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Limsoon Wong KRDL PowerPoint PPT Presentation

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Datamining: Turning Biological Data into Gold. Limsoon Wong KRDL. Jonathan’s blocks. Jessica’s blocks. Whose block is this?. What is Datamining?. Jonathan’s rules: Blue or Circle Jessica’s rules: All the rest. What is Datamining?. Question: Can you explain how?.

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Limsoon Wong KRDL

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Limsoon wong krdl


Turning Biological Data

into Gold

Limsoon Wong


What is datamining

Jonathan’s blocks

Jessica’s blocks

Whose block

is this?

What is Datamining?

Jonathan’s rules: Blue or Circle

Jessica’s rules: All the rest

What is datamining1

What is Datamining?

Question: Can you explain how?

What are the benefits

What are the Benefits?

  • To the patient:

    • Better drug, better treatment

  • To the pharma:

    • Save time, save cost, make more $

  • To the scientist:

    • Better science

The datamining process

The Datamining Process

Epitope prediction

Epitope Prediction
















Epitope prediction results

1 66 100

Epitope Prediction Results

  • Prediction by our ANN model for HLA-A11

    • 29 predictions

    • 22 epitopes

    • 76% specificity

  • Prediction by BIMAS matrix for HLA-A*1101

Number of experimental binders

19 (52.8%) 5 (13.9%) 12 (33.3%)

Rank by BIMAS

Gene expression analysis

Gene Expression Analysis

  • Clustering gene expression profiles

  • Classifying gene expression profiles

    • find stable differentially expressed genes

Gene expression analysis results

Gene Expression Analysis Results

  • The Discovery System

    • Correlation test

    • Voter selection

    • Class prediction

Protein interaction extraction


Protein Interaction Extraction

“What are the protein-protein interaction pathways

from the latest reported discoveries?”

Protein interaction extraction results

Protein Interaction Extraction Results

  • Rule-based system for processing free texts in scientific abstracts

  • Specialized in

    • extracting protein names

    • extracting protein-protein interactions


Transcription start prediction

Transcription Start Prediction

Transcription start prediction results

Transcription Start Prediction Results

Medical record analysis

Medical Record Analysis

  • Looking for patterns that are

    • valid

    • novel

    • useful

    • understandable

Medical record analysis results

Medical Record Analysis Results

  • DeEPs, a novel “emerging pattern’’ method

  • Beats C4.5, CBA, LB, NB, TAN in 21 out of 32 UCI benchmarks

  • Works for gene expressions

Under the hood

Under the Hood

  • Artificial neural network

  • Neighbourhood analysis

  • Non-linear analysis

  • Template matching

  • Emerging pattern

  • Hidden markov models

  • Bayesian inference

  • Decision tree induction

  • ...

Behind the scene

Epitope Prediction

Vladimir Brusic

Judice Koh

Seah Seng Hong

Zhang Guanglan

Yu Kun

Transcription Start Prediction

Vladimir Bajic

Seah Seng Hong

Gene Expression Analysis

Zhang Louxin

Zhang Zhuo

Zhu Song

Medical Records

Li Jinyan

Protein Interaction Extraction

Ng See Kiong

Zhang Zhuo

Behind the Scene

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