Package de.julielab.genemapper.hpo

Class GenesetsOptimizationRoute

java.lang.Object

de.julielab.geneexpbase.hpo.HpoRoute

de.julielab.genemapper.hpo.GenesetsOptimizationRoute

All Implemented Interfaces:

Serializable, spark.Route

public class GenesetsOptimizationRoute
extends de.julielab.geneexpbase.hpo.HpoRoute

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class de.julielab.geneexpbase.hpo.HpoRoute

de.julielab.geneexpbase.hpo.HpoRoute.Metric

Field Summary

Fields

Modifier and Type	Field	Description
static String	GET_GENESET_SCORE

Fields inherited from class de.julielab.geneexpbase.hpo.HpoRoute

configuration, injector, KNOWN_ML_ALGORITHMS, loadedCorpora, runCounter

Constructor Summary

Constructors

Constructor	Description
GenesetsOptimizationRoute(Configuration configuration)

Method Summary

Modifier and Type	Method	Description
protected String	calculateScore(de.julielab.geneexpbase.hpo.HpoInstance si, de.julielab.geneexpbase.configuration.Parameters parameterMap, int seed, int cutoffTime, int resourceBudget, int maxResourceBudget, de.julielab.geneexpbase.hpo.HpoRoute.Metric returnMetric, int runId)
protected com.google.inject.Injector	createGuiceInjector(de.julielab.geneexpbase.configuration.Configuration configuration)
protected List<de.julielab.geneexpbase.hpo.HpoInstance>	getActiveCorpora()
protected de.julielab.geneexpbase.hpo.HpoRoute.Metric	getDefaultMetric()
int	getDevSamplingFrequency()
int	getNumSplits()
String	getRouteEndpoint()
protected String	getTaskName()
static void	main(String[] args)
protected void	printInspectionFile(String idType, double fileMetricValue, Map<String,Double> documentScores, de.julielab.geneexpbase.hpo.HpoInstance hpoInstance, List<de.julielab.geneexpbase.genemodel.GeneDocument> documents)

Methods inherited from class de.julielab.geneexpbase.hpo.HpoRoute

getAllCorporaTrainingDocuments4Instance, getCorpusPartition, getCorpusSplitByType, getDocuments4Budget, getDocuments4Budget4Instance, getDocuments4Instance, getDocuments4Instance, getMachineLearningPrefixes, getResultScalingFactors, getSplitMappingFile, getTrainDevSplit, getTrainingData, getTrainingData4Budget4Instance, handle, loadData, loadDataSplits, parseInstanceName, parseParameters, saveDataSplit, train

Methods inherited from class java.lang.Object

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

Field Detail

GET_GENESET_SCORE

public static final String GET_GENESET_SCORE

See Also:

Constant Field Values

Constructor Detail

GenesetsOptimizationRoute

public GenesetsOptimizationRoute(Configuration configuration)

Method Detail

main

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

Throws:

IOException

GeneMapperInitializationException

createGuiceInjector

protected com.google.inject.Injector createGuiceInjector(de.julielab.geneexpbase.configuration.Configuration configuration)

Specified by:

createGuiceInjector in class de.julielab.geneexpbase.hpo.HpoRoute

getRouteEndpoint

public String getRouteEndpoint()

Specified by:

getRouteEndpoint in class de.julielab.geneexpbase.hpo.HpoRoute

getNumSplits

public int getNumSplits()

Specified by:

getNumSplits in class de.julielab.geneexpbase.hpo.HpoRoute

getDevSamplingFrequency

public int getDevSamplingFrequency()

Specified by:

getDevSamplingFrequency in class de.julielab.geneexpbase.hpo.HpoRoute

getActiveCorpora

protected List<de.julielab.geneexpbase.hpo.HpoInstance> getActiveCorpora()

Specified by:

getActiveCorpora in class de.julielab.geneexpbase.hpo.HpoRoute

getTaskName

protected String getTaskName()

Specified by:

getTaskName in class de.julielab.geneexpbase.hpo.HpoRoute

getDefaultMetric

protected de.julielab.geneexpbase.hpo.HpoRoute.Metric getDefaultMetric()

Specified by:

getDefaultMetric in class de.julielab.geneexpbase.hpo.HpoRoute

calculateScore

protected String calculateScore(de.julielab.geneexpbase.hpo.HpoInstance si,
                                de.julielab.geneexpbase.configuration.Parameters parameterMap,
                                int seed,
                                int cutoffTime,
                                int resourceBudget,
                                int maxResourceBudget,
                                de.julielab.geneexpbase.hpo.HpoRoute.Metric returnMetric,
                                int runId)

Specified by:

calculateScore in class de.julielab.geneexpbase.hpo.HpoRoute

printInspectionFile

protected void printInspectionFile(String idType,
                                   double fileMetricValue,
                                   Map<String,Double> documentScores,
                                   de.julielab.geneexpbase.hpo.HpoInstance hpoInstance,
                                   List<de.julielab.geneexpbase.genemodel.GeneDocument> documents)