weso satbi 2011

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