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For a clustered graph, i.e, a graph whose vertex set is recursively partitioned into clusters, the C-Planarity Testing problem asks whether it is possible to find a planar embedding of the graph and a representation of each cluster as a region homeomorphic to a closed disk such that 1. the subgraph induced by each cluster is drawn in the interior of the corresponding disk, 2. each edge intersects any disk at most once, and 3. the nesting between clusters is reflected by the representation, i.e., child clusters are properly contained in their parent cluster. The computational complexity of this problem, whose study has been central to the theory of graph visualization since its introduction in 1995 [Qing-Wen Feng, Robert F. Cohen, and Peter Eades. Planarity for clustered graphs. ESA'95], has only been recently settled [Radoslav Fulek and Csaba D. T\'oth. Atomic Embeddability, Clustered Planarity, and Thickenability. To appear at SODA'20]. Before such a breakthrough, the complexity question was still unsolved even when the graph has a prescribed planar embedding, i.e, for embedded clustered graphs. We show that the C-Planarity Testing problem admits a single-exponential single-parameter FPT algorithm for embedded clustered graphs, when parameterized by the carving-width of the dual graph of the input. This is the first FPT algorithm for this long-standing open problem with respect to a single notable graph-width parameter. Moreover, in the general case, the polynomial dependency of our FPT algorithm is smaller than the one of the algorithm by Fulek and T\'oth. To further strengthen the relevance of this result, we show that the C-Planarity Testing problem retains its computational complexity when parameterized by several other graph-width parameters, which may potentially lead to faster algorithms., Comment: Extended version of the paper "C-Planarity Testing of Embedded Clustered Graphs with Bounded Dual Carving-Width" to appear in the Proceedings of the 14th International Symposium on Parameterized and Exact Computation (IPEC 2019)

We study the version of the C-Planarity problem in which edges connecting the same pair of clusters must be grouped into pipes, which generalizes the Strip Planarity problem. We give algorithms to decide several families of instances for the two variants in which the order of the pipes around each cluster is given as part of the input or can be chosen by the algorithm., 19 pages, 9 figures, extended version of the paper appeared at ISAAC 2016

In this paper we study the clustered graphs whose underlying graph is a cycle. This is a simple family of clustered graphs that are “highly non connected”. We start by studying 3-cluster cycles, that are clustered graphs such that the underlying graph is a simple cycle and there are three clusters all at the same level. We show that in this case testing the c-planarity can be done efficiently and give an efficient drawing algorithm. Also, we characterize 3-cluster cycles in terms of formal grammars. Finally, we generalize the results on 3-cluster cycles considering clustered graphs that at each level of the inclusion tree have a cycle structure. Even in this case we show efficient c-planarity testing and drawing algorithms.

In a drawing of a clustered graph vertices and edges are drawn as points and curves, respectively, while clusters are represented by simple closed regions. A drawing of a clustered graph is c-planar if it has no edge–edge, edge–region, or region–region crossings. Determining the complexity of testing whether a clustered graph admits a c-planar drawing is a long-standing open problem in the Graph Drawing research area. An obvious necessary condition for c-planarity is the planarity of the graph underlying the clustered graph. However, this condition is not sufficient and the consequences on the problem due to the requirement of not having edge–region and region–region crossings are not yet fully understood. In order to shed light on the c-planarity problem, we consider a relaxed version of it, where some kinds of crossings (either edge–edge, edge–region, or region–region) are allowed even if the underlying graph is planar. We investigate the relationships among the minimum number of edge–edge, edge–region, and region–region crossings for drawings of the same clustered graph. Also, we consider drawings in which only crossings of one kind are admitted. In this setting, we prove that drawings with only edge–edge or with only edge– region crossings always exist, while drawings with only region–region crossings may not. Further, we provide upper and lower bounds for the number of such crossings. Finally, we give a polynomial-time algorithm to test whether a drawing with only region–region crossings exists for biconnected graphs, hence identifying a first non-trivial necessary condition for c-planarity that can be tested in polynomial time for a noticeable class of graphs.

This thesis investigates the requirements for graph drawing stemming from practical applications, and presents both theoretical as well as practical results and approaches to handle them. Many approaches to compute graph layouts in various drawing styles exist, but the results are often not sufficient for use in practice. Drawing conventions, graphical notation standards, and user-defined requirements restrict the set of admissible drawings. These restrictions can be formalized as constraints for the layout computation. We investigate the requirements and give an overview and categorization of the corresponding constraints. Of main importance for the readability of a graph drawing is the number of edge crossings. In case the graph is planar it should be drawn without crossings, otherwise we should aim to use the minimum number of crossings possible. However, several types of constraints may impose restrictions on the way the graph can be embedded in the plane. These restrictions may have a strong impact on crossing minimization. For two types of such constraints we present specific solutions how to consider them in layout computation: We introduce the class of so-called embedding constraints, which restrict the order of the edges around a vertex. For embedding constraints we describe approaches for planarity testing, embedding, and edge insertion with the minimum number of crossings. These problems can be solved in linear time with our approaches. The second constraint type that we tackle are clusters. Clusters describe a hierarchical grouping of the graph's vertices that has to be reflected in the drawing. The complexity of the corresponding clustered planarity testing problem for clustered graphs is unknown so far. We describe a technique to compute a maximum clustered planar subgraph of a clustered graph. Our solution is based on an Integer Linear Program (ILP) formulation and includes also the first practical clustered planarity test for general clustered graphs. The resulting subgraph can be used within the first step of the planarization approach for clustered graphs. In addition, we describe how to improve the performance for pure clustered planarity testing by implying a branch-and-price approach. Large and complex graphs nowadays arise in many application domains. These graphs require interaction and navigation techniques to allow exploration of the underlying data. The corresponding concepts are presented and solutions for three practical applications are proposed: First, we describe Scaffold Hunter, a tool for the exploration of chemical space. We show how to use a hierarchical classification of molecules for the visual navigation in chemical space. The resulting visualization is embedded into an interactive environment that allows visual analysis of chemical compound databases. Finally, two interactive visualization approaches for two types of biological networks, protein-domain networks and residue interaction networks, are presented., In zahlreichen Anwendungsgebieten werden Informationen als Graphen modelliert und mithilfe dieser Graphen visualisiert. Eine übersichtliche Darstellung hilft bei der Analyse und unterstützt das Verständnis bei der Präsentation von Informationen mittels graph-basierter Diagramme. Neben allgemeinen ästhetischen Kriterien bestehen für eine solche Darstellung Anforderungen, die sich aus der Charakteristik der Daten, etablierten Darstellungskonventionen und der konkreten Fragestellung ergeben. Zusätzlich ist häufig eine individuelle Anpassung der Darstellung durch den Anwender gewünscht. Diese Anforderungen können mithilfe von Nebenbedingungen für die Berechnung eines Layouts formuliert werden. Trotz einer Vielzahl unterschiedlicher Anforderungen aus zahlreichen Anwendungsgebieten können die meisten Anforderungen über einige generische Nebenbedingungen formuliert werden. In dieser Arbeit untersuchen wir die Anforderungen aus der Praxis und beschreiben eine Zuordnung zu Nebenbedingungen für die Layoutberechnung. Wir geben eine Übersicht über den aktuellen Stand der Behandlung von Nebenbedingungen beim Zeichnen von Graphen und kategorisieren diese nach grundlegenden Eigenschaften. Von besonderer Wichtigkeit für die Qualität einer Darstellung ist die Anzahl der Kreuzungen. Planare Graphen sollten kreuzungsfrei gezeichnet werden, bei nicht-planaren Graphen sollte die minimale Anzahl Kreuzungen erreicht werden. Einige Nebenbedingungen beschränken jedoch die Möglichkeit, den Graph in die Ebene einzubetten. Dies kann starke Auswirkungen auf das Ergebnis der Kreuzungsminimierung haben. Zwei wichtige Typen solcher Nebenbedingungen werden in dieser Arbeit näher untersucht. Mit den Embedding Constraints führen wir eine Klasse von Nebenbedingungen ein, welche die mögliche Reihenfolge der Kanten um einen Knoten beschränken. Für diese Klasse präsentieren wir Linearzeitalgorithmen für das Testen der Planarität und das optimale Einfügen von Kanten unter Beachtung der Einbettungsbeschränkungen. Der zweite Typ von Nebenbedingungen sind Cluster, die eine hierarchische Gruppierung von Knoten vorgeben. Für das Testen der Cluster-Planarität unter solchen Nebenbedingungen ist die Komplexität bisher unbekannt. Wir beschreiben ein Verfahren, um einen maximalen Cluster-planaren Untergraphen zu berechnen. Wir nutzen dabei eine Formulierung als ganzzahliges lineares Programm sowie einen Branch-and-Cut Ansatz zur Lösung. Das Verfahren erlaubt auch die Bestimmung der Cluster-Planarität und stellt damit den ersten praktischen Ansatz zum Testen allgemeiner Clustergraphen dar. Zusätzlich beschreiben wir eine Verbesserung für den Fall, dass lediglich Cluster-Planarität getestet werden muss, der maximale Cluster-planare Untergraph aber nicht von Interesse ist. Für dieses Szenario geben wir eine vereinfachte Formulierung und präsentieren ein Lösungsverfahren, das auf einem Branch-and-Price Ansatz beruht. In der Praxis müssen häufig sehr große oder komplexe Graphen untersucht werden. Dazu werden entsprechende Interaktions- und Navigationsmethoden benötigt. Wir beschreiben die entsprechenden Konzepte und stellen Lösungen für drei Anwendungsbereiche vor: Zunächst beschreiben wir Scaffold Hunter, eine Software zur Navigation im chemischen Strukturraum. Scaffold Hunter benutzt eine hierarchische Klassifikation von Molekülen als Grundlage für die visuelle Navigation. Die Visualisierung ist eingebettet in eine interaktive Oberfläche die eine visuelle Analyse von chemischen Strukturdatenbanken erlaubt. Für zwei Typen von biologischen Netzwerken, Protein-Domänen Netzwerke und Residue-Interaktionsnetzwerke, stellen wir Ansätze für die interaktive Visualisierung dar. Die entsprechenden Layoutverfahren unterliegen einer Reihe von Nebenbedingungen für eine sinnvolle Darstellung.

Consider a planar drawing Gamma of a planar graph G such that the vertices are drawn as small circles and the edges are drawn as thin stripes. Consider a non-simple cycle c of G. Is it possible to draw c as a non-intersecting closed curve inside Gamma, following the circles that correspond in Gamma to the vertices of c and the stripes that connect them? We show that this test can be done in polynomial time and study this problem in the framework of clustered planarity for highly non-connected clustered graphs.

Knapsack problems give a simple framework for decision making. A classical example is the min-knapsack problem (MinKnap): choose a subset of items with minimum total cost, whose total profit is above a given threshold. While this model successfully generalizes to problems in scheduling, network design and capacited location, its dynamic programming approaches do not. One often relies on strong polyhedral relaxations for corresponding integer programs instead. Among other results, we construct such a relaxation for the time-invariant incremental knapsack problem (IIK), and study classes of valid inequalities for MinKnap. IIK is covered in the first part of this thesis. It is a generalization of the max-knapsack problem to a discrete multi-period setting. At each time, capacity increases and items can be added, but not removed from the knapsack. The goal is to maximize the sum of profits over all times. IIK models scenarios in specific financial markets and governmental decision processes. It is known to be strongly NP-hard and there has been work on approximation algorithms for special cases. We settle the complexity of IIK by designing a PTAS, and provide several extensions of the technique. The second part is on MinKnap and divided into two chapters. One is motivated by a recent work on disjunctive relaxations for MinKnap with fixed objective function, where we reduce the size of the construction. The other focuses on a class of bounded pitch inequalities, that generalize the unweighted cover inequalities for MinKnap. While separating over pitch-1 inequalities is NP-hard, we show that approximate separation over the set of pitch-1 and pitch-2 inequalities can be done in polynomial time. We also investigate integrality gaps of linear relaxations for MinKnap when these inequalities are added. Consequently we show that, for any fixed t, the t-th CG closure of the natural relaxation has unbounded gap. The last chapter deals with questions in clustered planarity testing. The Hanani-Tutte theorem is a classical result that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. We conclude by a short proof, using matroid intersection, for a result by Di Battista and Frati on embedded clustered graphs.