Download - WESO SATBI 2011
![Page 1: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/1.jpg)
Application of the Spreading Activation Technique for Recommending
Concepts of well-known Ontologies inMedical Systems
José María Álvarez Rodríguez
WESO-Universidad de Oviedohttp://purl.org/weso/
First International Workshop on Semantic Applied Technologies on Biomedical Informatics (SATBI 2011)
In conjunction with ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB)
Chicago, IL, U.S.A. August 1-3, 2011
![Page 2: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/2.jpg)
Introduction
Psycho linguistics and
Semantic priming
![Page 3: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/3.jpg)
Retrieve data as brain can do
...a connectionist method
![Page 4: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/4.jpg)
New information realm...
Semantic TechnologiesLinked Data...
Different scopes...
E-Health, E -procurement, etc.
![Page 5: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/5.jpg)
E-Health SectorNeed to automate
processes combine and synthesize complex
related pieces of information
facilitate access to clinical information
identify patterns within the patient data
…
![Page 6: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/6.jpg)
How to select related concepts
(symptoms & diseases)?
![Page 7: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/7.jpg)
Tagging of EHR
CDSS
![Page 8: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/8.jpg)
Graph ExplorationDocument Retrieval
Information Retrieval
Semantic Search Engines
Recommending engines
Annotation & Tagging
![Page 9: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/9.jpg)
Open GALEN
“Ontologies” are considered categories: 23,141 concepts
950 relations…
to facilitate clinical apps & statistics
![Page 10: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/10.jpg)
SNOMED CT765,000 active English -language
descriptions830,000 logically -defining
relationships…
Data retrieve & analysis, tagging…
![Page 11: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/11.jpg)
Summary...ConceptsRelations
Apps to retrieve, analyze, annotate
…a huge amount of medical data
![Page 12: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/12.jpg)
GRAPH EXPLORATION?
![Page 13: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/13.jpg)
Spreading Activation (SA)
3 StagesActivation function
Calculation of activation valueConstrained SAStop condition
![Page 14: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/14.jpg)
3 Stages
PreadjustmentInitial nodes, weights of relations, set
functions…
ExecutionSpread the activation value, graph
exploration…
PostadjustmentRank nodes…
![Page 15: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/15.jpg)
Variables & ConstantsID Description
Number of total inputs of node
Number of connections between
Weight of relation between
1 if the node has been activated 0 otherwise
Activation threshold
![Page 16: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/16.jpg)
Activation function
Calculation of activation value
![Page 17: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/17.jpg)
Graphically Activation function
![Page 18: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/18.jpg)
Constrained SA
DistanceNodes far from an activate node should be penalized
PathPath of activation built by the algorithm
Fan outNodes highly connected should not be representative
Activation -thresholdSpread nodes have an activation value >= threshold
![Page 19: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/19.jpg)
Stop Condition
There is no node to spread with an activation value
>Min Activation Value
Threshold
![Page 20: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/20.jpg)
ONTOSPREADhttp://code.google.com/p/ontospread/
API Java Extensible (intensive use of design patterns)
Add new constraints to SAContext, time, output degradation …
3 Toolslibrary, test module & graphical
debugger
![Page 21: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/21.jpg)
New constraints1) Context of activation2) Min activation value*3) Max & Min spread
concepts4) Time of execution5) Degradation Functions
![Page 22: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/22.jpg)
Degradation Functions1) Generic
2) Distance -Based
3) Beats -based (k number of iterations)
![Page 23: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/23.jpg)
Converging Paths Reward
![Page 24: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/24.jpg)
Implementation1) Set of activated nodes
2) Set of spread nodes
3) Activation value
![Page 25: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/25.jpg)
![Page 26: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/26.jpg)
ONTOSPREAD in Action
![Page 27: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/27.jpg)
Search and Recommend
«best nodes»
according to the initial set
![Page 28: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/28.jpg)
Methodology1. Select well-known ontologies2. Define a set of initial concepts3. Specify the weight of relations4. Combine restrictions5. Select degradation function6. Add reward function7. Test & repeat!
![Page 29: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/29.jpg)
Open GALEN1. Ontology2. #Advanced-BreastCancer &
NAMEDSymptom3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
![Page 30: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/30.jpg)
![Page 31: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/31.jpg)
SNOMED-CT1. Ontology2. #Articular cartilage of lunate &
#Articular tissue sample3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
![Page 32: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/32.jpg)
![Page 33: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/33.jpg)
Use Cases
BOPA Project (semantic searh engine of legal documents)http://www.w3.org/2001/sw/sweo/public/UseCases/CTIC/
10ders Project(recommendation of public procurement notices)
http://purl.org/weso/moldeas/
![Page 34: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/34.jpg)
Evaluation1. Close to the human brain
behaviour2. Configurable & extensible
framework3. Flexibility & scalability
..but...
A domain-expert is still needed
![Page 35: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/35.jpg)
Further Steps
1. Automatic configuration of the algorithm
2. Development of Map -Reduce version of SA (to be published)
![Page 36: WESO SATBI 2011](https://reader033.vdocuments.mx/reader033/viewer/2022051816/546db7a2af79597b298b54b2/html5/thumbnails/36.jpg)
Application of the Spreading Activation Technique for Recommending
Concepts of well-known Ontologies inMedical Systems
José María Álvarez Rodríguez
WESO-Universidad de Oviedohttp://purl.org/weso/
First International Workshop on Semantic Applied Technologies on Biomedical Informatics (SATBI 2011)
In conjunction with ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB)
Chicago, IL, U.S.A. August 1-3, 2011