def visulizeDataSet(network, data, seqno, in_labels, out_labels):
seq = data.getSequence(seqno)
tmpDs = SequentialDataSet(data.indim, data.outdim)
tmpDs.newSequence()
for i in xrange(data.getSequenceLength(seqno)):
tmpDs.addSample(seq[0][i], seq[1][i])
nplots = len(in_labels) + len(out_labels)
for i in range(len(in_labels)):
p = PL.subplot(nplots, 1, i + 1)
p.clear()
p.plot(tmpDs['input'][:, i])
p.set_ylabel(in_labels[i])
for i in range(len(out_labels)):
p = PL.subplot(nplots, 1, i + 1 + len(in_labels))
p.clear()
output = ModuleValidator.calculateModuleOutput(network, tmpDs)
p.plot(tmpDs['target'][:, i], label='train')
p.plot(output[:, i], label='sim')
p.legend()
p.set_ylabel(out_labels[i])
def visulizeDataSet(network, data, seqno, in_labels, out_labels):
seq = data.getSequence(seqno)
tmpDs = SequentialDataSet(data.indim, data.outdim)
tmpDs.newSequence()
for i in xrange(data.getSequenceLength(seqno)):
tmpDs.addSample(seq[0][i], seq[1][i])
nplots = len(in_labels) + len(out_labels)
for i in range(len(in_labels)):
p = PL.subplot(nplots, 1, i + 1)
p.clear()
p.plot(tmpDs['input'][:, i])
p.set_ylabel(in_labels[i])
for i in range(len(out_labels)):
p = PL.subplot(nplots, 1, i + 1 + len(in_labels))
p.clear()
output = ModuleValidator.calculateModuleOutput(network, tmpDs)
p.plot(tmpDs['target'][:, i], label='train')
p.plot(output[:, i], label='sim')
p.legend()
p.set_ylabel(out_labels[i])
def testOnSequenceData(module, dataset):
"""
Fetch targets and calculate the modules output on dataset.
Output and target are in one-of-many format. The class for each sequence is
determined by argmax OF THE LAST ITEM IN THE SEQUENCE.
"""
target = dataset.getField("target")
output = ModuleValidator.calculateModuleOutput(module, dataset)
# determine last indices of the sequences inside dataset
ends = SequenceHelper.getSequenceEnds(dataset)
class_output = array([argmax(output[end]) for end in ends])
class_target = array([argmax(target[end]) for end in ends])
return Validator.classificationPerformance(class_output, class_target)
def main():
train, val = getData()
train_errs = []
val_errs = []
for hiddensize in range(10, 100, 5):
net = buildNetwork(39,
hiddensize,
1,
hiddenclass=SigmoidLayer,
outclass=SigmoidLayer)
trainer = BackpropTrainer(net, train)
for i in range(20):
trainer.train()
verr = ModuleValidator.MSE(net, val)
print hiddensize, ": ", verr
val_errs.append(verr)
train_errs.append(trainer.train())
return (train_errs, val_errs)
def get_segregation(
file_path= "/computed/sentence_analysis_reg.pkl.gz",
error_metric = regression_metric):
# Loading necessary data.
best_module, testData, Y_test = data.load( root + file_path )
n_samples = len(Y_test)
# Computing error and sorting and grouping errors by rating groups
Y_pred = ModuleValidator.calculateModuleOutput(best_module, testData)
error = [ error_metric(Y_pred[i],Y_test[i]) for i in xrange(n_samples) ]
err_and_revidx = zip( error, range(n_samples) )
sorted_err = {0:[], 1:[], 2:[], 3:[], 4:[]}
# for some reason the last n_samples/2 are corrupted and are not alligned to the reviews.
for idx in range(n_samples/2):
sorted_err[ Y_test[idx] ].append( err_and_revidx[idx] )
for idx in range(5):
sorted_err[idx] = sorted( sorted_err[idx] )
return sorted_err
def train(self, args):
if(self.data.ds == None):
print("Can't train without loaded data")
return
if(args != [] and len(args) >= 2):
self.net.epochs = int(args[1])
if(self.net.trainingType == "gradient"):
if(self.trainer == None):
self.trainer, self.returnsNet = self.__getGradientTrainer();
self.__train(self.trainer.trainEpochs, self.returnsNet)
elif(self.net.trainingType == "optimization"):
if(self.trainer == None):
self.trainer, self.returnsNet = self.__getOptimizationTrainer();
self.__train(self.trainer.learn, self.returnsNet)
return
elif(self.trainingType == "crossval"):
if(self.trainer == None):
self.trainer, self.returnsNet = self.__getGradientTrainer();
evaluation = ModuleValidator.classificationPerformance(self.trainer.module, self.data.ds)
validator = CrossValidator(trainer=self.trainer, dataset=self.trainer.ds, n_folds=5, valfunc=evaluation, verbose=True, max_epochs=1)
print(validator.validate())
else:
raise Exception("Cannot create trainer, no network type specified" + self.trainingType)
if tstsplot and ctstsplot:
pylab.plot(tsts['input'], ctsts, c='g')
pylab.xlabel('x')
pylab.ylabel('y')
pylab.title('Neuron Number:' + str(nneuron))
pylab.grid(True)
plotname = os.path.join(plotdir, ('jpq2layers_plot' + str(iter)))
pylab.savefig(plotname)
# set-up the neural network
nneuron = 5
mom = 0.98
netname = "LSL-" + str(nneuron) + "-" + str(mom)
mv = ModuleValidator()
v = Validator()
#create the test DataSet
x = numpy.arange(0.0, 1.0 + 0.01, 0.01)
s = 0.5 + 0.4 * numpy.sin(2 * numpy.pi * x)
tsts = SupervisedDataSet(1, 1)
tsts.setField('input', x.reshape(len(x), 1))
tsts.setField('target', s.reshape(len(s), 1))
#read the train DataSet from file
trndata = SupervisedDataSet.loadFromFile(os.path.join(os.getcwd(), 'trndata'))
myneuralnet = os.path.join(os.getcwd(), 'myneuralnet.xml')
if os.path.isfile(myneuralnet):
n = NetworkReader.readFrom(myneuralnet, name=netname)
#calculate the test DataSet based on the trained Neural Network
starttime = time.time()
print("Training Network 6")
trainer6 = backprop.BackpropTrainer(net6, dataset=train)
score6 = trainer6.train()
trainerrorlist.append(score6)
timeTaken.append(time.time() - starttime)
print("BackPropTrainer 1 has an error rate of " + score1.__str__())
print("BackPropTrainer 2 has an error rate of " + score2.__str__())
print("BackPropTrainer 3 has an error rate of " + score3.__str__())
print("BackPropTrainer 4 has an error rate of " + score4.__str__())
print("BackPropTrainer 5 has an error rate of " + score5.__str__())
print("BackPropTrainer 6 has an error rate of " + score6.__str__())
testErrorArray = []
score1a = ModuleValidator.MSE(net1, test)
testErrorArray.append(score1a)
score2a = ModuleValidator.MSE(net2, test)
testErrorArray.append(score2a)
score3a = ModuleValidator.MSE(net3, test)
testErrorArray.append(score3a)
score4a = ModuleValidator.MSE(net4, test)
testErrorArray.append(score4a)
score5a = ModuleValidator.MSE(net5, test)
testErrorArray.append(score5a)
score6a = ModuleValidator.MSE(net6, test)
testErrorArray.append(score6a)
print("Printing mean square error values")
print("BackPropTrainer 1 has a test error rate of " + score1a.__str__())
print("BackPropTrainer 2 has a test error rate of " + score2a.__str__())
alldata.addSample([-1, -1], [0]) alldata.addSample([-1, -1], [0]) alldata.addSample([-1, -1], [0]) alldata.addSample([-1, -1], [0]) alldata.addSample([1, 1], [1]) alldata.addSample([1, 1], [1]) alldata.addSample([1, 1], [1]) alldata.addSample([1, 1], [1]) alldata.addSample([1, 1], [1]) tstdata, trndata = alldata.splitWithProportion(0.25) trndata._convertToOneOfMany() tstdata._convertToOneOfMany() # We can also examine the dataset print "Number of training patterns: ", len(trndata) print "Input and output dimensions: ", trndata.indim, trndata.outdim print "First sample (input, target, class):" print trndata['input'][0], trndata['target'][0], trndata['class'][0] fnn = buildNetwork( trndata.indim, 5, trndata.outdim, recurrent=False ) trainer = BackpropTrainer( fnn, dataset=trndata, momentum=0.1, verbose=True, weightdecay=0.01 ) # I am not sure about this, I don't think my production code is implemented like this modval = ModuleValidator() trainer.trainEpochs(20) trainer.trainOnDataset(dataset=trndata) cv = CrossValidator( trainer, trndata, n_folds=5, valfunc=modval.MSE ) print "MSE %f" %( cv.validate() )
if tstsplot and ctstsplot:
pylab.plot(tsts['input'], ctsts,c='g')
pylab.xlabel('x')
pylab.ylabel('y')
pylab.title('Neuron Number:'+str(nneuron))
pylab.grid(True)
plotname = os.path.join(plotdir,('jpq2layers_plot'+ str(iter)))
pylab.savefig(plotname)
# set-up the neural network
nneuron = 5
mom = 0.98
netname="LSL-"+str(nneuron)+"-"+str(mom)
mv=ModuleValidator()
v = Validator()
n=FeedForwardNetwork(name=netname)
inLayer = LinearLayer(1,name='in')
hiddenLayer = SigmoidLayer(nneuron,name='hidden0')
outLayer = LinearLayer(1,name='out')
biasinUnit = BiasUnit(name="bhidden0")
biasoutUnit = BiasUnit(name="bout")
n.addInputModule(inLayer)
n.addModule(hiddenLayer)
n.addModule(biasinUnit)
n.addModule(biasoutUnit)
n.addOutputModule(outLayer)
in_to_hidden = FullConnection(inLayer,hiddenLayer)
bias_to_hidden = FullConnection(biasinUnit,hiddenLayer)
bias_to_out = FullConnection(biasoutUnit,outLayer)
def main():
config = MU.ConfigReader('configs/%s' % sys.argv[1])
config.read()
logDir = '%s-%s' % (__file__, sys.argv[1])
os.mkdir(logDir)
with open('%s/config.txt' % logDir, 'w') as outfile:
json.dump(config.getConfigDict(), outfile, indent=4)
dr = MU.DataReader(config['input_tsv_path'])
data = dr.read(config['interested_columns'])
inLabels = config['input_columns']
outLabels = config['output_columns']
tds, vds = seqDataSetPair(data, inLabels, outLabels,
config['seq_label_column'], config['test_seqno'],
config['validation_seqno'])
inScale = config.getDataScale(inLabels)
outScale = config.getDataScale(outLabels)
normalizeDataSet(tds, ins=inScale, outs=outScale)
normalizeDataSet(vds, ins=inScale, outs=outScale)
trainData = tds
validationData = vds
fdim = tds.indim / 5 + 5
xdim = tds.outdim * 2
rnn = buildNetwork(tds.indim,
fdim,
fdim,
fdim,
xdim,
tds.outdim,
hiddenclass=SigmoidLayer,
recurrent=True)
rnn.addRecurrentConnection(FullConnection(rnn['hidden0'], rnn['hidden0']))
rnn.addRecurrentConnection(FullConnection(rnn['hidden1'], rnn['hidden1']))
rnn.addRecurrentConnection(FullConnection(rnn['hidden2'], rnn['hidden2']))
rnn.sortModules()
trainer = RPropMinusTrainer(rnn,
dataset=trainData,
batchlearning=True,
verbose=True,
weightdecay=0.005)
errTime = []
errTrain = []
errValidation = []
epochNo = 0
while True:
for i in range(config['epochs_per_update']):
trainer.train()
epochNo += config['epochs_per_update']
NetworkWriter.writeToFile(rnn, '%s/Epoch_%d.xml' % (logDir, epochNo))
NetworkWriter.writeToFile(rnn, '%s/Latest.xml' % logDir)
tOut = ModuleValidator.calculateModuleOutput(rnn, trainData)
vOut = ModuleValidator.calculateModuleOutput(rnn, validationData)
tScaler = config.getDataScale([config['output_scalar_label']])[0][1]
tAvgErr = NP.sqrt(NP.mean((trainData['target'] - tOut)**2)) * tScaler
vAvgErr = NP.sqrt(NP.mean(
(validationData['target'] - vOut)**2)) * tScaler
tMaxErr = NP.max(NP.abs(trainData['target'] - tOut)) * tScaler
vMaxErr = NP.max(NP.abs(validationData['target'] - vOut)) * tScaler
errTrain.append(tAvgErr)
errValidation.append(vAvgErr)
errTime.append(epochNo)
print "Training error: avg %5.3f max %5.3f" % (tAvgErr,
tMaxErr)
print "Validation error: avg %5.3f max %5.3f" % (vAvgErr,
vMaxErr)
print "------------------------------------------------------------------------------"
if (config['visualize_on_training'] == 'yes'):
PL.figure(1)
PL.ioff()
visulizeDataSet(rnn, trainData, 0,
config['visualized_columns']['input'],
config['visualized_columns']['output'])
PL.ion()
PL.draw()
PL.figure(2)
PL.ioff()
visulizeDataSet(rnn, validationData, 0,
config['visualized_columns']['input'],
config['visualized_columns']['output'])
PL.ion()
PL.draw()
p = PL.figure(3)
PL.ioff()
p.clear()
PL.plot(errTime, errTrain, label='Train')
PL.plot(errTime, errValidation, label='Validation')
PL.legend()
PL.ion()
PL.draw()
timeSpentBuilding.append(end - start)
print("Trainer created")
start = time.clock()
trainer = BackpropTrainer(LSTMNetwork, dataset=train)
error = trainer.train()
end = time.clock()
print str(end - start) + " seconds for the training the network"
print("LSTMNetwork" + str(LSTMNetworkNumber) + " has an error rate of: " +
str(error))
overallError.append(error)
timeSpentTraining.append(end - start)
print("Validating the trained network to the testing one")
start = time.clock()
validation = ModuleValidator.MSE(LSTMNetwork, test)
end = time.clock()
print str(end - start) + " seconds for testing the network"
print("Backpropagation Trainer " + str(LSTMNetworkNumber) +
" has test error rate of: " + str(validation))
testComparison.append(validation)
timeSpentTesting.append(end - start)
LSTMNetworkNumber += 1
# Values for OverallError and TestComparison
print str(overallError)
print str(testComparison)
# Plot of network's error after training
plt.plot([1, 2, 3, 4], overallError)
def runTraining(self, convergence=0, **kwargs):
""" Trains the network on the stored dataset. If convergence is >0, check after that many epoch increments
whether test error is going down again, and stop training accordingly.
CAVEAT: No support for Sequential datasets!"""
assert isinstance(self.Trainer, Trainer)
if self.Graph is not None:
self.Graph.setLabels(x='epoch', y='normalized regression error')
self.Graph.setLegend(['training','test'],loc='upper right')
epoch = 0
inc = self.epoinc
best_error = Infinity
best_epoch = 0
learncurve_x = [0]
learncurve_y = [0.0]
valcurve_y = [0.0]
converged = False
convtest = 0
if convergence>0:
logging.info("Convergence criterion: %d batches of %d epochs w/o improvement" % (convergence, inc))
while epoch<=self.maxepochs and not converged:
self.Trainer.trainEpochs(inc)
epoch+=inc
learncurve_x.append(epoch)
# calculate errors on TRAINING data
err_trn = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.DS)
learncurve_y.append(err_trn)
if self.TDS is None:
logging.info("epoch: %6d, err_trn: %10g" % (epoch, err_trn))
else:
# calculate same errors on TEST data
err_tst = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.TDS)
valcurve_y.append(err_tst)
if err_tst < best_error:
# store best error and parameters
best_epoch = epoch
best_error = err_tst
bestweights = self.Trainer.module.params.copy()
convtest = 0
else:
convtest += 1
logging.info("epoch: %6d, err_trn: %10g, err_tst: %10g, best_tst: %10g" % (epoch, err_trn, err_tst, best_error))
if self.Graph is not None:
self.Graph.addData(1, epoch, err_tst)
# check if convegence criterion is fulfilled (no improvement after N epoincs)
if convtest >= convergence:
converged = True
if self.Graph is not None:
self.Graph.addData(0, epoch, err_trn)
self.Graph.update()
# training finished!
logging.info("Best epoch: %6d, with error: %10g" % (best_epoch, best_error))
if self.VDS is not None:
# calculate same errors on VALIDATION data
self.Trainer.module.params[:] = bestweights.copy()
err_val = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.VDS)
logging.info("Result on evaluation data: %10g" % err_val)
# store training curve for saving into file
self.trainCurve = (learncurve_x, learncurve_y, valcurve_y)
def main():
config = MU.ConfigReader('configs/%s' % sys.argv[1])
config.read()
logDir = '%s-%s' % (__file__, sys.argv[1])
os.mkdir(logDir)
with open('%s/config.txt' % logDir, 'w') as outfile:
json.dump(config.getConfigDict(), outfile, indent=4)
dr = MU.DataReader(config['input_tsv_path'])
data = dr.read(config['interested_columns'])
inLabels = config['input_columns']
outLabels = config['output_columns']
tds, vds = seqDataSetPair(data, inLabels, outLabels, config['seq_label_column'],
config['test_seqno'], config['validation_seqno'])
inScale = config.getDataScale(inLabels)
outScale = config.getDataScale(outLabels)
normalizeDataSet(tds, ins = inScale, outs = outScale)
normalizeDataSet(vds, ins = inScale, outs = outScale)
trainData = tds
validationData = vds
fdim = tds.indim / 2 + 15
xdim = tds.outdim * 2
rnn = buildNetwork(tds.indim,
fdim, fdim, xdim,
tds.outdim,
hiddenclass=SigmoidLayer,
recurrent=True)
rnn.addRecurrentConnection(FullConnection(rnn['hidden2'], rnn['hidden0']))
rnn.sortModules()
trainer = RPropMinusTrainer(rnn, dataset=trainData, batchlearning=True, verbose=True, weightdecay=0.005)
#trainer = RPropMinusTrainer(rnn, dataset=trainData, batchlearning=True, verbose=True)
#trainer = BackpropTrainer(rnn, dataset=trainData, learningrate=0.0001,
# lrdecay=1.0, momentum=0.4, verbose=True, batchlearning=False,
# weightdecay=0)
errTime = []
errTrain = []
errValidation = []
epochNo = 0
while True:
for i in range(config['epochs_per_update']):
trainer.train()
epochNo += config['epochs_per_update']
NetworkWriter.writeToFile(rnn, '%s/Epoch_%d.xml' % (logDir, epochNo))
NetworkWriter.writeToFile(rnn, '%s/Latest.xml' % logDir)
tOut = ModuleValidator.calculateModuleOutput(rnn, trainData)
vOut = ModuleValidator.calculateModuleOutput(rnn, validationData)
tScaler = config.getDataScale([config['output_scalar_label']])[0][1]
tAvgErr = NP.sqrt(NP.mean((trainData['target'] - tOut) ** 2)) * tScaler
vAvgErr = NP.sqrt(NP.mean((validationData['target'] - vOut) ** 2)) * tScaler
tMaxErr = NP.max(NP.abs(trainData['target'] - tOut)) * tScaler
vMaxErr = NP.max(NP.abs(validationData['target'] - vOut)) * tScaler
errTrain.append(tAvgErr)
errValidation.append(vAvgErr)
errTime.append(epochNo)
print "Training error: avg %5.3f degC max %5.3f degC" % (tAvgErr, tMaxErr)
print "Validation error: avg %5.3f degC max %5.3f degC" % (vAvgErr, vMaxErr)
print "------------------------------------------------------------------------------"
if (config['visualize_on_training'] == 'yes'):
PL.figure(1)
PL.ioff()
visulizeDataSet(rnn, trainData, 0,
config['visualized_columns']['input'],
config['visualized_columns']['output'])
PL.ion()
PL.draw()
PL.figure(2)
PL.ioff()
visulizeDataSet(rnn, validationData, 0,
config['visualized_columns']['input'],
config['visualized_columns']['output'])
PL.ion()
PL.draw()
p = PL.figure(3)
PL.ioff()
p.clear()
PL.plot(errTime, errTrain, label = 'Train')
PL.plot(errTime, errValidation, label = 'Validation')
PL.legend()
PL.ion()
PL.draw()
import pylab, numpy
from pybrain.tools.shortcuts import buildNetwork
from pybrain.structure import TanhLayer
from pybrain.datasets import SupervisedDataSet
from pybrain.supervised.trainers import BackpropTrainer
from pybrain.tools.validation import CrossValidator, ModuleValidator
results = pylab.loadtxt('credit.txt')
target = results[:, -1]
data = numpy.delete(results, -1, 1)
#print "data", tuple(data[0])
#print "target", (target[0],)
#net = buildNetwork(14, 10, 1)
net = buildNetwork(14, 10, 1, hiddenclass=TanhLayer)
#print net.activate([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14])
ds = SupervisedDataSet(14, 1)
for i in range(len(data)):
ds.addSample(tuple(data[i]), (target[i], ))
trainer = BackpropTrainer(net, ds)
evaluation = ModuleValidator()
validator = CrossValidator(trainer=trainer,
dataset=trainer.ds,
n_folds=5,
valfunc=evaluation.MSE)
print(validator.validate())
def correct(output, target): return ModuleValidator.validate(correctValFunc, output, target)
if tstsplot and ctstsplot:
pylab.plot(tsts['input'], ctsts,c='g')
pylab.xlabel('x')
pylab.ylabel('y')
pylab.title('Neuron Number:'+str(nneuron))
pylab.grid(True)
plotname = os.path.join(plotdir,('jpq2layers_plot'+ str(iter)))
pylab.savefig(plotname)
# set-up the neural network
nneuron = 5
mom = 0.98
netname="LSL-"+str(nneuron)+"-"+str(mom)
mv=ModuleValidator()
v = Validator()
#create the test DataSet
x = numpy.arange(0.0, 1.0+0.01, 0.01)
s = 0.5+0.4*numpy.sin(2*numpy.pi*x)
tsts = SupervisedDataSet(1,1)
tsts.setField('input',x.reshape(len(x),1))
tsts.setField('target',s.reshape(len(s),1))
#read the train DataSet from file
trndata = SupervisedDataSet.loadFromFile(os.path.join(os.getcwd(),'trndata'))
myneuralnet = os.path.join(os.getcwd(),'myneuralnet.xml')
if os.path.isfile(myneuralnet):
n = NetworkReader.readFrom(myneuralnet,name=netname)
treinadorSupervisionado = BackpropTrainer(rn, dados)
numeroDeAcessos = 10
numeroDeEpocasPorAcesso = 50
fig1 = plt.figure()
ax1 = fig1.add_subplot(111)
ax1.axis([0, 2 * math.pi, -1.5, 1.5])
fig1.hold()
fig2 = plt.figure()
ax2 = fig2.add_subplot(111)
ax2.axis([-50, numeroDeAcessos * numeroDeEpocasPorAcesso + 50, 0.00001, 4])
ax2.set_yscale('log')
fig2.hold()
meansq = ModuleValidator()
erro2 = meansq.MSE(treinadorSupervisionado.module, dados)
print erro2
ax2.plot([0], [erro2], 'bo')
tempoPausa = 1
for i in range(numeroDeAcessos):
treinadorSupervisionado.trainEpochs(numeroDeEpocasPorAcesso)
meansq = ModuleValidator()
erro2 = meansq.MSE(treinadorSupervisionado.module, dados)
print erro2
ax1.plot(dados['input'],
dados['target'],
'bo',
markersize=7,
markeredgewidth=0)
trainer = ReinforcedTrainer(module=nn, rewarder=rewardFunc)
from pybrain.tools.validation import ModuleValidator
import thread
def userthread():
from IPython.Shell import IPShellEmbed
ipshell = IPShellEmbed()
ipshell()
#thread.start_new_thread(userthread, ())
# carry out the training
while True:
trndata = generateData(nseq=20, ratevarlimit=random.uniform(0.0, 0.3))
tstdata = generateData(nseq=20)
trainer.setData(trndata)
trainer.train()
trnresult = 100. * (ModuleValidator.MSE(nn, trndata))
tstresult = 100. * (ModuleValidator.MSE(nn, tstdata))
print "train error: %5.2f%%" % trnresult, ", test error: %5.2f%%" % tstresult
s = getRandomSeq(100, ratevarlimit=random.uniform(0.0, 1.0))
print " real:", seqStr(s)
print " nn:", getSeqOutputFromNN(nn, s)
hidden_layer_size=200
net = buildNetwork( t-1 , hidden_layer_size, 1 ,bias = True )
trainer = BackpropTrainer( module=net, dataset=ds1, momentum=0.1, verbose=True, weightdecay=0.01)
for i in range(20):
print("Training Epoch #"+str(i))
trainer.trainEpochs( 1 )
p = net.activateOnDataset(ds2)
p = p.argmax(axis=1) # the highest output activation gives the class
p = p.reshape(-1,-1)
print p
hitrate = ModuleValidator.classificationPerformance(module=net,dataset=ds1)
print hitrate
#trainer.trainUntilConvergence( verbose = True, validationProportion = 0.15, maxEpochs = 20)
# for i in range(20):
# trainer.trainEpochs(3)
# trnresult = percentError(trainer.testOnClassData(),y_train)
# tstresult = percentError(trainer.testOnClassData(dataset=ds2),y_test)
# print "epoch: %4d" % trainer.totalepochs, \
# "train error: %5.2f%%" % trnresult, \
# "test error: %5.2f%%" % tstresult
# out = net.activateOnDataset(ds1)
# out = out.argmax(axis=1) # the highest output activation gives the class
# #print out
# figure(1)
def correct(output, target):
return ModuleValidator.validate(correctValFunc, output, target)
def eval_nn(params):
global nn, trndata
nn.reset()
nn.params[:] = params
return ModuleValidator.MSE(nn, trndata)
def runTraining(self, convergence=0, **kwargs):
""" Trains the network on the stored dataset. If convergence is >0, check after that many epoch increments
whether test error is going down again, and stop training accordingly.
CAVEAT: No support for Sequential datasets!"""
assert isinstance(self.Trainer, Trainer)
if self.Graph is not None:
self.Graph.setLabels(x='epoch', y='normalized regression error')
self.Graph.setLegend(['training','test'],loc='upper right')
epoch = 0
inc = self.epoinc
best_error = Infinity
best_epoch = 0
learncurve_x = [0]
learncurve_y = [0.0]
valcurve_y = [0.0]
converged = False
convtest = 0
if convergence>0:
logging.info("Convergence criterion: %d batches of %d epochs w/o improvement" % (convergence, inc))
while epoch<=self.maxepochs and not converged:
self.Trainer.trainEpochs(inc)
epoch+=inc
learncurve_x.append(epoch)
# calculate errors on TRAINING data
err_trn = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.DS)
learncurve_y.append(err_trn)
if self.TDS is None:
logging.info("epoch: %6d, err_trn: %10g" % (epoch, err_trn))
else:
# calculate same errors on TEST data
err_tst = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.TDS)
valcurve_y.append(err_tst)
if err_tst < best_error:
# store best error and parameters
best_epoch = epoch
best_error = err_tst
bestweights = self.Trainer.module.params.copy()
convtest = 0
else:
convtest += 1
logging.info("epoch: %6d, err_trn: %10g, err_tst: %10g, best_tst: %10g" % (epoch, err_trn, err_tst, best_error))
if self.Graph is not None:
self.Graph.addData(1, epoch, err_tst)
# check if convegence criterion is fulfilled (no improvement after N epoincs)
if convtest >= convergence:
converged = True
if self.Graph is not None:
self.Graph.addData(0, epoch, err_trn)
self.Graph.update()
# training finished!
logging.info("Best epoch: %6d, with error: %10g" % (best_epoch, best_error))
if self.VDS is not None:
# calculate same errors on VALIDATION data
self.Trainer.module.params[:] = bestweights.copy()
err_val = ModuleValidator.validate(Validator.MSE, self.Trainer.module, self.VDS)
logging.info("Result on evaluation data: %10g" % err_val)
# store training curve for saving into file
self.trainCurve = (learncurve_x, learncurve_y, valcurve_y)
def score(self, x_data, y_datas):
return ModuleValidator.validate(regression_score, self.net, self._prepare_dataset(x_data, y_datas))
trainer = RPropMinusTrainer(net, dataset=train_ds)
train_errors = []
# save errors for plotting later
EPOCHS_PER_CYCLE = 10
CYCLES = 10
EPOCHS = EPOCHS_PER_CYCLE * CYCLES
for a in xrange(CYCLES):
trainer.trainEpochs(EPOCHS_PER_CYCLE)
train_errors.append(trainer.testOnData())
epoch = (a+1) * EPOCHS_PER_CYCLE
print("\r epoch {}/{}".format(epoch, EPOCHS), end="")
stdout.flush()
print("final error for training =", train_errors[-1])
err_tst = ModuleValidator.validate(Validator.MSE, net, dataset=test_ds)
eval_err.append(err_tst)
modnet.append(net)
print("test_Err", err_tst)
print(eval_err)
pmin = eval_err.index(min(eval_err))
print(pmin)
net = modnet[pmin]
hypernet.append(net)
hypereval.append(min(eval_err))
hypermin = hypereval.index(min(eval_err))
net = hypernet[hypermin]
print("number of hidden layers", hypermin+1)
def main():
config = MU.ConfigReader("configs/%s" % sys.argv[1])
config.read()
logDir = "%s-%s" % (__file__, sys.argv[1])
os.mkdir(logDir)
with open("%s/config.txt" % logDir, "w") as outfile:
json.dump(config.getConfigDict(), outfile, indent=4)
dr = MU.DataReader(config["input_tsv_path"])
data = dr.read(config["interested_columns"])
inLabels = config["input_columns"]
outLabels = config["output_columns"]
tds, vds = seqDataSetPair(
data, inLabels, outLabels, config["seq_label_column"], config["test_seqno"], config["validation_seqno"]
)
inScale = config.getDataScale(inLabels)
outScale = config.getDataScale(outLabels)
normalizeDataSet(tds, ins=inScale, outs=outScale)
normalizeDataSet(vds, ins=inScale, outs=outScale)
trainData = tds
validationData = vds
fdim = tds.indim / 5 + 5
xdim = tds.outdim * 2
rnn = buildNetwork(tds.indim, fdim, fdim, xdim, tds.outdim, hiddenclass=SigmoidLayer, recurrent=True)
rnn.addRecurrentConnection(FullConnection(rnn["hidden0"], rnn["hidden0"]))
rnn.addRecurrentConnection(FullConnection(rnn["hidden1"], rnn["hidden1"]))
rnn.sortModules()
trainer = RPropMinusTrainer(rnn, dataset=trainData, batchlearning=True, verbose=True)
errTime = []
errTrain = []
errValidation = []
epochNo = 0
while True:
for i in range(config["epochs_per_update"]):
trainer.train()
epochNo += config["epochs_per_update"]
NetworkWriter.writeToFile(rnn, "%s/Epoch_%d.xml" % (logDir, epochNo))
NetworkWriter.writeToFile(rnn, "%s/Latest.xml" % logDir)
tOut = ModuleValidator.calculateModuleOutput(rnn, trainData)
vOut = ModuleValidator.calculateModuleOutput(rnn, validationData)
tScaler = config.getDataScale([config["output_scalar_label"]])[0][1]
tAvgErr = NP.sqrt(NP.mean((trainData["target"] - tOut) ** 2)) * tScaler
vAvgErr = NP.sqrt(NP.mean((validationData["target"] - vOut) ** 2)) * tScaler
tMaxErr = NP.max(NP.abs(trainData["target"] - tOut)) * tScaler
vMaxErr = NP.max(NP.abs(validationData["target"] - vOut)) * tScaler
errTrain.append(tAvgErr)
errValidation.append(vAvgErr)
errTime.append(epochNo)
print "Training error: avg %5.3f degC max %5.3f degC" % (tAvgErr, tMaxErr)
print "Validation error: avg %5.3f degC max %5.3f degC" % (vAvgErr, vMaxErr)
print "------------------------------------------------------------------------------"
if config["visualize_on_training"] == "yes":
PL.figure(1)
PL.ioff()
visulizeDataSet(
rnn, trainData, 0, config["visualized_columns"]["input"], config["visualized_columns"]["output"]
)
PL.ion()
PL.draw()
PL.figure(2)
PL.ioff()
visulizeDataSet(
rnn, validationData, 0, config["visualized_columns"]["input"], config["visualized_columns"]["output"]
)
PL.ion()
PL.draw()
p = PL.figure(3)
PL.ioff()
p.clear()
PL.plot(errTime, errTrain, label="Train")
PL.plot(errTime, errValidation, label="Validation")
PL.legend()
PL.ion()
PL.draw()
