JN 5/29/2016 SeeGraph: A System for Visualizing Weighted-Edge Graphs Joshua New Dr. Jian Huang Dr. Elissa Chesler
www.cs.utk.edu/~seelab

Introduction • Design Decisions • Current Capabilities – Data options – View options • Results • Future Work – Input Features – Result Statistics – Interactivity – Publications JN 5/29/2016
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Design Decisions
– Langston’s Pearson’s correlation of 7443 genes (*_at) to define a weighted edgelist – Data to be added: Paraclique, Phenotype, and Statistical Model – Apply spring-embedding in order to create a graph layout where distance to adjacent vertices is based on the edge’s weight
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JN 5/29/2016

Design Decisions
– First attempt using GraphViz for creating a 2D layout – Note: edges occlude the data & vertices are too cluttered
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JN 5/29/2016

Design Decisions
– Use a 3D Layout • More space between individual nodes • Customizable view for specific areas of interest • More advanced rendering techniques to visually compare separate areas – Nodes always visible • Line edges don’t occlude the nodes of interest • Perspective projection preserves 3D relation
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JN 5/29/2016

Design Decisions
– Interaction with multiple thresholds – Interactive querying of per-vertex data features – Display of relevant statistics for the results – Psycho-visual contrast for node delineation – Use of lighting to give 3D shape to nodes – Customizable view and rendering
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JN 5/29/2016

JN 5/29/2016 Current Capabilities
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Data Options
(uses GEM3D’s algorithm) – Stand-alone program for computing the spring-embedded layout of an edgelist; converts a weighted edgelist (*.wel) to a graph vertex layout (*.gvl) – Usage: ./laymeout filename.wel threshold[0.0-1.0] absValFlag[0,1] – Ex: ./laymeout rma_pearsons.85.wel 0.85 1
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JN 5/29/2016

Data Options
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JN 5/29/2016

Data Options • SeeGraph Command Line Parameters 1) View a single spring-embedded layout w/ one thresh – ./Seegraph viewOption[1] filename.wel threshold[0.0-1.0] absValFlag[0,1] – Ex: ./Seegraph 1 rma_pearsons.85.wel 0.85 1 2) View multiple spring-embedded layouts – ./Seegraph viewOption[2] filename.wel startThresh endThresh stepThresh absValFlag – Ex: ./Seegraph 2 rma_pearsons.85.wel 0.85 0.95 0.01 1 3) View a single spring-embedded layout w/ multiple threshes – ./Seegraph viewOption[3] filename.wel startThresh stepThresh absValFlag – Ex: ./Seegraph 3 rma_pearsons.85.wel 0.85 0.01 1
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JN 5/29/2016

P A R A M 2
0.85
0.91
0.92
0.95
P A R A M 3
0.85
0.91
0.92
0.98
JN 5/29/2016 Data Options
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View Options • • – – – – SeeGraph Key Commands F1-F12 – different viewing options Left/Right arrow – change threshold Up/Down arrow – zoom in/out Change query – F0=[‘z’-’a’+,’q’-’1’+] – Display information current threshold setting – – – number of vertices number of edges current query
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JN 5/29/2016

View Options • View Quadrics (F2) – Good but slow (15 fps) – Scales well w/ resolution • View Splats (F3) – Fuzzy but fast (72 fps) – Doesn’t scale well w/ res.
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JN 5/29/2016

View Options • View Sphere (F12) – Shows off lighting well • View Normals (F4) – Shows light reflection – Reveals internal structure
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JN 5/29/2016

View Options • Toggle Edges (F5) – Show for relationships – Hide for performance – Edges are color-coded based upon their corresponding weight • Edge Colors (Menu) – Hot/Cold – easy to understand edges – Full Color – maximizes edge contrast • Edge Options – Normalize to full color (F6) – Separate negative edges (F7)
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JN 5/29/2016

View Options H o t / C o l d F u l l C o l o r JN 5/29/2016 N&S [0-.5,.5-1] !N&S [0-.15,.85-1] N&!S
[0-1] !N&!S
[.85-1]
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View Options • Rm Disco Off (F8) – Contextual View – Red/Blue psycho-contrast • Rm Disco On (F8) – Occlusion-free view
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JN 5/29/2016

View Options • Rm Disco Verts (F8) – Shows only the selection with no occlusion • Show LCC (F9) – Shows only the largest connected-component
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JN 5/29/2016

View Options • !All Edges (F10) – Shows only edges above the current threshold • All Edges (F10) – Shows connected edges regardless of the thresh
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JN 5/29/2016

View Options • Query on Degree – 7442 Verts w/ [1,1486] • New Query – 4892 Verts with [11,1486]
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JN 5/29/2016

Results Number of total edges, blue indicates edges with negative weight Number of non-disconnected vertices for varying thresholds
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JN 5/29/2016

Findings
Number of Edges in LCC
800000 700000 696525 600000 550726 500000 425457 400000 300000 320899 232046 200000 100000 0 0.85 0.86 0.87 0.88 0.89
0.9
160851 104999 63147 34223 160865020 1433 131 8 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99
0
Number of Vertices in LCC
8000 7236 7000 6662 6000 6054 5426 5000 4771 4000 4141 3498 3000 2683 2000 2081 1496 1000 0 0.85
0.86
0.87
0.88
0.89
0.9
0.91
0.92
0.93
0.94
0.95
618 0.96
299 0.97
78 0.98
9 0.99
0
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JN 5/29/2016

Results • Connected vs. LCC – Number of Vertices for varying thresholds
Number of Connected Vertices
8000 7000 6000 5000 4000 3000 2000 1000 0 7443 7236 6916 6662 6342 6054 5780 5426 5092 4771 4475 4141 3798 3498 3128 2683 2450 2081 1844 1496 1181 618 585 299 0.85
0.86
0.87
0.88
0.89
0.9
0.91
0.92
0.93
0.94
0.95
0.96
0.97
0.98
0.99
Number of Connected Edges
800000 700000 696525 600000 550726 500000 425457 400000 300000 320899 232046 200000 100000 0 0.85 0.86 0.87 0.88 0.89
0.9
160851 104999 63147 34223 160865020 1433 131 8 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99
0 • Connected vs. LCC – Number of Edges for varying thresholds
www.cs.utk.edu/~seelab
JN 5/29/2016

Results • Display Performance – Q=Quadrics (F2) – S=Splats (F3)
Windows FPS at 800x600 Graphs with Edges
40 30 20 10 0 80 70 60 50 36 18 15 24 19 24 5 6 10 6 11 8 8 12 9 6 0.85
0.86
0.87
0.88
0.89
0.9
Threshold
0.91
0.92
0.93
0.94
0.95
72 36
Without Edges
1-screen (800x600) 1-screen (full – 1280x1024) 2x2 (2560x2048) 3x3 (3840x3072)
Quads (4,4) Splatting
16 16 5 5 246 105 33 17 Splatting S-Connected S-LCC Quadrics Q-Connected Q-LCC
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JN 5/29/2016

Future Work
1.
degree.txt
– vertex,positive edges,percent positive,negative edges,percent negative,total,percent total
2.
3.
100005_at 700 9.41% 144 1.93% 844 11.34%
newconnc.txt
newconnp.txt
– Same per-node info for each of 38 Cliques – Same per-node info for each of 38 Paracliques – – –
Clique/Paraclique membership Clique/Paraclique connectivity Cluster by paraclique
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JN 5/29/2016

Future Work
1.
2.
Phenotypes Regulatory Models
– 3 different thresholds for edges, phenotypes, and regulatory models – Different-colored nodes for each of these 3
– What others besides degree and the above?
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JN 5/29/2016

Future Work • Result Statistics: displayed on screen – Number of vertices – Number of edges – More data written to output*.txt file (~) • What other statistics?
– Average degree – Average edge weight
www.cs.utk.edu/~seelab
JN 5/29/2016

Future Work • Interactivity – Selection of a specific node within the scene – Picking/brushing for mouse-based selection of node(s)/edge(s) of interest – Scripting language to formally define parameters and requests to the system – GUI to allow for easy definition/refinement of queries
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JN 5/29/2016

Future Work • Publications (1 domain-specific with useful/important findings) – SIGGRAPH deadline – January 24 th • • Conference: Boston, MA; July 30-August 3, 2006 http://www.siggraph.org/s2006/ – EuroVis deadline – October/November • • Conference: Lisbon, Portugal; May 8-10, 2006 http://www.gris.uni-tuebingen.de/~bartz/egdv/events.html
– EuroGraphics deadline – January 27 th • • Conference: Braga, Portugal; May 11-12, 2006 http://www.di.uminho.pt/egpgv06/
www.cs.utk.edu/~seelab
JN 5/29/2016

SeeGraph v4.0 Reference Card Function Keys
F1 – Toggle Full-Screen Mode F2 – View Quadrics F3 – View Splats F4 – Show/Hide Lighting Normals F5 – Show/Hide Edges F6 – Toggle Edge Normalization F7 – Toggle Edge Separation F8 – Show/Hide Disconnected Verts F9 – Show/Hide LCC F10 – Show All Edges F11 – Toggle Active Querying F12 – View Sphere
Keyboard
Esc – Exit → – Increase Threshold ← – Decrease Threshold +, ↑ – Zoom In -, ↓ – Zoom Out ~ – Write selected data to output*.txt
1 – Increase ceiling for feature 0 Q – Decrease ceiling for feature 0 A – Increase floor for feature 0 Z – Decrease floor for feature 0 * Move to the right for each consecutive feature