Presentation to Engineering Science Summer Institute, 31 May 2001

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Bioinformatics and Machine LearningBuilding
Probabilistic Modelsof Gene Expression from
Microarray Data
William H. Hsu with Prashanth Boddhireddy,
Haipeng Guo, Rengakrishnan Subramanian, Ben
Perry, and Julie A. Thornton Department of
Computing and Information Sciences Kansas State
University Laboratory for Knowledge Discovery in
Databases http//www.kddresearch.org/Groups/Bioinf
ormatics
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Overview

• Bioinformatics
• Genomics
• Proteomics
• Other Metabolomics and Enzyme Kinetics, etc.
• Artificial Intelligence (AI) Approaches
• Clustering
• Graphical Models and Temporal Modeling
• Hidden Markov Models (HMMs) in Proteomics
• Dynamic Bayesian Networks DBNs (aka TPNs, TBNs,
  DPNs)
• Microarray Data Mining
• Current Projects and Open Problems
• Data Modeling
• User Modeling and Collaborative Filtering (CF) -
  DESCRIBER
• New Algorithms for Learning, Inference in
  Graphical Models
• Integrative Approaches to Gene Profiling

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Information Retrieval (IR) and Text Mining
Commercial Applications
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Visual Programming andSoftware Engineering
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Stages of Data Mining andKnowledge Discovery in
Databases
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Clustering Approaches
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Genetic Algorithms for Parameter Tuning in
Bayesian Network Structure Learning 1
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Genetic Algorithms for Parameter Tuning in
Bayesian Network Structure Learning 2
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Experimenters Workbench
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Microarrays
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A Gene Network for YeastFriedman, Nachman,
Linial, Peer, 2000
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Components of A Microarray ExperimentHybridizati
on
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Components of A Microarray ExperimentComputation
al Gene Expression Modeling
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DESCRIBER An ExperimentalIntelligent Filter

• Example Queries
• What experiments have found cell cycle-regulated
  metabolic pathways in Saccharomyces?
• What codes and microarray data were used, and why?

Users of Scientific Document Repository

DESCRIBER
Learning and Inference Components
Historical Use Case Query Data
Personalized Interface
New Queries
Domain-Specific Collaborative Filtering
Decision Support Models
Interface(s) to Distributed Repository
Domain-Specific Repositories Experimental
Data Source Codes and Specifications Data
Models Ontologies Models
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DESCRIBEROverview
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DESCRIBERCollaborative Filtering Module