Bayesian modelling and sampling strategies for ordering and clustering problems with a focus on next-generation sequencing data

This thesis presents novel methods for ordering and clustering problems. The first two parts focus on the development of models and sampling strategies specifically tailored for next-generation sequencing data. Most high-throughput measurements for single-cell data are destructive, resulting in the loss of longitudinal information. I developed a new, Bayesian, way of reconstructing this information computationally, sampling orders efficiently using MCMC on a space of permutations. This Bayesian approach provides novel insights into biological phenomena and experimental artefacts. The second part presents a new clustering method for single-cell data, which specifically models the uncertainty of the clustering structure that results in part from the uncertainty of the orders discussed above. The proposed method uses nonparametric Bayesian methods, consensus clustering and efficient MCMC sampling to identify differences in dynamic patterns for different branches of gene expression data. It also categorises genes in a way consistent with biological function in an application to stimulated dendritic cells, and integrates data from different cell lines in a principled way. The third part of the thesis adapts some of the methods developed in the first two parts to applications with very sparsely and irregularly sampled data, and explores through simulations the applicability of such models in different circumstances. The fourth part discusses clustering methods for samples in a variety of different contexts, such as RNA expression, methylation or protein expression, and develops and critically discusses a novel hierarchical Bayesian method that integrates both different contexts and different groups of samples, for example different cancer types. The unifying underlying theme of the thesis is the development of methods and efficient sampling and approximation strategies capable of capturing the uncertainty inherent in any statistical analysis of high-dimensional and noisy data.Medical research counci

Analysing functional genomics data using novel ensemble, consensus and data fusion techniques

Motivation: A rapid technological development in the biosciences and in computer science in the last decade has enabled the analysis of high-dimensional biological datasets on standard desktop computers. However, in spite of these technical advances, common properties of the new high-throughput experimental data, like small sample sizes in relation to the number of features, high noise levels and outliers, also pose novel challenges. Ensemble and consensus machine learning techniques and data integration methods can alleviate these issues, but often provide overly complex models which lack generalization capability and interpretability. The goal of this thesis was therefore to develop new approaches to combine algorithms and large-scale biological datasets, including novel approaches to integrate analysis types from different domains (e.g. statistics, topological network analysis, machine learning and text mining), to exploit their synergies in a manner that provides compact and interpretable models for inferring new biological knowledge. Main results: The main contributions of the doctoral project are new ensemble, consensus and cross-domain bioinformatics algorithms, and new analysis pipelines combining these techniques within a general framework. This framework is designed to enable the integrative analysis of both large- scale gene and protein expression data (including the tools ArrayMining, Top-scoring pathway pairs and RNAnalyze) and general gene and protein sets (including the tools TopoGSA , EnrichNet and PathExpand), by combining algorithms for different statistical learning tasks (feature selection, classification and clustering) in a modular fashion. Ensemble and consensus analysis techniques employed within the modules are redesigned such that the compactness and interpretability of the resulting models is optimized in addition to the predictive accuracy and robustness. The framework was applied to real-word biomedical problems, with a focus on cancer biology, providing the following main results: (1) The identification of a novel tumour marker gene in collaboration with the Nottingham Queens Medical Centre, facilitating the distinction between two clinically important breast cancer subtypes (framework tool: ArrayMining) (2) The prediction of novel candidate disease genes for Alzheimer’s disease and pancreatic cancer using an integrative analysis of cellular pathway definitions and protein interaction data (framework tool: PathExpand, collaboration with the Spanish National Cancer Centre) (3) The prioritization of associations between disease-related processes and other cellular pathways using a new rule-based classification method integrating gene expression data and pathway definitions (framework tool: Top-scoring pathway pairs) (4) The discovery of topological similarities between differentially expressed genes in cancers and cellular pathway definitions mapped to a molecular interaction network (framework tool: TopoGSA, collaboration with the Spanish National Cancer Centre) In summary, the framework combines the synergies of multiple cross-domain analysis techniques within a single easy-to-use software and has provided new biological insights in a wide variety of practical settings

Analysing functional genomics data using novel ensemble, consensus and data fusion techniques

Motivation: A rapid technological development in the biosciences and in computer science in the last decade has enabled the analysis of high-dimensional biological datasets on standard desktop computers. However, in spite of these technical advances, common properties of the new high-throughput experimental data, like small sample sizes in relation to the number of features, high noise levels and outliers, also pose novel challenges. Ensemble and consensus machine learning techniques and data integration methods can alleviate these issues, but often provide overly complex models which lack generalization capability and interpretability. The goal of this thesis was therefore to develop new approaches to combine algorithms and large-scale biological datasets, including novel approaches to integrate analysis types from different domains (e.g. statistics, topological network analysis, machine learning and text mining), to exploit their synergies in a manner that provides compact and interpretable models for inferring new biological knowledge. Main results: The main contributions of the doctoral project are new ensemble, consensus and cross-domain bioinformatics algorithms, and new analysis pipelines combining these techniques within a general framework. This framework is designed to enable the integrative analysis of both large- scale gene and protein expression data (including the tools ArrayMining, Top-scoring pathway pairs and RNAnalyze) and general gene and protein sets (including the tools TopoGSA , EnrichNet and PathExpand), by combining algorithms for different statistical learning tasks (feature selection, classification and clustering) in a modular fashion. Ensemble and consensus analysis techniques employed within the modules are redesigned such that the compactness and interpretability of the resulting models is optimized in addition to the predictive accuracy and robustness. The framework was applied to real-word biomedical problems, with a focus on cancer biology, providing the following main results: (1) The identification of a novel tumour marker gene in collaboration with the Nottingham Queens Medical Centre, facilitating the distinction between two clinically important breast cancer subtypes (framework tool: ArrayMining) (2) The prediction of novel candidate disease genes for Alzheimer’s disease and pancreatic cancer using an integrative analysis of cellular pathway definitions and protein interaction data (framework tool: PathExpand, collaboration with the Spanish National Cancer Centre) (3) The prioritization of associations between disease-related processes and other cellular pathways using a new rule-based classification method integrating gene expression data and pathway definitions (framework tool: Top-scoring pathway pairs) (4) The discovery of topological similarities between differentially expressed genes in cancers and cellular pathway definitions mapped to a molecular interaction network (framework tool: TopoGSA, collaboration with the Spanish National Cancer Centre) In summary, the framework combines the synergies of multiple cross-domain analysis techniques within a single easy-to-use software and has provided new biological insights in a wide variety of practical settings

Learning from complex networks

Graph Theory has proven to be a universal language for describing modern complex systems. The elegant theoretical framework of graphs drew the researchers' attention over decades. Therefore, graphs have emerged as a ubiquitous data structure in various applications where a relational characteristic is evident. Graph-driven applications are found, e.g., in social network analysis, telecommunication networks, logistic processes, recommendation systems, modeling kinetic interactions in protein networks, or the 'Internet of Things' (IoT) where modeling billions of interconnected web-enabled devices is of paramount importance. This thesis dives deep into the challenges of modern graph applications. It proposes a robustified and accelerated spectral clustering model in homogeneous graphs and novel transformer-driven graph shell models for attributed graphs. A new data structure is introduced for probabilistic graphs to compute the information flow efficiently. Moreover, a metaheuristic algorithm is designed to find a good solution to an optimization problem composed of an extended vehicle routing problem. The thesis closes with an analysis of trend flows in social media data. Detecting communities within a graph is a fundamental data mining task of interest in virtually all areas and also serves as an unsupervised preprocessing step for many downstream tasks. One most the most well-established clustering methods is Spectral Clustering. However, standard spectral clustering is highly sensitive to noisy input data, and the eigendecomposition has a high, cubic runtime complexity O(n^3). Tackling one of these problems often exacerbates the other. This thesis presents a new model which accelerates the eigendecomposition step by replacing it with a Nyström approximation. Robustness is achieved by iteratively separating the data into a cleansed and noisy part of the data. In this process, representing the input data as a graph is vital to identify parts of the data being well connected by analyzing the vertices' distances in the eigenspace. With the advances in deep learning architectures, we also observe a surge in research on graph representation learning. The message-passing paradigm in Graph Neural Networks (GNNs) formalizes a predominant heuristic for multi-relational and attributed graph data to learn node representations. In downstream applications, we can use the representations to tackle theoretical problems known as node classification, graph classification/regression, and relation prediction. However, a common issue in GNNs is known as over-smoothing. By increasing the number of iterations within the message-passing, the nodes' representations of the input graph align and become indiscernible. This thesis shows an efficient way of relaxing the GNN architecture by employing a routing heuristic in the general workflow. Specifically, an additional layer routes the nodes' representations to dedicated experts. Each expert calculates the representations according to their respective GNN workflow. The definitions of distinguishable GNNs result from k-localized views starting from a central node. This procedure is referred to as Graph Shell Attention (SEA), where experts process different subgraphs in a transformer-motivated fashion. Reliable propagation of information through large communication networks, social networks, or sensor networks is relevant to applications concerning marketing, social analysis, or monitoring physical or environmental conditions. However, social ties of friendship may be obsolete, and communication links may fail, inducing the notion of uncertainty in such networks. This thesis addresses the problem of optimizing information propagation in uncertain networks given a constrained budget of edges. A specialized data structure, called F-tree, addresses two NP-hard subproblems: the computation of the expected information flow and the optimal choice of edges. The F-tree identifies independent components of a probabilistic input graph for which the information flow can either be computed analytically and efficiently or for which traditional Monte-Carlo sampling can be applied independently of the remaining network. The next part of the thesis covers a graph problem from the Operations Research point of view. A new variant of the well-known vehicle routing problem (VRP) is introduced, where customers are served within a specific time window (TW), as well as flexible delivery locations (FL) including capacity constraints. The latter implies that each customer is scheduled in one out of a set of capacitated delivery service locations. Practically, the VRPTW-FL problem is relevant for applications in parcel delivery, routing with limited parking space, or, for example, in the scope of hospital-wide scheduling of physical therapists. This thesis presents a metaheuristic built upon a hybrid Adaptive Large Neighborhood Search (ALNS). Moreover, a backtracking mechanism in the construction phase is introduced to alter unsatisfactory decisions at early stages. In the computational study, hospital data is used to evaluate the utility of flexible delivery locations and various cost functions. In the last part of the thesis, social media trends are analyzed, which yields insights into user sentiment and newsworthy topics. Such trends consist of bursts of messages concerning a particular topic within a time frame, significantly deviating from the average appearance frequency of the same subject. This thesis presents a method to classify trend archetypes to predict future dissemination by investigating the dissemination of such trends in space and time. Generally, with the ever-increasing scale and complexity of graph-structured datasets and artificial intelligence advances, AI-backed models will inevitably play an important role in analyzing, modeling, and enhancing knowledge extraction from graph data.Die Graphentheorie hat sich zur einer universellen Sprache entwickelt, mit Hilfe derer sich moderne und komplexe Systeme und Zusammenhänge beschreiben lassen. Diese theoretisch elegante und gut fundierte Rahmenstruktur attrahierte über Dekaden hinweg die Aufmerksamkeit von Wissenschaftlern/-innen. In der heutigen Informationstechnologie-Landschaft haben sich Graphen längst zu einer allgegenwärtigen Datenstruktur in Anwendungen etabliert, innerhalb derer charakteristische Zusammenhangskomponenten eine zentrale Rolle spielen. Anwendungen, die über Graphen unterstützt werden, finden sich u.a. in der Analyse von sozialen Netzwerken, Telekommunikationsnetwerken, logistische Prozessverwaltung, Analyse von Empfehlungsdiensten, in der Modellierung kinetischer Interaktionen von Proteinstrukturen, oder auch im "Internet der Dinge" (engl.: 'Internet Of Things' (IoT)), welches das Zusammenspiel von abermillionen web-unterstützte Endgeräte abbildet und eine prädominierende Rolle für große IT-Unternehmen spielt. Diese Dissertation beleuchtet die Herausforderungen moderner Graphanwendungen. Im Bereich homogener Netzwerken wird ein beschleunigtes und robustes spektrales Clusteringverfahren, sowie ein Modell zur Untersuchung von Teilgraphen mittels Transformer-Architekturen für attribuierte Graphen vorgestellt. Auf wahrscheinlichkeitsbasierten homogenen Netzwerken wird eine neue Datenstruktur eingeführt, die es erlaubt einen effizienten Informationsfluss innerhalb eines Graphen zu berechnen. Darüber hinaus wird ein Optimierungsproblem in Transportnetzwerken beleuchtet, sowie eine Untersuchung von Trendflüssen in sozialen Medien diskutiert. Die Untersuchung von Verbünden (engl.: 'Clusters') von Graphdaten stellt einen Eckpfeiler im Bereich der Datengewinnung dar. Die Erkenntnisse sind nahezu in allen praktischen Bereichen von Relevanz und dient im Bereich des unüberwachten Lernens als Vorverarbeitungsschritt für viele nachgeschaltete Aufgaben. Einer der weit verbreitetsten Methodiken zur Verbundanalyse ist das spektrale Clustering. Die Qualität des spektralen Clusterings leidet, wenn die Eingabedaten sehr verrauscht sind und darüber hinaus ist die Eigenwertzerlegung mit O(n^3) eine teure Operation und damit wesentlich für die hohe, kubische Laufzeitkomplexität verantwortlich. Die Optimierung von einem dieser Kriterien exazerbiert oftmals das verbleibende Kriterium. In dieser Dissertation wird ein neues Modell vorgestellt, innerhalb dessen die Eigenwertzerlegung über eine Nyström Annäherung beschleunigt wird. Die Robustheit wird über ein iteratives Verfahren erreicht, das die gesäuberten und die verrauschten Daten voneinander trennt. Die Darstellung der Eingabedaten über einen Graphen spielt hierbei die zentrale Rolle, die es erlaubt die dicht verbundenen Teile des Graphen zu identifizieren. Dies wird über eine Analyse der Distanzen im Eigenraum erreicht. Parallel zu neueren Erkenntnissen im Bereich des Deep Learnings lässt sich auch ein Forschungsdrang im repräsentativen Lernen von Graphen erkennen. Graph Neural Networks (GNN) sind eine neue Unterform von künstlich neuronalen Netzen (engl.: 'Artificial Neural Networks') auf der Basis von Graphen. Das Paradigma des sogenannten 'message-passing' in neuronalen Netzen, die auf Graphdaten appliziert werden, hat sich hierbei zur prädominierenden Heuristik entwickelt, um Vektordarstellungen von Knoten aus (multi-)relationalen, attribuierten Graphdaten zu lernen. Am Ende der Prozesskette können wir somit theoretische Probleme angehen und lösen, die sich mit Fragestellungen über die Klassifikation von Knoten oder Graphen, über regressive Ausdrucksmöglichkeiten bis hin zur Vorhersage von relationaler Verbindungen beschäftigen. Ein klassisches Problem innerhalb graphischer neuronaler Netze ist bekannt unter der Terminologie des 'over-smoothing' (dt.: 'Überglättens'). Es beschreibt, dass sich mit steigender Anzahl an Iterationen des wechselseitigen Informationsaustausches, die Knotenrepräsentationen im vektoriellen Raum angleichen und somit nicht mehr unterschieden werden können. In dieser Forschungsarbeit wird eine effiziente Methode vorgestellt, die die klassische GNN Architektur aufbricht und eine Vermittlerschicht in den herkömmlichen Verarbeitungsfluss einarbeitet. Konkret gesprochen werden hierbei Knotenrepräsentationen an ausgezeichnete Experten geschickt. Jeder Experte verarbeitet auf idiosynkratischer Basis die Knoteninformation. Ausgehend von einem Anfrageknoten liegt das Kriterium für die Unterscheidbarkeit von Experten in der restriktiven Verarbeitung lokaler Information. Diese neue Heuristik wird als 'Graph Shell Attention' (SEA) bezeichnet und beschreibt die Informationsverarbeitung unterschiedlicher Teilgraphen von Experten unter der Verwendung der Transformer-technologie. Eine zuverlässige Weiterleitung von Informationen über größere Kommunikationsnetzwerken, sozialen Netzwerken oder Sensorennetzwerken spielen eine wichtige Rolle in Anwendungen der Marktanalyse, der Analyse eines sozialen Gefüges, oder der Überwachung der physischen und umweltorientierten Bedingungen. Innerhalb dieser Anwendungen können Fälle auftreten, wo Freundschaftsbeziehungen nicht mehr aktuell sind, wo die Kommunikation zweier Endpunkte zusammenbricht, welches mittels einer Unsicherheit des Informationsaustausches zweier Endpunkte ausgedrückt werden kann. Diese Arbeit untersucht die Optimierung des Informationsflusses in Netzwerken, deren Verbindungen unsicher sind, hinsichtlich der Bedingung, dass nur ein Bruchteil der möglichen Kanten für den Informationsaustausch benutzt werden dürfen. Eine eigens entwickelte Datenstruktur - der F-Baum - wird eingeführt, die 2 NP-harte Teilprobleme auf einmal adressiert: zum einen die Berechnung des erwartbaren Informationsflusses und zum anderen die Auswahl der optimalen Kanten. Der F-Baum unterscheidet hierbei unabhängige Zusammenhangskomponenten der wahrscheinlichkeitsbasierten Eingabedaten, deren Informationsfluss entweder analytisch korrekt und effizient berechnet werden können, oder lokal über traditionelle Monte-Carlo sampling approximiert werden können. Der darauffolgende Abschnitt dieser Arbeit befasst sich mit einem Graphproblem aus Sicht der Optimierungsforschung angewandter Mathematik. Es wird eine neue Variante der Tourenplanung vorgestellt, welches neben kundenspezifischer Zeitfenster auch flexible Zustellstandorte beinhaltet. Darüber hinaus obliegt den Zielorten, an denen Kunden bedient werden können, weiteren Kapazitätslimitierungen. Aus praktischer Sicht ist das VRPTW-FL (engl.: "Vehicle Routing Problem with Time Windows and Flexible Locations") eine bedeutende Problemstellung für Paketdienstleister, Routenplanung mit eingeschränkten Stellplätzen oder auch für die praktische Planung der Arbeitsaufteilung von behandelnden Therapeuten/-innen und Ärzten/-innen in einem Krankenhaus. In dieser Arbeit wird für die Bewältigung dieser Problemstellung eine Metaheuristik vorgestellt, die einen hybriden Ansatz mit der sogenannten Adaptive Large Neighborhood Search (ALNS) impliziert. Darüber hinaus wird als Konstruktionsheuristik ein 'Backtracking'-Mechanismus (dt.: Rückverfolgung) angewandt, um initiale Startlösungen aus dem Lösungssuchraum auszuschließen, die weniger vielversprechend sind. In der Evaluierung dieses neuen Ansatz werden Krankenhausdaten untersucht, um auch die Nützlichkeit von flexiblen Zielorten unter verschiedenen Kostenfunktionen herauszuarbeiten. Im letzten Kapitel dieser Dissertation werden Trends in sozialen Daten analysiert, die Auskunft über die Stimmung der Benutzer liefern, sowie Einblicke in tagesaktuelle Geschehnisse gewähren. Ein Kennzeichen solcher Trends liegt in dem Aufbraußen von inhaltsspezifischen Themen innerhalb eines Zeitfensters, die von der durchschnittlichen Erscheinungshäufigkeit desselben Themas signifikant abweichen. Die Untersuchung der Verbreitung solches Trends über die zeitliche und örtliche Dimension erlaubt es, Trends in Archetypen zu klassifizieren, um somit die Ausbreitung zukünftiger Trends hervorzusagen. Mit der immerwährenden Skalierung von Graphdaten und deren Komplexität, und den Fortschritten innerhalb der künstlichen Intelligenz, wird das maschinelle Lernen unweigerlich weiterhin eine wesentliche Rolle spielen, um Graphdaten zu modellieren, analysieren und schlussendlich die Wissensextraktion aus derartigen Daten maßgeblich zu fördern.La théorie des graphes s'est révélée être une langue universel pour décrire les systèmes complexes modernes. L'élégant cadre théorique des graphes a attiré l'attention des chercheurs pendant des décennies. Par conséquent, les graphes sont devenus une structure de données omniprésente dans diverses applications où une caractéristique relationnelle est évidente. Les applications basées sur les graphes se retrouvent, par exemple, dans l'analyse des réseaux sociaux, les réseaux de télécommunication, les processus logistiques, les systèmes de recommandation, la modélisation des interactions cinétiques dans les réseaux de protéines, ou l'"Internet des objets" (IoT) où la modélisation de milliards de dispositifs interconnectés basés sur le web est d'une importance capitale. Cette thèse se penche sur les défis posés par les applications modernes des graphes. Elle propose un modèle de regroupement spectral robuste et accéléré dans les graphes homogènes et de nouveaux modèles d'enveloppe de graphe pilotés par transformateur pour les graphes attribués. Une nouvelle structure de données est introduite pour les graphes probabilistes afin de calculer efficacement le flux d'informations. De plus, un algorithme métaheuristique est conçu pour trouver une bonne solution à un problème d'optimisation composé d'un problème étendu de routage de véhicules. La thèse se termine par une analyse des flux de tendances dans les données des médias sociaux. La détection de communautés au sein d'un graphe est une tâche fondamentale d'exploration de données qui présente un intérêt dans pratiquement tous les domaines et sert également d'étape de prétraitement non supervisé pour de nombreuses tâches en aval. L'une des méthodes de regroupement les mieux établies est le regroupement spectral. Cependant, le regroupement spectral standard est très sensible aux données d'entrée bruitées, et l'eigendecomposition a une complexité d'exécution cubique élevée O(n^3). S'attaquer à l'un de ces problèmes exacerbe souvent l'autre. Cette thèse présente un nouveau modèle qui accélère l'étape d'eigendecomposition en la remplaçant par une approximation de Nyström. La robustesse est obtenue en séparant itérativement les données en une partie nettoyée et une partie bruyante. Dans ce processus, la représentation des données d'entrée sous forme de graphe est essentielle pour identifier les parties des données qui sont bien connectées en analysant les distances des sommets dans l'espace propre. Avec les progrès des architectures de Deep Learning, nous observons également une poussée de la recherche sur l'apprentissage de la représentation graphique. Le paradigme du passage de messages dans les réseaux neuronaux graphiques (GNN) formalise une heuristique prédominante pour les données graphiques multi-relationnelles et attribuées afin d'apprendre les représentations des nœuds. Dans les applications en aval, nous pouvons utiliser les représentations pour résoudre des problèmes théoriques tels que la classification des nœuds, la classification/régression des graphes et la prédiction des relations. Cependant, un problème courant dans les GNN est connu sous le nom de lissage excessif. En augmentant le nombre d'itérations dans le passage de messages, les représentations des nœuds du graphe d'entrée s'alignent et deviennent indiscernables. Cette thèse montre un moyen efficace d'assouplir l'architecture GNN en employant une heuristique de routage dans le flux de travail général. Plus précisément, une couche supplémentaire achemine les représentations des nœuds vers des experts spécialisés. Chaque expert calcule les représentations en fonction de son flux de travail GNN respectif. Les définitions de GNN distincts résultent de k vues localisées à partir d'un nœud central. Cette procédure est appelée Graph Shell Attention (SEA), dans laquelle les experts traitent différents sous-graphes à l'aide d'un transformateur. La propagation fiable d'informations par le biais de grands réseaux de communication, de réseaux sociaux ou de réseaux de capteurs est importante pour les applications concernant le marketing, l'analyse sociale ou la surveillance des conditions physiques ou environnementales. Cependant, les liens sociaux d'amitié peuvent être obsolètes, et les liens de communication peuvent échouer, induisant la notion d'incertitude dans de tels réseaux. Cette thèse aborde le problème de l'optimisation de la propagation de l'information dans les réseaux incertains compte tenu d'un budget contraint d'arêtes. Une structure de données spécialisée, appelée F-tree, traite deux sous-problèmes NP-hard: le calcul du flux d'information attendu et le choix optimal des arêtes. L'arbre F identifie les composants indépendants d'un graphe d'entrée probabiliste pour lesquels le flux d'informations peut être calculé analytiquement et efficacement ou pour lesquels l'échantillonnage Monte-Carlo traditionnel peut être appliqué indépendamment du reste du réseau. La partie suivante de la thèse couvre un problème de graphe du point de vue de la recherche opérationnelle. Une nouvelle variante du célèbre problème d'acheminement par véhicule (VRP) est introduite, où les clients sont servis dans une fenêtre temporelle spécifique (TW), ainsi que des lieux de livraison flexibles (FL) incluant des contraintes de capacité. Ces dernières impliquent que chaque client est programmé dans l'un des emplacements de service de livraison à capacité. En pratique, le problème VRPTW-FL est pertinent pour des applications de livraison de colis, d'acheminement avec un espace de stationnement limité ou, par exemple, dans le cadre de la programmation de kinésithérapeutes à l'échelle d'un hôpital. Cette thèse présente une métaheuristique construite sur une recherche hybride de grands voisinages adaptatifs (ALNS). En outre, un mécanisme de retour en arrière dans la phase de construction est introduit pour modifier les décisions insatisfaisantes à des stades précoces. Dans l'étude computationnelle, des données hospitalières sont utilisées pour évaluer l'utilité de lieux de livraison flexibles et de diverses fonctions de coût. Dans la dernière partie de la thèse, les tendances des médias sociaux sont analysées, ce qui donne un aperçu du sentiment des utilisateurs et des sujets d'actualité. Ces tendances consistent en des rafales de messages concernant un sujet particulier dans un laps de temps donné, s'écartant de manière significative de la fréquence moyenne d'apparition du même sujet. Cette thèse présente une méthode de classification des archétypes de tendances afin de prédire leur diffusion future en étudiant la diffusion de ces tendances dans l'espace et dans le temps. D'une manière générale, avec l'augmentation constante de l'échelle et de la complexité des ensembles de données structurées en graphe et les progrès de l'intelligence artificielle, les modèles soutenus par l'IA joueront inévitablement un rôle important dans l'analyse, la modélisation et l'amélioration de l'extraction de connaissances à partir de données en graphe

Exploratory search in time-oriented primary data

In a variety of research fields, primary data that describes scientific phenomena in an original condition is obtained. Time-oriented primary data, in particular, is an indispensable data type, derived from complex measurements depending on time. Today, time-oriented primary data is collected at rates that exceed the domain experts’ abilities to seek valuable information undiscovered in the data. It is widely accepted that the magnitudes of uninvestigated data will disclose tremendous knowledge in data-driven research, provided that domain experts are able to gain insight into the data. Domain experts involved in data-driven research urgently require analytical capabilities. In scientific practice, predominant activities are the generation and validation of hypotheses. In analytical terms, these activities are often expressed in confirmatory and exploratory data analysis. Ideally, analytical support would combine the strengths of both types of activities. Exploratory search (ES) is a concept that seamlessly includes information-seeking behaviors ranging from search to exploration. ES supports domain experts in both gaining an understanding of huge and potentially unknown data collections and the drill-down to relevant subsets, e.g., to validate hypotheses. As such, ES combines predominant tasks of domain experts applied to data-driven research. For the design of useful and usable ES systems (ESS), data scientists have to incorporate different sources of knowledge and technology. Of particular importance is the state-of-the-art in interactive data visualization and data analysis. Research in these factors is at heart of Information Visualization (IV) and Visual Analytics (VA). Approaches in IV and VA provide meaningful visualization and interaction designs, allowing domain experts to perform the information-seeking process in an effective and efficient way. Today, bestpractice ESS almost exclusively exist for textual data content, e.g., put into practice in digital libraries to facilitate the reuse of digital documents. For time-oriented primary data, ES mainly remains at a theoretical state. Motivation and Problem Statement. This thesis is motivated by two main assumptions. First, we expect that ES will have a tremendous impact on data-driven research for many research fields. In this thesis, we focus on time-oriented primary data, as a complex and important data type for data-driven research. Second, we assume that research conducted to IV and VA will particularly facilitate ES. For time-oriented primary data, however, novel concepts and techniques are required that enhance the design and the application of ESS. In particular, we observe a lack of methodological research in ESS for time-oriented primary data. In addition, the size, the complexity, and the quality of time-oriented primary data hampers the content-based access, as well as the design of visual interfaces for gaining an overview of the data content. Furthermore, the question arises how ESS can incorporate techniques for seeking relations between data content and metadata to foster data-driven research. Overarching challenges for data scientists are to create usable and useful designs, urgently requiring the involvement of the targeted user group and support techniques for choosing meaningful algorithmic models and model parameters. Throughout this thesis, we will resolve these challenges from conceptual, technical, and systemic perspectives. In turn, domain experts can benefit from novel ESS as a powerful analytical support to conduct data-driven research. Concepts for Exploratory Search Systems (Chapter 3). We postulate concepts for the ES in time-oriented primary data. Based on a survey of analysis tasks supported in IV and VA research, we present a comprehensive selection of tasks and techniques relevant for search and exploration activities. The assembly guides data scientists in the choice of meaningful techniques presented in IV and VA. Furthermore, we present a reference workflow for the design and the application of ESS for time-oriented primary data. The workflow divides the data processing and transformation process into four steps, and thus divides the complexity of the design space into manageable parts. In addition, the reference workflow describes how users can be involved in the design. The reference workflow is the framework for the technical contributions of this thesis. Visual-Interactive Preprocessing of Time-Oriented Primary Data (Chapter 4). We present a visual-interactive system that enables users to construct workflows for preprocessing time-oriented primary data. In this way, we introduce a means of providing content-based access. Based on a rich set of preprocessing routines, users can create individual solutions for data cleansing, normalization, segmentation, and other preprocessing tasks. In addition, the system supports the definition of time series descriptors and time series distance measures. Guidance concepts support users in assessing the workflow generalizability, which is important for large data sets. The execution of the workflows transforms time-oriented primary data into feature vectors, which can subsequently be used for downstream search and exploration techniques. We demonstrate the applicability of the system in usage scenarios and case studies. Content-Based Overviews (Chapter 5). We introduce novel guidelines and techniques for the design of contentbased overviews. The three key factors are the creation of meaningful data aggregates, the visual mapping of these aggregates into the visual space, and the view transformation providing layouts of these aggregates in the display space. For each of these steps, we characterize important visualization and interaction design parameters allowing the involvement of users. We introduce guidelines supporting data scientists in choosing meaningful solutions. In addition, we present novel visual-interactive quality assessment techniques enhancing the choice of algorithmic model and model parameters. Finally, we present visual interfaces enabling users to formulate visual queries of the time-oriented data content. In this way, we provide means of combining content-based exploration with content-based search. Relation Seeking Between Data Content and Metadata (Chapter 6). We present novel visual interfaces enabling domain experts to seek relations between data content and metadata. These interfaces can be integrated into ESS to bridge analytical gaps between the data content and attached metadata. In three different approaches, we focus on different types of relations and define algorithmic support to guide users towards most interesting relations. Furthermore, each of the three approaches comprises individual visualization and interaction designs, enabling users to explore both the data and the relations in an efficient and effective way. We demonstrate the applicability of our interfaces with usage scenarios, each conducted together with domain experts. The results confirm that our techniques are beneficial for seeking relations between data content and metadata, particularly for data-centered research. Case Studies - Exploratory Search Systems (Chapter 7). In two case studies, we put our concepts and techniques into practice. We present two ESS constructed in design studies with real users, and real ES tasks, and real timeoriented primary data collections. The web-based VisInfo ESS is a digital library system facilitating the visual access to time-oriented primary data content. A content-based overview enables users to explore large collections of time series measurements and serves as a baseline for content-based queries by example. In addition, VisInfo provides a visual interface for querying time oriented data content by sketch. A result visualization combines different views of the data content and metadata with faceted search functionality. The MotionExplorer ESS supports domain experts in human motion analysis. Two content-based overviews enhance the exploration of large collections of human motion capture data from two perspectives. MotionExplorer provides a search interface, allowing domain experts to query human motion sequences by example. Retrieval results are depicted in a visual-interactive view enabling the exploration of variations of human motions. Field study evaluations performed for both ESS confirm the applicability of the systems in the environment of the involved user groups. The systems yield a significant improvement of both the effectiveness and the efficiency in the day-to-day work of the domain experts. As such, both ESS demonstrate how large collections of time-oriented primary data can be reused to enhance data-centered research. In essence, our contributions cover the entire time series analysis process starting from accessing raw time-oriented primary data, processing and transforming time series data, to visual-interactive analysis of time series. We present visual search interfaces providing content-based access to time-oriented primary data. In a series of novel explorationsupport techniques, we facilitate both gaining an overview of large and complex time-oriented primary data collections and seeking relations between data content and metadata. Throughout this thesis, we introduce VA as a means of designing effective and efficient visual-interactive systems. Our VA techniques empower data scientists to choose appropriate models and model parameters, as well as to involve users in the design. With both principles, we support the design of usable and useful interfaces which can be included into ESS. In this way, our contributions bridge the gap between search systems requiring exploration support and exploratory data analysis systems requiring visual querying capability. In the ESS presented in two case studies, we prove that our techniques and systems support data-driven research in an efficient and effective way

Enriched spatial comparison of clusterings through discovery of deviating subspaces

Full text embargoed until: 2016-01-3

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested