def CrossValidationDriver(examples, attrs, nPossibleValues, nQuantBounds, mEstimateVal=0.0,
holdOutFrac=0.3, modelBuilder=makeNBClassificationModel, silent=0,
calcTotalError=0, **kwargs):
nTot = len(examples)
if not kwargs.get('replacementSelection', 0):
testIndices, trainIndices = SplitData.SplitIndices(nTot, holdOutFrac, silent=1, legacy=1,
replacement=0)
else:
testIndices, trainIndices = SplitData.SplitIndices(nTot, holdOutFrac, silent=1, legacy=0,
replacement=1)
trainExamples = [examples[x] for x in trainIndices]
testExamples = [examples[x] for x in testIndices]
NBmodel = modelBuilder(trainExamples, attrs, nPossibleValues, nQuantBounds, mEstimateVal,
**kwargs)
if not calcTotalError:
xValError, _ = CrossValidate(NBmodel, testExamples, appendExamples=1)
else:
xValError, _ = CrossValidate(NBmodel, examples, appendExamples=0)
if not silent:
print('Validation error was %%%4.2f' % (100 * xValError))
NBmodel._trainIndices = trainIndices
return NBmodel, xValError
def test_exceptions(self):
self.assertRaises(ValueError, SplitData.SplitIndices, 10, -0.1)
self.assertRaises(ValueError, SplitData.SplitIndices, 10, 1.1)
f = StringIO()
with redirect_stdout(f):
SplitData.SplitIndices(10, 0.5, replacement=True, silent=False)
s = f.getvalue()
self.assertIn('Training', s)
self.assertIn('hold-out', s)
def test_SplitData(self):
self.assertRaises(ValueError, SplitData.SplitDataSet, None, -1.1)
self.assertRaises(ValueError, SplitData.SplitDataSet, None, 1.1)
data = list(range(10))
DataUtils.InitRandomNumbers((23, 42))
f = StringIO()
with redirect_stdout(f):
result = SplitData.SplitDataSet(data, 0.5)
self.assertEqual(set(result[0]).intersection(result[1]), set())
self.assertEqual(len(result[0]), 5)
s = f.getvalue()
self.assertIn('Training', s)
self.assertIn('hold-out', s)
def CrossValidationDriver(examples,
attrs,
nPossibleValues,
numNeigh,
modelBuilder=makeClassificationModel,
distFunc=DistFunctions.EuclideanDist,
holdOutFrac=0.3,
silent=0,
calcTotalError=0,
**kwargs):
""" Driver function for building a KNN model of a specified type
**Arguments**
- examples: the full set of examples
- numNeigh: number of neighbors for the KNN model (basically k in k-NN)
- knnModel: the type of KNN model (a classification vs regression model)
- holdOutFrac: the fraction of the data which should be reserved for the hold-out set
(used to calculate error)
- silent: a toggle used to control how much visual noise this makes as it goes
- calcTotalError: a toggle used to indicate whether the classification error
of the tree should be calculated using the entire data set (when true) or just
the training hold out set (when false)
"""
nTot = len(examples)
if not kwargs.get('replacementSelection', 0):
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=1,
replacement=0)
else:
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=0,
replacement=1)
trainExamples = [examples[x] for x in trainIndices]
testExamples = [examples[x] for x in testIndices]
nTrain = len(trainExamples)
if not silent:
print "Training with %d examples" % (nTrain)
knnMod = modelBuilder(numNeigh, attrs, distFunc)
knnMod.SetTrainingExamples(trainExamples)
knnMod.SetTestExamples(testExamples)
if not calcTotalError:
xValError, badExamples = CrossValidate(knnMod,
testExamples,
appendExamples=1)
else:
xValError, badExamples = CrossValidate(knnMod,
examples,
appendExamples=0)
if not silent:
'Validation error was %%%4.2f' % (100 * xValError)
knnMod._trainIndices = trainIndices
return knnMod, xValError
pickVects = {}
halfwayPts = [1e8] * len(models)
for whichModel, model in enumerate(models):
tmpD = dataSet
try:
seed = model._randomSeed
except AttributeError:
pass
else:
DataUtils.InitRandomNumbers(seed)
if details.shuffleActivities:
DataUtils.RandomizeActivities(tmpD, shuffle=1)
if hasattr(model, '_splitFrac') and (details.doHoldout
or details.doTraining):
trainIdx, testIdx = SplitData.SplitIndices(tmpD.GetNPts(),
model._splitFrac,
silent=1)
if details.filterFrac != 0.0:
trainFilt, temp = DataUtils.FilterData(tmpD,
details.filterVal,
details.filterFrac,
-1,
indicesToUse=trainIdx,
indicesOnly=1)
testIdx += temp
trainIdx = trainFilt
if details.doTraining:
testIdx, trainIdx = trainIdx, testIdx
else:
testIdx = range(tmpD.GetNPts())
def RunOnData(details, data, progressCallback=None, saveIt=1, setDescNames=0):
nExamples = data.GetNPts()
if details.lockRandom:
seed = details.randomSeed
else:
import random
seed = (random.randint(0, 1e6), random.randint(0, 1e6))
DataUtils.InitRandomNumbers(seed)
testExamples = []
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data, shuffle=1, runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data, shuffle=0, runDetails=details)
namedExamples = data.GetNamedData()
if details.splitRun == 1:
trainIdx, testIdx = SplitData.SplitIndices(len(namedExamples),
details.splitFrac,
silent=not _verbose)
trainExamples = [namedExamples[x] for x in trainIdx]
testExamples = [namedExamples[x] for x in testIdx]
else:
testExamples = []
testIdx = []
trainIdx = range(len(namedExamples))
trainExamples = namedExamples
if details.filterFrac != 0.0:
# if we're doing quantization on the fly, we need to handle that here:
if hasattr(details, 'activityBounds') and details.activityBounds:
tExamples = []
bounds = details.activityBounds
for pt in trainExamples:
pt = pt[:]
act = pt[-1]
placed = 0
bound = 0
while not placed and bound < len(bounds):
if act < bounds[bound]:
pt[-1] = bound
placed = 1
else:
bound += 1
if not placed:
pt[-1] = bound
tExamples.append(pt)
else:
bounds = None
tExamples = trainExamples
trainIdx, temp = DataUtils.FilterData(tExamples,
details.filterVal,
details.filterFrac,
-1,
indicesOnly=1)
tmp = [trainExamples[x] for x in trainIdx]
testExamples += [trainExamples[x] for x in temp]
trainExamples = tmp
counts = DataUtils.CountResults(trainExamples, bounds=bounds)
ks = counts.keys()
ks.sort()
message('Result Counts in training set:')
for k in ks:
message(str((k, counts[k])))
counts = DataUtils.CountResults(testExamples, bounds=bounds)
ks = counts.keys()
ks.sort()
message('Result Counts in test set:')
for k in ks:
message(str((k, counts[k])))
nExamples = len(trainExamples)
message('Training with %d examples' % (nExamples))
nVars = data.GetNVars()
attrs = range(1, nVars + 1)
nPossibleVals = data.GetNPossibleVals()
for i in range(1, len(nPossibleVals)):
if nPossibleVals[i - 1] == -1:
attrs.remove(i)
if details.pickleDataFileName != '':
pickleDataFile = open(details.pickleDataFileName, 'wb+')
cPickle.dump(trainExamples, pickleDataFile)
cPickle.dump(testExamples, pickleDataFile)
pickleDataFile.close()
if details.bayesModel:
composite = BayesComposite.BayesComposite()
else:
composite = Composite.Composite()
composite._randomSeed = seed
composite._splitFrac = details.splitFrac
composite._shuffleActivities = details.shuffleActivities
composite._randomizeActivities = details.randomActivities
if hasattr(details, 'filterFrac'):
composite._filterFrac = details.filterFrac
if hasattr(details, 'filterVal'):
composite._filterVal = details.filterVal
composite.SetModelFilterData(details.modelFilterFrac,
details.modelFilterVal)
composite.SetActivityQuantBounds(details.activityBounds)
nPossibleVals = data.GetNPossibleVals()
if details.activityBounds:
nPossibleVals[-1] = len(details.activityBounds) + 1
if setDescNames:
composite.SetInputOrder(data.GetVarNames())
composite.SetDescriptorNames(details._descNames)
else:
composite.SetDescriptorNames(data.GetVarNames())
composite.SetActivityQuantBounds(details.activityBounds)
if details.nModels == 1:
details.internalHoldoutFrac = 0.0
if details.useTrees:
from rdkit.ML.DecTree import CrossValidate, PruneTree
if details.qBounds != []:
from rdkit.ML.DecTree import BuildQuantTree
builder = BuildQuantTree.QuantTreeBoot
else:
from rdkit.ML.DecTree import ID3
builder = ID3.ID3Boot
driver = CrossValidate.CrossValidationDriver
pruner = PruneTree.PruneTree
composite.SetQuantBounds(details.qBounds)
nPossibleVals = data.GetNPossibleVals()
if details.activityBounds:
nPossibleVals[-1] = len(details.activityBounds) + 1
composite.Grow(trainExamples,
attrs,
nPossibleVals=[0] + nPossibleVals,
buildDriver=driver,
pruner=pruner,
nTries=details.nModels,
pruneIt=details.pruneIt,
lessGreedy=details.lessGreedy,
needsQuantization=0,
treeBuilder=builder,
nQuantBounds=details.qBounds,
startAt=details.startAt,
maxDepth=details.limitDepth,
progressCallback=progressCallback,
holdOutFrac=details.internalHoldoutFrac,
replacementSelection=details.replacementSelection,
recycleVars=details.recycleVars,
randomDescriptors=details.randomDescriptors,
silent=not _verbose)
elif details.useSigTrees:
from rdkit.ML.DecTree import CrossValidate
from rdkit.ML.DecTree import BuildSigTree
builder = BuildSigTree.SigTreeBuilder
driver = CrossValidate.CrossValidationDriver
nPossibleVals = data.GetNPossibleVals()
if details.activityBounds:
nPossibleVals[-1] = len(details.activityBounds) + 1
if hasattr(details, 'sigTreeBiasList'):
biasList = details.sigTreeBiasList
else:
biasList = None
if hasattr(details, 'useCMIM'):
useCMIM = details.useCMIM
else:
useCMIM = 0
if hasattr(details, 'allowCollections'):
allowCollections = details.allowCollections
else:
allowCollections = False
composite.Grow(trainExamples,
attrs,
nPossibleVals=[0] + nPossibleVals,
buildDriver=driver,
nTries=details.nModels,
needsQuantization=0,
treeBuilder=builder,
maxDepth=details.limitDepth,
progressCallback=progressCallback,
holdOutFrac=details.internalHoldoutFrac,
replacementSelection=details.replacementSelection,
recycleVars=details.recycleVars,
randomDescriptors=details.randomDescriptors,
biasList=biasList,
useCMIM=useCMIM,
allowCollection=allowCollections,
silent=not _verbose)
elif details.useKNN:
from rdkit.ML.KNN import CrossValidate
from rdkit.ML.KNN import DistFunctions
driver = CrossValidate.CrossValidationDriver
dfunc = ''
if (details.knnDistFunc == "Euclidean"):
dfunc = DistFunctions.EuclideanDist
elif (details.knnDistFunc == "Tanimoto"):
dfunc = DistFunctions.TanimotoDist
else:
assert 0, "Bad KNN distance metric value"
composite.Grow(trainExamples,
attrs,
nPossibleVals=[0] + nPossibleVals,
buildDriver=driver,
nTries=details.nModels,
needsQuantization=0,
numNeigh=details.knnNeighs,
holdOutFrac=details.internalHoldoutFrac,
distFunc=dfunc)
elif details.useNaiveBayes or details.useSigBayes:
from rdkit.ML.NaiveBayes import CrossValidate
driver = CrossValidate.CrossValidationDriver
if not (hasattr(details, 'useSigBayes') and details.useSigBayes):
composite.Grow(trainExamples,
attrs,
nPossibleVals=[0] + nPossibleVals,
buildDriver=driver,
nTries=details.nModels,
needsQuantization=0,
nQuantBounds=details.qBounds,
holdOutFrac=details.internalHoldoutFrac,
replacementSelection=details.replacementSelection,
mEstimateVal=details.mEstimateVal,
silent=not _verbose)
else:
if hasattr(details, 'useCMIM'):
useCMIM = details.useCMIM
else:
useCMIM = 0
composite.Grow(trainExamples,
attrs,
nPossibleVals=[0] + nPossibleVals,
buildDriver=driver,
nTries=details.nModels,
needsQuantization=0,
nQuantBounds=details.qBounds,
mEstimateVal=details.mEstimateVal,
useSigs=True,
useCMIM=useCMIM,
holdOutFrac=details.internalHoldoutFrac,
replacementSelection=details.replacementSelection,
silent=not _verbose)
## elif details.useSVM:
## from rdkit.ML.SVM import CrossValidate
## driver = CrossValidate.CrossValidationDriver
## composite.Grow(trainExamples, attrs, nPossibleVals=[0]+nPossibleVals,
## buildDriver=driver, nTries=details.nModels,
## needsQuantization=0,
## cost=details.svmCost,gamma=details.svmGamma,
## weights=details.svmWeights,degree=details.svmDegree,
## type=details.svmType,kernelType=details.svmKernel,
## coef0=details.svmCoeff,eps=details.svmEps,nu=details.svmNu,
## cache_size=details.svmCache,shrinking=details.svmShrink,
## dataType=details.svmDataType,
## holdOutFrac=details.internalHoldoutFrac,
## replacementSelection=details.replacementSelection,
## silent=not _verbose)
else:
from rdkit.ML.Neural import CrossValidate
driver = CrossValidate.CrossValidationDriver
composite.Grow(trainExamples,
attrs, [0] + nPossibleVals,
nTries=details.nModels,
buildDriver=driver,
needsQuantization=0)
composite.AverageErrors()
composite.SortModels()
modelList, counts, avgErrs = composite.GetAllData()
counts = numpy.array(counts)
avgErrs = numpy.array(avgErrs)
composite._varNames = data.GetVarNames()
for i in range(len(modelList)):
modelList[i].NameModel(composite._varNames)
# do final statistics
weightedErrs = counts * avgErrs
averageErr = sum(weightedErrs) / sum(counts)
devs = (avgErrs - averageErr)
devs = devs * counts
devs = numpy.sqrt(devs * devs)
avgDev = sum(devs) / sum(counts)
message('# Overall Average Error: %%% 5.2f, Average Deviation: %%% 6.2f' %
(100. * averageErr, 100. * avgDev))
if details.bayesModel:
composite.Train(trainExamples, verbose=0)
# blow out the saved examples and then save the composite:
composite.ClearModelExamples()
if saveIt:
composite.Pickle(details.outName)
details.model = DbModule.binaryHolder(cPickle.dumps(composite))
badExamples = []
if not details.detailedRes and (not hasattr(details, 'noScreen')
or not details.noScreen):
if details.splitRun:
message('Testing all hold-out examples')
wrong = testall(composite, testExamples, badExamples)
message('%d examples (%% %5.2f) were misclassified' %
(len(wrong),
100. * float(len(wrong)) / float(len(testExamples))))
_runDetails.holdout_error = float(len(wrong)) / len(testExamples)
else:
message('Testing all examples')
wrong = testall(composite, namedExamples, badExamples)
message('%d examples (%% %5.2f) were misclassified' %
(len(wrong),
100. * float(len(wrong)) / float(len(namedExamples))))
_runDetails.overall_error = float(len(wrong)) / len(namedExamples)
if details.detailedRes:
message('\nEntire data set:')
resTup = ScreenComposite.ShowVoteResults(range(data.GetNPts()), data,
composite, nPossibleVals[-1],
details.threshold)
nGood, nBad, nSkip, avgGood, avgBad, avgSkip, voteTab = resTup
nPts = len(namedExamples)
nClass = nGood + nBad
_runDetails.overall_error = float(nBad) / nClass
_runDetails.overall_correct_conf = avgGood
_runDetails.overall_incorrect_conf = avgBad
_runDetails.overall_result_matrix = repr(voteTab)
nRej = nClass - nPts
if nRej > 0:
_runDetails.overall_fraction_dropped = float(nRej) / nPts
if details.splitRun:
message('\nHold-out data:')
resTup = ScreenComposite.ShowVoteResults(range(len(testExamples)),
testExamples, composite,
nPossibleVals[-1],
details.threshold)
nGood, nBad, nSkip, avgGood, avgBad, avgSkip, voteTab = resTup
nPts = len(testExamples)
nClass = nGood + nBad
_runDetails.holdout_error = float(nBad) / nClass
_runDetails.holdout_correct_conf = avgGood
_runDetails.holdout_incorrect_conf = avgBad
_runDetails.holdout_result_matrix = repr(voteTab)
nRej = nClass - nPts
if nRej > 0:
_runDetails.holdout_fraction_dropped = float(nRej) / nPts
if details.persistTblName and details.dbName:
message('Updating results table %s:%s' %
(details.dbName, details.persistTblName))
details.Store(db=details.dbName, table=details.persistTblName)
if details.badName != '':
badFile = open(details.badName, 'w+')
for i in range(len(badExamples)):
ex = badExamples[i]
vote = wrong[i]
outStr = '%s\t%s\n' % (ex, vote)
badFile.write(outStr)
badFile.close()
composite.ClearModelExamples()
return composite
def BalanceComposite(details,composite,data1=None,data2=None):
""" balances the composite using the parameters provided in details
**Arguments**
- details a _CompositeRun.RunDetails_ object
- composite: the composite model to be balanced
- data1: (optional) if provided, this should be the
data set used to construct the original models
- data2: (optional) if provided, this should be the
data set used to construct the new individual models
"""
if not details.balCnt or details.balCnt > len(composite):
return composite
message("Balancing Composite")
#
# start by getting data set 1: which is the data set used to build the
# original models
#
if data1 is None:
message("\tReading First Data Set")
fName = details.balTable.strip()
tmp = details.tableName
details.tableName = fName
dbName = details.dbName
details.dbName = details.balDb
data1 = details.GetDataSet()
details.tableName = tmp
details.dbName = dbName
if data1 is None:
return composite
details.splitFrac = composite._splitFrac
details.randomSeed = composite._randomSeed
DataUtils.InitRandomNumbers(details.randomSeed)
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data1,shuffle=1,runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data1,shuffle=0,runDetails=details)
namedExamples = data1.GetNamedData()
if details.balDoHoldout or details.balDoTrain:
trainIdx,testIdx = SplitData.SplitIndices(len(namedExamples),details.splitFrac,
silent=1)
trainExamples = [namedExamples[x] for x in trainIdx]
testExamples = [namedExamples[x] for x in testIdx]
if details.filterFrac != 0.0:
trainIdx,temp = DataUtils.FilterData(trainExamples,details.filterVal,
details.filterFrac,-1,
indicesOnly=1)
tmp = [trainExamples[x] for x in trainIdx]
testExamples += [trainExamples[x] for x in temp]
trainExamples = tmp
if details.balDoHoldout:
testExamples,trainExamples = trainExamples,testExamples
else:
trainExamples = namedExamples
dataSet1 = trainExamples
cols1 = [x.upper() for x in data1.GetVarNames()]
data1 = None
#
# now grab data set 2: the data used to build the new individual models
#
if data2 is None:
message("\tReading Second Data Set")
data2 = details.GetDataSet()
if data2 is None:
return composite
details.splitFrac = composite._splitFrac
details.randomSeed = composite._randomSeed
DataUtils.InitRandomNumbers(details.randomSeed)
if details.shuffleActivities == 1:
DataUtils.RandomizeActivities(data2,shuffle=1,runDetails=details)
elif details.randomActivities == 1:
DataUtils.RandomizeActivities(data2,shuffle=0,runDetails=details)
dataSet2 = data2.GetNamedData()
cols2 = [x.upper() for x in data2.GetVarNames()]
data2 = None
# and balance it:
res = []
weights = details.balWeight
if type(weights) not in (types.TupleType,types.ListType):
weights = (weights,)
for weight in weights:
message("\tBalancing with Weight: %.4f"%(weight))
res.append(AdjustComposite.BalanceComposite(composite,dataSet1,dataSet2,
weight,
details.balCnt,
names1=cols1,names2=cols2))
return res
def CrossValidationDriver(examples,
attrs=[],
nPossibleVals=[],
holdOutFrac=.3,
silent=0,
tolerance=0.3,
calcTotalError=0,
hiddenSizes=None,
**kwargs):
"""
**Arguments**
- examples: the full set of examples
- attrs: a list of attributes to consider in the tree building
*This argument is ignored*
- nPossibleVals: a list of the number of possible values each variable can adopt
*This argument is ignored*
- holdOutFrac: the fraction of the data which should be reserved for the hold-out set
(used to calculate the error)
- silent: a toggle used to control how much visual noise this makes as it goes.
- tolerance: the tolerance for convergence of the net
- calcTotalError: if this is true the entire data set is used to calculate
accuracy of the net
- hiddenSizes: a list containing the size(s) of the hidden layers in the network.
if _hiddenSizes_ is None, one hidden layer containing the same number of nodes
as the input layer will be used
**Returns**
a 2-tuple containing:
1) the net
2) the cross-validation error of the net
**Note**
At the moment, this is specific to nets with only one output
"""
nTot = len(examples)
if not kwargs.get('replacementSelection', 0):
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=1,
replacement=0)
else:
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=0,
replacement=1)
trainExamples = [examples[x] for x in trainIndices]
testExamples = [examples[x] for x in testIndices]
nTrain = len(trainExamples)
if not silent:
print('Training with %d examples' % (nTrain))
nInput = len(examples[0]) - 1
nOutput = 1
if hiddenSizes is None:
nHidden = nInput
netSize = [nInput, nHidden, nOutput]
else:
netSize = [nInput] + hiddenSizes + [nOutput]
net = Network.Network(netSize)
t = Trainers.BackProp()
t.TrainOnLine(trainExamples,
net,
errTol=tolerance,
useAvgErr=0,
silent=silent)
nTest = len(testExamples)
if not silent:
print('Testing with %d examples' % nTest)
if not calcTotalError:
xValError, _ = CrossValidate(net, testExamples, tolerance)
else:
xValError, _ = CrossValidate(net, examples, tolerance)
if not silent:
print('Validation error was %%%4.2f' % (100 * xValError))
net._trainIndices = trainIndices
return net, xValError
def CrossValidationDriver(examples,
attrs,
nPossibleVals,
holdOutFrac=.3,
silent=0,
calcTotalError=0,
treeBuilder=ID3.ID3Boot,
lessGreedy=0,
startAt=None,
nQuantBounds=[],
maxDepth=-1,
**kwargs):
""" Driver function for building trees and doing cross validation
**Arguments**
- examples: the full set of examples
- attrs: a list of attributes to consider in the tree building
- nPossibleVals: a list of the number of possible values each variable can adopt
- holdOutFrac: the fraction of the data which should be reserved for the hold-out set
(used to calculate the error)
- silent: a toggle used to control how much visual noise this makes as it goes.
- calcTotalError: a toggle used to indicate whether the classification error
of the tree should be calculated using the entire data set (when true) or just
the training hold out set (when false)
- treeBuilder: the function to call to build the tree
- lessGreedy: toggles use of the less greedy tree growth algorithm (see
_ChooseOptimalRoot_).
- startAt: forces the tree to be rooted at this descriptor
- nQuantBounds: an optional list. If present, it's assumed that the builder
algorithm takes this argument as well (for building QuantTrees)
- maxDepth: an optional integer. If present, it's assumed that the builder
algorithm takes this argument as well
**Returns**
a 2-tuple containing:
1) the tree
2) the cross-validation error of the tree
"""
nTot = len(examples)
if not kwargs.get('replacementSelection', 0):
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=1,
replacement=0)
else:
testIndices, trainIndices = SplitData.SplitIndices(nTot,
holdOutFrac,
silent=1,
legacy=0,
replacement=1)
trainExamples = [examples[x] for x in trainIndices]
testExamples = [examples[x] for x in testIndices]
nTrain = len(trainExamples)
if not silent:
print('Training with %d examples' % (nTrain))
if not lessGreedy:
if nQuantBounds is None or nQuantBounds == []:
tree = treeBuilder(trainExamples,
attrs,
nPossibleVals,
initialVar=startAt,
maxDepth=maxDepth,
**kwargs)
else:
tree = treeBuilder(trainExamples,
attrs,
nPossibleVals,
nQuantBounds,
initialVar=startAt,
maxDepth=maxDepth,
**kwargs)
else:
tree = ChooseOptimalRoot(examples,
trainExamples,
testExamples,
attrs,
nPossibleVals,
treeBuilder,
nQuantBounds,
maxDepth=maxDepth,
**kwargs)
nTest = len(testExamples)
if not silent:
print('Testing with %d examples' % nTest)
if not calcTotalError:
xValError, badExamples = CrossValidate(tree,
testExamples,
appendExamples=1)
else:
xValError, badExamples = CrossValidate(tree,
examples,
appendExamples=0)
if not silent:
print('Validation error was %%%4.2f' % (100 * xValError))
tree.SetBadExamples(badExamples)
tree.SetTrainingExamples(trainExamples)
tree.SetTestExamples(testExamples)
tree._trainIndices = trainIndices
return tree, xValError