Datamining:
Download
1 / 17

Limsoon Wong KRDL - PowerPoint PPT Presentation


  • 135 Views
  • Uploaded on

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?.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Limsoon Wong KRDL' - evan


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Datamining:

Turning Biological Data

into Gold

Limsoon Wong

KRDL


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



Epitope prediction
Epitope Prediction

TRAP-559AA

MNHLGNVKYLVIVFLIFFDLFLVNGRDVQNNIVDEIKYSE

EVCNDQVDLYLLMDCSGSIRRHNWVNHAVPLAMKLIQQLN

LNDNAIHLYVNVFSNNAKEIIRLHSDASKNKEKALIIIRS

LLSTNLPYGRTNLTDALLQVRKHLNDRINRENANQLVVIL

TDGIPDSIQDSLKESRKLSDRGVKIAVFGIGQGINVAFNR

FLVGCHPSDGKCNLYADSAWENVKNVIGPFMKAVCVEVEK

TASCGVWDEWSPCSVTCGKGTRSRKREILHEGCTSEIQEQ

CEEERCPPKWEPLDVPDEPEDDQPRPRGDNSSVQKPEENI

IDNNPQEPSPNPEEGKDENPNGFDLDENPENPPNPDIPEQ

KPNIPEDSEKEVPSDVPKNPEDDREENFDIPKKPENKHDN

QNNLPNDKSDRNIPYSPLPPKVLDNERKQSDPQSQDNNGN

RHVPNSEDRETRPHGRNNENRSYNRKYNDTPKHPEREEHE

KPDNNKKKGESDNKYKIAGGIAGGLALLACAGLAYKFVVP

GAATPYAGEPAPFDETLGEEDKDLDEPEQFRLPEENEWN


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

WEB

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

Jak1




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


ad