org.apache.ctakes.ytex.semil

Class SemiLEvaluationParser

java.lang.Object

org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser

org.apache.ctakes.ytex.semil.SemiLEvaluationParser

All Implemented Interfaces:

ClassifierEvaluationParser

public class SemiLEvaluationParser
extends BaseClassifierEvaluationParser

Parse semiL output, store in DB. With semiL there is no test data set - just training data & unlabelled data. Need the following files:

• *.output - semil prediction output
• options.properties - options passed to semil (semil.distance), other options (kernel.name, kernel.experiment)
• _test_data.txt - test class ids
• _train_id.txt - training label ids
• _test_id.txt - test label ids

The semil output may contain the output of multiple runs. Will create a classifier_eval record for each run. SemiL may change the label of labeled data (soft label); currently the relabled instances will not be stored.

Author:

vhacongarlav

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser

BaseClassifierEvaluationParser.InstanceClassInfo

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

ClassifierEvaluationParser.ParseOption

Field Summary

Fields

Modifier and Type	Field and Description
static org.apache.commons.logging.Log	log
static Pattern	pGamma parse options
static Pattern	pLabel
static Pattern	pLambda
static Pattern	pLaplacian
static Pattern	pMu
static Pattern	pOutput distance files of the form label1_dist_pearson_5.txt parse out the metric and degree from the file name.
static Pattern	pPercent

Fields inherited from class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser

wsDotPattern, wsPattern

Fields inherited from interface org.apache.ctakes.ytex.kernel.ClassifierEvaluationParser

NO, YES

Constructor Summary

Constructors

Constructor and Description
SemiLEvaluationParser()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] args)
void	parseDirectory(File dataDir, File outputDir)

Methods inherited from class org.apache.ctakes.ytex.kernel.BaseClassifierEvaluationParser

checkFileRead, extractFirstToken, getClassifierEvaluationDao, getFileBaseName, initClassifierEvaluation, initClassifierEvaluationFromProperties, loadClassIdMap, loadClassInfo, loadInstanceClassInfo, loadProps, parseDoubleOption, parseInstanceIds, parseIntOption, setClassifierEvaluationDao, storeSemiSupervised, updateSemiSupervisedPredictions, updateSemiSupervisedPredictions

Methods inherited from class java.lang.Object

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

Field Detail

log

public static final org.apache.commons.logging.Log log

pGamma

public static Pattern pGamma

parse options

  gamma=10.000000 mu=0.500000 lambda=0.010100 hard_label=1 Laplacian=1 percentage of labeled points =0.000000
 

pMu

public static Pattern pMu

pLambda

public static Pattern pLambda

pLabel

public static Pattern pLabel

pLaplacian

public static Pattern pLaplacian

pPercent

public static Pattern pPercent

pOutput

public static Pattern pOutput

distance files of the form label1_dist_pearson_5.txt parse out the metric and degree from the file name.

Constructor Detail

SemiLEvaluationParser

public SemiLEvaluationParser()

Method Detail

parseDirectory

public void parseDirectory(File dataDir,
                           File outputDir)
                    throws IOException

Parameters:

fileBaseName - e.g. label1_run1_fold1

dataDir - where train, test, id files are located

outputDir - where classifier output is stored

Throws:

IOException

main

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

Throws:

IOException