das tecnologias de informação e comunicação torna crescente a quantidade de itens disponíveis para a escolha, impondo custo para o usuário no processo de tomada de decisão. A Computação Afetiva tem entre seus objetivos identificar o estado emocional/afetivo do usuário durante uma interação computacional, para automaticamente responder a ele. Já Sistemas de Recomendação auxiliam a tomada de decisão, selecionando e sugerindo itens em situações onde há grandes volumes de informação, tradicionalmente, utilizando as preferências dos usuários para a seleção e sugestão. Esse processo pode ser melhorado com o uso do contexto (físico, ambiental, social), surgindo os Sistemas de Recomendação Sensíveis ao Contexto. Tendo em vista a importância das emoções em nossas vidas, e a possibilidade de tratamento delas com a Computação Afetiva, este trabalho utiliza o contexto afetivo do usuário como variável da situação, durante o processo de recomendação, propondo o Affective-Recommender um sistema de recomendação que faz uso do estado afetivo do usuário para selecionar e sugerir itens. O sistema foi modelado a partir de quatro componentes: (i) detector, que identifica o estado afetivo, utilizando o modelo multidimensional Pleasure, Arousal e Dominance e o instrumento Self-Assessment Manikin, solicitando que o usuário informe como se sente; (ii) recomendador, que escolhe e sugere itens, utilizando uma abordagem baseada em filtragem colaborativa, em que a preferência de um usuário para um item é vista como sua reação estado afetivo detectado após o contato ao item; (iii) aplicação, que interage com o usuário, exibe os itens de provável maior interesse definidos pelo recomendador, e solicita que o estado seja identificado, sempre que necessário; e (iv) base de dados, que armazena os itens disponíveis para serem sugeridos e as preferências de cada usuário. Como um caso de uso e prova de conceito, o Affective-Recommender é empregado em um cenário de e-learning, devido à importância da personalização, obtida com a recomendação, e das emoções no processo de aprendizagem. O sistema foi implementado utilizando-se como base o AVEA Moodle. Para expor o funcionamento, estruturou-se um cenário de uso, simulando-se o processo de recomendação. Para verificar a aplicabilidade real do sistema, ele foi empregado em três turmas de cursos de graduação da UFSM, sendo analisados dados de acesso e aplicado um questionário para identificar as impressões do alunos quanto a informar como se sentem e receber recomendações. Como resultados, percebeu-se que os alunos conseguiram informar seus estados afetivos, e que houve uma mudança em neste estado com base no item acessado, embora não tenham vislumbrado melhorias com as recomendações, em virtude da pequena quantidade de dados disponível para processamento e do curto tempo de aplicação.

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The original intention of the recommender system is to solve the problem of information explosion, hoping to help users find the content they need more efficiently. In an e-commerce platform, users typically interact with items that they are interested in or need in a variety of ways. For example, buying, browsing details, etc. These interactions are recorded as time-series information. How to use this sequential information to predict user behaviors in the future and give an efficient and effective recommendation is a very important problem. For content providers, such as merchants in e-commerce platforms, more accurate recommendation means higher traffic, CTR (click-through rate), and revenue. Therefore, in the industry, the CTR model for recommendation systems is a research hotspot. However, in the fine ranking stage of the recommendation system, the existing models have some limitations. No researcher has attempted to predict multiple behaviors of one user simultaneously by processing sequential information. We define this problem as the multi-task sequential recommendation problem. In response to this problem, we study the CTR model, sequential recommendation, and multi-task learning. Based on these studies, this paper proposes AMBSN (Attention-based Multi-Behavior Sequential Network). Specifically, we added a transformer layer, the activation unit, and the multi-task tower to the traditional Embedding&MLP (multi-layer perceptron) model. The transformer layer enables our model to efficiently extract sequential behavior information, the activation unit can understand user interests, and the multi-task tower structure makes the model give the prediction of different user behaviors at the same time. We choose user behavior data from Taobao for recommendation published on TianChi as the dataset, and AUC as the evaluation criterion. We compare the performance of AMBSN and some other models on the test set after training. The final results of the experiment show that our model outperforms some existing models. / L’intenzione originale del sistema di raccomandazione è risolvere il problema dell’esplosione delle informazioni, sperando di aiutare gli utenti a trovare il contenuto di cui hanno bisogno in modo più efficiente. In una piattaforma di e-commerce, gli utenti in genere interagiscono con gli articoli a cui sono interessati o di cui hanno bisogno in vari modi. Ad esempio, acquisti, dettagli di navigazione, ecc. Queste interazioni vengono registrate come informazioni di serie temporali. Come utilizzare queste informazioni sequenziali per prevedere i comportamenti degli utenti in futuro e fornire una raccomandazione efficiente ed efficace è un problema molto importante. Per i fornitori di contenuti, come i commercianti nelle piattaforme di e-commerce, una raccomandazione più accurata significa traffico, CTR (percentuale di clic) ed entrate più elevati. Pertanto, nel settore, il modello CTR per i sistemi di raccomandazione è un hotspot di ricerca. Tuttavia, nella fase di classificazione fine del sistema di raccomandazione, i modelli esistenti presentano alcune limitazioni. Nessun ricercatore ha tentato di prevedere più comportamenti di un utente contemporaneamente elaborando informazioni sequenziali. Definiamo questo problema come il problema di raccomandazione sequenziale multi-task. In risposta a questo problema, studiamo il modello CTR, la raccomandazione sequenziale e l’apprendimento multi-task. Sulla base di questi studi, questo documento propone AMBSN (Attention-based Multi-Behavior Sequential Network). In particolare, abbiamo aggiunto uno strato trasformatore, l’unità di attivazione e la torre multi-task al tradizionale modello Embedding&MLP (multi-layer perceptron). Il livello del trasformatore consente al nostro modello di estrarre in modo efficiente le informazioni sul comportamento sequenziale, l’unità di attivazione può comprendere gli interessi degli utenti e la struttura della torre multi-task fa sì che il modello fornisca la previsione di diversi comportamenti degli utenti contemporaneamente. Scegliamo i dati sul comportamento degli utenti da Taobao per la raccomandazione pubblicata su TianChi come set di dati e l’AUC come criterio di valutazione. Confrontiamo le prestazioni di AMBSN e di alcuni altri modelli sul set di test dopo l’allenamento. I risultati finali dell’esperimento mostrano che il nostro modello supera alcuni modelli esistenti.