Search results for "Graph drawing"
showing 10 items of 15 documents
Heuristics for the min–max arc crossing problem in graphs
2018
Abstract In this paper, we study the visualization of complex structures in the context of automatic graph drawing. Constructing geometric representations of combinatorial structures, such as networks or graphs, is a difficult task that requires an expert system. The automatic generation of drawings of graphs finds many applications from software engineering to social media. The objective of graph drawing expert systems is to generate layouts that are easy to read and understand. This main objective is achieved by solving several optimization problems. In this paper we focus on the most important one: reducing the number of arc crossings in the graph. This hard optimization problem has been…
Variable neighborhood descent for the incremental graph drawing
2017
Abstract Graphs are used to represent reality in several areas of knowledge. Drawings of graphs have many applications, from project scheduling to software diagrams. The main quality desired for drawings of graphs is readability, and crossing reduction is a fundamental aesthetic criterion for a good representation of a graph. In this paper we target the edge crossing reduction in the context of incremental graph drawing, in which we want to preserve the layout of a graph over successive drawings. We propose a hybrid method based on the GRASP (Greedy Randomized Adaptive Search Procedure) and VND (Variable Neighborhood Descent) methodologies and compare it with previous methods via simulation.
Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data
2018
In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
Tabu search for min-max edge crossing in graphs
2020
Abstract Graph drawing is a key issue in the field of data analysis, given the ever-growing amount of information available today that require the use of automatic tools to represent it. Graph Drawing Problems (GDP) are hard combinatorial problems whose applications have been widely relevant in fields such as social network analysis and project management. While classically in GDPs the main aesthetic concern is related to the minimization of the total sum of crossing in the graph (min-sum), in this paper we focus on a particular variant of the problem, the Min-Max GDP, consisting in the minimization of the maximum crossing among all egdes. Recently proposed in scientific literature, the Min…
Curved Edge Routing
2001
We consider the problem of drawing a graph where edges are represented by smooth curves between the associated nodes. Previously curved edges were drawn as splines defined by carefully calculated control points. We present a completely different approach where finding an edge is reduced to solving a differential equation. This approach allows to represent the graph drawing aesthetics directly, even the most complex ones denoting the dependencies among the paths.
Arc crossing minimization in graphs with GRASP
2001
Graphs are commonly used to represent information in many fields of science and engineering. Automatic drawing tools generate comprehensible graphs from data, taking into account a variety of properties, enabling users to see important relationships in the data. The goal of limiting the number of arc crossings is a well-admitted criterion for a good drawing. In this paper, we present a Greedy Randomized Adaptive Search Procedure (GRASP) for the problem of minimizing arc crossings in graphs. Computational experiments with 200 graphs with up to 350 vertices are presented to assess the merit of the method. We show that simple heuristics are very fast but result in inferior solutions, while hig…
A tabu search algorithm for the bipartite drawing problem
1998
Graphs are used to represent reality in several areas of knowledge. This has generated considerable interest in graph drawing algorithms. Arc crossing minimization is a fundamental aesthetic criterion to obtain a readable map of a graph. The problem of minimizing the number of arc crossings in a bipartite graph (BDP) is NP-complete. In this paper we present a Tabu Search (TS) scheme for the BDP. Several algorithms can be obtained with this scheme by implementing different evaluators in the move definitions. In this paper we propose two variants. Computational results are reported on a set of 300 randomly generated test problems. The two algorithms have been compared with the best heuristics…
Variable Neighborhood Search for the Vertex Separation Problem
2012
The vertex separation problem belongs to a family of optimization problems in which the objective is to nd the best separator of vertices or edges in a generic graph. This optimization problem is strongly related to other well-known graph problems; such as the Path-Width, the Node Search Number or the Interval Thickness, among others. All of these optimization problems are NP-hard and have practical applications in VLSI, computer language compiler design or graph drawing. Up to know, they have been generally tackled with exact approaches, presenting polynomial-time algorithms to obtain the optimal solution for speci c types of graphs. However, in spite of their practical applications, these…
IMFLer: A Web Application for Interactive Metabolic Flux Analysis and Visualization.
2021
Increasing genome-wide data in biological sciences and medicine has contributed to the development of a variety of visualization tools. Several automatic, semiautomatic, and manual visualization tools have already been developed. Some even have integrated flux balance analysis (FBA), but in most cases, it depends on separately installed third party software that is proprietary and does not allow customization of its functionality and has many restrictions for easy data distribution and analysis. In this study, we present an interactive metabolic flux analyzer and visualizer (IMFLer)-a static single-page web application that enables the reading and management of metabolic model layout maps, …