Petra Mutzel

Graph Drawing Software

References.- Technical Foundations.- 1 Introduction.- 2 Graphs and Their Representation.- 3 Graph Planarity and Embeddings.- 4 Graph Drawing Methods.- References.- WilmaScope - A 3D Graph Visualization System.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Pajek - Analysis and Visualization of Large Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Tulip - A Huge Graph Visualization Framework.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Graphviz and Dynagraph - Static and Dynamic Graph Drawing Tools.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- AGD - A Library of Algorithms for Graph Drawing.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- yFiles - Visualization and Automatic Layout of Graphs.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- GDS - A Graph Drawing Server on the Internet.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- BioPath - Exploration and Visualization of Biochemical Pathways.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- DBdraw - Automatic Layout of Relational Database Schemas.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- GoVisual - A Diagramming Software for UML Class Diagrams.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- CrocoCosmos - 3D Visualization of Large Object-oriented Programs.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- ViSta - Visualizing Statecharts.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- visone - Analysis and Visualization of Social Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.- Polyphemus and Hermes - Exploration and Visualization of Computer Networks.- 1 Introduction.- 2 Applications.- 3 Algorithms.- 4 Implementation.- 5 Examples.- 6 Software.- References.

A Linear Time Implementation of SPQR-Trees

The data structure SPQR-tree represents the decomposition of a biconnected graph with respect to its triconnected components. SPQR-trees have been introduced by Di Battista and Tamassia [8] and, since then, became quite important in the field of graph algorithms. Theoretical papers using SPQR-trees claim that they can be implemented in linear time using a modification of the algorithm by Hopcroft and Tarjan [15] for decomposing a graph into its triconnected components. So far no correct linear time implementation of either triconnectivity decomposition or SPQR-trees is known to us. Here, we show the incorrectness of the Hopcroft and Tarjan algorithm [15], and correct the faulty parts. We describe the relationship between SPQR-trees and triconnected components and apply the resulting algorithm to the computation of SPQR-trees. Our implementation is publically available in AGD [1].

2-layer straightline crossing minimization: Performance of exact and heuristic algorithms.

We present algorithms for the two layer straightline crossing minimization problem that are able to compute exact optima. Our computational results lead us to the conclusion that there is no need for heuristics if one layer is xed, even though the problem is NP-hard, and that for the general problem with two variable layers, true optima can be computed for sparse instances in which the smaller layer contains up to 15 nodes. For bigger instances, the iterated barycenter method turns out to be the method of choice among several popular heuristics whose performance we could assess by comparing their results to optimum solutions.

Interactive exploration of chemical space with Scaffold Hunter.

We describe Scaffold Hunter, a highly interactive computer-based tool for navigation in chemical space that fosters intuitive recognition of complex structural relationships associated with bioactivity. The program reads compound structures and bioactivity data, generates compound scaffolds, correlates them in a hierarchical tree-like arrangement, and annotates them with bioactivity. Brachiation along tree branches from structurally complex to simple scaffolds allows identification of new ligand types. We provide proof of concept for pyruvate kinase.

An Algorithmic Framework for the Exact Solution of the Prize-Collecting Steiner Tree Problem

The Prize-Collecting Steiner Tree Problem (PCST) on a graph with edge costs and vertex profits asks for a subtree minimizing the sum of the total cost of all edges in the subtree plus the total profit of all vertices not contained in the subtree. PCST appears frequently in the design of utility networks where profit generating customers and the network connecting them have to be chosen in the most profitable way.Our main contribution is the formulation and implementation of a branch-and-cut algorithm based on a directed graph model where we combine several state-of-the-art methods previously used for the Steiner tree problem. Our method outperforms the previously published results on the standard benchmark set of problems.We can solve all benchmark instances from the literature to optimality, including some of them for which the optimum was not known. Compared to a recent algorithm by Lucena and Resende, our new method is faster by more than two orders of magnitude. We also introduce a new class of more challenging instances and present computational results for them. Finally, for a set of large-scale real-world instances arising in the design of fiber optic networks, we also obtain optimal solution values.

A graph–theoretic approach to steganography

We suggest a graph-theoretic approach to steganography based on the idea of exchanging rather than overwriting pixels. We construct a graph from the cover data and the secret message. Pixels that need to be modified are represented as vertices and possible partners of an exchange are connected by edges. An embedding is constructed by solving the combinatorial problem of calculating a maximum cardinality matching. The secret message is then embedded by exchanging those samples given by the matched edges. This embedding preserves first-order statistics. Additionally, the visual changes can be minimized by introducing edge weights. We have implemented an algorithm based on this approach with support for several types of image and audio files and we have conducted computational studies to evaluate the performance of the algorithm.

Exact Ground States of Ising Spin Glasses: New Experimental Results With a Branch and Cut Algorithm

In this paper we study two-dimensional Ising spin glasses on a grid with nearest neighbor and periodic boundary interactions, based on a Gaussian bond distribution, and an exterior magnetic field. We show how using a technique called branch and cut, the exact ground states of grids of sizes up to 100×100 can be determined in a moderate amount of computation time, and we report on extensive computational tests. With our method we produce results based on more than 20,000 experiments on the properties of spin glasses whose errors depend only on the assumptions on the model and not on the computational process. This feature is a clear advantage of the method over other, more popular ways to compute the ground state, like Monte Carlo simulation including simulated annealing, evolutionary, and genetic algorithms, that provide only approximate ground states with a degree of accuracy that cannot be determineda priori. Our ground-state energy estimation at zero field is −1.317.

The Thickness of Graphs: A Survey

Abstract. We give a state-of-the-art survey of the thickness of a graph from both a theoretical and a practical point of view. After summarizing the relevant results concerning this topological invariant of a graph, we deal with practical computation of the thickness. We present some modifications of a basic heuristic and investigate their usefulness for evaluating the thickness and determining a decomposition of a graph in planar subgraphs.

Retention time alignment algorithms for LC/MS data must consider non-linear shifts

MOTIVATION Proteomics has particularly evolved to become of high interest for the field of biomarker discovery and drug development. Especially the combination of liquid chromatography and mass spectrometry (LC/MS) has proven to be a powerful technique for analyzing protein mixtures. Clinically orientated proteomic studies will have to compare hundreds of LC/MS runs at a time. In order to compare different runs, sophisticated preprocessing steps have to be performed. An important step is the retention time (rt) alignment of LC/MS runs. Especially non-linear shifts in the rt between pairs of LC/MS runs make this a crucial and non-trivial problem. RESULTS For the purpose of demonstrating the particular importance of correcting non-linear rt shifts, we evaluate and compare different alignment algorithms. We present and analyze two versions of a new algorithm that is based on regression techniques, once assuming and estimating only linear shifts and once also allowing for the estimation of non-linear shifts. As an example for another type of alignment method we use an established alignment algorithm based on shifting vectors that we adapted to allow for correcting non-linear shifts also. In a simulation study, we show that rt alignment procedures that can estimate non-linear shifts yield clearly better alignments. This is even true under mild non-linear deviations. AVAILABILITY R code for the regression-based alignment methods and simulated datasets are available at http://www.statistik.tu-dortmund.de/genetik-publikationen-alignment.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Maximum planar subgraphs and nice embeddings: Practical layout tools

In automatic graph drawing a given graph has to be laid out in the plane, usually according to a number of topological and aesthetic constraints. Nice drawings for sparse nonplanar graphs can be achieved by determining a maximum planar subgraph and augmenting an embedding of this graph. This approach appears to be of limited value in practice, because the maximum planar subgraph problem is NP-hard.We attack the maximum planar subgraph problem with a branch-and-cut technique which gives us quite good, and in many cases provably optimum, solutions for sparse graphs and very dense graphs. In the theoretical part of the paper, the polytope of all planar subgraphs of a graphG is defined and studied. All subgraphs of a graphG, which are subdivisions ofK5 orK3,3, turn out to define facets of this polytope. For cliques contained inG, the Euler inequalities turn out to be facet-defining for the planar subgraph polytope. Moreover, we introduce the subdivision inequalities,V2k inequalities, and the flower inequalities, all of which are facet-defining for the polytope. Furthermore, the composition of inequalities by 2-sums is investigated.We also present computational experience with a branch-and-cut algorithm for the above problem. Our approach is based on an algorithm which searches for forbidden substructures in a graph that contains a subdivision ofK5 orK3,3. These structures give us inequalities which are used as cutting planes.Finally, we try to convince the reader that the computation of maximum planar subgraphs is indeed a practical tool for finding nice embeddings by applying this method to graphs taken from the literature.