weso satbi 2011
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TRANSCRIPT
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
Introduction
Psycho linguistics and
Semantic priming
Retrieve data as brain can do
...a connectionist method
New information realm...
Semantic TechnologiesLinked Data...
Different scopes...
E-Health, E -procurement, etc.
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
…
How to select related concepts
(symptoms & diseases)?
Tagging of EHR
CDSS
Graph ExplorationDocument Retrieval
Information Retrieval
Semantic Search Engines
Recommending engines
Annotation & Tagging
Open GALEN
“Ontologies” are considered categories: 23,141 concepts
950 relations…
to facilitate clinical apps & statistics
SNOMED CT765,000 active English -language
descriptions830,000 logically -defining
relationships…
Data retrieve & analysis, tagging…
Summary...ConceptsRelations
Apps to retrieve, analyze, annotate
…a huge amount of medical data
GRAPH EXPLORATION?
Spreading Activation (SA)
3 StagesActivation function
Calculation of activation valueConstrained SAStop condition
3 Stages
PreadjustmentInitial nodes, weights of relations, set
functions…
ExecutionSpread the activation value, graph
exploration…
PostadjustmentRank nodes…
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
Activation function
Calculation of activation value
Graphically Activation function
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
Stop Condition
There is no node to spread with an activation value
>Min Activation Value
Threshold
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
New constraints1) Context of activation2) Min activation value*3) Max & Min spread
concepts4) Time of execution5) Degradation Functions
Degradation Functions1) Generic
2) Distance -Based
3) Beats -based (k number of iterations)
Converging Paths Reward
Implementation1) Set of activated nodes
2) Set of spread nodes
3) Activation value
ONTOSPREAD in Action
Search and Recommend
«best nodes»
according to the initial set
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!
Open GALEN1. Ontology2. #Advanced-BreastCancer &
NAMEDSymptom3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
SNOMED-CT1. Ontology2. #Articular cartilage of lunate &
#Articular tissue sample3. Default value 1.04. Constrained SA + New restrictions5. H1 H26. No | Yes
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/
Evaluation1. Close to the human brain
behaviour2. Configurable & extensible
framework3. Flexibility & scalability
..but...
A domain-expert is still needed
Further Steps
1. Automatic configuration of the algorithm
2. Development of Map -Reduce version of SA (to be published)
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