Evolution of Knowledge Discovery and Management

Evolution of Knowledge Discovery and Management Dr. A. Fazel Famili National Research Council of Canada Ottawa, ON K1A 0R6 Canada [email_address] October 28 th 2066

Outline ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Sequence data: C T A GG C T CC A G C T Time series The data mining process Discovered Knowledge: - Informative attributes - Thresholds - Relationships - Strength of Discovery ,[object Object],[object Object],[object Object],[object Object],Knowledge Discovery: The process of discovering useful and previously unknown knowledge from historical or real-time data - Data Extraction and Selection - Data Pre-processing - Data Analysis (e.g. Pattern Recognition) - Post-processing This is what I need!

Roots of knowledge Discovery Knowledge Discovery Parallel algorithms Machine Learning High performance computing Visualisation Database and Data Warehousing Data Visualization Applied Statistics

Motivation Analysis capability (Software/Hardware Understanding the value of data Data production/ storage Knowledge Discovery

Knowledge Discovery Efforts ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Typical Applications of Data Mining ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The real challenge: Bioinformatics - Genomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The real challenge (cont’d) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Data in Genomics and Proteomics Genomics - Microarrays ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Proteomics MS 2D/3D GELs Protein Arrays Sequence data

Biological Data Analysis Normalization ,[object Object],[object Object],[object Object],- Validation - Documentation Knowledge Discovery Microarray Data Data Pre-processing (Understanding the data) ,[object Object],[object Object],[object Object]

Contributions and applications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Comparative Genomics ,[object Object]

Comparative Genomics ,[object Object],Control Test Full samples Hybridize and wash Microarray Data Identify Patterns of Gene Expression

Looking at some case studies Bioinformatics

Disease Modeling: Leukemia case study ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Golub et al. 13 37 37 BioMiner Golub et al. & BioMiner

Understanding the data P20 p17 P17 P20 VRLLGam_train_lab_t_20020709_173359.html

[object Object],[object Object],[object Object],Predictor Model and informative Genes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Effects of anomalies on modeling ,[object Object],[object Object],[object Object]

Gene Identification in Alzheimer Disease ,[object Object],[object Object],[object Object],[object Object],[object Object],BioMiner 19.2K arrays from healthy & AD patients Identified 67 genes in 3 categories

[object Object],[object Object],[object Object],[object Object],Gene Identification in HCV (CHEO) BioMiner from normal & infected mice Identified 7 genes most informative 15.6K arrays

Case study – multiple experiments ,[object Object],[object Object],Experiments: Myriam 12693281, Nan 12693388 and China were rejected Data:

Data Analysis process CM SAM RP G1 G2 G3 Final Results Biological problem - Microarray Experiments Methods Results Biological/Literature Validation CM - Cluster mapping; SAM - Significant Analysis of Microarrays RP - Rank products

Methods: SAM, RP and CM ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],En E1 E2

Results: Significant genes discovered by different methods 1. Genes are common to Nan and Myriam 2. Genes are common to Nan, Myriam and LPS 3. Genes are common to Nan and Myriam, but not LPS CM&SAM&RP (coverage rate) 18/46 known genes= 39% 22/48 known genes = 45.8% 2/9 known genes = 22% SAM&RP (No CM) (coverage rate) 4/14 known genes = 28.6% 12/58 known genes = 20.1% ?/4 known genes =? SAM&RP (total coverage rate) 22/60 known genes= 36.6% 34/106 known genes = 32% ? Group1: Group2: Group3 :

Some lessons learned ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Short Summary and the evolution ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Short Summary (Cont’d) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

A simple comparison . . . ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Knowledge Management ,[object Object],[object Object],[object Object]

What is Knowledge Management? ,[object Object],[object Object],[object Object]

Why we need Knowledge Management? ,[object Object],[object Object],[object Object],[object Object],[object Object]

How can we manage it? ,[object Object],[object Object],[object Object],[object Object],[object Object]

Current Directions – Evolution of Knowledge Discovery (specific examples) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Resources ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Evolution of Knowledge Discovery and Management

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Evolution of Knowledge Discovery and Management