def createLeaveOneOutJobs(
srcRoot,
jobDir,
jobNameFmt,
finalJobName,
outputDir,
numObservations,
dataLoader,
lambdas,
shouldRegBias,
matlabDeclarations,
):
jobNamePart = jobNameFmt.format("NA", "NA")
foldIndices = range(1, numObservations + 1)
if matlabDeclarations is None:
matlabDeclarations = list()
logRegRoot = os.path.join(srcRoot, "shared", "logisticRegression")
addpathFmt = "addpath(genpath('{0}'));"
matlabDeclarations.append(addpathFmt.format(logRegRoot))
if shouldRegBias:
shouldRegBiasStr = "true"
else:
shouldRegBiasStr = "false"
cvFuncFmt = "LogRegSingleLambdaSingleFoldCVFromLoader({0}, {1}, {2}, {3}, {4})".format(
dataLoader, "{0}", numObservations, "{1}", shouldRegBiasStr
)
looJobDictionary = QSubHelpers.createGridJobs(
jobDir, outputDir, jobNameFmt, cvFuncFmt, matlabDeclarations, [lambdas, foldIndices], 50
)
mergeJobDictionary = QSubHelpers.createMergeAllJobOutputsJob(
jobDir, outputDir, outputDir, jobNameFmt, "loo_mrg_" + jobNamePart, [lambdas, foldIndices]
)
finalizeFunc = "LogRegChooseLambdaAndTrainAll({0}, {1}, '{2}')".format(
dataLoader, shouldRegBiasStr, os.path.join(outputDir, "output_loo_mrg_" + jobNamePart + ".mat")
)
finalizeJobDictionary = QSubHelpers.createGridJobs(
jobDir, outputDir, finalJobName, finalizeFunc, matlabDeclarations, ()
)
finalJobManifestName = "looLogRegFinalJobManifest_" + jobNamePart + ".txt"
return [looJobDictionary, mergeJobDictionary, finalizeJobDictionary]
def createLeaveOneOutJobsForEachParameterCombination(
srcRoot, jobDir, outputDir, jobNameFmt, dataLoaderFmt, parameters, lambdas, shouldRegBias, matlabDeclarations
):
combinedJobDictionaries = list()
formatArgsForFinalJob = list()
for (indexParameterList, parameterList) in enumerate(parameters):
formatArgsForFinalJob.append("{" + "{0}".format(indexParameterList) + "}")
formatArgsForFinalJob.append("NA")
formatArgsForFinalJob.append("NA")
jobNameSuffixFmt = jobNameFmt.format(*tuple(formatArgsForFinalJob))
finalJobNameFormat = "fnl_loo_" + jobNameSuffixFmt
dataSizeOutputFmt = writeDataSizes(
srcRoot, jobDir, outputDir, jobNameSuffixFmt, dataLoaderFmt, matlabDeclarations, parameters
)
combinedDictionaries = None
for parameterCombination in QSubHelpers.parameterCombinationIterator(parameters):
dataLoader = dataLoaderFmt.format(*parameterCombination)
parameterCombinationWithPlaceholders = list()
for parameter in parameterCombination:
parameterCombinationWithPlaceholders.append(parameter)
parameterCombinationWithPlaceholders.append("{0}")
parameterCombinationWithPlaceholders.append("{1}")
jobNameFmtPartial = jobNameFmt.format(*tuple(parameterCombinationWithPlaceholders))
print("Creating jobs for parameter combination: " + str(parameterCombination))
dataSize = readDataSize(dataSizeOutputFmt.format(*parameterCombination))
numObservations = dataSize[0]
print("num observations: {0}".format(numObservations))
jobDictionaries = createLeaveOneOutJobs(
srcRoot,
jobDir,
jobNameFmtPartial,
finalJobNameFormat.format(*parameterCombination),
outputDir,
numObservations,
dataLoader,
lambdas,
shouldRegBias,
matlabDeclarations,
)
if not combinedDictionaries:
combinedDictionaries = jobDictionaries
else:
for (indexDictionary, jobDictionary) in enumerate(jobDictionaries):
for (jobName, outputs) in jobDictionary.items():
combinedDictionaries[indexDictionary][jobName] = outputs
return (combinedDictionaries, finalJobNameFormat)
def writeDataSizes(srcRoot, jobDir, outputDir, jobNameSuffixFmt, dataLoaderFmt, matlabDeclarations, parameters):
if matlabDeclarations is None:
matlabDeclarations = list()
logRegRoot = os.path.join(srcRoot, "shared", "logisticRegression")
addpathFmt = "addpath(genpath('{0}'));"
matlabDeclarations.append(addpathFmt.format(logRegRoot))
jobNameFmt = "plllogreg_getsz_" + jobNameSuffixFmt
writeSizeFuncFmt = "WriteSize( {0}, '{1}' );".format(
dataLoaderFmt, os.path.join(outputDir, "output_" + jobNameFmt + ".txt")
)
writeDataSizeJobDict = QSubHelpers.createGridJobs(
jobDir, outputDir, jobNameFmt, writeSizeFuncFmt, matlabDeclarations, parameters
)
QSubHelpers.runScripts(jobDir, outputDir, writeDataSizeJobDict, 100, None, None)
return os.path.join(outputDir, "output_" + jobNameFmt + ".txt")
def runLeaveOneOutJobs(jobDir, outputDir, jobDictionaries, maxSimulataneousJobs, resourceStr, pool):
for jobDictionary in jobDictionaries:
QSubHelpers.runScripts(jobDir, outputDir, jobDictionary, maxSimulataneousJobs, resourceStr, pool)
