def getSetup(learnerName, dataDir, outputDir, numProcesses):
if learnerName=="SVM":
learner = LibSVM(kernel='gaussian', type="C_SVC", processes=numProcesses)
loadMethod = ModelSelectUtils.loadRatschDataset
dataDir += "benchmark/"
outputDir += "classification/" + learnerName + "/"
paramDict = {}
paramDict["setC"] = learner.getCs()
paramDict["setGamma"] = learner.getGammas()
elif learnerName=="SVR":
learner = LibSVM(kernel='gaussian', type="Epsilon_SVR", processes=numProcesses)
learner.normModelSelect = True
loadMethod = ModelSelectUtils.loadRegressDataset
dataDir += "regression/"
outputDir += "regression/" + learnerName + "/"
paramDict = {}
paramDict["setC"] = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
paramDict["setGamma"] = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
paramDict["setEpsilon"] = learner.getEpsilons()
elif learnerName=="CART":
learner = DecisionTreeLearner(criterion="mse", maxDepth=30, minSplit=1, pruneType="CART", processes=numProcesses)
learner.setChunkSize(2)
loadMethod = ModelSelectUtils.loadRegressDataset
dataDir += "regression/"
outputDir += "regression/" + learnerName + "/"
paramDict = {}
paramDict["setGamma"] = numpy.array(numpy.round(2**numpy.arange(1, 7.5, 0.5)-1), dtype=numpy.int)
else:
raise ValueError("Unknown learnerName: " + learnerName)
return learner, loadMethod, dataDir, outputDir, paramDict
def computeIdealPenalty(args):
"""
Find the complete penalty.
"""
(X, y, fullX, C, gamma, gridPoints, pdfX, pdfY1X, pdfYminus1X) = args
svm = LibSVM('gaussian', gamma, C)
svm.learnModel(X, y)
predY = svm.predict(X)
predFullY, decisionsY = svm.predict(fullX, True)
decisionGrid = numpy.reshape(decisionsY, (gridPoints.shape[0], gridPoints.shape[0]), order="F")
trueError = ModelSelectUtils.bayesError(gridPoints, decisionGrid, pdfX, pdfY1X, pdfYminus1X)
idealPenalty = trueError - Evaluator.binaryError(predY, y)
return idealPenalty
def testGetModel(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 50
numFeatures = 3
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
svm.learnModel(X, y)
weights, b = svm.getWeights()
def testGetModel(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 50
numFeatures = 3
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
svm.learnModel(X, y)
weights, b = svm.getWeights()
def testStr(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
def testPredict(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel()
y = numpy.array(y > 0, numpy.int32)*2 -1
svm = LibSVM()
svm.learnModel(X, y)
y2, d = svm.predict(X, True)
def testPredict(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel()
y = numpy.array(y > 0, numpy.int32) * 2 - 1
svm = LibSVM()
svm.learnModel(X, y)
y2, d = svm.predict(X, True)
def testComputeTestError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0]*0.5
trainX, trainY = self.X[0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeTestError(args)
svm = LibSVM('gaussian', gamma, C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
self.assertEquals(Evaluator.binaryError(predY, testY), error)
def profileParallelPen(self):
learner = LibSVM(processes=8)
learner.setChunkSize(2)
numExamples = 10000
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
Y = numpy.array(numpy.random.rand(numExamples) < 0.1, numpy.int)*2-1
Cvs = [self.folds-1]
def run():
for i in range(2):
print("Iteration " + str(i))
idx = Sampling.crossValidation(self.folds, numExamples)
learner.parallelPen(X, Y, idx, self.paramDict, Cvs)
ProfileUtils.profile('run()', globals(), locals())
def profileParallelPen(self):
learner = LibSVM(processes=8)
learner.setChunkSize(2)
numExamples = 10000
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
Y = numpy.array(numpy.random.rand(numExamples) < 0.1,
numpy.int) * 2 - 1
Cvs = [self.folds - 1]
def run():
for i in range(2):
print("Iteration " + str(i))
idx = Sampling.crossValidation(self.folds, numExamples)
learner.parallelPen(X, Y, idx, self.paramDict, Cvs)
ProfileUtils.profile('run()', globals(), locals())
def testGetWeights(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2] ,[3]], numpy.float64)
#X = numpy.random.rand(numExamples, 10)
y = numpy.array([[-1], [-1], [-1], [1], [1] ,[1]])
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.zeros(numExamples)
decisions2 = numpy.dot(X, weights) - b
self.assertTrue((decisions == decisions2).all())
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
#Do the same test on a random datasets
numExamples = 50
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
y = numpy.sign(numpy.random.rand(numExamples)-0.5)
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.dot(X, weights) + b
tol = 10**-6
self.assertTrue(numpy.linalg.norm(decisions - decisions2) < tol)
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
def setUp(self):
try:
import sklearn
except ImportError as error:
logging.debug(error)
return
numpy.random.seed(21)
numExamples = 100
numFeatures = 10
eg = ExamplesGenerator()
self.X, self.y = eg.generateBinaryExamples(numExamples, numFeatures)
self.svm = LibSVM()
self.svm.Cs = 2.0**numpy.arange(-2, 2, dtype=numpy.float)
self.svm.gammas = 2.0**numpy.arange(-3, 1, dtype=numpy.float)
self.svm.epsilons = 2.0**numpy.arange(-2, 0, dtype=numpy.float)
numpy.set_printoptions(linewidth=150, suppress=True, precision=3)
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
def testLearnModel(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Test for wrong labels
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2] ,[3]], numpy.float)
y = numpy.array([[-1], [-1], [-1], [1], [1] ,[5]])
self.assertRaises(ValueError, self.svm.learnModel, X, y)
#Try the regression SVM
svm = LibSVM(type="Epsilon_SVR")
y = numpy.random.rand(self.X.shape[0])
svm.learnModel(self.X, self.y)
def testComputeBootstrapError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0] * 0.5
trainX, trainY = self.X[
0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeBootstrapError(args)
def testLearnModel(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Test for wrong labels
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2], [3]], numpy.float)
y = numpy.array([[-1], [-1], [-1], [1], [1], [5]])
self.assertRaises(ValueError, self.svm.learnModel, X, y)
#Try the regression SVM
svm = LibSVM(type="Epsilon_SVR")
y = numpy.random.rand(self.X.shape[0])
svm.learnModel(self.X, self.y)
def profileModelSelect(self):
learner = LibSVM()
numExamples = 10000
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
Y = numpy.array(numpy.random.rand(numExamples) < 0.1,
numpy.int) * 2 - 1
def run():
for i in range(5):
print("Iteration " + str(i))
idx = Sampling.crossValidation(self.folds, numExamples)
learner.parallelModelSelect(X, Y, idx, self.paramDict)
ProfileUtils.profile('run()', globals(), locals())
def __init__(self, examplesFileName):
"""
Create the class by reading examples from a Matlab file. Instantiate the SVM
and create a preprocesor to standarise examples to have zero mean and unit variance.
"""
self.examplesList = ExamplesList.readFromFile(examplesFileName)
self.examplesList.setDefaultExamplesName("X")
self.examplesList.setLabelsName("y")
(freqs, items) = Util.histogram(self.examplesList.getSampledDataField("y").ravel())
logging.info("Distribution of labels: " + str((freqs, items)))
logging.info("The base error rate is " + str(float(min(freqs))/self.examplesList.getNumExamples()))
self.classifier = LibSVM()
self.errorMethod = Evaluator.balancedError
self.preprocessor = Standardiser()
X = self.preprocessor.standardiseArray(self.examplesList.getDataField(self.examplesList.getDefaultExamplesName()))
self.examplesList.overwriteDataField(self.examplesList.getDefaultExamplesName(), X)
def testComputeTestError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0] * 0.5
trainX, trainY = self.X[
0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeTestError(args)
svm = LibSVM('gaussian', gamma, C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
self.assertEquals(Evaluator.binaryError(predY, testY), error)
def setUp(self):
try:
import sklearn
except ImportError as error:
logging.debug(error)
return
numpy.random.seed(21)
numExamples = 100
numFeatures = 10
eg = ExamplesGenerator()
self.X, self.y = eg.generateBinaryExamples(numExamples, numFeatures)
self.svm = LibSVM()
self.svm.Cs = 2.0**numpy.arange(-2, 2, dtype=numpy.float)
self.svm.gammas = 2.0**numpy.arange(-3, 1, dtype=numpy.float)
self.svm.epsilons = 2.0**numpy.arange(-2, 0, dtype=numpy.float)
numpy.set_printoptions(linewidth=150, suppress=True, precision=3)
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
def testComputeIdealPenalty(self):
C = 10.0
gamma = 0.5
svm = LibSVM("gaussian", gamma, C)
args = (self.X, self.y, self.X, self.y, svm)
error = computeIdealPenalty(args)
def testSetErrorCost(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 1000
numFeatures = 100
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
C = 0.1
kernel = "linear"
kernelParam = 0
svm.setKernel(kernel, kernelParam)
svm.setC(C)
svm.setErrorCost(0.1)
svm.learnModel(X, y)
predY = svm.classify(X)
e1 = Evaluator.binaryErrorP(y, predY)
svm.setErrorCost(0.9)
svm.learnModel(X, y)
predY = svm.classify(X)
e2 = Evaluator.binaryErrorP(y, predY)
self.assertTrue(e1 > e2)
Cs = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
gammas = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
epsilons = numpy.array([2**-2])
paramDict = {}
paramDict["setC"] = Cs
paramDict["setGamma"] = gammas
paramDict["setEpsilon"] = epsilons
sampleMethod = Sampling.crossValidation
numProcesses = multiprocessing.cpu_count()
j = 0
trainX, trainY, testX, testY = ModelSelectUtils.loadRegressDataset(dataDir, datasetName, j)
learner = LibSVM(kernel='gaussian', type="Epsilon_SVR", processes=numProcesses)
for sampleSize in sampleSizes:
print("Sample size " +str(sampleSize))
trainInds = numpy.random.permutation(trainX.shape[0])[0:sampleSize]
validX = trainX[trainInds,:]
validY = trainY[trainInds]
#errors = learner.parallelPenaltyGrid(validX, validY, testX, testY, paramDict, computeTestError)
#errors = numpy.squeeze(errors)
errors = numpy.zeros((Cs.shape[0], gammas.shape[0]))
norms = numpy.zeros((Cs.shape[0], gammas.shape[0]))
for i, C in enumerate(Cs):
i = 0
datasetName = datasetNames[i][0]
numRealisations = datasetNames[i][1]
logging.debug("Learning using dataset " + datasetName)
data = numpy.load(dataDir + datasetName + ".npz")
gridPoints, trainX, trainY, pdfX, pdfY1X, pdfYminus1X = data["arr_0"], data["arr_1"], data["arr_2"], data["arr_3"], data["arr_4"], data["arr_5"]
#We form a test set from the grid points
testX = numpy.zeros((gridPoints.shape[0]**2, 2))
for m in range(gridPoints.shape[0]):
testX[m*gridPoints.shape[0]:(m+1)*gridPoints.shape[0], 0] = gridPoints
testX[m*gridPoints.shape[0]:(m+1)*gridPoints.shape[0], 1] = gridPoints[m]
svm = LibSVM()
logging.debug("Using sample size " + str(sampleSize) + " and " + str(folds) + " folds")
perm = numpy.random.permutation(trainX.shape[0])
trainInds = perm[0:sampleSize]
validX = trainX[trainInds, :]
validY = trainY[trainInds]
logging.debug("Finding ideal grid of penalties")
idealGrid = parallelPenaltyGridRbf(svm, validX, validY, testX, gridPoints, pdfX, pdfY1X, pdfYminus1X)
for s in range(len(sampleMethods)):
sampleMethod = sampleMethods[s][1]
logging.debug("Sampling method :" + str(sampleMethod))
idx = sampleMethod(folds, validY.shape[0])
def testModelSelect(self):
"""
We test the results on some data and compare to SVR.
"""
numExamples = 200
X, y = data.make_regression(numExamples, noise=0.5)
X = Standardiser().standardiseArray(X)
y = Standardiser().standardiseArray(y)
trainX = X[0:100, :]
trainY = y[0:100]
testX = X[100:, :]
testY = y[100:]
learner = DecisionTreeLearner(maxDepth=20, minSplit=10, pruneType="REP-CV")
learner.setPruneCV(8)
paramDict = {}
paramDict["setGamma"] = numpy.linspace(0.0, 1.0, 10)
paramDict["setPruneCV"] = numpy.arange(6, 11, 2, numpy.int)
folds = 5
idx = Sampling.crossValidation(folds, trainX.shape[0])
bestTree, cvGrid = learner.parallelModelSelect(trainX, trainY, idx, paramDict)
predY = bestTree.predict(testX)
error = Evaluator.rootMeanSqError(testY, predY)
print(error)
learner = DecisionTreeLearner(maxDepth=20, minSplit=5, pruneType="CART")
paramDict = {}
paramDict["setGamma"] = numpy.linspace(0.0, 1.0, 50)
folds = 5
idx = Sampling.crossValidation(folds, trainX.shape[0])
bestTree, cvGrid = learner.parallelModelSelect(trainX, trainY, idx, paramDict)
predY = bestTree.predict(testX)
error = Evaluator.rootMeanSqError(testY, predY)
print(error)
return
#Let's compare to the SVM
learner2 = LibSVM(kernel='gaussian', type="Epsilon_SVR")
paramDict = {}
paramDict["setC"] = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
paramDict["setGamma"] = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
paramDict["setEpsilon"] = learner2.getEpsilons()
idx = Sampling.crossValidation(folds, trainX.shape[0])
bestSVM, cvGrid = learner2.parallelModelSelect(trainX, trainY, idx, paramDict)
predY = bestSVM.predict(testX)
error = Evaluator.rootMeanSqError(testY, predY)
print(error)
def testSetSvmType(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
X = Standardiser().standardiseArray(X)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + 1
y2 = numpy.array(y > 0, numpy.int32) * 2 - 1
svm = LibSVM()
svm.setSvmType("Epsilon_SVR")
self.assertEquals(svm.getType(), "Epsilon_SVR")
#Try to get a good error
Cs = 2**numpy.arange(-6, 4, dtype=numpy.float)
epsilons = 2**numpy.arange(-6, 4, dtype=numpy.float)
bestError = 10
for C in Cs:
for epsilon in epsilons:
svm.setEpsilon(epsilon)
svm.setC(C)
svm.learnModel(X, y)
yp = svm.predict(X)
if Evaluator.rootMeanSqError(y, yp) < bestError:
bestError = Evaluator.rootMeanSqError(y, yp)
self.assertTrue(
bestError < Evaluator.rootMeanSqError(y, numpy.zeros(y.shape[0])))
svm.setSvmType("C_SVC")
svm.learnModel(X, y2)
yp2 = svm.predict(X)
self.assertTrue(0 <= Evaluator.binaryError(y2, yp2) <= 1)
import matplotlib.pyplot as plt
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
numpy.seterr(all="raise")
numpy.random.seed(21)
dataDir = PathDefaults.getDataDir()
dataDir += "modelPenalisation/regression/"
outputDir = PathDefaults.getOutputDir() + "modelPenalisation/regression/SVR/"
figInd = 0
loadMethod = ModelSelectUtils.loadRegressDataset
datasets = ModelSelectUtils.getRegressionDatasets(True)
numProcesses = multiprocessing.cpu_count()
learner = LibSVM(kernel="rbf", processes=numProcesses, type="Epsilon_SVR")
learner.setChunkSize(3)
Cs = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
gammas = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
epsilons = learner.getEpsilons()
numCs = Cs.shape[0]
numGammas = gammas.shape[0]
numEpsilons = epsilons.shape[0]
learner.normModelSelect = True
paramDict = {}
paramDict["setC"] = Cs
paramDict["setGamma"] = gammas
def testSetSvmType(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
X = Standardiser().standardiseArray(X)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + 1
y2 = numpy.array(y > 0, numpy.int32)*2 -1
svm = LibSVM()
svm.setSvmType("Epsilon_SVR")
self.assertEquals(svm.getType(), "Epsilon_SVR")
#Try to get a good error
Cs = 2**numpy.arange(-6, 4, dtype=numpy.float)
epsilons = 2**numpy.arange(-6, 4, dtype=numpy.float)
bestError = 10
for C in Cs:
for epsilon in epsilons:
svm.setEpsilon(epsilon)
svm.setC(C)
svm.learnModel(X, y)
yp = svm.predict(X)
if Evaluator.rootMeanSqError(y, yp) < bestError:
bestError = Evaluator.rootMeanSqError(y, yp)
self.assertTrue(bestError < Evaluator.rootMeanSqError(y, numpy.zeros(y.shape[0])))
svm.setSvmType("C_SVC")
svm.learnModel(X, y2)
yp2 = svm.predict(X)
self.assertTrue(0 <= Evaluator.binaryError(y2, yp2) <= 1)
def testSaveParams(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.5)
svm.setEpsilon(12.1)
svm.setErrorCost(1.8)
svm.setSvmType("Epsilon_SVR")
svm.setTermination(0.12)
svm.setKernel("gaussian", 0.43)
outputDir = PathDefaults.getOutputDir()
fileName = outputDir + "test/testSvmParams"
svm.saveParams(fileName)
svm2 = LibSVM()
svm2.loadParams(fileName)
self.assertEquals(svm.getC(), 10.5)
self.assertEquals(svm.getEpsilon(), 12.1)
self.assertEqual(svm.getErrorCost(), 1.8)
self.assertEqual(svm.getSvmType(), "Epsilon_SVR")
self.assertEqual(svm.getTermination(), 0.12)
self.assertEqual(svm.getKernel(), "gaussian")
self.assertEqual(svm.getKernelParams(), 0.43)
def testSetEpsilon(self):
"""
Test out the parameter for the regressive SVM, vary epsilon and look at
number of support vectors.
"""
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.0)
svm.setEpsilon(0.1)
svm.setSvmType("Epsilon_SVR")
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + numpy.random.randn(100)
svm.setEpsilon(1.0)
svm.learnModel(X, y)
numSV = svm.getModel().support_.shape
svm.setEpsilon(0.5)
svm.learnModel(X, y)
numSV2 = svm.getModel().support_.shape
svm.setEpsilon(0.01)
svm.learnModel(X, y)
numSV3 = svm.getModel().support_.shape
#There should be fewer SVs as epsilon increases
self.assertTrue(numSV < numSV2)
self.assertTrue(numSV2 < numSV3)
def testSaveParams(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.5)
svm.setEpsilon(12.1)
svm.setErrorCost(1.8)
svm.setSvmType("Epsilon_SVR")
svm.setTermination(0.12)
svm.setKernel("gaussian", 0.43)
outputDir = PathDefaults.getOutputDir()
fileName = outputDir + "test/testSvmParams"
svm.saveParams(fileName)
svm2 = LibSVM()
svm2.loadParams(fileName)
self.assertEquals(svm.getC(), 10.5)
self.assertEquals(svm.getEpsilon(), 12.1)
self.assertEqual(svm.getErrorCost(), 1.8)
self.assertEqual(svm.getSvmType(), "Epsilon_SVR")
self.assertEqual(svm.getTermination(), 0.12)
self.assertEqual(svm.getKernel(), "gaussian")
self.assertEqual(svm.getKernelParams(), 0.43)
def testSetEpsilon(self):
"""
Test out the parameter for the regressive SVM, vary epsilon and look at
number of support vectors.
"""
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.0)
svm.setEpsilon(0.1)
svm.setSvmType("Epsilon_SVR")
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + numpy.random.randn(100)
svm.setEpsilon(1.0)
svm.learnModel(X, y)
numSV = svm.getModel().support_.shape
svm.setEpsilon(0.5)
svm.learnModel(X, y)
numSV2 = svm.getModel().support_.shape
svm.setEpsilon(0.01)
svm.learnModel(X, y)
numSV3 = svm.getModel().support_.shape
#There should be fewer SVs as epsilon increases
self.assertTrue(numSV < numSV2)
self.assertTrue(numSV2 < numSV3)
class LibSVMTest(unittest.TestCase):
def setUp(self):
try:
import sklearn
except ImportError as error:
logging.debug(error)
return
numpy.random.seed(21)
numExamples = 100
numFeatures = 10
eg = ExamplesGenerator()
self.X, self.y = eg.generateBinaryExamples(numExamples, numFeatures)
self.svm = LibSVM()
self.svm.Cs = 2.0**numpy.arange(-2, 2, dtype=numpy.float)
self.svm.gammas = 2.0**numpy.arange(-3, 1, dtype=numpy.float)
self.svm.epsilons = 2.0**numpy.arange(-2, 0, dtype=numpy.float)
numpy.set_printoptions(linewidth=150, suppress=True, precision=3)
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
def testLearnModel(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Test for wrong labels
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2], [3]], numpy.float)
y = numpy.array([[-1], [-1], [-1], [1], [1], [5]])
self.assertRaises(ValueError, self.svm.learnModel, X, y)
#Try the regression SVM
svm = LibSVM(type="Epsilon_SVR")
y = numpy.random.rand(self.X.shape[0])
svm.learnModel(self.X, self.y)
def testSetErrorCost(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 1000
numFeatures = 100
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
C = 0.1
kernel = "linear"
kernelParam = 0
svm.setKernel(kernel, kernelParam)
svm.setC(C)
svm.setErrorCost(0.1)
svm.learnModel(X, y)
predY = svm.classify(X)
e1 = Evaluator.binaryErrorP(y, predY)
svm.setErrorCost(0.9)
svm.learnModel(X, y)
predY = svm.classify(X)
e2 = Evaluator.binaryErrorP(y, predY)
self.assertTrue(e1 > e2)
def testClassify(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Now, permute examples
perm = numpy.random.permutation(self.X.shape[0])
predY = self.svm.classify(self.X[perm, :])
y = y[perm]
e2 = Evaluator.binaryError(y, predY)
self.assertEquals(e, e2)
def testEvaluateCv(self):
try:
import sklearn
except ImportError as error:
return
folds = 10
(means, vars) = self.svm.evaluateCv(self.X, self.y, folds)
self.assertTrue((means <= 1).all())
self.assertTrue((means >= 0).all())
self.assertTrue((vars <= 1).all())
self.assertTrue((vars >= 0).all())
@apgl.skip("")
def testGetModel(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 50
numFeatures = 3
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
svm.learnModel(X, y)
weights, b = svm.getWeights()
#logging.debug(weights)
#logging.debug(b)
@apgl.skip("")
def testGetWeights(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2], [3]], numpy.float64)
#X = numpy.random.rand(numExamples, 10)
y = numpy.array([[-1], [-1], [-1], [1], [1], [1]])
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.zeros(numExamples)
decisions2 = numpy.dot(X, weights) - b
self.assertTrue((decisions == decisions2).all())
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
#Do the same test on a random datasets
numExamples = 50
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
y = numpy.sign(numpy.random.rand(numExamples) - 0.5)
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.dot(X, weights) + b
tol = 10**-6
self.assertTrue(numpy.linalg.norm(decisions - decisions2) < tol)
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
def testSetTermination(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
self.svm.setTermination(0.1)
self.svm.learnModel(self.X, self.y)
def testSetSvmType(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
X = Standardiser().standardiseArray(X)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + 1
y2 = numpy.array(y > 0, numpy.int32) * 2 - 1
svm = LibSVM()
svm.setSvmType("Epsilon_SVR")
self.assertEquals(svm.getType(), "Epsilon_SVR")
#Try to get a good error
Cs = 2**numpy.arange(-6, 4, dtype=numpy.float)
epsilons = 2**numpy.arange(-6, 4, dtype=numpy.float)
bestError = 10
for C in Cs:
for epsilon in epsilons:
svm.setEpsilon(epsilon)
svm.setC(C)
svm.learnModel(X, y)
yp = svm.predict(X)
if Evaluator.rootMeanSqError(y, yp) < bestError:
bestError = Evaluator.rootMeanSqError(y, yp)
self.assertTrue(
bestError < Evaluator.rootMeanSqError(y, numpy.zeros(y.shape[0])))
svm.setSvmType("C_SVC")
svm.learnModel(X, y2)
yp2 = svm.predict(X)
self.assertTrue(0 <= Evaluator.binaryError(y2, yp2) <= 1)
@apgl.skip("")
def testSaveParams(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.5)
svm.setEpsilon(12.1)
svm.setErrorCost(1.8)
svm.setSvmType("Epsilon_SVR")
svm.setTermination(0.12)
svm.setKernel("gaussian", 0.43)
outputDir = PathDefaults.getOutputDir()
fileName = outputDir + "test/testSvmParams"
svm.saveParams(fileName)
svm2 = LibSVM()
svm2.loadParams(fileName)
self.assertEquals(svm.getC(), 10.5)
self.assertEquals(svm.getEpsilon(), 12.1)
self.assertEqual(svm.getErrorCost(), 1.8)
self.assertEqual(svm.getSvmType(), "Epsilon_SVR")
self.assertEqual(svm.getTermination(), 0.12)
self.assertEqual(svm.getKernel(), "gaussian")
self.assertEqual(svm.getKernelParams(), 0.43)
def testStr(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
#logging.debug(svm)
def testSetEpsilon(self):
"""
Test out the parameter for the regressive SVM, vary epsilon and look at
number of support vectors.
"""
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.0)
svm.setEpsilon(0.1)
svm.setSvmType("Epsilon_SVR")
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + numpy.random.randn(100)
svm.setEpsilon(1.0)
svm.learnModel(X, y)
numSV = svm.getModel().support_.shape
svm.setEpsilon(0.5)
svm.learnModel(X, y)
numSV2 = svm.getModel().support_.shape
svm.setEpsilon(0.01)
svm.learnModel(X, y)
numSV3 = svm.getModel().support_.shape
#There should be fewer SVs as epsilon increases
self.assertTrue(numSV < numSV2)
self.assertTrue(numSV2 < numSV3)
def testPredict(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel()
y = numpy.array(y > 0, numpy.int32) * 2 - 1
svm = LibSVM()
svm.learnModel(X, y)
y2, d = svm.predict(X, True)
#self.assertTrue((numpy.sign(d) == y2).all())
#@unittest.skip("")
def testParallelVfcvRbf(self):
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
bestSVM, meanErrors = svm.parallelVfcvRbf(self.X, self.y, idx)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += Evaluator.binaryError(predY, testY)
meanErrors2[i, j] = error / len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
def testParallelVfcvRbf2(self):
#In this test we try SVM regression
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
bestSVM, meanErrors = svm.parallelVfcvRbf(self.X,
self.y,
idx,
type="Epsilon_SVR")
tol = 10**-6
bestError = 100
meanErrors2 = numpy.zeros(
(svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += svm.getMetricMethod()(predY, testY)
meanErrors2[j, k, i] = error / len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
bestEpsilon = epsilon
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertEquals(bestEpsilon, bestSVM.getEpsilon())
self.assertTrue(numpy.linalg.norm(meanErrors2 - meanErrors) < tol)
def testParallelVfPenRbf(self):
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
resultsList = svm.parallelVfPenRbf(self.X, self.y, idx, Cv)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += Evaluator.binaryError(
predY, self.y) - Evaluator.binaryError(
predTrainY, trainY)
penalty = penalty * Cv[0] / len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
meanErrors2[i,
j] = Evaluator.binaryError(predY, self.y) + penalty
if meanErrors2[i, j] < bestError:
bestC = C
bestGamma = gamma
bestError = meanErrors2[i, j]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
#@unittest.skip("")
def testParallelVfPenRbf2(self):
#Test support vector regression
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
resultsList = svm.parallelVfPenRbf(self.X,
self.y,
idx,
Cv,
type="Epsilon_SVR")
tol = 10**-6
bestError = 100
meanErrors2 = numpy.zeros(
(svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += svm.getMetricMethod()(
predY, self.y) - svm.getMetricMethod()(predTrainY,
trainY)
penalty = penalty * Cv[0] / len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
meanErrors2[j, k, i] = svm.getMetricMethod()(
predY, self.y) + penalty
if meanErrors2[j, k, i] < bestError:
bestC = C
bestGamma = gamma
bestEpsilon = epsilon
bestError = meanErrors2[j, k, i]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertEquals(bestEpsilon, bestSVM.getEpsilon())
self.assertTrue(numpy.linalg.norm(meanErrors2 - meanErrors) < tol)
def testGetC(self):
svm = LibSVM()
svm.setC(10.0)
C = svm.getC()
self.assertTrue(C == 10.0)
def testGetGamma(self):
svm = LibSVM()
svm.setKernel("gaussian", 12.0)
gamma = svm.getKernelParams()
self.assertTrue(gamma == 12.0)
def testComputeTestError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0] * 0.5
trainX, trainY = self.X[
0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeTestError(args)
svm = LibSVM('gaussian', gamma, C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
self.assertEquals(Evaluator.binaryError(predY, testY), error)
def testComputeBootstrapError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0] * 0.5
trainX, trainY = self.X[
0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeBootstrapError(args)
def testComputeIdealPenalty(self):
C = 10.0
gamma = 0.5
svm = LibSVM("gaussian", gamma, C)
args = (self.X, self.y, self.X, self.y, svm)
error = computeIdealPenalty(args)
def testParallelPenaltyGridRbf(self):
svm = self.svm
svm.setKernel("gaussian")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
idealPenalties = svm.parallelPenaltyGridRbf(trainX, trainY, self.X,
self.y)
idealPenalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
idealPenalties3 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = Evaluator.binaryError(
predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
idealPenalties2[i, j] = penalty
args = (trainX, trainY, self.X, self.y, svm)
idealPenalties3[i, j] = computeIdealPenalty(args)
tol = 10**-6
self.assertTrue(
numpy.linalg.norm(idealPenalties2.T - idealPenalties) < tol)
def testParallelPenaltyGridRbf2(self):
#Test with SVM regression
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
idealPenalties = svm.parallelPenaltyGridRbf(trainX,
trainY,
self.X,
self.y,
type="Epsilon_SVR")
idealPenalties2 = numpy.zeros(
(svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = svm.getMetricMethod()(
predY, self.y) - svm.getMetricMethod()(predTrainY,
trainY)
idealPenalties2[j, k, i] = penalty
tol = 10**-6
self.assertTrue(
numpy.linalg.norm(idealPenalties2 - idealPenalties) < tol)
def testParallelModelSelect(self):
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
bestSVM, meanErrors = svm.parallelModelSelect(self.X, self.y, idx,
paramDict)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
print("Computing real grid")
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += Evaluator.binaryError(predY, testY)
meanErrors2[i, j] = error / len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
def testParallelPenaltyGrid2(self):
#Test with SVM regression
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
paramDict["setEpsilon"] = svm.getEpsilons()
#print(paramDict.keys())
idealPenalties = svm.parallelPenaltyGrid(trainX, trainY, self.X,
self.y, paramDict)
idealPenalties2 = numpy.zeros(
(svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = svm.getMetricMethod()(
predY, self.y) - svm.getMetricMethod()(predTrainY,
trainY)
idealPenalties2[j, k, i] = penalty
tol = 10**-6
self.assertTrue(
numpy.linalg.norm(idealPenalties2 - idealPenalties) < tol)
def testParallelPen(self):
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
resultsList = svm.parallelPen(self.X, self.y, idx, paramDict, Cv)
tol = 10**-6
bestError = 1
trainErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
penalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += Evaluator.binaryError(
predY, self.y) - Evaluator.binaryError(
predTrainY, trainY)
penalty = penalty * Cv[0] / len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
trainErrors2[i, j] = Evaluator.binaryError(predY, self.y)
penalties2[i, j] = penalty
meanErrors2[i,
j] = Evaluator.binaryError(predY, self.y) + penalty
if meanErrors2[i, j] < bestError:
bestC = C
bestGamma = gamma
bestError = meanErrors2[i, j]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
self.assertTrue(numpy.linalg.norm(trainErrors2.T - trainErrors) < tol)
self.assertTrue(
numpy.linalg.norm(penalties2.T - currentPenalties) < tol)
def testParallelPenaltyGrid(self):
svm = self.svm
svm.setKernel("gaussian")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
idealPenalties = svm.parallelPenaltyGrid(trainX, trainY, self.X,
self.y, paramDict)
idealPenalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
idealPenalties3 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = Evaluator.binaryError(
predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
idealPenalties2[i, j] = penalty
args = (trainX, trainY, self.X, self.y, svm)
idealPenalties3[i, j] = computeIdealPenalty(args)
tol = 10**-6
self.assertTrue(
numpy.linalg.norm(idealPenalties2.T - idealPenalties) < tol)
def testGetBestLearner(self):
svm = self.svm
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
errors = numpy.random.rand(svm.getCs().shape[0],
svm.getGammas().shape[0])
folds = 5
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm.normModelSelect = True
svm.setKernel("gaussian")
learner = svm.getBestLearner(errors, paramDict, self.X, self.y, idx)
bestC = learner.getC()
#Find the best norm
bestInds = numpy.unravel_index(numpy.argmin(errors), errors.shape)
learner.setC(svm.getCs()[bestInds[0]])
learner.setGamma(svm.getGammas()[bestInds[1]])
norms = []
for trainInds, testInds in idx:
validX = self.X[trainInds, :]
validY = self.y[trainInds]
learner.learnModel(validX, validY)
norms.append(learner.weightNorm())
bestNorm = numpy.array(norms).mean()
norms = numpy.zeros(paramDict["setC"].shape[0])
for i, C in enumerate(paramDict["setC"]):
learner.setC(C)
learner.learnModel(self.X, self.y)
norms[i] = learner.weightNorm()
bestC2 = paramDict["setC"][numpy.abs(norms - bestNorm).argmin()]
self.assertEquals(bestC, bestC2)
def testSetErrorCost(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 1000
numFeatures = 100
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
C = 0.1
kernel = "linear"
kernelParam = 0
svm.setKernel(kernel, kernelParam)
svm.setC(C)
svm.setErrorCost(0.1)
svm.learnModel(X, y)
predY = svm.classify(X)
e1 = Evaluator.binaryErrorP(y, predY)
svm.setErrorCost(0.9)
svm.learnModel(X, y)
predY = svm.classify(X)
e2 = Evaluator.binaryErrorP(y, predY)
self.assertTrue(e1 > e2)
import matplotlib.pyplot as plt logging.basicConfig(stream=sys.stdout, level=logging.DEBUG) numpy.seterr(all="raise") numpy.random.seed(21) dataDir = PathDefaults.getDataDir() dataDir += "modelPenalisation/regression/" outputDir = PathDefaults.getOutputDir() + "modelPenalisation/regression/SVR/" figInd = 0 loadMethod = ModelSelectUtils.loadRegressDataset datasets = ModelSelectUtils.getRegressionDatasets(True) numProcesses = multiprocessing.cpu_count() learner = LibSVM(kernel="rbf", processes=numProcesses, type="Epsilon_SVR") learner.setChunkSize(3) Cs = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float) gammas = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float) epsilons = learner.getEpsilons() gammaInd = 3 gamma = gammas[gammaInd] learner.setGamma(gamma) epsilonInd = 0 epsilon = epsilons[epsilonInd] learner.setEpsilon(epsilon) learner.normModelSelect = True
class LibSVMTest(unittest.TestCase):
def setUp(self):
try:
import sklearn
except ImportError as error:
logging.debug(error)
return
numpy.random.seed(21)
numExamples = 100
numFeatures = 10
eg = ExamplesGenerator()
self.X, self.y = eg.generateBinaryExamples(numExamples, numFeatures)
self.svm = LibSVM()
self.svm.Cs = 2.0**numpy.arange(-2, 2, dtype=numpy.float)
self.svm.gammas = 2.0**numpy.arange(-3, 1, dtype=numpy.float)
self.svm.epsilons = 2.0**numpy.arange(-2, 0, dtype=numpy.float)
numpy.set_printoptions(linewidth=150, suppress=True, precision=3)
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
def testLearnModel(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Test for wrong labels
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2] ,[3]], numpy.float)
y = numpy.array([[-1], [-1], [-1], [1], [1] ,[5]])
self.assertRaises(ValueError, self.svm.learnModel, X, y)
#Try the regression SVM
svm = LibSVM(type="Epsilon_SVR")
y = numpy.random.rand(self.X.shape[0])
svm.learnModel(self.X, self.y)
def testSetErrorCost(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 1000
numFeatures = 100
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
C = 0.1
kernel = "linear"
kernelParam = 0
svm.setKernel(kernel, kernelParam)
svm.setC(C)
svm.setErrorCost(0.1)
svm.learnModel(X, y)
predY = svm.classify(X)
e1 = Evaluator.binaryErrorP(y, predY)
svm.setErrorCost(0.9)
svm.learnModel(X, y)
predY = svm.classify(X)
e2 = Evaluator.binaryErrorP(y, predY)
self.assertTrue(e1 > e2)
def testClassify(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
predY = self.svm.classify(self.X)
y = self.y
e = Evaluator.binaryError(y, predY)
#Now, permute examples
perm = numpy.random.permutation(self.X.shape[0])
predY = self.svm.classify(self.X[perm, :])
y = y[perm]
e2 = Evaluator.binaryError(y, predY)
self.assertEquals(e, e2)
def testEvaluateCv(self):
try:
import sklearn
except ImportError as error:
return
folds = 10
(means, vars) = self.svm.evaluateCv(self.X, self.y, folds)
self.assertTrue((means <= 1).all())
self.assertTrue((means>= 0).all())
self.assertTrue((vars <= 1).all())
self.assertTrue((vars>= 0).all())
@apgl.skip("")
def testGetModel(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 50
numFeatures = 3
eg = ExamplesGenerator()
X, y = eg.generateBinaryExamples(numExamples, numFeatures)
svm = LibSVM()
svm.learnModel(X, y)
weights, b = svm.getWeights()
#logging.debug(weights)
#logging.debug(b)
@apgl.skip("")
def testGetWeights(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2] ,[3]], numpy.float64)
#X = numpy.random.rand(numExamples, 10)
y = numpy.array([[-1], [-1], [-1], [1], [1] ,[1]])
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.zeros(numExamples)
decisions2 = numpy.dot(X, weights) - b
self.assertTrue((decisions == decisions2).all())
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
#Do the same test on a random datasets
numExamples = 50
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
y = numpy.sign(numpy.random.rand(numExamples)-0.5)
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.dot(X, weights) + b
tol = 10**-6
self.assertTrue(numpy.linalg.norm(decisions - decisions2) < tol)
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
def testSetTermination(self):
try:
import sklearn
except ImportError as error:
return
self.svm.learnModel(self.X, self.y)
self.svm.setTermination(0.1)
self.svm.learnModel(self.X, self.y)
def testSetSvmType(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
X = Standardiser().standardiseArray(X)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + 1
y2 = numpy.array(y > 0, numpy.int32)*2 -1
svm = LibSVM()
svm.setSvmType("Epsilon_SVR")
self.assertEquals(svm.getType(), "Epsilon_SVR")
#Try to get a good error
Cs = 2**numpy.arange(-6, 4, dtype=numpy.float)
epsilons = 2**numpy.arange(-6, 4, dtype=numpy.float)
bestError = 10
for C in Cs:
for epsilon in epsilons:
svm.setEpsilon(epsilon)
svm.setC(C)
svm.learnModel(X, y)
yp = svm.predict(X)
if Evaluator.rootMeanSqError(y, yp) < bestError:
bestError = Evaluator.rootMeanSqError(y, yp)
self.assertTrue(bestError < Evaluator.rootMeanSqError(y, numpy.zeros(y.shape[0])))
svm.setSvmType("C_SVC")
svm.learnModel(X, y2)
yp2 = svm.predict(X)
self.assertTrue(0 <= Evaluator.binaryError(y2, yp2) <= 1)
@apgl.skip("")
def testSaveParams(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.5)
svm.setEpsilon(12.1)
svm.setErrorCost(1.8)
svm.setSvmType("Epsilon_SVR")
svm.setTermination(0.12)
svm.setKernel("gaussian", 0.43)
outputDir = PathDefaults.getOutputDir()
fileName = outputDir + "test/testSvmParams"
svm.saveParams(fileName)
svm2 = LibSVM()
svm2.loadParams(fileName)
self.assertEquals(svm.getC(), 10.5)
self.assertEquals(svm.getEpsilon(), 12.1)
self.assertEqual(svm.getErrorCost(), 1.8)
self.assertEqual(svm.getSvmType(), "Epsilon_SVR")
self.assertEqual(svm.getTermination(), 0.12)
self.assertEqual(svm.getKernel(), "gaussian")
self.assertEqual(svm.getKernelParams(), 0.43)
def testStr(self):
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
#logging.debug(svm)
def testSetEpsilon(self):
"""
Test out the parameter for the regressive SVM, vary epsilon and look at
number of support vectors.
"""
try:
import sklearn
except ImportError as error:
return
svm = LibSVM()
svm.setC(10.0)
svm.setEpsilon(0.1)
svm.setSvmType("Epsilon_SVR")
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel() + numpy.random.randn(100)
svm.setEpsilon(1.0)
svm.learnModel(X, y)
numSV = svm.getModel().support_.shape
svm.setEpsilon(0.5)
svm.learnModel(X, y)
numSV2 = svm.getModel().support_.shape
svm.setEpsilon(0.01)
svm.learnModel(X, y)
numSV3 = svm.getModel().support_.shape
#There should be fewer SVs as epsilon increases
self.assertTrue(numSV < numSV2)
self.assertTrue(numSV2 < numSV3)
def testPredict(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 100
numFeatures = 10
X = numpy.random.randn(numExamples, numFeatures)
c = numpy.random.randn(numFeatures)
y = numpy.dot(X, numpy.array([c]).T).ravel()
y = numpy.array(y > 0, numpy.int32)*2 -1
svm = LibSVM()
svm.learnModel(X, y)
y2, d = svm.predict(X, True)
#self.assertTrue((numpy.sign(d) == y2).all())
#@unittest.skip("")
def testParallelVfcvRbf(self):
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
bestSVM, meanErrors = svm.parallelVfcvRbf(self.X, self.y, idx)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += Evaluator.binaryError(predY, testY)
meanErrors2[i, j] = error/len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
def testParallelVfcvRbf2(self):
#In this test we try SVM regression
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
bestSVM, meanErrors = svm.parallelVfcvRbf(self.X, self.y, idx, type="Epsilon_SVR")
tol = 10**-6
bestError = 100
meanErrors2 = numpy.zeros((svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += svm.getMetricMethod()(predY, testY)
meanErrors2[j, k, i] = error/len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
bestEpsilon = epsilon
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertEquals(bestEpsilon, bestSVM.getEpsilon())
self.assertTrue(numpy.linalg.norm(meanErrors2 - meanErrors) < tol)
def testParallelVfPenRbf(self):
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
resultsList = svm.parallelVfPenRbf(self.X, self.y, idx, Cv)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += Evaluator.binaryError(predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
penalty = penalty*Cv[0]/len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
meanErrors2[i, j] = Evaluator.binaryError(predY, self.y) + penalty
if meanErrors2[i, j] < bestError:
bestC = C
bestGamma = gamma
bestError = meanErrors2[i, j]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
#@unittest.skip("")
def testParallelVfPenRbf2(self):
#Test support vector regression
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
resultsList = svm.parallelVfPenRbf(self.X, self.y, idx, Cv, type="Epsilon_SVR")
tol = 10**-6
bestError = 100
meanErrors2 = numpy.zeros((svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += svm.getMetricMethod()(predY, self.y) - svm.getMetricMethod()(predTrainY, trainY)
penalty = penalty*Cv[0]/len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
meanErrors2[j, k, i] = svm.getMetricMethod()(predY, self.y) + penalty
if meanErrors2[j, k, i] < bestError:
bestC = C
bestGamma = gamma
bestEpsilon = epsilon
bestError = meanErrors2[j, k, i]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertEquals(bestEpsilon, bestSVM.getEpsilon())
self.assertTrue(numpy.linalg.norm(meanErrors2 - meanErrors) < tol)
def testGetC(self):
svm = LibSVM()
svm.setC(10.0)
C = svm.getC()
self.assertTrue(C == 10.0)
def testGetGamma(self):
svm = LibSVM()
svm.setKernel("gaussian", 12.0)
gamma = svm.getKernelParams()
self.assertTrue(gamma == 12.0)
def testComputeTestError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0]*0.5
trainX, trainY = self.X[0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeTestError(args)
svm = LibSVM('gaussian', gamma, C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
self.assertEquals(Evaluator.binaryError(predY, testY), error)
def testComputeBootstrapError(self):
C = 10.0
gamma = 0.5
numTrainExamples = self.X.shape[0]*0.5
trainX, trainY = self.X[0:numTrainExamples, :], self.y[0:numTrainExamples]
testX, testY = self.X[numTrainExamples:, :], self.y[numTrainExamples:]
svm = LibSVM('gaussian', gamma, C)
args = (trainX, trainY, testX, testY, svm)
error = computeBootstrapError(args)
def testComputeIdealPenalty(self):
C = 10.0
gamma = 0.5
svm = LibSVM("gaussian", gamma, C)
args = (self.X, self.y, self.X, self.y, svm)
error = computeIdealPenalty(args)
def testParallelPenaltyGridRbf(self):
svm = self.svm
svm.setKernel("gaussian")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
idealPenalties = svm.parallelPenaltyGridRbf(trainX, trainY, self.X, self.y)
idealPenalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
idealPenalties3 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = Evaluator.binaryError(predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
idealPenalties2[i, j] = penalty
args = (trainX, trainY, self.X, self.y, svm)
idealPenalties3[i, j] = computeIdealPenalty(args)
tol = 10**-6
self.assertTrue(numpy.linalg.norm(idealPenalties2.T - idealPenalties) < tol)
def testParallelPenaltyGridRbf2(self):
#Test with SVM regression
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
idealPenalties = svm.parallelPenaltyGridRbf(trainX, trainY, self.X, self.y, type="Epsilon_SVR")
idealPenalties2 = numpy.zeros((svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = svm.getMetricMethod()(predY, self.y) - svm.getMetricMethod()(predTrainY, trainY)
idealPenalties2[j, k, i] = penalty
tol = 10**-6
self.assertTrue(numpy.linalg.norm(idealPenalties2 - idealPenalties) < tol)
def testParallelModelSelect(self):
folds = 3
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
bestSVM, meanErrors = svm.parallelModelSelect(self.X, self.y, idx, paramDict)
tol = 10**-6
bestError = 1
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
print("Computing real grid")
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
error = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
testX = self.X[testInds, :]
testY = self.y[testInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(testX)
error += Evaluator.binaryError(predY, testY)
meanErrors2[i, j] = error/len(idx)
if error < bestError:
bestC = C
bestGamma = gamma
bestError = error
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
def testParallelPenaltyGrid2(self):
#Test with SVM regression
svm = self.svm
svm.setKernel("gaussian")
svm.setSvmType("Epsilon_SVR")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
paramDict["setEpsilon"] = svm.getEpsilons()
#print(paramDict.keys())
idealPenalties = svm.parallelPenaltyGrid(trainX, trainY, self.X, self.y, paramDict)
idealPenalties2 = numpy.zeros((svm.gammas.shape[0], svm.epsilons.shape[0], svm.Cs.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
for k in range(svm.epsilons.shape[0]):
epsilon = svm.epsilons[k]
svm.setGamma(gamma)
svm.setC(C)
svm.setEpsilon(epsilon)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = svm.getMetricMethod()(predY, self.y) - svm.getMetricMethod()(predTrainY, trainY)
idealPenalties2[j, k, i] = penalty
tol = 10**-6
self.assertTrue(numpy.linalg.norm(idealPenalties2 - idealPenalties) < tol)
def testParallelPen(self):
folds = 3
Cv = numpy.array([4.0])
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm = self.svm
svm.setKernel("gaussian")
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
resultsList = svm.parallelPen(self.X, self.y, idx, paramDict, Cv)
tol = 10**-6
bestError = 1
trainErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
penalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
meanErrors2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
penalty = 0
for trainInds, testInds in idx:
trainX = self.X[trainInds, :]
trainY = self.y[trainInds]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty += Evaluator.binaryError(predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
penalty = penalty*Cv[0]/len(idx)
svm.learnModel(self.X, self.y)
predY = svm.predict(self.X)
trainErrors2[i, j] = Evaluator.binaryError(predY, self.y)
penalties2[i, j] = penalty
meanErrors2[i, j] = Evaluator.binaryError(predY, self.y) + penalty
if meanErrors2[i, j] < bestError:
bestC = C
bestGamma = gamma
bestError = meanErrors2[i, j]
bestSVM, trainErrors, currentPenalties = resultsList[0]
meanErrors = trainErrors + currentPenalties
self.assertEquals(bestC, bestSVM.getC())
self.assertEquals(bestGamma, bestSVM.getGamma())
self.assertTrue(numpy.linalg.norm(meanErrors2.T - meanErrors) < tol)
self.assertTrue(numpy.linalg.norm(trainErrors2.T - trainErrors) < tol)
self.assertTrue(numpy.linalg.norm(penalties2.T - currentPenalties) < tol)
def testParallelPenaltyGrid(self):
svm = self.svm
svm.setKernel("gaussian")
trainX = self.X[0:40, :]
trainY = self.y[0:40]
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
idealPenalties = svm.parallelPenaltyGrid(trainX, trainY, self.X, self.y, paramDict)
idealPenalties2 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
idealPenalties3 = numpy.zeros((svm.Cs.shape[0], svm.gammas.shape[0]))
for i in range(svm.Cs.shape[0]):
C = svm.Cs[i]
for j in range(svm.gammas.shape[0]):
gamma = svm.gammas[j]
svm.setGamma(gamma)
svm.setC(C)
svm.learnModel(trainX, trainY)
predY = svm.predict(self.X)
predTrainY = svm.predict(trainX)
penalty = Evaluator.binaryError(predY, self.y) - Evaluator.binaryError(predTrainY, trainY)
idealPenalties2[i, j] = penalty
args = (trainX, trainY, self.X, self.y, svm)
idealPenalties3[i, j] = computeIdealPenalty(args)
tol = 10**-6
self.assertTrue(numpy.linalg.norm(idealPenalties2.T - idealPenalties) < tol)
def testGetBestLearner(self):
svm = self.svm
paramDict = {}
paramDict["setC"] = svm.getCs()
paramDict["setGamma"] = svm.getGammas()
errors = numpy.random.rand(svm.getCs().shape[0], svm.getGammas().shape[0])
folds = 5
idx = Sampling.crossValidation(folds, self.X.shape[0])
svm.normModelSelect = True
svm.setKernel("gaussian")
learner = svm.getBestLearner(errors, paramDict, self.X, self.y, idx)
bestC = learner.getC()
#Find the best norm
bestInds = numpy.unravel_index(numpy.argmin(errors), errors.shape)
learner.setC(svm.getCs()[bestInds[0]])
learner.setGamma(svm.getGammas()[bestInds[1]])
norms = []
for trainInds, testInds in idx:
validX = self.X[trainInds, :]
validY = self.y[trainInds]
learner.learnModel(validX, validY)
norms.append(learner.weightNorm())
bestNorm = numpy.array(norms).mean()
norms = numpy.zeros(paramDict["setC"].shape[0])
for i, C in enumerate(paramDict["setC"]):
learner.setC(C)
learner.learnModel(self.X, self.y)
norms[i] = learner.weightNorm()
bestC2 = paramDict["setC"][numpy.abs(norms-bestNorm).argmin()]
self.assertEquals(bestC, bestC2)
def testGetC(self):
svm = LibSVM()
svm.setC(10.0)
C = svm.getC()
self.assertTrue(C == 10.0)
def runToyExp(datasetNames, sampleSizes, foldsSet, cvScalings, sampleMethods, numProcesses, fileNameSuffix):
dataDir = PathDefaults.getDataDir() + "modelPenalisation/toy/"
outputDir = PathDefaults.getOutputDir() + "modelPenalisation/"
svm = LibSVM()
numCs = svm.getCs().shape[0]
numGammas = svm.getGammas().shape[0]
numMethods = 1 + (1 + cvScalings.shape[0])
numParams = 2
runIdeal = True
runCv = True
runVfpen = True
for i in range(len(datasetNames)):
datasetName = datasetNames[i][0]
numRealisations = datasetNames[i][1]
logging.debug("Learning using dataset " + datasetName)
for s in range(len(sampleMethods)):
sampleMethod = sampleMethods[s][1]
outfileName = outputDir + datasetName + sampleMethods[s][0] + fileNameSuffix
fileLock = FileLock(outfileName + ".npz")
if not fileLock.isLocked() and not fileLock.fileExists():
fileLock.lock()
errors = numpy.zeros((numRealisations, len(sampleSizes), foldsSet.shape[0], numMethods))
params = numpy.zeros((numRealisations, len(sampleSizes), foldsSet.shape[0], numMethods, numParams))
errorGrids = numpy.zeros(
(numRealisations, len(sampleSizes), foldsSet.shape[0], numMethods, numCs, numGammas)
)
approxGrids = numpy.zeros(
(numRealisations, len(sampleSizes), foldsSet.shape[0], numMethods, numCs, numGammas)
)
idealGrids = numpy.zeros((numRealisations, len(sampleSizes), foldsSet.shape[0], numCs, numGammas))
data = numpy.load(dataDir + datasetName + ".npz")
gridPoints, trainX, trainY, pdfX, pdfY1X, pdfYminus1X = (
data["arr_0"],
data["arr_1"],
data["arr_2"],
data["arr_3"],
data["arr_4"],
data["arr_5"],
)
# We form a test set from the grid points
testX = numpy.zeros((gridPoints.shape[0] ** 2, 2))
for m in range(gridPoints.shape[0]):
testX[m * gridPoints.shape[0] : (m + 1) * gridPoints.shape[0], 0] = gridPoints
testX[m * gridPoints.shape[0] : (m + 1) * gridPoints.shape[0], 1] = gridPoints[m]
for j in range(numRealisations):
Util.printIteration(j, 1, numRealisations, "Realisation: ")
for k in range(sampleSizes.shape[0]):
sampleSize = sampleSizes[k]
for m in range(foldsSet.shape[0]):
folds = foldsSet[m]
logging.debug("Using sample size " + str(sampleSize) + " and " + str(folds) + " folds")
perm = numpy.random.permutation(trainX.shape[0])
trainInds = perm[0:sampleSize]
validX = trainX[trainInds, :]
validY = trainY[trainInds]
svm = LibSVM(processes=numProcesses)
# Find ideal penalties
if runIdeal:
logging.debug("Finding ideal grid of penalties")
idealGrids[j, k, m, :, :] = parallelPenaltyGridRbf(
svm, validX, validY, testX, gridPoints, pdfX, pdfY1X, pdfYminus1X
)
# Cross validation
if runCv:
logging.debug("Running V-fold cross validation")
methodInd = 0
idx = sampleMethod(folds, validY.shape[0])
if sampleMethod == Sampling.bootstrap:
bootstrap = True
else:
bootstrap = False
bestSVM, cvGrid = svm.parallelVfcvRbf(validX, validY, idx, True, bootstrap)
predY, decisionsY = bestSVM.predict(testX, True)
decisionGrid = numpy.reshape(
decisionsY, (gridPoints.shape[0], gridPoints.shape[0]), order="F"
)
errors[j, k, m, methodInd] = ModelSelectUtils.bayesError(
gridPoints, decisionGrid, pdfX, pdfY1X, pdfYminus1X
)
params[j, k, m, methodInd, :] = numpy.array([bestSVM.getC(), bestSVM.getKernelParams()])
errorGrids[j, k, m, methodInd, :, :] = cvGrid
# v fold penalisation
if runVfpen:
logging.debug("Running penalisation")
# BIC penalisation
Cv = float((folds - 1) * numpy.log(validX.shape[0]) / 2)
tempCvScalings = cvScalings * (folds - 1)
tempCvScalings = numpy.insert(tempCvScalings, 0, Cv)
# Use cross validation
idx = sampleMethod(folds, validY.shape[0])
svmGridResults = svm.parallelVfPenRbf(validX, validY, idx, tempCvScalings)
for n in range(len(tempCvScalings)):
bestSVM, trainErrors, approxGrid = svmGridResults[n]
methodInd = n + 1
predY, decisionsY = bestSVM.predict(testX, True)
decisionGrid = numpy.reshape(
decisionsY, (gridPoints.shape[0], gridPoints.shape[0]), order="F"
)
errors[j, k, m, methodInd] = ModelSelectUtils.bayesError(
gridPoints, decisionGrid, pdfX, pdfY1X, pdfYminus1X
)
params[j, k, m, methodInd, :] = numpy.array(
[bestSVM.getC(), bestSVM.getKernelParams()]
)
errorGrids[j, k, m, methodInd, :, :] = trainErrors + approxGrid
approxGrids[j, k, m, methodInd, :, :] = approxGrid
meanErrors = numpy.mean(errors, 0)
print(meanErrors)
meanParams = numpy.mean(params, 0)
print(meanParams)
meanErrorGrids = numpy.mean(errorGrids, 0)
stdErrorGrids = numpy.std(errorGrids, 0)
meanIdealGrids = numpy.mean(idealGrids, 0)
stdIdealGrids = numpy.std(idealGrids, 0)
meanApproxGrids = numpy.mean(approxGrids, 0)
stdApproxGrids = numpy.std(approxGrids, 0)
numpy.savez(
outfileName,
errors,
params,
meanErrorGrids,
stdErrorGrids,
meanIdealGrids,
stdIdealGrids,
meanApproxGrids,
stdApproxGrids,
)
logging.debug("Saved results as file " + outfileName + ".npz")
fileLock.unlock()
else:
logging.debug("Results already computed")
logging.debug("All done!")
def testGetGamma(self):
svm = LibSVM()
svm.setKernel("gaussian", 12.0)
gamma = svm.getKernelParams()
self.assertTrue(gamma == 12.0)
from apgl.util import Util
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
numpy.seterr(all="raise")
numpy.random.seed(21)
dataDir = PathDefaults.getDataDir()
dataDir += "modelPenalisation/regression/"
outputDir = PathDefaults.getOutputDir() + "modelPenalisation/regression/SVR/"
figInd = 0
loadMethod = ModelSelectUtils.loadRegressDataset
datasets = ModelSelectUtils.getRegressionDatasets(True)
numProcesses = multiprocessing.cpu_count()
learner = LibSVM(kernel="rbf", processes=numProcesses, type="Epsilon_SVR")
learner.setChunkSize(3)
Cs = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
gammas = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
epsilons = learner.getEpsilons()
numCs = Cs.shape[0]
numGammas = gammas.shape[0]
paramDict = {}
paramDict["setC"] = Cs
paramDict["setGamma"] = gammas
paramDict["setEpsilon"] = epsilons
print(learner)
def testGetWeights(self):
try:
import sklearn
except ImportError as error:
return
numExamples = 6
X = numpy.array([[-3], [-2], [-1], [1], [2], [3]], numpy.float64)
#X = numpy.random.rand(numExamples, 10)
y = numpy.array([[-1], [-1], [-1], [1], [1], [1]])
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.zeros(numExamples)
decisions2 = numpy.dot(X, weights) - b
self.assertTrue((decisions == decisions2).all())
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
#Do the same test on a random datasets
numExamples = 50
numFeatures = 10
X = numpy.random.rand(numExamples, numFeatures)
y = numpy.sign(numpy.random.rand(numExamples) - 0.5)
svm = LibSVM()
svm.learnModel(X, y.ravel())
weights, b = svm.getWeights()
#Let's see if we can compute the decision values
y, decisions = svm.predict(X, True)
decisions2 = numpy.dot(X, weights) + b
tol = 10**-6
self.assertTrue(numpy.linalg.norm(decisions - decisions2) < tol)
predY = numpy.sign(decisions2)
self.assertTrue((y.ravel() == predY).all())
import logging
import numpy
import os
datasets = ModelSelectUtils.getRegressionDatasets()
numProcesses = 8
dataDir = PathDefaults.getDataDir() + "modelPenalisation/regression/"
datasetName = datasets[9]
print(datasetName)
j = 0
trainX, trainY, testX, testY = ModelSelectUtils.loadRegressDataset(dataDir, datasetName, j)
learner = LibSVM(kernel='gaussian', type="Epsilon_SVR", processes=numProcesses)
paramDict = {}
paramDict["setC"] = 2.0**numpy.arange(-10, 14, 2, dtype=numpy.float)
paramDict["setGamma"] = 2.0**numpy.arange(-10, 4, 2, dtype=numpy.float)
paramDict["setEpsilon"] = learner.getEpsilons()
foldsSet = numpy.arange(2, 31, 2)
Cvs = numpy.array([1.0])
sampleMethod = Sampling.crossValidation
sampleSize = 100
trainInds = numpy.random.permutation(trainX.shape[0])[0:sampleSize]
validX = trainX[trainInds,:]
validY = trainY[trainInds]
def testGetC(self):
svm = LibSVM()
svm.setC(10.0)
C = svm.getC()
self.assertTrue(C == 10.0)
class SvmEgoSimulator(AbstractDiffusionSimulator):
"""
A class which combines SVM classification with the EgoSimulation. There are methods
to run modelSelection, train the SVM and then run the simulation. The simulation itself
is run using EgoSimulator.
"""
def __init__(self, examplesFileName):
"""
Create the class by reading examples from a Matlab file. Instantiate the SVM
and create a preprocesor to standarise examples to have zero mean and unit variance.
"""
self.examplesList = ExamplesList.readFromFile(examplesFileName)
self.examplesList.setDefaultExamplesName("X")
self.examplesList.setLabelsName("y")
(freqs, items) = Util.histogram(self.examplesList.getSampledDataField("y").ravel())
logging.info("Distribution of labels: " + str((freqs, items)))
logging.info("The base error rate is " + str(float(min(freqs))/self.examplesList.getNumExamples()))
self.classifier = LibSVM()
self.errorMethod = Evaluator.balancedError
self.preprocessor = Standardiser()
X = self.preprocessor.standardiseArray(self.examplesList.getDataField(self.examplesList.getDefaultExamplesName()))
self.examplesList.overwriteDataField(self.examplesList.getDefaultExamplesName(), X)
def getPreprocessor(self):
"""
Returns the preprocessor
"""
return self.preprocessor
def sampleExamples(self, sampleSize):
"""
This function exists so that we can sample the same examples used in model
selection and exclude them when running evaluateClassifier.
"""
self.examplesList.randomSubData(sampleSize)
def modelSelection(self, Cs, kernel, kernelParams, errorCosts, folds, sampleSize):
"""
Perform model selection using an SVM
"""
Parameter.checkInt(sampleSize, 0, self.examplesList.getNumExamples())
Parameter.checkInt(folds, 0, sampleSize)
Parameter.checkString(kernel, ["linear", "polynomial", "gaussian"])
Parameter.checkList(Cs, Parameter.checkFloat, [0.0, float("inf")])
Parameter.checkList(errorCosts, Parameter.checkFloat, [0.0, float("inf")])
#Perform model selection
self.examplesList.randomSubData(sampleSize)
(freqs, items) = Util.histogram(self.examplesList.getSampledDataField("y").ravel())
logging.info("Using " + str(sampleSize) + " examples for model selection")
logging.info("Distribution of labels: " + str((freqs, items)))
logging.info("List of Cs " + str(Cs))
logging.info("List of kernels " + str(kernel))
logging.info("List of kernelParams " + str(kernelParams))
logging.info("List of errorCosts " + str(errorCosts))
CVal, kernelParamVal, errorCost, error = self.classifier.cvModelSelection(self.examplesList, Cs, kernelParams, kernel, folds, errorCosts, self.errorMethod)
logging.info("Model selection returned C = " + str(CVal) + " kernelParam = " + str(kernelParamVal) + " errorCost = " + str(errorCost) + " with error " + str(error))
return CVal, kernelParamVal, errorCost, error
def evaluateClassifier(self, CVal, kernel, kernelParamVal, errorCost, folds, sampleSize, invert=True):
"""
Evaluate the SVM with the given parameters. Often model selection is done before this step
and in that case, invert=True uses a sample excluding those used for model selection.
"""
Parameter.checkFloat(CVal, 0.0, float('inf'))
Parameter.checkFloat(errorCost, 0.0, float('inf'))
Parameter.checkString(kernel, ["linear", "polynomial", "gaussian"])
if kernel == "gaussian":
Parameter.checkFloat(kernelParamVal, 0.0, float('inf'))
elif kernel == "polynomial":
Parameter.checkInt(kernelParamVal, 2, float('inf'))
Parameter.checkInt(folds, 0, sampleSize)
Parameter.checkInt(sampleSize, 0, self.examplesList.getNumExamples())
if invert:
allIndices = numpy.array(list(range(0, self.examplesList.getNumExamples())))
testIndices = numpy.setdiff1d(allIndices, self.examplesList.getPermutationIndices())
testIndices = numpy.random.permutation(testIndices)[0:sampleSize]
else:
testIndices = Util.sampleWithoutReplacement(sampleSize, self.examplesList.getNumExamples())
logging.info("Using " + str(testIndices.shape[0]) + " examples for SVM evaluation")
self.examplesList.setPermutationIndices(testIndices)
self.classifier.setParams(C=CVal, kernel=kernel, kernelParam=kernelParamVal)
self.classifier.setErrorCost(errorCost)
(means, vars) = self.classifier.evaluateCv(self.examplesList, folds)
logging.info("--- Classification evaluation ---")
logging.info("Error on " + str(testIndices.shape[0]) + " examples is " + str(means[0]) + "(" + str(vars[0]) + ")")
logging.info("Sensitivity (recall = TP/(TP+FN)): " + str(means[1]) + "(" + str(vars[1]) + ")")
logging.info("Specificity (TN/TN+FP): " + str(means[2]) + "(" + str(vars[2]) + ")")
logging.info("Error on positives: " + str(means[3]) + "(" + str(vars[3]) + ")")
logging.info("Error on negatives: " + str(means[4]) + "(" + str(vars[4]) + ")")
logging.info("Balanced error: " + str(means[5]) + "(" + str(vars[5]) + ")")
return (means, vars)
def trainClassifier(self, CVal, kernel, kernelParamVal, errorCost, sampleSize):
Parameter.checkFloat(CVal, 0.0, float('inf'))
Parameter.checkString(kernel, ["linear", "gaussian", "polynomial"])
Parameter.checkFloat(kernelParamVal, 0.0, float('inf'))
Parameter.checkFloat(errorCost, 0.0, float('inf'))
Parameter.checkInt(sampleSize, 0, self.examplesList.getNumExamples())
logging.info("Training SVM with C=" + str(CVal) + ", " + kernel + " kernel" + ", param=" + str(kernelParamVal) + ", sampleSize=" + str(sampleSize) + ", errorCost=" + str(errorCost))
self.examplesList.randomSubData(sampleSize)
self.classifier.setC(C=CVal)
self.classifier.setKernel(kernel=kernel, kernelParam=kernelParamVal)
self.classifier.setErrorCost(errorCost)
X = self.examplesList.getSampledDataField(self.examplesList.getDefaultExamplesName())
y = self.examplesList.getSampledDataField(self.examplesList.getLabelsName())
y = y.ravel()
self.classifier.learnModel(X, y)
return self.classifier
def getWeights(self):
return self.classifier.getWeights()
def runSimulation(self, maxIterations):
Parameter.checkInt(maxIterations, 1, float('inf'))
#Notice that the data is preprocessed in the same way as the survey data
egoSimulator = EgoSimulator(self.graph, self.classifier, self.preprocessor)
totalInfo = numpy.zeros(maxIterations+1)
totalInfo[0] = EgoUtils.getTotalInformation(self.graph)
logging.info("Total number of people with information: " + str(totalInfo[0]))
logging.info("--- Simulation Started ---")
for i in range(0, maxIterations):
logging.info("--- Iteration " + str(i) + " ---")
self.graph = egoSimulator.advanceGraph()
totalInfo[i+1] = EgoUtils.getTotalInformation(self.graph)
logging.info("Total number of people with information: " + str(totalInfo[i+1]))
#Compute distribution of ages etc. in alters
alterIndices = egoSimulator.getAlters(i)
alterAges = numpy.zeros(len(alterIndices))
alterGenders = numpy.zeros(len(alterIndices))
for j in range(0, len(alterIndices)):
currentVertex = self.graph.getVertex(alterIndices[j])
alterAges[j] = currentVertex[self.egoQuestionIds.index(("Q5X", 0))]
alterGenders[j] = currentVertex[self.egoQuestionIds.index(("Q4", 0))]
(freqs, items) = Util.histogram(alterAges)
logging.info("Distribution of ages " + str(freqs) + " " + str(items))
(freqs, items) = Util.histogram(alterGenders)
logging.info("Distribution of genders " + str(freqs) + " " + str(items))
logging.info("--- Simulation Finished ---")
return totalInfo, egoSimulator.getTransmissions()
def getVertexFeatureDistribution(self, fIndex, vIndices=None):
return self.graph.getVertexFeatureDistribution(fIndex, vIndices)
def getPreProcessor(self):
return self.preprocessor
def getClassifier(self):
return self.classifier
preprocessor = None
examplesList = None
classifier = None
graph = None
edgeWeight = 1
def testGetGamma(self):
svm = LibSVM()
svm.setKernel("gaussian", 12.0)
gamma = svm.getKernelParams()
self.assertTrue(gamma == 12.0)