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for Bioinformatics, Part I
1Lecture at Yang Ming National University, Taipei, June 2006
Knowledge Discovery Techniques
for Bioinformatics
Limsoon Wong
Lecture at Yang Ming National University, Taipei, June 2006 Copyright 2006 ? Limsoon Wong
2
Course Plan
? Knowledge discovery
essence (1.5 hrs)
– Feature generation, feature
selection, feature integration
– Understanding accuracy
– Cross validation
? Machine learning methods
(1.5 hrs)
– Decision trees
– Ensemble classifiers
– K-NN
– Na?ve Bayes
– HMM
? Gene feature recognition
(1.5 hrs)
– Translation initiation site
– Transcription start site
? Gene expr analysis (1.5 hrs)
– Gene expr profile classification
– Gene expr profile clustering
– Extreme sample selection
? Protein subcellular
localization recognition (1.0
hrs)
– Sorting signals
– Amino acid domain
compositions
? Data Cleansing (0.5 hrs)
– Association rules mining
– Errors in databases
– Data de-duplication
? Sequence homology
interpretation (1.5 hrs)
– Guilt by various types of assoc
2Lecture at Yang Ming National University, Taipei, June 2006
For written notes on this lecture, please read chapter 3 of The Practical Bioinformatician,
Knowledge Discovery Techniques
for Bioinformatics, Part I:
Essence of Knowledge Discovery
Limsoon Wong
Lecture at Yang Ming National University, Taipei, June 2006 Copyright 2006 ? Limsoon Wong
4
Jonathan’s rules : Blue or Circle
Jessica’s rules : All the rest
What is Knowledge Discovery?
Whose block
is this?
Jonathan’s blocks
Jessica’s blocks
3Lecture at Yang Ming National University, Taipei, June 2006 Copyright 2006 ? Limsoon Wong
5
What is Knowledge Discovery?
Question: Can you explain how?
Lecture at Yang Ming National University, Taipei, June 2006 Copyright 2006 ? Limsoon Wong
6
The Steps of Knowledge Discovery
? Training data gathering
? Feature generation
– k-grams, colour, texture, domain know-how, ...
? Feature selection
– Entropy, χ2, CFS, t-test, domain know-how...
? Feature integration
– SVM, ANN, PCL, CART, C4.5, kNN, ...
Some
classi
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