Visual analytics for relationships in scientific data

Domain scientists hope to address grand scientific challenges by exploring the abundance of data generated and made available through modern high-throughput techniques. Typical scientific investigations can make use of novel visualization tools that enable dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These general tools should be applicable to many disciplines: allowing biologists to develop an intuitive understanding of the structure of coexpression networks and discover genes that reside in critical positions of biological pathways, intelligence analysts to decompose social networks, and climate scientists to model extrapolate future climate conditions. By using a graph as a universal data representation of correlation, our novel visualization tool employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool integrates techniques such as graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by querying an optimized B-tree, dynamic level-of-detail graph abstraction, and template-based fuzzy classification using neural networks. We demonstrate our system using real-world workflows from several large-scale studies. Parallel coordinates has proven to be a scalable visualization and navigation framework for multivariate data. However, when data with thousands of variables are at hand, we do not have a comprehensive solution to select the right set of variables and order them to uncover important or potentially insightful patterns. We present algorithms to rank axes based upon the importance of bivariate relationships among the variables and showcase the efficacy of the proposed system by demonstrating autonomous detection of patterns in a modern large-scale dataset of time-varying climate simulation

Explorative Graph Visualization

Netzwerkstrukturen (Graphen) sind heutzutage weit verbreitet. Ihre Untersuchung dient dazu, ein besseres Verständnis ihrer Struktur und der durch sie modellierten realen Aspekte zu gewinnen. Die Exploration solcher Netzwerke wird zumeist mit Visualisierungstechniken unterstützt. Ziel dieser Arbeit ist es, einen Überblick über die Probleme dieser Visualisierungen zu geben und konkrete Lösungsansätze aufzuzeigen. Dabei werden neue Visualisierungstechniken eingeführt, um den Nutzen der geführten Diskussion für die explorative Graphvisualisierung am konkreten Beispiel zu belegen.Network structures (graphs) have become a natural part of everyday life and their analysis helps to gain an understanding of their inherent structure and the real-world aspects thereby expressed. The exploration of graphs is largely supported and driven by visual means. The aim of this thesis is to give a comprehensive view on the problems associated with these visual means and to detail concrete solution approaches for them. Concrete visualization techniques are introduced to underline the value of this comprehensive discussion for supporting explorative graph visualization

Large-Scale Networks: Algorithms, Complexity and Real Applications

Networks have broad applicability to real-world systems, due to their ability to model and represent complex relationships. The discovery and forecasting of insightful patterns from networks are at the core of analytical intelligence in government, industry, and science. Discoveries and forecasts, especially from large-scale networks commonly available in the big-data era, strongly rely on fast and efficient network algorithms. Algorithms for dealing with large-scale networks are the first topic of research we focus on in this thesis. We design, theoretically analyze and implement efficient algorithms and parallel algorithms, rigorously proving their worst-case time and space complexities. Our main contributions in this area are novel, parallel algorithms to detect k-clique communities, special network groups which are widely used to understand complex phenomena. The proposed algorithms have a space complexity which is the square root of that of the current state-of-the-art. Time complexity achieved is optimal, since it is inversely proportional to the number of processing units available. Extensive experiments were conducted to confirm the efficiency of the proposed algorithms, even in comparison to the state-of-the-art. We experimentally measured a linear speedup, substantiating the optimal performances attained. The second focus of this thesis is the application of networks to discover insights from real-world systems. We introduce novel methodologies to capture cross correlations in evolving networks. We instantiate these methodologies to study the Internet, one of the most, if not the most, pervasive modern technological system. We investigate the dynamics of connectivity among Internet companies, those which interconnect to ensure global Internet access. We then combine connectivity dynamics with historical worldwide stock markets data, and produce graphical representations to visually identify high correlations. We find that geographically close Internet companies offering similar services are driven by common economic factors. We also provide evidence on the existence and nature of hidden factors governing the dynamics of Internet connectivity. Finally, we propose network models to effectively study the Internet Domain Name System (DNS) traffic, and leverage these models to obtain rankings of Internet domains as well as to identify malicious activities

Data integration for biological network databases: MetNetDB labeled graph model and graph matching algorithm

To understand the cellular functions of genes requires investigating a variety of biological data, including experimental data, annotation from online databases and literatures, information about cellular interactions, and domain knowledge from biologists. These requirements demand a flexible and powerful biological data management system. MetNetDB is the biological database component of the MetNet platform (http://metnetdb.org/), a software platform for Arabidopsis system biology. This work describes a labeled graph model that addresses the challenges associated with biological network databases, and discusses the implementation of this model in MetNetDB. MetNetDB integrates most recent data from various sources, including biological networks, gene annotation, metabolite information, and protein localization data. The integration contains four steps: data model transformation and integration; semantic mapping; data conversion and integration; and conflict resolution. MetNetDB is established as a labeled graph model. The graph structure supports network data storage and application of graph analysis algorithm. The node and edge labels have the same extension capability as object data model. In addition, rules are used to guarantee the biological network data integrity; operations are defined for graph edit and comparison. To facilitate the integration of network data, which is often inaccurate or incomplete, a subgraph extraction algorithm is designed for MetNetDB. This algorithm allows subgraph querying based on user-specified biomolecules. Both exact matching and approximate matching with biomolecules in networks are supported. The similarity among biomolecules is inferred from expression patterns, gene ontology, chemical ontology, and protein-gene relationships. Combined with the implementation of Messmer\u27s approximate subgraph isomorphism algorithm, MetNetDB supports exact and approximate graph matching. Based on the MetNetDB labeled graph model and the graph matching algorithms, the MetNetDB curator tool is built with several innovative features, including active biological rule checking during network curation, tracking data change history, and a biologist-friendly visual graph query system

Real-time analytics on large dynamic graphs

In today's fast-paced and interconnected digital world, the data generated by an increasing number of applications is being modeled as dynamic graphs. The graph structure encodes relationships among data items, while the structural changes to the graphs as well as the continuous stream of information produced by the entities in these graphs make them dynamic in nature. Examples include social networks where users post status updates, images, videos, etc.; phone call networks where nodes may send text messages or place phone calls; road traffic networks where the traffic behavior of the road segments changes constantly, and so on. There is a tremendous value in storing, managing, and analyzing such dynamic graphs and deriving meaningful insights in real-time. However, a majority of the work in graph analytics assumes a static setting, and there is a lack of systematic study of the various dynamic scenarios, the complexity they impose on the analysis tasks, and the challenges in building efficient systems that can support such tasks at a large scale. In this dissertation, I design a unified streaming graph data management framework, and develop prototype systems to support increasingly complex tasks on dynamic graphs. In the first part, I focus on the management and querying of distributed graph data. I develop a hybrid replication policy that monitors the read-write frequencies of the nodes to decide dynamically what data to replicate, and whether to do eager or lazy replication in order to minimize network communication and support low-latency querying. In the second part, I study parallel execution of continuous neighborhood-driven aggregates, where each node aggregates the information generated in its neighborhoods. I build my system around the notion of an aggregation overlay graph, a pre-compiled data structure that enables sharing of partial aggregates across different queries, and also allows partial pre-computation of the aggregates to minimize the query latencies and increase throughput. Finally, I extend the framework to support continuous detection and analysis of activity-based subgraphs, where subgraphs could be specified using both graph structure as well as activity conditions on the nodes. The query specification tasks in my system are expressed using a set of active structural primitives, which allows the query evaluator to use a set of novel optimization techniques, thereby achieving high throughput. Overall, in this dissertation, I define and investigate a set of novel tasks on dynamic graphs, design scalable optimization techniques, build prototype systems, and show the effectiveness of the proposed techniques through extensive evaluation using large-scale real and synthetic datasets

Community Detection in Hypergraphen

Viele Datensätze können als Graphen aufgefasst werden, d.h. als Elemente (Knoten) und binäre Verbindungen zwischen ihnen (Kanten). Unter dem Begriff der "Complex Network Analysis" sammeln sich eine ganze Reihe von Verfahren, die die Untersuchung von Datensätzen allein aufgrund solcher struktureller Eigenschaften erlauben. "Community Detection" als Untergebiet beschäftigt sich mit der Identifikation besonders stark vernetzter Teilgraphen. Über den Nutzen hinaus, den eine Gruppierung verwandter Element direkt mit sich bringt, können derartige Gruppen zu einzelnen Knoten zusammengefasst werden, was einen neuen Graphen von reduzierter Komplexität hervorbringt, der die Makrostruktur des ursprünglichen Graphen unter Umständen besser hervortreten lässt. Fortschritte im Bereich der "Community Detection" verbessern daher auch das Verständnis komplexer Netzwerke im allgemeinen. Nicht jeder Datensatz lässt sich jedoch angemessen mit binären Relationen darstellen - Relationen höherer Ordnung führen zu sog. Hypergraphen. Gegenstand dieser Arbeit ist die Verallgemeinerung von Ansätzen zur "Community Detection" auf derartige Hypergraphen. Im Zentrum der Aufmerksamkeit stehen dabei "Social Bookmarking"-Datensätze, wie sie von Benutzern von "Bookmarking"-Diensten erzeugt werden. Dabei ordnen Benutzer Dokumenten frei gewählte Stichworte, sog. "Tags" zu. Dieses "Tagging" erzeugt, für jede Tag-Zuordnung, eine ternäre Verbindung zwischen Benutzer, Dokument und Tag, was zu Strukturen führt, die 3-partite, 3-uniforme (im folgenden 3,3-, oder allgemeiner k,k-) Hypergraphen genannt werden. Die Frage, der diese Arbeit nachgeht, ist wie diese Strukturen formal angemessen in "Communities" unterteilt werden können, und wie dies das Verständnis dieser Datensätze erleichtert, die potenziell sehr reich an latenten Informationen sind. Zunächst wird eine Verallgemeinerung der verbundenen Komponenten für k,k-Hypergraphen eingeführt. Die normale Definition verbundener Komponenten weist auf den untersuchten Datensätzen, recht uninformativ, alle Elemente einer einzelnen Riesenkomponente zu. Die verallgemeinerten, so genannten hyper-inzidenten verbundenen Komponenten hingegen zeigen auf den "Social Bookmarking"-Datensätzen eine charakteristische Größenverteilung, die jedoch bspw. von Spam-Verhalten zerstört wird - was eine Verbindung zwischen Verhaltensmustern und strukturellen Eigenschaften zeigt, der im folgenden weiter nachgegangen wird. Als nächstes wird das allgemeine Thema der "Community Detection" auf k,k-Hypergraphen eingeführt. Drei Herausforderungen werden definiert, die mit der naiven Anwendung bestehender Verfahren nicht gemeistert werden können. Außerdem werden drei Familien synthetischer Hypergraphen mit "Community"-Strukturen von steigender Komplexität eingeführt, die prototypisch für Situationen stehen, die ein erfolgreicher Detektionsansatz rekonstruieren können sollte. Der zentrale methodische Beitrag dieser Arbeit besteht aus der im folgenden dargestellten Entwicklung eines multipartiten (d.h. für k,k-Hypergraphen geeigneten) Verfahrens zur Erkennung von "Communities". Es basiert auf der Optimierung von Modularität, einem etablierten Verfahrung zur Erkennung von "Communities" auf nicht-partiten, d.h. "normalen" Graphen. Ausgehend vom einfachst möglichen Ansatz wird das Verfahren iterativ verfeinert, um den zuvor definierten sowie neuen, in der Praxis aufgetretenen Herausforderungen zu begegnen. Am Ende steht die Definition der "ausgeglichenen multi-partiten Modularität". Schließlich wird ein interaktives Werkzeug zur Untersuchung der so gewonnenen "Community"-Zuordnungen vorgestellt. Mithilfe dieses Werkzeugs können die Vorteile der zuvor eingeführten Modularität demonstriert werden: So können komplexe Zusammenhänge beobachtet werden, die den einfacheren Verfahren entgehen. Diese Ergebnisse werden von einer stärker quantitativ angelegten Untersuchung bestätigt: Unüberwachte Qualitätsmaße, die bspw. den Kompressionsgrad berücksichtigen, können über eine größere Menge von Beispielen die Vorteile der ausgeglichenen multi-partiten Modularität gegenüber den anderen Verfahren belegen. Zusammenfassend lassen sich die Ergebnisse dieser Arbeit in zwei Bereiche einteilen: Auf der praktischen Seite werden Werkzeuge zur Erforschung von "Social Bookmarking"-Daten bereitgestellt. Demgegenüber stehen theoretische Beiträge, die für Graphen etablierte Konzepte - verbundene Komponenten und "Community Detection" - auf k,k-Hypergraphen übertragen.Many datasets can be interpreted as graphs, i.e. as elements (nodes) and binary relations between them (edges). Under the label of complex network analysis, a vast array of graph-based methods allows the exploration of datasets purely based on such structural properties. Community detection, as a subfield of network analysis, aims to identify well-connected subparts of graphs. While the grouping of related elements is useful in itself, these groups can furthermore be collapsed into single nodes, creating a new graph of reduced complexity which may better reveal the original graph's macrostructure. Therefore, advances in community detection improve the understanding of complex networks in general. However, not every dataset can be modelled properly with binary relations - higher-order relations give rise to so-called hypergraphs. This thesis explores the generalization of community detection approaches to hypergraphs. In the focus of attention are social bookmarking datasets, created by users of online bookmarking services who assign freely chosen keywords, so-called "tags", to documents. This "tagging" creates, for each tag assignment, a ternary connection between the user, the document, and the tag, inducing particular structures called 3-partite, 3-uniform hypergraphs (henceforth called 3,3- or more generally k,k-hypergraphs). The question pursued here is how to decompose these structures in a formally adequate manner, and how this improves the understanding of these rich datasets. First, a generalization of connected components to k,k-hypergraphs is proposed. The standard definition of connected components here rather uninformatively assigns almost all elements to a single giant component. The generalized so-called hyperincident connected components, however, show a characteristic size distribution on the social bookmarking datasets that is disrupted by, e.g., spamming activity - demonstrating a link between behavioural patterns and structural features that is further explored in the following. Next, the general topic of community detection in k,k-hypergraphs is introduced. Three challenges are posited that are not met by the naive application of standard techniques, and three families of synthetic hypergraphs are introduced containing increasingly complex community setups that a successful detection approach must be able to identify. The main methodical contribution of this thesis consists of the following development of a multi-partite (i.e. suitable for k,k-hypergraphs) community detection algorithm. It is based on modularity optimization, a well-established algorithm to detect communities in non-partite, i.e. "normal" graphs. Starting from the simplest approach possible, the method is successively refined to meet the previously defined as well as empirically encountered challenges, culminating in the definition of the "balanced multi-partite modularity". Finally, an interactive tool for exploring the obtained community assignments is introduced. Using this tool, the benefits of balanced multi-partite modularity can be shown: Intricate patters can be observed that are missed by the simpler approaches. These findings are confirmed by a more quantitative examination: Unsupervised quality measures considering, e.g., compression document the advantages of this approach on a larger number of samples. To conclude, the contributions of this thesis are twofold. It provides practical tools for the analysis of social bookmarking data, complemented with theoretical contributions, the generalization of connected components and modularity from graphs to k,k-hypergraphs

Graph-based approaches to word sense induction

This thesis is a study of Word Sense Induction (WSI), the Natural Language Processing (NLP) task of automatically discovering word meanings from text. WSI is an open problem in NLP whose solution would be of considerable benefit to many other NLP tasks. It has, however, has been studied by relatively few NLP researchers and often in set ways. Scope therefore exists to apply novel methods to the problem, methods that may improve upon those previously applied. This thesis applies a graph-theoretic approach to WSI. In this approach, word senses are identifed by finding particular types of subgraphs in word co-occurrence graphs. A number of original methods for constructing, analysing, and partitioning graphs are introduced, with these methods then incorporated into graphbased WSI systems. These systems are then shown, in a variety of evaluation scenarios, to return results that are comparable to those of the current best performing WSI systems. The main contributions of the thesis are a novel parameter-free soft clustering algorithm that runs in time linear in the number of edges in the input graph, and novel generalisations of the clustering coeficient (a measure of vertex cohesion in graphs) to the weighted case. Further contributions of the thesis include: a review of graph-based WSI systems that have been proposed in the literature; analysis of the methodologies applied in these systems; analysis of the metrics used to evaluate WSI systems, and empirical evidence to verify the usefulness of each novel method introduced in the thesis for inducing word senses

Physics based supervised and unsupervised learning of graph structure

Graphs are central tools to aid our understanding of biological, physical, and social systems. Graphs also play a key role in representing and understanding the visual world around us, 3D-shapes and 2D-images alike. In this dissertation, I propose the use of physical or natural phenomenon to understand graph structure. I investigate four phenomenon or laws in nature: (1) Brownian motion, (2) Gauss\u27s law, (3) feedback loops, and (3) neural synapses, to discover patterns in graphs

Rule-based Modeling of Cell Signaling: Advances in Model Construction, Visualization and Simulation

Rule-based modeling is a graph-based approach to specifying the kinetics of cell signaling systems. A reaction rule is a compact and explicit graph-based representation of a kinetic process, and it matches a class of reactions that involve identical sites and identical kinetics. Compact rule- based models have been used to generate large and combinatorially complex reaction networks, and rules have also been used to compile databases of kinetic interactions targeting specific cells and pathways. In this work, I address three technological challenges associated with rule-based modeling. First, I address the ability to generate an automated global visualization of a rule-based model as a network of signal flows. I showed how to analyze a reaction rule and extract a set of bipartite regulatory relationships, which can be aggregated across rules into a global network. I also provide a set of coarse-graining approaches to compress an automatically generated network into a compact pathway diagram, even for models with 100s of rules. Second, I resolved an incompatibility between two recent advances in rule-based modeling: network-free simulation (which enables simulation without generating a reaction network), and energy-based rule-based modeling (which enables specifying a model using cooperativity parameters and automated accounting of free energy). The incompatibility arose because calculating the reaction rate requires computing the reaction free energy in an energy-based model, and this requires knowledge of both reactants and products of the reaction, but the products are not available in a network-free simulation until after the reaction event has fired. This was resolved by expanding each energy- based rule into a number of normal reaction rules for which reaction free energies can be calculated unambiguously. Third, I demonstrated a particular type of modularization that is based on treating a set of rules as a module. This enables building models from combinations of modular hypotheses and supplements the other modularization strategies such as macros, types and energy-based compression