Package de.julielab.genemapper.mappingcores

Class DypsisCandidateRanker

java.lang.Object

de.julielab.genemapper.mappingcores.DypsisCandidateRanker

public class DypsisCandidateRanker
extends Object

Uses machine learning methods to create features for the mapping candidates of a gene mention.

Only prediction is handled directly in this class. Training is done by HpoRoute.train(InstanceList, Parameters, String, int).

This class requires the tax2originalCandidates map and populates the tax2lexicallyRerankedCandidates field of a gene's MentionMappingResult.

Field Summary

Fields

Modifier and Type	Field	Description
static double	avgDiffCorrect
static double	avgDiffWrong
static double	avgRatioCorrect
static double	avgRatioWrong
static int	correct
static double	wrong

Constructor Summary

Constructors

Constructor	Description
DypsisCandidateRanker(de.julielab.geneexpbase.configuration.Configuration configuration, CandidateRetrieval candidateRetrieval, de.julielab.geneexpbase.services.CacheService cacheService)

Method Summary

Modifier and Type	Method	Description
void	clear()	Sets the internal state to null.
de.julielab.geneexpbase.configuration.Parameters	getModelParameters()
List<de.julielab.geneexpbase.candidateretrieval.SynHit>	getOriginalExactMatches(de.julielab.geneexpbase.genemodel.GeneMention gm, de.julielab.geneexpbase.configuration.Parameters parameters, List<de.julielab.geneexpbase.candidateretrieval.SynHit> candidates4tax)
void	loadModel(File modelSource)
void	loadModel(InputStream modelIs)
@NotNull de.julielab.geneexpbase.configuration.Parameters	mergeParameters(de.julielab.geneexpbase.configuration.Parameters parameterMap)	Merges the stored model parameters with the externally passed parameters.
void	rankCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm, AtomicInteger gmidCounter, de.julielab.geneexpbase.configuration.Parameters parameterMap)
void	saveModel(File modelDestination, de.julielab.geneexpbase.configuration.Parameters parameters)
static void	setGoldRelevanceScores(de.julielab.geneexpbase.genemodel.GeneMention gm, de.julielab.geneexpbase.genemodel.MentionMappingResult mmr)

Methods inherited from class java.lang.Object

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

Field Detail

avgDiffCorrect

public static double avgDiffCorrect

avgRatioCorrect

public static double avgRatioCorrect

correct

public static int correct

avgDiffWrong

public static double avgDiffWrong

avgRatioWrong

public static double avgRatioWrong

wrong

public static double wrong

Constructor Detail

DypsisCandidateRanker

@Inject
public DypsisCandidateRanker(de.julielab.geneexpbase.configuration.Configuration configuration,
                             CandidateRetrieval candidateRetrieval,
                             de.julielab.geneexpbase.services.CacheService cacheService)

Method Detail

setGoldRelevanceScores

public static void setGoldRelevanceScores(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                          de.julielab.geneexpbase.genemodel.MentionMappingResult mmr)

saveModel

public void saveModel(File modelDestination,
                      de.julielab.geneexpbase.configuration.Parameters parameters)

loadModel

public void loadModel(File modelSource)
               throws IOException,
                      ClassNotFoundException

Throws:

IOException

ClassNotFoundException

mergeParameters

@NotNull
public @NotNull de.julielab.geneexpbase.configuration.Parameters mergeParameters(de.julielab.geneexpbase.configuration.Parameters parameterMap)

Merges the stored model parameters with the externally passed parameters. This is especially important to set settings required by the DypsisContextRanker but have been set differently in the training of this ranker because they just weren't needed.

Parameters:

parameterMap -

Returns:

rankCandidates

public void rankCandidates(de.julielab.geneexpbase.genemodel.GeneMention gm,
                           AtomicInteger gmidCounter,
                           de.julielab.geneexpbase.configuration.Parameters parameterMap)

getOriginalExactMatches

public List<de.julielab.geneexpbase.candidateretrieval.SynHit> getOriginalExactMatches(de.julielab.geneexpbase.genemodel.GeneMention gm,
                                                                                       de.julielab.geneexpbase.configuration.Parameters parameters,
                                                                                       List<de.julielab.geneexpbase.candidateretrieval.SynHit> candidates4tax)

clear

public void clear()

Sets the internal state to null. No trained classifiers or parameters will be available any more.

loadModel

public void loadModel(InputStream modelIs)
               throws IOException,
                      ClassNotFoundException

Throws:

IOException

ClassNotFoundException

getModelParameters

public de.julielab.geneexpbase.configuration.Parameters getModelParameters()