Visualizing Networks: Beyond the Hairball
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The document discusses network visualization techniques. It begins by describing how visualizations of complex networks often result in "hairballs" that are difficult to interpret. It then discusses different approaches to laying out networks in ways that make their structures clearer, such as algorithmic layouts, matrix representations, and focusing on attributes of nodes and edges. The document provides examples of network visualization tools and techniques and emphasizes the importance of choosing visualizations based on the intended audience and goals.
Visualizing Networks: Beyond the Hairball
- 1. Visualizing Networks Beyond the “Hairball” Lynn Cherny @arnicas O’Reilly Strata NYC 2012
- 2. Visualizing Networks Beyond the “Hairball” Lynn Cherny @arnicas O’Reilly Strata NYC 2012
- 3. PS(A): I AM NOT JASON SUNDRAM He could not make it, and asked me to take over. 2
- 4. The Hairball: A Metaphor for Complexity http://www.nd.edu/~networks/Publication%20Categories/01%20Review%20Articles/ScaleFree_Scientific%20Ameri %20288,%2060-69%20(2003).pdf
- 7. WHAT IS A NETWORK? It’s not a visualization. Think of it as a data structure.
- 8. Data relationship: entities + relationships to other objects (node/edge, vertex/link) Nodes and Edges may have attributes, eg. gender, age, weight, tv prefs connection date, frequency of contact, type of exchange, directionality of relationship attributes may be calculated from network itself
- 12. Best! A User Study on Visualizing Directed Edges in Graphs” Danny Holten and Jarke J. van Wijk, 27th SIGCHI Conference on Human Factors in Computing Systems (Proceedings of CHI 2009), http://blog.visual.ly/network-visualizations/ 9
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- 15. 10
- 16. It’s a natural human trait to see visual similarity and proximity as meaningful. Be very careful about your display choices and layout methods! 10
- 17. Reading a network visualization There’s obviously something important going on here, structurally....
- 18. Reading a network visualization Lo o k a t th is o utl ier cas e! There’s obviously something important going on here, structurally....
- 19. Reading a network visualization à Lo o age k a mé n ere t th A ver h is o i s o utl tro ier cas e! There’s obviously something important going on here, structurally....
- 20. S? MIReading a network visualization à Lo o age k a mé n ere t th A ver h is o i s o utl tro ier cas e! There’s obviously something important going on here, structurally.... Using a “random” Gephi layout on the dolphins
- 21. S? MIReading a network visualization à Lo o age k a mé n ere t th A ver h is o i s o utl tro ier cas e! Rando m! There’s obviously something important going on here, structurally.... Using a “random” Gephi layout on the dolphins
- 22. Design Examples s! lp h in o it h D w
- 23. The Dolphins of Doubtful Sound http://www.doc.govt.nz/documents/conservation/native-animals/marine-mammals/abundance-population- structure-bottlenose-dolphins-doubtful-dusky-sounds.pdf
- 24. “The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations. Can geographic isolation explain this unique trait?” David Lusseau et al. BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY Volume 54, Number 4 (2003) http://www.springerlink.com/content/pepxvj4lu42ur2gw/
- 25. “The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations. Can geographic isolation explain this unique trait?” ! ti tle p er l pa tua ac e Th David Lusseau et al. BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY Volume 54, Number 4 (2003) http://www.springerlink.com/content/pepxvj4lu42ur2gw/
- 26. “SF” “ULT” 2 hung out D. Lusseau, Evidence for Social Role in a Dolphin Social Network. Evol Ecol (2007) 21:357–366
- 27. Citation: Lusseau D (2007) Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?. PLoS ONE 2(4): e348. doi:10.1371/journal.pone.0000348
- 28. Citation: Lusseau D (2007) Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?. PLoS ONE 2(4): e348. doi:10.1371/journal.pone.0000348 define relationship Using “mirroring” to
- 29. Citation: Lusseau D (2007) Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?. PLoS ONE 2(4): e348. doi:10.1371/journal.pone.0000348 define edges “headbutting” to define relationship UsingUsing “mirroring” to
- 30. TOOLS FOR TODAY Creating network layouts... 17
- 31. Gephi 18
- 32. Or “D3” (d3js.org) • A “build it yourself” svg-based visualization library • Import graphs as (or parse to create) a json node-link structure
- 33. Making a Network Who is your audience? What’s the goal? Exploration / Iterative visualization during data analysis? End-user communication?
- 34. Making a Network Who is your audience? What’s the goal? Exploration / Iterative visualization during data analysis? End-user communication? Layout choices: by hand, algorithmic, style... Understand the global and local context with some stats about actors and roles in the network Improve your layout with stats / attributes - inherent (such as gender) or calculated (e.g., degree) Add interactivity for end users if appropriate
- 35. J Bertin: Semiology of Graphics Linear Circular Irregular Regular (Tree) 3D Matrix / Bipartite Bertin, J. Semiology of Graphics: Diagrams, Networks, Maps (1967)
- 36. Algorithmic Approaches Frank van Ham talk slides: http://bit.ly/s6udpy
- 37. (Trees are a whole other subject) Treevis.net: http://www.informatik.uni-rostock.de/~hs162/treeposter/poster.html
- 40. Real social networks are generally quite sparse. http://www.cise.ufl.edu/research/sparse/matrices/Newman/ dolphins.html
- 41. D3 demo by me http://www.ghostweather.com/essays/talks/networkx/adjacency.html
- 42. NodeTrix: A Hybrid Visualization of Social Networks. Nathalie Henry, Jean-Daniel Fekete, and Michael J. McGuffin. (2007) http://arxiv.org/abs/0705.0599
- 45. ARC / LINEAR LAYOUTS
- 46. Philipp Steinweber and Andreas Koller Similar Diversity, 2007 For a D3 example in another domain: http://tradearc.laserdeathstehr.com/
- 50. Design Interlude
- 51. Bertin’s Thought Process Bertin, J. Semiology of Graphics: Diagrams, Networks, Maps (1967)
- 53. (P) Paris (Z) Paris Suburbs (+50) Communes of >50K (+10) Communes of >10K (-10) Communes of <10K (R) Rural
- 54. CIRCULAR / CHORD LAYOUTS
- 55. “If it's Circos pro bab rou ly d nd, o it Circ os ” can http://circos.ca/images/
- 56. Simple Orderings of Nodes Circular Layout “Dual Circle” layout with Sorted by ordered by Degree most popular dolphin in center Modularity 41 Dolphins colored by modularity class (community) in Gephi
- 59. Hierarchical Edge Bundling "Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data”, Danny Holten, IEEE Transactions on Visualization and Computer Graphics (TVCG; Proceedings of Vis/InfoVis 2006), Vol. 12, No. 5,
- 60. A D3 Example by M. Bostock D3: http://bl.ocks.org/1044242
- 61. A very short detour into maps...
- 62. 46 Flow Map Layout, Phan et al (2005) http://graphics.stanford.edu/papers/flow_map_layout/
- 63. 46 Flow Map Layout, Phan et al (2005) http://graphics.stanford.edu/papers/flow_map_layout/
- 64. "Force-Directed Edge Bundling for Graph Visualization”, Danny Holten and Jarke J. van Wijk, 11th Eurographics/IEEE-VGTC Symposium on Visualization (Computer Graphics Forum; Proceedings of EuroVis 2009), Pages 983 - 990, 2009.
- 65. Divided Edge Bundling for Directional Network Data David Selassie, Brandon Heller, Jeffrey Heer IEEE Trans. Visualization & Comp. Graphics (Proc. InfoVis), 2011 48
- 66. Design Example
- 69. 51 Jerome’s version with the map is not available online, sorry.
- 70. Yet Another Design Example
- 71. Moritz Stefaner’s Muesli Problem https://speakerdeck.com/u/moritzstefaner/p/omg-its-all-connected
- 73. s li ke iou ch lic u m ot de o “ To s, n h!” el f o om oug ims hr en to h us m i tz or -M https://speakerdeck.com/u/moritzstefaner/p/omg-its-all-connected
- 74. Final https://speakerdeck.com/u/moritzstefaner/p/omg-its-all-connected
- 75. ALGORITHMIC LAYOUTS Gephi / D3.js / Other tools
- 76. Gephi Sigma.js Gephi.org: Open source, runs on Mac, Linux, PC Can be run from a python-esque console plugin or UI Can be run “headless” for layouts (Jason Sundram) https://github.com/jsundram/pygephi Plugins include a Neo4j graph db access, and streaming support Sigma.js : Will display a gexf gephi layout file with minimal work, using a plugin interpreter for sigma Also offers a force-directed layout plugin for graphs without x&y coords Does CANVAS drawing, not SVG
- 78. Movie: Sigma.js version of the Gephi export http://exploringdata.github.com/vis/human-disease-
- 79. Using Sigma.js basic_sigma.js <div class="sigma-expand“ function init() { // Instanciate sigma.js and customize rendering : id="sigma-example"></div> var sigInst = sigma.init(document.getElementById('sigma-example')) .drawingProperties({ defaultLabelColor: '#fff', defaultLabelSize: 14, defaultLabelBGColor: '#fff', defaultLabelHoverColor: '#000', labelThreshold: 6, defaultEdgeType: 'curve' }).graphProperties({ minNodeSize: 0.5, maxNodeSize: 5, minEdgeSize: 1, maxEdgeSize: 1 }).mouseProperties({ Where maxRatio: 32 }); to put // Parse a GEXF encoded file to fill the graph the <script src="../js/sigma.min.js"></script> // (requires "sigma.parseGexf.js" to be included) <script src="../js/sigma.parseGexf.js"></script> sigInst.parseGexf('color_by_mod.gexf'); graph <script src="basic_sigma.js"></script> // Draw the graph : sigInst.draw(); } Your graph if (document.addEventListener) { document.addEventListener("DOMContentLoaded", init, false); } else { window.onload = init; } In sigma.js’s github (under plugins!)
- 80. Sample Layout Plugins in Gephi https://gephi.org/tutorials/gephi-tutorial-layouts.pdf
- 81. Gephi Plugin Layout Details Layout Complexity Graph Size Author Comment Circular O(N) 1 to 1M nodes Matt Groeninger Used to show distribution, ordered layout Radial Axis O(N) 1 to 1M nodes Matt Groeninger Show ordered groups (homophily) Force Atlas O(N²) 1 to 10K nodes Mathieu Jacomy Slow, but uses edge weight and few biases Force Atlas 2 O(N*log(N)) 1 to 1M nodes Mathieu (does not use Jacomy weight) OpenOrd O(N*log(N)) 100 to 1M nodes S. Martin, W. M. Focus on clustering Brown, R. Klavans, (uses edge weight) Yifan Hu O(N*log(N)) 100 to 100K nodes and K. Boyack Yifan Hu (no edge weight) Fruchterman- O(N²) 1 to 1K nodes Fruchterman & Particle system, slow Rheingold Rheingold! (no edge weight) GeoLayout O(N) 1 to 1M nodes Alexis Jacomy Uses Lat/Long for layout https://gephi.org/2011/new-tutorial-layouts-in-gephi/
- 82. Dolphins Again OpenOrd + “No Overlap” ForceAtlas2 63
- 83. Dolphins Again OpenOrd + “No Overlap” ForceAtlas2 63
- 84. Dolphins Again OpenOrd + “No Overlap” ForceAtlas2 63
- 85. Unweighted dolphins, Force Atlas Weight 2: Force Atlas Weight 4: Force Atlas 64
- 86. Unweighted dolphins, Force Atlas Weight 2: Force Atlas Weight 4: Force Atlas Weight 4: Yifan Hu 64
- 87. Canvas/SVG benchmarks from the d3.js group: https://docs.google.com/spreadsheet/ ccc? Nick Diakapolous: http://nad.webfactional.com/ntap/graphscale/ key=0AtvlFoSBUC5kdEZJNVFySG9wSHZk
- 88. Canvas/SVG benchmarks from the d3.js group: https://docs.google.com/spreadsheet/ ccc? Nick Diakapolous: http://nad.webfactional.com/ntap/graphscale/ key=0AtvlFoSBUC5kdEZJNVFySG9wSHZk
- 89. SIMPLE CALCULATIONS ON NETWORKS CAN TELL YOU Often you need to visualize the structure/role of the graph elements as part of the visualization: So, do some simple math.
- 90. Degree (In, Out) “Degree” is a measure of the edges in (directed), out (directed), or total (in directed or undirected graphs) to a node “Hub” nodes have high in- degree. In scale-free networks, we see preferential attachment to the popular kids. http://mlg.ucd.ie/files/summer/tutorial.pdf
- 91. Scale-free Networks Image from Lada Adamic’s SNA Course on Coursera pdf 3D
- 92. The Threat of Hub-Loss Albert-László Barabási and Eric Bonabeau, Scale-Free Networks, 2003.http://www.scientificamerican.com/ article.cfm?id=scale-free-networks
- 93. Visualization Aside: If Some Names are Huge, the Others are Invisible-? 70 Correcting for text size by degree display issue
- 94. Visualization Aside: If Some Names are Huge, the Others are Invisible-? Gephi Panel 70 Correcting for text size by degree display issue
- 95. Visualization Aside: If Some Names are Huge, the Others are Invisible-? Gephi Panel 70 Correcting for text size by degree display issue
- 96. Visualization Aside: If Some Names are Huge, the Others are Invisible-? Gephi Panel 70 Correcting for text size by degree display issue
- 97. Betweenness A measure of connectedness between (sub)components of the graph “Betweenness centrality thus tends to pick out boundary individuals who play the role of brokers between communities.” Lusseau and Newman. http://www.ncbi.nlm.nih.gov/pmc/ articles/PMC1810112/pdf/15801609.pdf http://en.wikipedia.org/wiki/Centrality#Betweenness_centrality
- 98. Judging By Eye Will Probably Be Wrong... 72
- 99. Judging By Eye Will Probably Be Wrong... ? This one? 72
- 100. Judging By Eye Will Probably Be Wrong... ? This one? Sized by Betweenness 72
- 101. Eigenvector Centrality Intuition: A node is important if it is connected to other important nodes A node with a small number of influential contacts may outrank one with a larger number of mediocre contacts http://mlg.ucd.ie/files/summer/tutorial.pdf http://demonstrations.wolfram.com/
- 103. Community Detection E.g., the Louvain method, in Gephi as “Modularity.” Many layout algorithms help you intuit these structures, but don’t rely on perception of layout! http://en.wikipedia.org/wiki/File:Network_Community_Structure.png
- 104. Citation: Lusseau D (2007) Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?. PLoS ONE 2(4): e348. doi:10.1371/journal.pone.0000348
- 105. Citation: Lusseau D (2007) Why Are Male Social Relationships Complex in the Doubtful Sound Bottlenose Dolphin Population?. PLoS ONE 2(4): e348. doi:10.1371/journal.pone.0000348 77
- 106. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 107. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 108. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 109. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 110. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 111. Identifying the role that animals play in their social networks (2004) D Lusseau, MEJ Newman Proceedings of the Royal Society of London. Series B: Biological Sciences
- 112. Eduarda Mendes Rodrigues, Natasa Milic-Frayling, Marc Smith, Ben Shneiderman, Derek Hansen, Group-in-a- box Layout for Multi-faceted Analysis of Communities. IEEE Third International Conference on Social
- 115. Movie: Ger Hobbelt D3: http://bl.ocks.org/3616279
- 116. Movie: Ger Hobbelt D3: http://bl.ocks.org/3616279
- 117. Design Example
- 118. 100 nodes, size by degree, Clustered by partition, no edges shaded by Betweenness, in until you click on one, node size is a d3.js force directed layout. choice of attributes, nodes represented by labels/colors…. http://www.ghostweather.com/essays/talks/networkx/ http://www.ghostweather.com/essays/talks/networkx/
- 119. Movie: 84 http://www.ghostweather.com/essays/talks/networkx/force_fonts.html
- 120. Movie: by @moebio 85 http://intuitionanalytics.com/pleiades/
- 121. ! LOL SO YOU WANT TO LAY IT OUT YOURSELF... Perfectionist? Artist? Don’t like algorithms? 86
- 123. Design Examples
- 124. Conspiracy Theorist Mark Learning from Lombardi: http://benfry.com/exd09/
- 125. Conspiracy Theorist Mark Learning from Lombardi: http://benfry.com/exd09/
- 127. Roche Applied Science Biochemical Pathways Map: http://web.expasy.org/cgi-bin/pathways/
- 128. Roche Applied Science Biochemical Pathways Map: http://web.expasy.org/cgi-bin/pathways/
- 129. Hybrid Method: Use algorithmic layout, and then adjust nodes by Ger Hobbelt in D3: http://bl.ocks.org/3637711
- 130. Tweaking your layout is addictive! Yo ned wa u r ha ! ve ! be en Jason Davies: http://www.jasondavies.com/planarity/
- 131. STEP BACK, SCALE UP... 94
- 132. C.Dunne & B.Shneiderman. Network Motif Simplification. http://hcil2.cs.umd.edu/trs/
- 133. GraphPrism: Compact Visualization of Network Structure Sanjay Kairam, Diana MacLean, Manolis Savva, Jeffrey Heer Advanced Visual Interfaces, 2012
- 135. Video: 98 http://graphics.wsj.com/political-moneyball/
- 136. Wrap it up on design...
- 137. Reminders Choose your visual encodings, layout, interaction to make it a visualization, rather than raw data vomit. Take care: people will infer things from proximity/similarity even if it was not intended! Do data analysis / reduction - why would you want to show 1T of network data? Allow interactivity if needed for end users. Help people find things in your network!
- 138. Reminders Choose your visual encodings, layout, interaction to make it a visualization, rather than raw data vomit. Take care: people will infer things from To ot sci proximity/similarity even if it was not =N o m wa ce d intended! at uc al en a h d go Do data analysis / reduction - why at ys ! a would you want to show 1T of network o d data? Allow interactivity if needed for end users. Help people find things in your network!
- 139. More Reminders! Different layouts communicate different things to your viewer - choose wisely Reducing noise: Don’t show edges (perhaps on demand) Show details only on demand: zoom in Cluster your nodes/edges Consider if it has to be a “network” display at all: Is it the stats you care about? Or the hairball? 101
- 140. The Map is Not the Territory… Forest Pitts (thanks to Noah Friedkin) http://www.analytictech.com/networks/pitts.htm
- 141. The Map is Not the Territory… Forest Pitts (thanks to Noah Friedkin) http://www.analytictech.com/networks/pitts.htm
- 143. Thanks! @arnicas [email protected] And thanks to twitter vis friends for content: @jsundram, @laneharrison, @moritz_stefaner, @jcukier, @jeff1024, @vlandham, @moebio, @jeffrey_heer, @mbostock, @eagereyes, @jasondavies, @stefpos, @sarahslo, @ndiakopoulos, @gephi
- 144. A Few More References Jeff Heer class slides: http:// Robert Kosara’s post: http:// hci.stanford.edu/courses/cs448b/ eagereyes.org/techniques/graphs- w09/lectures/20090204- hairball GraphsAndTrees.pdf Lane Harrison’s post: http:// A great in-progress book on networks: blog.visual.ly/network- http://barabasilab.neu.edu/ visualizations/ networksciencebook/ MS Lima’s book Visual Complexity Mark Newman’s many papers: http:// Jason Sundram’s tool to drive Gephi www-personal.umich.edu/~mejn/ layout from command line: https:// Eyeo Festival videos from Moritz github.com/jsundram/pygephi Stefaner, Manuel Lima, Stefanie A couple articles on community Posavec structure: Journal of Graph Algorithms and Overlapping Community Detection Applications: http://jgaa.info/ in Networks: State of the Art home.html and Comparative Study by Jierui Jim Vallandingham’s D3 network Xie, Stephen Kelley, Boleslaw K. tutorials: http://flowingdata.com/ Szymanski 2012/08/02/how-to-make-an- Empirical Comparison of interactive-network-visualization/, Algorithms for Network
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