Richard Tzong-Han Tsai

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HypertenGene Extracting key hypertension
genesfrom biomedical literature

• Richard Tzong-Han Tsai
• , Po-Ting Lai
• , Hong-Jie Dai
• , Chi-Hsin Huang
• ,Yue-Yang Bow
• Yen-Ching Chang
• ,Wen-Harn Pan
• , Wen-Lian Hsu

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Where are we from?
Institute of Information ScienceAcademia
SinicaTaiwan
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InCoB 2009
Institute of Information ScienceAcademia
Sinica Taiwan
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HypertenGene Extracting key hypertension
genesfrom biomedical literature with position
and automatically-generated template features

• Richard Tzong-Han Tsai
• , Po-Ting Lai
• , Hong-Jie Dai
• , Chi-Hsin Huang
• ,Yue-Yang Bow
• Yen-Ching Chang
• ,Wen-Harn Pan
• , Wen-Lian Hsu

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Outline

• Motivation
• Major tasks
• Dataset
• Evaluation
• Conclusion

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What Causes Hypertension
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GAD Database
Disease View        Search for All       Record
found  930
About 930 PubMed ID about genes associate to
hypertension recorded in GAD Database update
to 2008
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Articles about Hypertension
Over three hundred thousands abstracts about
hypertension in PubMed
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Key Hypertension Genes

• Genes which cause hypertension genetically

Example
The GNB3 may be considered a genetic marker for hypertension. PMID 14557282
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HG Pair in a Sentence
S

• The GNB3 may be considered a genetic
• marker for hypertension.

G
HG Pair
H
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Outline

• Motivation
• Major tasks
• Dataset
• Evaluation
• Conclusion

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Major Task

1. Gene named entity recognition (NER) and gene
   normalization (GN)
2. Hypertension named entity recognition
3. Gene-hypertension relation extraction

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Gene Named Entity Recognition
Example
The GNB3 may be considered a genetic marker for hypertension. PMID 14557282
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Gene Named Entity Recognition
Example
The GNB3 may be considered a genetic marker for hypertension. PMID 14557282
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Gene Normalization
Example
The GNB3 may be considered a genetic marker for hypertension. PMID 14557282
Gene ID 2784
guanine nucleotide binding protein (G protein), beta polypeptide 3 guanine nucleotide-binding protein, beta-3 subunit transducin beta chain 3 G protein, beta-3 subunit GTP-binding regulatory protein beta-3 chain GNB3
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Major Task

1. Gene named entity recognition (NER) and gene
   normalization (GN)
2. Hypertension named entity recognition
3. Gene-hypertension relation extraction

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Disease NER
Example
The GNB3 may be considered a genetic marker for hypertension. PMID 14557282
In conclusion, REN 10631A alleles are significantly associated with EHT in the Emirati population. PMID 16138564
EHT Essential HyperTension
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Disease NEs in Evident Sentences
OBJECTIVE We sought to determine whether
polymorphisms in the transforming growth factor
(TGF)-beta3 gene are associated with risk of
pregnancy-induced hypertension (PIH) in
case-control mother-baby dyads. ... CONCLUSION A
fetal TGF-beta3 polymorphism (rs11466414) is
associated with PIH in a predominantly Hispanic
population.
PMID 19628198
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List of Hypertension Acronym
Original Name Acronym
pregnancy-induced hypertension PIH
Primary pulmonary hypertension PPH
Family history of hypertension FH
Pulmonary hypertension PH
More than 30 pairs were collected by acronym
recognition component
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Major Task

1. Gene named entity recognition (NER) and gene
   normalization (GN)
2. Hypertension named entity recognition
3. Gene-hypertension relation extraction

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Formulation
Key Relation
Binary Classificationif one target HG pair has relation or not
Not a Key Relation
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Outline

• Motivation
• Major tasks
• Dataset
• Evaluation
• Conclusion

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Datasets

• Our data set consists of 939 sentences from 195
  abstracts selected from the GAD
• 1395 HG pairs can be extracted from these 939
  sentences

Positive HG pair Negative HG pair
Number of HG pairs 349 1046
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Training Testing

• Randomly selected 90 HG pairs for training
  set 10 HG pairs for test set
• Repeat 30 times
• Calculated the averages to compare their
  performance

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Outline

• Motivation
• Major tasks
• Dataset
• Evaluation
• Conclusion

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Scoring Method F-score

• The weighted harmonic mean of precision and
  recall

Key Gene Prediction
Dataset HG1HG10
HG4
HG5
HG6
HG1
HG6
HG1
HG7
HG2
HG7
precision 1/5 0.2
HG3
HG8
recall 1/3 0.33
HG4
HG9
F-score (20.20.33)/(0.20.33)0.25
HG5
HG10
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AUC of the iP/R curve
n is the total number of correct HG pairs
rj the recall at that HG pairs
pi is the highest interpolated precision for
the correct HG pairs j at rj
Interpolated precision pi is calculated for
each recall r by taking the highest precision at
r or any r gt r.
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Scoring Method AUC
Key Gene Prediction
1st
HG1
2nd
HG6
3rd
HG7
4th
HG2
5th
HG3
Dataset HG1HG10
HG1
HG6
Precision 0.6, Recall 1, F-score 0.75AUC
0.733333
HG2
HG7
HG3
HG8
Key Gene Prediction
HG4
HG9
1st
HG1
2nd
HG6
3rd
HG2
4th
HG3
5th
HG7
HG5
HG10
Precision 0.6, Recall 1, F-score 0.75 AUC
0.833333
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Select Features for Classification
Features
Binary Classification
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Select Features for Classification
The GNB3 may be considered a genetic marker for hypertension.
Key HG pair or not
Features
Binary Classification
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Features

• Basic Word Features
• Chunk Features
• Parse Tree Path Features
• Template Features
• Position Features

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Basic Word Features
The GNB3 may be considered a genetic marker for hypertension. The GNB3 may be considered a genetic marker for hypertension.
Words between may, be, considered, a, genetic, marker, of, predisposition, for
Words between (bigram) may_be, be_considered, considered_a, a_genetic,genetic_marker, marker_of, of_predisposition,predisposition_for
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Parse Tree Path Features
Parse Tree Path Features NP_S_VP_NP_PP_NP
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Chunk Features
Word The GNB3 may be considered a genetic marker for hypertension
Chunk B-NP I-NP B-VP I-VP I-VP B-NP I-NP I-NP B-PP B-NP
The GNB3 may be considered a genetic marker for hypertension. The GNB3 may be considered a genetic marker for hypertension.
Inter-HG chunk types VP_NP_PP
Inter-HG chunk head words consider_marker_hypertension
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Result of Baseline Features
 Config Precision Recall F-score AUC SAUC
Baseline 0.704 0.536 0.603 0.493 0.126
Baseline Basic word Chunk Parse Tree SAUC
Standard Variation of AUC
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Template Features
Especially, a polymorphism in SLC12A was
significantly associated with hypertension in
women even after correction by the Bonferroni
method.
The leptin gene polymorphism was associated with
hypertension independent of obesity .
On analysis of covariance , the interaction
between ND2 - 237 Leu / Met polymorphism and
habitual drinking was significantly associated
with both systolic blood pressure and diastolic
blood pressure.
gene associated with hypertension
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Result of BT Features
 Config P R F-score AUC SAUC ?AUC t AUCgtAUCB? (t gt1.67?)
Baseline 0.704 0.536 0.603 0.493 0.126 N/A N/A N/A
BT 0.733 0.540 0.615 0.513 0.105 0.011 0.65 No
B Baseline feature (words feature, chunk
feature, parse tree) T Template features t t
test
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Position Features

• Relative position features

Value 010

• Section featuresDivide an abstract into four
  sections

Objective Methods Result Conclusions
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Before Section Categorization
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After Section Categorization
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PubMed EX
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Result
 Config P R F-score AUC SAUC ?AUC t AUCgtAUCB? (t gt1.67?)
Baseline 0.704 0.536 0.603 0.493 0.126 N/A N/A N/A
BT 0.733 0.540 0.615 0.513 0.105 0.011 0.65 No
BP 0.825 0.823 0.820 0.814 0.087 0.360 11.44 Yes
BPT 0.815 0.879 0.841 0.818 0.084 0.378 11.75 Yes
 
B Baseline feature (words feature, chunk
feature, parse tree) P Position features T
Template features
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Outline

• Motivation
• Major tasks
• Dataset
• Evaluation
• Conclusion

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Conclusions-1

• The first systematic study of extracting
  hypertension-related genes.

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Conclusions-2

• The first attempt to create a hypertension-gene
  relation corpus base on the GAD database.

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Conclusions-3

• Propose a supervised learning approach for
  extracting key hypertension-related genes.

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Thanks for your attention