1. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org cDNA Microarray- Experiment Gene Protein protein-product role pathway functional- description canonical- name accession-number protein-ID Relational Link (Reference Key) Probabilistic Dependency cDNA-sequence treatment hybridization normalization data regulation DNA-sequence Pathway pathway- descriptor pathway-name pathway-ID pathway Relational Graphical Models (RGMs): Computational Genomics Domain

2. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Workflows in TAVERNA [1] TAVERNA Workbench my Grid Project © 2003 Oinn et al.i

3. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Workflows in TAVERNA [2] TAVERNA Workbench my Grid Project © 2004 Oinn et al.i

4. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org TIGR TM4 Workflows [1]: MIDAS – Microarray Suite TIGR MIDAS © 2005 Saeed et al.

5. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org TIGR TM4 Workflows [2]: Multi-Experiment Viewer (MeV) TIGR MeV 4.1 © 2005 Saeed et al.

6. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Module 1 Collaborative Recommendation Front-End Personalized User Interface: Workflow Development and Repurposing Graphical Relational Models of Past User Queries Learning to Predict User Preferences Decision Support: Selection of Workflows, Components, and Services to Reuse/Adapt Models for CR Recommendations to User New Queries, Evaluations from User DESCRIBER Graphical Relational Models of Workflows, Components User Queries (Use Case Data) to Module 4 Workflow Instances, Logs, Templates, Components to Module 2 from Module 3 from Module 5 DESCRIBER: Using Relational Graphical Models

7. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Application: Workflow Modeling in Bioinformatics –Collaborative recommendation –Example: gene expression modeling Methodology: Relational Graphical Models (RGMs) –DESCRIBER project: using RGMs –Other workflows: proteomics, metabolomics Link Analysis Problems –Finding dynamic relational attributes –Identity uncertainty Other Applications –Market basket analysis: cross-selling –Spatial data cleaning Software for Building Graphical Models: BNJ, etc. Outline

8. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org BNJ Development History Bayesian Network Tools (BNTools, 2000-2002) –Junction Tree –Editor –Structure learning (K2) BNJ v1 (2002-2003) –Semistructured data format (XML) based on MSBN, XBN –ConverterFactory: Hugin, Ergo, Netica, MSBN –Importance sampling –Other inference algorithms (Guo: Multi-Start Hill Climbing, Tabu Search) BNJ v2 (2003-2004) –Relational Models –Wizards: Learning, Inference BNJ v3 (2004-present) –Visualization Framework –Run Mode: online constraint propagation –Refactoring for speed: 600-2000% speedup over v2 –Better memory management

9. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org BNJ Graphical User Interface [3]: Constraint Propagation (Run Mode) Asia (Chest Clinic) Network© 2004 KSU Bayesian Network tools in Java (BNJ) Development Team

10. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org BNJ Graphical User Interface [4] Network ALARM Network © 2005 KSU Bayesian Network tools in Java (BNJ) Development Team

11. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Genetic Algorithm for BN Structure Learning Results: Asia (Chest Clinic) Histogram of estimated fitness for all 8! = 40320 permutations of Asia variables K2FS Samples Best f of final gen 500015000.944 1000015000.960 200001500.935 200004500.977 2000015000.978 Results for Asia (5000 samples per fitness evaluation in D val and D test )

12. Kansas State University Department of Computing and Information Sciences Kansas State University KDD Lab (www.kddresearch.org)www.kddresearch.org Laboratory for Knowledge Discovery in Databases (KDD) –Computational science and engineering (CSE): decision support –Bioinformatics and Medical Informatics (BMI) working group www.kddresearch.org/Groups/Bioinformatics www.kddresearch.org/Groups/Bioinformatics –Human-Computer Interaction (HCI) - e.g., simulation-based training www.kddresearch.org/Groups/{Intelligent-HCI | Vislab} www.kddresearch.org/Groups/{Intelligent-HCI | Vislab} Programs and Workshops –PRISM: CIS (Hsu), EECE (Das), IMSE (Chang) www.kddresearch.org/Groups/Soft-Computing –Machine Learning and KDD (IJCAI-2001) www.kddresearch.org/Workshops/IJCAI-2001 –Real-Time Decision Support and Diagnosis (AAAI/UAI/KDD-2002) www.kddresearch.org/Workshops/RTDSDS-2002 –Learning Graphical Models for Computational Genomics (IJCAI-2003) www.kddresearch.org/Workshops/IJCAI-2003-Bioinformatics Research Partnerships –Defense (ONR), NSF (EPSCoR), industry (AIdentity Matrix), academia –Brown, North Carolina State, Wisconsin, TIGR, Manchester Graphical Models for KDD: Research Projects at K-State