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LEAP-KMC Workshop 2006LEAP-KMC Workshop 2006
Visualization of KMC Simulation Data Visualization of KMC Simulation Data and Evolutionary Computation:and Evolutionary Computation:
The LEAP Infrastructure andThe LEAP Infrastructure andContent Management SystemContent Management System
LEAP-KMC Workshop 2006LEAP-KMC Workshop 2006
Visualization of KMC Simulation Data Visualization of KMC Simulation Data and Evolutionary Computation:and Evolutionary Computation:
The LEAP Infrastructure andThe LEAP Infrastructure andContent Management SystemContent Management System
William H. Hsu and Andrew WaltersWilliam H. Hsu and Andrew Walters
Thursday, 18 May 2006Thursday, 18 May 2006
Laboratory for Knowledge Discovery in DatabasesLaboratory for Knowledge Discovery in Databases
Kansas State UniversityKansas State University
http://www.kddresearch.org/KSU/CIS/KMC-20060518-Vis.ppthttp://www.kddresearch.org/KSU/CIS/KMC-20060518-Vis.ppt
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Visualizing the Problem:Visualizing the Problem:2-D Models2-D Models
Occupancy Number (ON) =
1x20 + 1x2
1 + 0x2
2 + 1x2
3 + 1x2
4 + 1x2
5 = 59
Pattern Recognition SchemePattern Recognition Scheme
(Karim et al., 2005)
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Visualizing the Simulation:Visualizing the Simulation:3-D Models3-D Models
Based on (Thornton, 2005) © 2005 Charlie L. Thornton
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Visualizing the Database [1]:Visualizing the Database [1]:GrowthGrowth
© 2004 Rahman, Amar, Hsu, Kara, WallentineFrom proposal for NSF 0428826
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
cDNAMicroarray-Experiment
Gene Protein
protein-product
role
pathway
functional-description
canonical-name
accession-number
protein-ID
Relational Link (Reference Key)ProbabilisticDependency
cDNA-sequence
treatment
hybridization
normalization
data
regulation
DNA-sequence
Pathway
pathway-descriptor
pathway-name
pathway-ID
pathway
TAVERNA WorkbenchmyGrid Project
© 2004 Oinn et al.DESCRIBER example schema
© 2003 Hsu
Transactional View (cf. UML Sequence Diagram) Objective View (cf. UML Class Diagram)
Visualizing the Database [2]:Visualizing the Database [2]:Entity-Relational Models for Data MiningEntity-Relational Models for Data Mining
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Visualizing Models [1]:Visualizing Models [1]:Animation of Algorithms, BNJ v3Animation of Algorithms, BNJ v3
CPCS-54 Network© 2004 KSU Bayesian Network tools in Java (BNJ) Development Team
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Asia (Chest Clinic) Network© 2004 KSU Bayesian Network tools in Java (BNJ) Development Team
Visualizing Models [2]:Visualizing Models [2]:Constraint Propagation, BNJ v3Constraint Propagation, BNJ v3
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
ALARM Network
© 2005 KSU Bayesian Network tools in Java (BNJ) Development Team
Visualizing Models [3]:Visualizing Models [3]:Tree Propagation, BNJ v4Tree Propagation, BNJ v4
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
© 2005 William H. HsuFrom 1st Annual LEAP-KMC Workshop, 2005
Cluster Tree for 36-bit Occupancy VectorDatabase from Cobweb – WEKA238 merges, 186 splits, 1106 clusters
Visualization of Energy (x) vs. Cluster Membership (y)using Clusters found by Expectation-Maximization (EM) – WEKA20 clusters, log likelihood = -11.66
Visualizing Models [4]:Visualizing Models [4]:Clusters from EM and CobwebClusters from EM and Cobweb
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Visualizing Convergence:Visualizing Convergence:Adaptive Importance Sampling, K2, & GAAdaptive Importance Sampling, K2, & GA
© 2002 Hsu, Guo, Perry, Thornton
Inferential RMSE for Forward Simulation
0
0.05
0.1
0.15
0.2
0.25
1 2693 5385 8077 10769 13461
Samples
RM
SE
GoldStandardNetwork
K2 Outputon OptimalOrdering
K2 Outputon GAOrdering
K2: 20K FS: 1500
(Hsu, Guo, Perry & Stilson, 2002)
Frequency of Validation Set Fitness
0 200 400 600 800 1000 1200 1400
0.802
0.816
0.830
0.844
0.858
0.871
0.885
0.899
0.913
0.927
0.941
0.955
0.969
0.982
0.996
Histogram of estimated fitness for all 8! = 40320 permutations of
Asia variables
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Information Visualization Road MapInformation Visualization Road Map
Human Computer Intelligent Interaction (HCII) IssuesHuman Computer Intelligent Interaction (HCII) Issues
– Human factors: usability, ergonomicsHuman factors: usability, ergonomics
– Interface designInterface design
Simulator Visualization Wish ListSimulator Visualization Wish List
– 3-D view controls and automatic focus3-D view controls and automatic focus
– Color customization (automated and manual)Color customization (automated and manual)
– Animation speed and time index controlAnimation speed and time index control
– Overlays for comparisonOverlays for comparison
– Survey/discussion: your desiderata?Survey/discussion: your desiderata?
Visualization Toolkit (VTK/ITK) – Visualization Toolkit (VTK/ITK) – http://http://www.itk.orgwww.itk.org
Kansas State University CIS Department18 May 2006Second Annual KMC Workshop
Content Management System:Content Management System:The LEAP-KMC TikiWikiThe LEAP-KMC TikiWiki
FeaturesFeatures
– User-managed content (cf. Wikipedia’s MediaWiki)User-managed content (cf. Wikipedia’s MediaWiki)
– Database and server-side file maintenanceDatabase and server-side file maintenance
Applications: Glossary, Experiment Files, Codes, Outreach, EducationApplications: Glossary, Experiment Files, Codes, Outreach, Education
Try it! Try it! http://leap-kmc.user.cis.ksu.eduhttp://leap-kmc.user.cis.ksu.edu