88 research outputs found
A Sparse Stress Model
Force-directed layout methods constitute the most common approach to draw
general graphs. Among them, stress minimization produces layouts of
comparatively high quality but also imposes comparatively high computational
demands. We propose a speed-up method based on the aggregation of terms in the
objective function. It is akin to aggregate repulsion from far-away nodes
during spring embedding but transfers the idea from the layout space into a
preprocessing phase. An initial experimental study informs a method to select
representatives, and subsequent more extensive experiments indicate that our
method yields better approximations of minimum-stress layouts in less time than
related methods.Comment: Appears in the Proceedings of the 24th International Symposium on
Graph Drawing and Network Visualization (GD 2016
Node overlap removal by growing a tree
Node overlap removal is a necessary step in many scenarios including laying out a graph, or visualizing a tag cloud. Our contribution is a new overlap removal algorithm that iteratively builds a Minimum Spanning Tree on a Delaunay triangulation of the node centers and removes the node overlaps by ”growing” the tree. The algorithm is simple to implement yet produces high quality layouts. According to our experiments it runs several times faster than the current state-of-the-art methods
Edge Label Placement in Layered Graph Drawing
Many visual languages based on node-link diagrams use edge labels. We describe different strategies of placing edge labels in the context of the layered approach to graph drawing and investigate ways of encoding edge direction in labels. We evaluate the label placement strategies based on both common aesthetic criteria and a controlled experiment. We find that placing labels on their edge can lead to more compact diagrams. Also, placing labels with additional arrows indicating edge direction can help users navigate in large diagrams and is generally preferred by participants of our experiment, outperforming other ways of indicating edge direction
On Embeddability of Buses in Point Sets
Set membership of points in the plane can be visualized by connecting
corresponding points via graphical features, like paths, trees, polygons,
ellipses. In this paper we study the \emph{bus embeddability problem} (BEP):
given a set of colored points we ask whether there exists a planar realization
with one horizontal straight-line segment per color, called bus, such that all
points with the same color are connected with vertical line segments to their
bus. We present an ILP and an FPT algorithm for the general problem. For
restricted versions of this problem, such as when the relative order of buses
is predefined, or when a bus must be placed above all its points, we provide
efficient algorithms. We show that another restricted version of the problem
can be solved using 2-stack pushall sorting. On the negative side we prove the
NP-completeness of a special case of BEP.Comment: 19 pages, 9 figures, conference version at GD 201
Discovering duplicate tasks in transition systems for the simplification of process models
This work presents a set of methods to improve the understandability of process models. Traditionally, simplification methods trade off quality metrics, such as fitness or precision. Conversely, the methods proposed in this paper produce simplified models while preserving or even increasing fidelity metrics. The first problem addressed in the
paper is the discovery of duplicate tasks. A new method is proposed that avoids overfitting by working on the transition system generated by the log. The method is able to discover duplicate tasks even in the presence of concurrency and choice. The second problem is the structural simplification of the model by identifying optional and repetitive tasks. The tasks are substituted by annotated events that allow the removal of silent tasks and reduce the complexity of the
model. An important feature of the methods proposed in this paper is that they are independent from the actual miner used for process discovery.Peer ReviewedPostprint (author's final draft
Anisotropic Radial Layout for Visualizing Centrality and Structure in Graphs
This paper presents a novel method for layout of undirected graphs, where
nodes (vertices) are constrained to lie on a set of nested, simple, closed
curves. Such a layout is useful to simultaneously display the structural
centrality and vertex distance information for graphs in many domains,
including social networks. Closed curves are a more general constraint than the
previously proposed circles, and afford our method more flexibility to preserve
vertex relationships compared to existing radial layout methods. The proposed
approach modifies the multidimensional scaling (MDS) stress to include the
estimation of a vertex depth or centrality field as well as a term that
penalizes discord between structural centrality of vertices and their alignment
with this carefully estimated field. We also propose a visualization strategy
for the proposed layout and demonstrate its effectiveness using three social
network datasets.Comment: Appears in the Proceedings of the 25th International Symposium on
Graph Drawing and Network Visualization (GD 2017
A Generalization of the Directed Graph Layering Problem
The Directed Layering Problem (DLP) solves a step of the widely used layer-based layout approach to automatically draw directed acyclic graphs. To cater for cyclic graphs, classically a preprocessing step is used that solves the Feedback Arc Set Problem (FASP)to make the graph acyclic before a layering is determined. Here, we present the Generalized Layering Problem (GLP) which solves the combination of DLP and FASP simultaneously, allowing general graphs as input. We show GLP to be NP- complete, present integer programming models to solve it, and perform thorough evaluations on different sets of graphs and with different implementations for the steps of the layer- based approach. We observe that GLP reduces the number of dummy nodes significantly, can produce more compact drawings and improves on graphs where DLP yields poor aspect ratios
Phylogenetic comparative assembly
Husemann P, Stoye J. Phylogenetic Comparative Assembly. Algorithms for Molecular Biology. 2010;5(1): 3.BACKGROUND:Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. RESULTS:Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacencies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. CONCLUSIONS:Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same tim
Graphs in molecular biology
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network
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