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GUESS The Graph Exploration System

GUESS The Graph Exploration System. Eytan Adar November 23, 2005. Existing tools, toolkits. Really good options exist Prefuse (Heer et al) JUNG (Fischer et al) GVF (Marshall) But… Need to know how to program Not easy to use for prototyping Program -> compile -> run cycle Too general…

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GUESS The Graph Exploration System

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  1. GUESSThe Graph Exploration System Eytan Adar November 23, 2005

  2. Existing tools, toolkits • Really good options exist • Prefuse (Heer et al) • JUNG (Fischer et al) • GVF (Marshall) • But… • Need to know how to program • Not easy to use for prototyping • Program -> compile -> run cycle • Too general… • Don’t take into account the nature of graphs

  3. Existing tools, full programs • Biology focus • Cytoscope • Social network focus • UCINET/Krackplot • Pajek • Problems • Too specific • Overwhelming • Pajek interface

  4. Design requirements • Deal with different kinds of networks • But not by abstracting everything to a matrix • Nodes and edges have properties! • Exploratory tool • Tolerate mistakes made in exploration • Ability to easily do standard analysis • Ability to add new analysis routines • Scriptable • Compile into application/applet • Flexible front/back ends

  5. GUESS • Originally “Zoomgraph” • Limited scripting (big if-else loop) • Problem: actually got users • Users want things • GUESS was designed to handle new demands • Has a real programming language for scripting • Pluggable visualizations

  6. Screenshot

  7. GUESS • “Gython” • Python + graph data structures + operators + query language • Better (expandable/separable) architecture • Back-end storage abstracted • Front-end visualization abstracted • Prefuse • Touchgraph • Still have one main “zoomable” front end • The most complete

  8. Demo

  9. A Domain Specific (Embedded) Language • Took existing jython core and modified it • New operators ( ->, <-, <->, rcontains, etc.) • node1->node2 • (node1,node2)->(node3,node5) • Better integration with Java • Automatic set mapping • (node1,node2,node3).color = red • If you know python or jython you should be comfortable in this space, but can also write Java code if you prefer

  10. Query language built in • Nodes and Edges have properties • The usual types (text, numbers, Booleans) • Can use these to manipulate the display • (dept == ‘Human Resources’).color = blue • (freq > 10).width = 4 • (cell_location == ‘wall’) & (expression_levels > 100) • (name like ‘Bob%’)

  11. Users don’t care… • Top level namespace contains all the objects you may want to play with directly • g = the working graph • Each node uniquely named • Each edge set uniquely accessed • a->b • Property objects also automatically created • (freq > 100) and also... • freq.max • Immutable • EDA  shouldn’t have to start from scratch • Distinction between invisible and deleted • “deleted” objects actually sit around in special (queryable) state.

  12. Users don’t care… • Objects have methods • g.gemLayout() • But, users don’t remember… • Automatic script finds all methods and loads them as built in functions • In Gython: • g.gemLayout()  gemLayout()  gemLayout() • Calls appropriate Java code • someFunction(x,y) vs. someFunction(x)

  13. Getting data in • GUESS lets you define your own properties nodedef> name, country VARCHAR N1,”US” N2,”France” edgedef> node1,node2, delay INT default 5 N1,N2,20

  14. Visual properties built in… • GUESS knows about visual properties • Nodes • location, color, size, shape, label, etc. • Edges • width, color, etc. • (Non-visual) properties generated dynamically • e.g. indegree, pagerank, betweeenness • Everything accessed same way • v3.color v3.dept v3.indegree

  15. Visual shortcuts • Lots of syntactic sugar to do certain things • Color each department differently • colorize(dept) • Color each edge by frequency from red to blue • colorize(freq,red,blue) • Can group and sort by properties • depts = groupBy(dept) • freqs = sortBy(freq) • whatever = groupAndSortBy(…)

  16. Built in functions • Layouts • Clustering algorithms • Shortest path/Flow algorithms • Centrality measures • Graph statistics • Plots and charts • Can even connect to R for more

  17. Demo

  18. Connect interpreter to display • Unique feature of GUESS • Mouse motion over text results in highlighting of graph/visualization structures • [[v4,v5],[v6,v7,v8]] • Contextual menus • Same menus pop up in display and in text window • Menus contextualized to type • “Copy as variable”

  19. Demo

  20. States and Time • As if graphs weren’t complicated enough… • Time is a critical dimension • Graphs and properties change • We want to visualize them • And users in an exploratory mode want undo • Kill two birds with one stone…

  21. States and Time • Basics through simple commands • ss(‘state name’) • ls(‘state name’) • Queries work between states • v44[‘q105’].dept • freq[2005] > freq[2003] • Morphing • morph(‘state name’,time) • output as movie • Camera tracking (in Zoomgraph and soon in GUESS) • Also… “range” fields • “1,5-100,102-105” • Node rcontains (5,10) • Node rexact (102-105)

  22. Extending GUESS • Write your own routines/programs • Change mouseover/click behavior • E.g. pop up a web page • Control remotely or through Java • Add “dockable” widgets • Replace front end • Compile into applet

  23. Simple Example: Skitter

  24. Skitter def skitter(_field): _maxangle = 2 * Math.PI _ordering = sortBy(_field) _increment = _maxangle / len(_ordering) _curangle = 0 g.nodes[0].outdegree _maxdeg = outdegree.max + 1.0 for _n in _ordering: _radius = 1 - Math.log((_n.outdegree + 1.0) / _maxdeg) _radius = _radius * 500.0 _x = 500.0 + _radius * Math.cos(_curangle) _y = 500.0 + _radius * Math.sin(_curangle) _n.setX(_x) _n.setY(_y) _curangle += _increment

  25. Skitter

  26. Modify the interface import … class dockexample1(com.hp.hpl.guess.ui.DockableAdapter): def __init__(self): testButton = JButton("center") action = lambda event: center() testButton.actionPerformed = action self.add(testButton) def getTitle(self): return("dockexample1")

  27. Modify the interface def sc(self,evt): val = self.testSlider.getValue() g.nodes.visible = 1 (freq < val).visible = 0 (freq >= val).visible = 1 self.hideDisconnectedNodes() self.label.setText("Frequency threshold ("+str(val)+")")

  28. Modify the interface import … class dockexample2(com.hp.hpl.guess.ui.DockableAdapter): testSlider = JSlider() label = JLabel("Frequency threshold (0) ") def __init__(self): self.testSlider.setMinimum(freq.min) … self.testSlider.setValue(freq.min) # default value self.testSlider.mouseReleased = self.sc self.add(self.label) self.add(self.testSlider) ui.dock(self)

  29. Modify the interface def hideDisconnectedNodes(self): toHide = [] for nod in g.nodes: # for all nodes vis = 0 # default to invisble for ed in nod.getOutEdges(): if (ed.visible == 1): vis = 1 break if (vis == 0): # should we hide the node? toHide += [nod] # hide all the nodes we put in our list toHide.visible = 0

  30. Compiling and distributing… • Users build applets/applications • Network simulation • Political blogs • I’ve heard of: • Neuroscience and sewer/water lines

  31. Front end flexibility • Can replace the visualization • I like Piccolo • But… • Prefuse • Touchgraph • JUNG • and soon Wilma (3D) • Are also available

  32. Scaling… • Not bad… • Graphics will slow you down • Algorithms are pretty fast • You can… • Load up a big dataset • Do a faster layout (gemLayout()) • Go to lunch • Play with graph

  33. ~2000

  34. ~6000 nodes

  35. ~12000 nodes

  36. Politics and Blogs Adamic & Glance, 2005

  37. Viral marketing Leskovec, Adamic, and Huberman, 2005

  38. Social groups Adamic, Adar, 2003

  39. Email communications Adamic, Adar, 2005

  40. Information Flow Adar, Zhang, Adamic, Lukose, 2004

  41. Summary… (end Eytan’s slides) • Exploratory data analysis • Free (GPL) • http://www.graphexploration.org

  42. Other visualization tools: Walrus • developed at CAIDA available under the GNU GPL. • “…best suited to visualizing moderately sized graphs that are nearly trees. A graph with a few hundred thousand nodes and only a slightly greater number of links is likely to be comfortable to work with.” • Java-based • Implemented Features • rendering at a guaranteed frame rate regardless of graph size • coloring nodes and links with a fixed color, or by RGB values stored in attributes • labeling nodes • picking nodes to examine attribute values • displaying a subset of nodes or links based on a user-supplied boolean attribute • interactive pruning of the graph to temporarily reduce clutter and occlusion • zooming in and out

  43. Other visualization tools: GraphViz • Takes descriptions of graphs in simple text languages • Outputs images in useful formats • Options for shapes and colors • Standalone or use as a library • dot: hierarchical or layered drawings of directed graphs, by avoiding edge crossings and reducing edge length • neato (Kamada-Kawai) and fdp (Fruchterman-Reinhold with heuristics to handle larger graphs) • twopi – radial layout • circo – circular layout http://www.graphviz.org/

  44. Dot (GraphViz)

  45. Neato (Graphviz)

  46. YEd - JavaTM Graph Editorhttp://www.yworks.com/en/products_yed_about.htm(good primarily for layouts, maybe free)

  47. Perfuse • (free) user interface toolkit for interactive information visualization • built in Java using Java2D graphics library • data structures and algorithms • pipeline architecture featuring reusable, composable modules • animation and rendering support • architectural techniques for scalability • requires knowledge of Java programming • website: http://prefuse.sourceforge.net/ • CHI paper http://guir.berkeley.edu/pubs/chi2005/prefuse.pdf

  48. Simple prefuse visualizations

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