org.apache.ctakes.ytex.kernel.metric

Class ConceptSimilarityServiceImpl

java.lang.Object

org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl

All Implemented Interfaces:

ConceptSimilarityService

public class ConceptSimilarityServiceImpl
extends Object
implements ConceptSimilarityService

compute concept similarity

Author:

vijay

Nested Class Summary

Nested classes/interfaces inherited from interface org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityService

ConceptSimilarityService.SimilarityMetricEnum

Constructor Summary

Constructors

Constructor and Description
ConceptSimilarityServiceImpl()

Method Summary

Modifier and Type	Method and Description
Object[]	getBestLCS(Set<String> lcses, boolean intrinsicIC, Map<String,Double> conceptFilter) get the best lcs
Object[]	getBestLCS(Set<String> lcses, Map<String,Double> icMap)
net.sf.ehcache.CacheManager	getCacheManager()
ClassifierEvaluationDao	getClassifierEvaluationDao()
ConceptDao	getConceptDao()
ConceptGraph	getConceptGraph()
String	getConceptGraphName()
String	getConceptSetName()
String	getCorpusName()
Map<String,BitSet>	getCuiTuiMap() cui - tui map.
int	getDepth(String concept)
double	getIC(String concept, boolean intrinsicICMap)
int	getLCS(String concept1, String concept2, Set<String> lcses, List<LCSPath> lcsPaths) get the lcs(s) for the specified concepts
net.sf.ehcache.Cache	getLcsCache()
String	getLcsImputedType()
PageRankService	getPageRankService()
Map<ConceptSimilarityService.SimilarityMetricEnum,SimilarityMetric>	getSimilarityMetricMap()
org.springframework.transaction.PlatformTransactionManager	getTransactionManager()
List<String>	getTuiList() list of tuis that corresponds to bitset indices
void	init()
void	initCuiTuiMapFromCorpus() load cui-tui for the specified corpus from the MRSTY table
boolean	isPreload()
int	lcs(String concept1, String concept2, List<LCSPath> lcsPaths)
double	loadConceptFilter(String label, int rankCutoff, Map<String,Double> conceptFilter) For the given label and cutoff, get the corresponding concepts whose propagated ig meets the threshold.
static void	main(String[] args)
void	setCacheManager(net.sf.ehcache.CacheManager cacheManager)
void	setClassifierEvaluationDao(ClassifierEvaluationDao classifierEvaluationDao)
void	setConceptDao(ConceptDao conceptDao)
void	setConceptGraphName(String conceptGraphName)
void	setConceptSetName(String conceptSetName)
void	setCorpusName(String corpusName)
void	setLcsCache(net.sf.ehcache.Cache lcsCache)
void	setLcsImputedType(String lcsImputedType)
void	setPageRankService(PageRankService pageRankService)
void	setPreload(boolean preload)
void	setSimilarityMetricMap(Map<ConceptSimilarityService.SimilarityMetricEnum,SimilarityMetric> similarityMetricMap)
void	setTransactionManager(org.springframework.transaction.PlatformTransactionManager transactionManager)
List<ConceptPairSimilarity>	similarity(List<ConceptPair> conceptPairs, List<ConceptSimilarityService.SimilarityMetricEnum> metrics, Map<String,Double> conceptFilter, boolean lcs) compute similarity for a list of concept pairs
ConceptPairSimilarity	similarity(List<ConceptSimilarityService.SimilarityMetricEnum> metrics, String concept1, String concept2, Map<String,Double> conceptFilter, boolean lcs) compute similarity for a pair of concepts

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ConceptSimilarityServiceImpl

public ConceptSimilarityServiceImpl()

Method Detail

main

public static void main(String[] args)
                 throws IOException

Throws:

IOException

getBestLCS

public Object[] getBestLCS(Set<String> lcses,
                           boolean intrinsicIC,
                           Map<String,Double> conceptFilter)

Description copied from interface: ConceptSimilarityService

get the best lcs

Specified by:

getBestLCS in interface ConceptSimilarityService

Parameters:

lcses - set of lcses

intrinsicIC - should the intrinsic ic be used? false - use corpus-based ic. For multiple lcses not using concept filter, use the lcs with the lowest infocontent

conceptFilter - limit to lcses in the concept filter. The lcs with the highest value will be used.

Returns:

array with 2 entries. Entry 1 - lcs (String). Entry 2 - infocontent (double). Null if no lcses are in the concept filter.

getBestLCS

public Object[] getBestLCS(Set<String> lcses,
                           Map<String,Double> icMap)

getCacheManager

public net.sf.ehcache.CacheManager getCacheManager()

getClassifierEvaluationDao

public ClassifierEvaluationDao getClassifierEvaluationDao()

getConceptDao

public ConceptDao getConceptDao()

getConceptGraph

public ConceptGraph getConceptGraph()

Specified by:

getConceptGraph in interface ConceptSimilarityService

getConceptGraphName

public String getConceptGraphName()

Specified by:

getConceptGraphName in interface ConceptSimilarityService

getConceptSetName

public String getConceptSetName()

getCorpusName

public String getCorpusName()

getCuiTuiMap

public Map<String,BitSet> getCuiTuiMap()

Description copied from interface: ConceptSimilarityService

cui - tui map. tuis are bitsets, indices correspond to tuis in ConceptSimilarityService.getTuiList()

Specified by:

getCuiTuiMap in interface ConceptSimilarityService

Returns:

getDepth

public int getDepth(String concept)

Specified by:

getDepth in interface ConceptSimilarityService

getIC

public double getIC(String concept,
                    boolean intrinsicICMap)

Specified by:

getIC in interface ConceptSimilarityService

getLCS

public int getLCS(String concept1,
                  String concept2,
                  Set<String> lcses,
                  List<LCSPath> lcsPaths)

Description copied from interface: ConceptSimilarityService

get the lcs(s) for the specified concepts

Specified by:

getLCS in interface ConceptSimilarityService

Parameters:

concept1 - required

concept2 - required

lcses - required - will be filled with the lcs(s).

Returns:

distance of path through lcs

getLcsCache

public net.sf.ehcache.Cache getLcsCache()

getLcsImputedType

public String getLcsImputedType()

getPageRankService

public PageRankService getPageRankService()

getSimilarityMetricMap

public Map<ConceptSimilarityService.SimilarityMetricEnum,SimilarityMetric> getSimilarityMetricMap()

getTransactionManager

public org.springframework.transaction.PlatformTransactionManager getTransactionManager()

getTuiList

public List<String> getTuiList()

Description copied from interface: ConceptSimilarityService

list of tuis that corresponds to bitset indices

Specified by:

getTuiList in interface ConceptSimilarityService

Returns:

init

public void init()

initCuiTuiMapFromCorpus

public void initCuiTuiMapFromCorpus()

load cui-tui for the specified corpus from the MRSTY table

isPreload

public boolean isPreload()

lcs

public int lcs(String concept1,
               String concept2,
               List<LCSPath> lcsPaths)

Specified by:

lcs in interface ConceptSimilarityService

loadConceptFilter

public double loadConceptFilter(String label,
                                int rankCutoff,
                                Map<String,Double> conceptFilter)

For the given label and cutoff, get the corresponding concepts whose propagated ig meets the threshold. Used by lin kernel to find concepts that actually have a non-trivial similarity

Specified by:

loadConceptFilter in interface ConceptSimilarityService

Parameters:

label - label

rankCutoff - cutoff

conceptFilter - set to fill with concepts

Returns:

double minimum evaluation

setCacheManager

public void setCacheManager(net.sf.ehcache.CacheManager cacheManager)

setClassifierEvaluationDao

public void setClassifierEvaluationDao(ClassifierEvaluationDao classifierEvaluationDao)

setConceptDao

public void setConceptDao(ConceptDao conceptDao)

setConceptGraphName

public void setConceptGraphName(String conceptGraphName)

setConceptSetName

public void setConceptSetName(String conceptSetName)

setCorpusName

public void setCorpusName(String corpusName)

setLcsCache

public void setLcsCache(net.sf.ehcache.Cache lcsCache)

setLcsImputedType

public void setLcsImputedType(String lcsImputedType)

setPageRankService

public void setPageRankService(PageRankService pageRankService)

setPreload

public void setPreload(boolean preload)

setSimilarityMetricMap

public void setSimilarityMetricMap(Map<ConceptSimilarityService.SimilarityMetricEnum,SimilarityMetric> similarityMetricMap)

setTransactionManager

public void setTransactionManager(org.springframework.transaction.PlatformTransactionManager transactionManager)

similarity

public List<ConceptPairSimilarity> similarity(List<ConceptPair> conceptPairs,
                                              List<ConceptSimilarityService.SimilarityMetricEnum> metrics,
                                              Map<String,Double> conceptFilter,
                                              boolean lcs)

Description copied from interface: ConceptSimilarityService

compute similarity for a list of concept pairs

Specified by:

similarity in interface ConceptSimilarityService

Parameters:

conceptPairs - required, concept pairs for which similarity should be computed

metrics - required, similarity metrics to compute

conceptFilter - optional - only lcs's in this set will be used.

Returns:

similarities

similarity

public ConceptPairSimilarity similarity(List<ConceptSimilarityService.SimilarityMetricEnum> metrics,
                                        String concept1,
                                        String concept2,
                                        Map<String,Double> conceptFilter,
                                        boolean lcs)

Description copied from interface: ConceptSimilarityService

compute similarity for a pair of concepts

Specified by:

similarity in interface ConceptSimilarityService

Parameters:

metrics - required, similarity metrics to compute

concept1 - required

concept2 - required

conceptFilter - optional - only lcs's in this set will be used.

Returns:

similarities