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