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![Workflow
ENTITY
EXTRACTION
PRE
PROCESSING
RELATION
EXTRACTION
MACHINE
LEARNING
SUPPORT
VECTOR
MACHINE
(SVM)
JSRE
Expression of the sigma(K) dependent cwlH gene depended on gerR.
BETWEEN AFTERFORE [1] [2]
GLOBAL](https://image.slidesharecdn.com/groupmeeting2012121-141009084418-conversion-gate02/75/Relation-Extraction-52-2048.jpg)
![Workflow
ENTITY
EXTRACTION
PRE
PROCESSING
RELATION
EXTRACTION
MACHINE
LEARNING
SUPPORT
VECTOR
MACHINE
(SVM)
JSRE
Expression of the sigma(K) dependent cwlH gene depended on gerR.
BETWEEN AFTERFORE [1] [2]
GLOBAL](https://image.slidesharecdn.com/groupmeeting2012121-141009084418-conversion-gate02/75/Relation-Extraction-53-2048.jpg)
![Workflow
ENTITY
EXTRACTION
PRE
PROCESSING
RELATION
EXTRACTION
MACHINE
LEARNING
SUPPORT
VECTOR
MACHINE
(SVM)
JSRE
Expression of the sigma(K) dependent cwlH gene depended on gerR.
BETWEEN AFTERFORE [1] [2]
GLOBAL](https://image.slidesharecdn.com/groupmeeting2012121-141009084418-conversion-gate02/75/Relation-Extraction-54-2048.jpg)
![Workflow
ENTITY
EXTRACTION
PRE
PROCESSING
RELATION
EXTRACTION
MACHINE
LEARNING
SUPPORT
VECTOR
MACHINE
(SVM)
JSRE
Expression of the sigma(K) dependent cwlH gene depended on gerR.
BETWEEN AFTERFORE [1] [2]
GLOBAL](https://image.slidesharecdn.com/groupmeeting2012121-141009084418-conversion-gate02/75/Relation-Extraction-55-2048.jpg)
![Workflow
ENTITY
EXTRACTION
PRE
PROCESSING
RELATION
EXTRACTION
MACHINE
LEARNING
SUPPORT
VECTOR
MACHINE
(SVM)
JSRE
Expression of the sigma(K) dependent cwlH gene depended on gerR.
GLOBAL
BETWEEN AFTERFORE [1] [2]
FEATURES 3-GRAM
Expression_of_the
of_the_sigma(k)
the_sigma(k)_dependent
sigma(k)_dependent_cwlH dependent_cwlH_gene
cwlJ_gene_depended
gene_depended_on
depended_on_gerB
FORE-BETWEEN BETWEEN BETWEEN-AFTER](https://image.slidesharecdn.com/groupmeeting2012121-141009084418-conversion-gate02/75/Relation-Extraction-56-2048.jpg)
Uploaded byÀlex Bravo Serrano
Relation Extraction
The document describes a workflow for extracting biomedical entities and relations from text using machine learning techniques. The workflow involves preprocessing text, extracting entities, extracting relations between entities, and using support vector machines and kernel methods to classify relations with a global and local feature space. Key aspects include named entity recognition to identify genes and diseases, and using the JSRE tool to extract relations between extracted entities.
Relation Extraction
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- 2. Given a drugunder development, what are other drugs or biomedical compounds that it might interact with? Which are the proteins targeted by celecoxib? Which are the genes that cause lung cancer?
- 3. TEXT MINING Which are thegenes that cause lung cancer? Given a drug under development, what are other drugs or biomedical compounds that it might interact with? Which are the proteins targeted by celecoxib?
- 4. TEXT MINING Which are thegenes that cause lung cancer? Given a drug under development, what are other drugs or biomedical compounds that it might interact with? Which are the proteins targeted by celecoxib?
- 5. TEXT MINING Which are thegenes that cause lung cancer? Given a drug under development, what are other drugs or biomedical compounds that it might interact with? Which are the proteins targeted by celecoxib? INFORMATION EXTRACTION
- 6. TEXT MINING Which are thegenes that cause lung cancer? Given a drug under development, what are other drugs or biomedical compounds that it might interact with? Which are the proteins targeted by celecoxib? RESULTS
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- 20. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING Supervised classification algorthm TrainingBinary SUPPORT VECTOR MACHINE (SVM) SCORE
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- 38. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) TEXT MINING???KERNEL N-dimensional featurevector len position POS… len position POS… len position POS… SCORE
- 39. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) TEXT MINING???KERNEL N-dimensional featurevector len position POS… len position POS… len position POS… Trained Model SVM SYSTEM SCORE
- 40. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) TEXT MINING???KERNEL N-dimensional featurevector len position POS… len position POS… len position POS… Trained Model Or ? SVM SYSTEMlen position POS… SCORE
- 41. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) TEXT MINING???KERNEL N-dimensional featurevector len position POS… len position POS… len position POS… Trained Model Or ? Prediction SVM SYSTEMlen position POS… SCORE
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- 46. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) Feature vector Annotated Corpus InputSpace Feature Space Lib SVM JSRE Java tool for Relation Extraction. When (deep) linguistic processing is not available. Combination of kernel functions to integrate two different information sources: Global and Local. KERNEL
- 47. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) Feature vector Annotated Corpus InputSpace Feature Space Lib SVM JSRE K1 K2 K KERNEL U =
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- 49. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR.
- 50. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR. Expression of the sigma(K) dependent cwlH gene depended on gerR.
- 51. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR.
- 52. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. BETWEEN AFTERFORE [1] [2] GLOBAL
- 53. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. BETWEEN AFTERFORE [1] [2] GLOBAL
- 54. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. BETWEEN AFTERFORE [1] [2] GLOBAL
- 55. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. BETWEEN AFTERFORE [1] [2] GLOBAL
- 56. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. GLOBAL BETWEEN AFTERFORE [1] [2] FEATURES 3-GRAM Expression_of_the of_the_sigma(k) the_sigma(k)_dependent sigma(k)_dependent_cwlH dependent_cwlH_gene cwlJ_gene_depended gene_depended_on depended_on_gerB FORE-BETWEEN BETWEEN BETWEEN-AFTER
- 57. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. GLOBAL BASIC FEATURESLOCAL Token Stem POS Orthographic
- 58. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. GLOBAL LOCAL KERNEL
- 59. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. GLOBAL LOCAL KERNEL DEP
- 60. Workflow ENTITY EXTRACTION PRE PROCESSING RELATION EXTRACTION MACHINE LEARNING SUPPORT VECTOR MACHINE (SVM) JSRE Expression of thesigma(K) dependent cwlH gene depended on gerR. GLOBAL LOCAL KERNEL DEP ?
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- 63. Workflow: Gene-Disease PRE PROCESSING RELATION EXTRACTION The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION
- 64. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION The low frequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. The low frequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese.
- 65. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION The low frequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. The low frequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese.
- 66. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION GLOBAL LOCAL
- 67. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION Biolemmatizer Stanford Parser GLOBAL LOCAL DEP
- 68. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION Biolemmatizer Stanford Parser GLOBAL LOCAL DEP
- 69. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION Tokens + POS STANFORD PARSER
- 70. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION Tokens + POS STANFORD PARSER The low frequencies the risk alleles rs1048661 rs2165241 may be one the factors led the low prevalence exfoliation_syndrome the general populations the Chinese at
- 71. Workflow: Gene-Disease PRE PROCESSING The lowfrequencies of the at-risk alleles at rs1048661 and rs2165241 may be one of the factors that led to the low prevalence of exfoliation syndrome in the general populations of the Chinese. ENTITY EXTRACTION RELATION EXTRACTION Tokens + POS STANFORD PARSER DEP The low frequencies the risk alleles rs1048661 rs2165241 may be one the factors led the low prevalence exfoliation_syndrome the general populations the Chinese at
- 72. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP The low frequencies the risk alleles rs1048661 rs2165241 maybe one the factors led the low prevalence exfoliation_syndrome the general populations the Chinese at
- 73. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP The low frequencies the risk alleles rs1048661 rs2165241 maybe one the factors led the low prevalence exfoliation_syndrome the general populations the Chinese at Least Common Subsumer
- 74. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP The low frequencies the risk alleles rs1048661 rs2165241 maybe one the factors led the low prevalence exfoliation_syndrome the general populations the Chinese at Least Common Subsumer
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- 76. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer
- 77. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj
- 78. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj V-WalkE-Walk
- 79. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj V-WalkE-Walk
- 80. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj V-WalkE-Walk
- 81. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj V-WalkE-Walk POSi_dep_POSi+1 Lemmai_dep_Lemmai+1 Stemi_dep_Stemi+1 Rolei_dep_Rolei+1 Tokeni_dep_Tokeni+1 dep_POSi_dep dep_Lemmai_dep dep_Stemi_dep dep_Rolei_dep dep_Tokeni_dep
- 82. Workflow: Gene-Disease PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP frequenciesallelesrs1048661rs2165241 onefactors led prevalence exfoliation_syndromeat Least Common Subsumer We know: • Token • Stem • Lemma • Role NEW!!! • Dependency Type • Dependency Node frequencies oneat prep_of nsubj V-WalkE-Walk POSi_dep_POSi+1 Lemmai_dep_Lemmai+1 Stemi_dep_Stemi+1 Rolei_dep_Rolei+1 Tokeni_dep_Tokeni+1 dep_POSi_dep dep_Lemmai_dep dep_Stemi_dep dep_Rolei_dep dep_Tokeni_dep
- 83. Workflow PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP Annotated Corpus Drug-DiseaseDrug-Gene Gene-Disease •Positive Association • Negative Association • Speculative Association Global + Local Global + Local + Dependencies
- 84. Workflow PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP Annotated Corpus Drug-DiseaseDrug-Gene Gene-Disease •Positive Association • Negative Association • Speculative Association Global + Local Global + Local + Dependencies
- 85. Corpus Kernel V-walkE-walk Precision Recall F1 Drug-Gene GL + LC - - 0.68 0.72 0.69 GL + LC + DEP Token - 0.70 0.73 (0.81) 0.70 (0.72) Drug-Disease GL + LC - - 0.83 0.76 0.79 GL + LC + DEP Token - 0.81 (0.83) 0.83 (0.85) 0.82 (0.72) Target-Disease GL + LC - - 0.73 0.69 0.70 GL + LC + DEP Token - 0.73 (0.76) 0.77 (0.78) 0.74 (0.75) AIMed GL + LC - - 0.53 0.66 0.58 GL + LC + DEP - Token 0.57 (0.57) 0.62 (0.69) 0.59 (0.60) Workflow PRE PROCESSING ENTITY EXTRACTION RELATION EXTRACTION DEP 10-fold Cross Validation
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