A Graph Layout Framework Combining t-Distributed Neighbor Retrieval Visualizer and Energy Models

Graph layout investigates the structure of the graph in order to better obtain the information implied in the graph. To solve the shortcomings of dimension reduction layouts on local adjustment and the insufficiency of energy models to maintain the overall structure of the graphs, this paper proposes a new graph layout framework called “tNEM” that layouts graphs by combining t-distributed neighbor retrieval visualizer (t-NeRV) and energy models. In the process of layout, our algorithm considers global and local structures at the same time. The layout results are more conform to aesthetic standards, meanwhile, maintain the structural information of the graph. We evaluate our algorithm on a wide variety of datasets and compare it with many other methods. We produce better visualization results than tsNET and tsNET* methods by reducing the tendency to crowd points together, and can better capture the global structure of the graph.

[1]  Peter Eades,et al.  A Heuristic for Graph Drawing , 1984 .

[2]  Paul Vickers,et al.  A survey of two-dimensional graph layout techniques for information visualisation , 2013, Inf. Vis..

[3]  Stephen G. Kobourov,et al.  Graph Layouts by t‐SNE , 2017, Comput. Graph. Forum.

[4]  Andreas Ludwig,et al.  A Fast Adaptive Layout Algorithm for Undirected Graphs , 1994, GD.

[5]  Eric Bonabeau,et al.  Graph multidimensional scaling with self-organizing maps , 2002, Inf. Sci..

[6]  Andreas Noack,et al.  An Energy Model for Visual Graph Clustering , 2003, GD.

[7]  Paul Geladi,et al.  Principal Component Analysis , 1987, Comprehensive Chemometrics.

[8]  Samuel Kaski,et al.  Optimization Equivalence of Divergences Improves Neighbor Embedding , 2014, ICML.

[9]  Tiago P. Peixoto,et al.  The graph-tool python library , 2014 .

[10]  Ryan A. Rossi,et al.  The Network Data Repository with Interactive Graph Analytics and Visualization , 2015, AAAI.

[11]  Jarkko Venna,et al.  Information Retrieval Perspective to Nonlinear Dimensionality Reduction for Data Visualization , 2010, J. Mach. Learn. Res..

[12]  Iain S. Duff,et al.  Sparse matrix test problems , 1982 .

[13]  David Harel,et al.  A Fast Multi-scale Method for Drawing Large Graphs , 2000, Graph Drawing.

[14]  W. T. Tutte How to Draw a Graph , 1963 .

[15]  Jim Blythe,et al.  The Effect of Graph Layout on Inference from Social Network Data , 1995, GD.

[16]  HERBERT A. SIMON,et al.  The Architecture of Complexity , 1991 .

[17]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[18]  Ulrik Brandes,et al.  A Sparse Stress Model , 2016, J. Graph Algorithms Appl..

[19]  Bernd Meyer,et al.  Competitive learning of network diagram layout , 1998, Proceedings. 1998 IEEE Symposium on Visual Languages (Cat. No.98TB100254).

[20]  David Auber,et al.  Tulip - A Huge Graph Visualization Framework , 2004, Graph Drawing Software.

[21]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[22]  Geoffrey E. Hinton,et al.  Stochastic Neighbor Embedding , 2002, NIPS.

[23]  W. Torgerson Multidimensional scaling: I. Theory and method , 1952 .

[24]  Michael T. Goodrich,et al.  A Fast Multi-Dimensional Algorithm for Drawing Large Graphs? , 2000 .

[25]  William B. Cowan,et al.  Human Perception of Laid-Out Graphs , 1998, Graph Drawing.

[26]  W. T. Tutte Convex Representations of Graphs , 1960 .

[27]  Ulrik Brandes,et al.  Eigensolver Methods for Progressive Multidimensional Scaling of Large Data , 2006, GD.

[28]  Eric Bonabeau,et al.  Self-Organizing Maps for Drawing Large Graphs , 1998, Inf. Process. Lett..

[29]  Michael Jünger,et al.  Drawing Large Graphs with a Potential-Field-Based Multilevel Algorithm , 2004, GD.

[30]  Boštjan Pajntar OVERVIEW OF ALGORITHMS FOR GRAPH DRAWING , 2006 .

[31]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[32]  Mark E. J. Newman,et al.  The Structure and Function of Complex Networks , 2003, SIAM Rev..

[33]  Yifan Hu,et al.  A Maxent-Stress Model for Graph Layout , 2012, IEEE Transactions on Visualization and Computer Graphics.

[34]  Timothy A. Davis,et al.  The university of Florida sparse matrix collection , 2011, TOMS.