connectedCounts = connectedCounts.astype(uintType)
sp.getConnectedCounts(connectedCounts)
connectedCounts = connectedCounts.astype(realDType)
entropyTrace.append(
calculateEntropy(activeColumnsCurrentEpoch[:, aliveColumns]))
boostFactors = np.zeros((columnNumber, ), dtype=realDType)
sp.getBoostFactors(boostFactors)
meanBoostFactorTrace.append(np.mean(boostFactors))
activeDutyCycle = np.zeros((columnNumber, ), dtype=realDType)
sp.getActiveDutyCycles(activeDutyCycle)
if epoch >= 1:
stability = calculateStability(activeColumnsCurrentEpoch,
activeColumnsPreviousEpoch)
stabilityTrace.append(stability)
numConnectedSynapsesTrace.append(np.sum(connectedCounts))
numNewSynapses = connectedCounts - connectedCountsPreviousEpoch
numNewSynapses[numNewSynapses < 0] = 0
numNewlyConnectedSynapsesTrace.append(np.sum(numNewSynapses))
numEliminatedSynapses = connectedCountsPreviousEpoch - connectedCounts
numEliminatedSynapses[numEliminatedSynapses < 0] = 0
numEliminatedSynapsesTrace.append(np.sum(numEliminatedSynapses))
metrics = {
'connected syn': [numConnectedSynapsesTrace[-1]],
'new syn': [numNewlyConnectedSynapsesTrace[-1]],
def runSPexperiments(expConfig):
inputVectorType = expConfig.dataSet
params = getSDRDataSetParams(expConfig.dataSet, int(expConfig.seed))
expName = getExperimentName(expConfig)
createDirectories(expName)
sdrData = SDRDataSet(params)
inputVectors = sdrData.getInputVectors()
numInputVector, inputSize = inputVectors.shape
plt.figure()
plt.imshow(np.reshape(inputVectors[2], (params['nX'], params['nY'])),
interpolation='nearest',
cmap='gray')
plt.savefig('figures/exampleInputs/{}'.format(expName))
print
print "Runnning experiment: {}".format(expName)
print "Training Data Size {} Dimensions {}".format(numInputVector,
inputSize)
spParams = getSpatialPoolerParams(params, expConfig)
sp = createSpatialPooler(expConfig.spatialImp, spParams)
if expConfig.topology == 1 and expConfig.spatialImp in ['faulty_sp', 'py']:
initializeSPConnections(sp, potentialRaidus=10, initConnectionRadius=5)
numColumns = np.prod(sp.getColumnDimensions())
numTestInputs = int(numInputVector * 0.5)
testInputs = inputVectors[:numTestInputs, :]
connectedCounts = np.zeros((numColumns, ), dtype=uintType)
boostFactors = np.zeros((numColumns, ), dtype=realDType)
activeDutyCycle = np.zeros((numColumns, ), dtype=realDType)
metrics = {
'numConnectedSyn': [],
'numNewSyn': [],
'numRemoveSyn': [],
'stability': [],
'entropy': [],
'maxEntropy': [],
'sparsity': [],
'noiseRobustness': [],
'classification': [],
'meanBoostFactor': [],
'reconstructionError': [],
'witnessError': []
}
connectedSyns = getConnectedSyns(sp)
activeColumnsCurrentEpoch, dum = runSPOnBatch(sp, testInputs, learn=False)
inspectSpatialPoolerStats(sp, inputVectors, expName + "beforeTraining")
checkPoints = [
0, expConfig.changeDataSetAt - 1, expConfig.changeDataSetAt,
expConfig.numEpochs - 1
]
epoch = 0
while epoch < expConfig.numEpochs:
print "training SP epoch {} ".format(epoch)
if (expConfig.changeDataSetContinuously
or epoch == expConfig.changeDataSetAt):
params['seed'] = epoch
sdrData.generateInputVectors(params)
inputVectors = sdrData.getInputVectors()
numInputVector, inputSize = inputVectors.shape
testInputs = inputVectors[:numTestInputs, :]
if expConfig.killInputsAfter > 0 and epoch > expConfig.killInputsAfter:
if expConfig.topology == 1:
inputSpaceDim = (params['nX'], params['nY'])
centerColumn = indexFromCoordinates((15, 15), inputSpaceDim)
deadInputs = topology.wrappingNeighborhood(
centerColumn, 5, inputSpaceDim)
else:
zombiePermutation = np.random.permutation(inputSize)
deadInputs = zombiePermutation[:100]
inputVectors[:, deadInputs] = 0
if epoch == expConfig.killCellsAt:
if expConfig.spatialImp in ['faulty_sp', 'monitored_faulty_sp']:
if expConfig.topology == 1:
centerColumn = indexFromCoordinates((15, 15),
sp._columnDimensions)
sp.killCellRegion(centerColumn, 5)
else:
sp.killCells(expConfig.killCellPrct)
if expConfig.trackOverlapCurve:
noiseLevelList, inputOverlapScore, outputOverlapScore = \
calculateOverlapCurve(sp, testInputs)
metrics['noiseRobustness'].append(
np.trapz(np.flipud(np.mean(outputOverlapScore, 0)),
noiseLevelList))
np.savez(
'./results/input_output_overlap/{}/epoch_{}'.format(
expName, epoch), noiseLevelList, inputOverlapScore,
outputOverlapScore)
if expConfig.classification:
# classify SDRs with noise
noiseLevelList = np.linspace(0, 1.0, 21)
classification_accuracy = classificationAccuracyVsNoise(
sp, testInputs, noiseLevelList)
metrics['classification'].append(
np.trapz(classification_accuracy, noiseLevelList))
np.savez(
'./results/classification/{}/epoch_{}'.format(expName, epoch),
noiseLevelList, classification_accuracy)
# train SP here,
# Learn is turned off at the first epoch to gather stats of untrained SP
learn = False if epoch == 0 else True
# randomize the presentation order of input vectors
sdrOrders = np.random.permutation(np.arange(numInputVector))
activeColumnsTrain, meanBoostFactors = runSPOnBatch(
sp, inputVectors, learn, sdrOrders)
# run SP on test dataset and compute metrics
activeColumnsPreviousEpoch = copy.copy(activeColumnsCurrentEpoch)
activeColumnsCurrentEpoch, dum = runSPOnBatch(sp,
testInputs,
learn=False)
stability = calculateStability(activeColumnsCurrentEpoch,
activeColumnsPreviousEpoch)
if (expConfig.changeDataSetContinuously
or epoch == expConfig.changeDataSetAt):
stability = float('nan')
metrics['stability'].append(stability)
metrics['sparsity'].append(
np.mean(np.mean(activeColumnsCurrentEpoch, 1)))
metrics['entropy'].append(calculateEntropy(activeColumnsCurrentEpoch))
# generate ideal SP outputs where all columns have the same activation prob.
activeColumnsIdeal = np.random.rand(
numInputVector, numColumns) > metrics['sparsity'][-1]
metrics['maxEntropy'].append(calculateEntropy(activeColumnsIdeal))
connectedSynsPreviousEpoch = copy.copy(connectedSyns)
sp.getConnectedCounts(connectedCounts)
connectedSyns = getConnectedSyns(sp)
metrics['meanBoostFactor'].append(np.mean(meanBoostFactors))
sp.getActiveDutyCycles(activeDutyCycle)
metrics['numConnectedSyn'].append(np.sum(connectedCounts))
numNewSynapses = connectedSyns - connectedSynsPreviousEpoch
numNewSynapses[numNewSynapses < 0] = 0
metrics['numNewSyn'].append(np.sum(numNewSynapses))
numEliminatedSynapses = connectedSynsPreviousEpoch - connectedSyns
numEliminatedSynapses[numEliminatedSynapses < 0] = 0
metrics['numRemoveSyn'].append(np.sum(numEliminatedSynapses))
metrics['reconstructionError'].append(
reconstructionError(sp, testInputs, activeColumnsCurrentEpoch))
metrics['witnessError'].append(
witnessError(sp, testInputs, activeColumnsCurrentEpoch))
print tabulate(metrics, headers="keys")
if expConfig.checkRFCenters:
# check distribution of RF centers, useful to monitor recovery from trauma
RFcenters, avgDistToCenter = getRFCenters(sp,
params,
type='connected')
if expConfig.spatialImp == 'faulty_sp':
aliveColumns = sp.getAliveColumns()
else:
aliveColumns = np.arange(numColumns)
fig = plotReceptiveFieldCenter(RFcenters[aliveColumns, :],
connectedCounts[aliveColumns],
(params['nX'], params['nY']))
plt.savefig('figures/RFcenters/{}/epoch_{}.png'.format(
expName, epoch))
plt.close(fig)
np.savez('results/RFcenters/{}/epoch_{}'.format(expName, epoch),
RFcenters, avgDistToCenter)
if expConfig.checkInputSpaceCoverage:
# check coverage of input space, useful to monitor recovery from trauma
inputSpaceCoverage = calculateInputSpaceCoverage(sp)
np.savez(
'results/InputCoverage/{}/epoch_{}'.format(expName, epoch),
inputSpaceCoverage, connectedCounts)
plt.figure(2)
plt.clf()
plt.imshow(inputSpaceCoverage, interpolation='nearest', cmap="jet")
plt.colorbar()
plt.savefig('figures/InputCoverage/{}/epoch_{}.png'.format(
expName, epoch))
if expConfig.checkTestInput:
RFcenters, avgDistToCenter = getRFCenters(sp,
params,
type='connected')
inputIdx = 0
outputColumns = np.zeros((numColumns, 1), dtype=uintType)
sp.compute(testInputs[inputIdx, :], False, outputColumns)
activeColumns = np.where(outputColumns > 0)[0]
fig = plotReceptiveFieldCenter(RFcenters[aliveColumns, :],
connectedCounts[aliveColumns],
(params['nX'], params['nY']))
plt.scatter(RFcenters[activeColumns, 0],
RFcenters[activeColumns, 1],
color='r')
plt.savefig('figures/ResponseToTestInputs/{}/epoch_{}.png'.format(
expName, epoch))
if expConfig.saveBoostFactors:
np.savez('results/boostFactors/{}/epoch_{}'.format(expName, epoch),
meanBoostFactors)
if expConfig.showExampleRFs:
fig = plotReceptiveFields2D(sp, params['nX'], params['nY'])
plt.savefig('figures/exampleRFs/{}/epoch_{}'.format(
expName, epoch))
plt.close(fig)
if epoch in checkPoints:
# inspect SP again
inspectSpatialPoolerStats(sp, inputVectors,
expName + "epoch{}".format(epoch))
epoch += 1
# plot stats over training
fileName = 'figures/network_stats_over_training_{}.pdf'.format(expName)
plotSPstatsOverTime(metrics, fileName)
metrics['expName'] = expName
pickle.dump(metrics, open('results/traces/{}/trace'.format(expName), 'wb'))
plotReceptiveFields2D(sp, params['nX'], params['nY'])
inspectSpatialPoolerStats(sp, inputVectors,
inputVectorType + "afterTraining")
plotExampleInputOutput(sp, inputVectors, expName + "final")
return metrics, expName
def runSPexperiments(expConfig):
inputVectorType = expConfig.dataSet
params = getSDRDataSetParams(expConfig.dataSet, int(expConfig.seed))
expName = getExperimentName(expConfig)
createDirectories(expName)
sdrData = SDRDataSet(params)
inputVectors = sdrData.getInputVectors()
numInputVector, inputSize = inputVectors.shape
plt.figure()
plt.imshow(np.reshape(inputVectors[2], (params['nX'], params['nY'])),
interpolation='nearest', cmap='gray')
plt.savefig('figures/exampleInputs/{}'.format(expName))
print
print "Runnning experiment: {}".format(expName)
print "Training Data Size {} Dimensions {}".format(numInputVector, inputSize)
spParams = getSpatialPoolerParams(params, expConfig)
sp = createSpatialPooler(expConfig.spatialImp, spParams)
if expConfig.topology == 1 and expConfig.spatialImp in ['faulty_sp', 'py']:
initializeSPConnections(sp, potentialRaidus=10, initConnectionRadius=5)
numColumns = np.prod(sp.getColumnDimensions())
numTestInputs = int(numInputVector * 0.5)
testInputs = inputVectors[:numTestInputs, :]
connectedCounts = np.zeros((numColumns,), dtype=uintType)
boostFactors = np.zeros((numColumns,), dtype=realDType)
activeDutyCycle = np.zeros((numColumns,), dtype=realDType)
metrics = {'numConnectedSyn': [],
'numNewSyn': [],
'numRemoveSyn': [],
'stability': [],
'entropy': [],
'maxEntropy': [],
'sparsity': [],
'noiseRobustness': [],
'classification': [],
'meanBoostFactor': [],
'reconstructionError': [],
'witnessError': []}
connectedSyns = getConnectedSyns(sp)
activeColumnsCurrentEpoch, dum = runSPOnBatch(sp, testInputs, learn=False)
inspectSpatialPoolerStats(sp, inputVectors, expName + "beforeTraining")
checkPoints = [0, expConfig.changeDataSetAt - 1,
expConfig.changeDataSetAt, expConfig.numEpochs - 1]
epoch = 0
while epoch < expConfig.numEpochs:
print "training SP epoch {} ".format(epoch)
if (expConfig.changeDataSetContinuously or
epoch == expConfig.changeDataSetAt):
params['seed'] = epoch
sdrData.generateInputVectors(params)
inputVectors = sdrData.getInputVectors()
numInputVector, inputSize = inputVectors.shape
testInputs = inputVectors[:numTestInputs, :]
if expConfig.killInputsAfter > 0 and epoch > expConfig.killInputsAfter:
if expConfig.topology == 1:
inputSpaceDim = (params['nX'], params['nY'])
centerColumn = indexFromCoordinates((15, 15), inputSpaceDim)
deadInputs = topology.wrappingNeighborhood(centerColumn, 5, inputSpaceDim)
else:
zombiePermutation = np.random.permutation(inputSize)
deadInputs = zombiePermutation[:100]
inputVectors[:, deadInputs] = 0
if epoch == expConfig.killCellsAt:
if expConfig.spatialImp in ['faulty_sp', 'monitored_faulty_sp']:
if expConfig.topology == 1:
centerColumn = indexFromCoordinates((15, 15), sp._columnDimensions)
sp.killCellRegion(centerColumn, 5)
else:
sp.killCells(expConfig.killCellPrct)
if expConfig.trackOverlapCurve:
noiseLevelList, inputOverlapScore, outputOverlapScore = \
calculateOverlapCurve(sp, testInputs)
metrics['noiseRobustness'].append(
np.trapz(np.flipud(np.mean(outputOverlapScore, 0)),
noiseLevelList))
np.savez(
'./results/input_output_overlap/{}/epoch_{}'.format(expName, epoch),
noiseLevelList, inputOverlapScore, outputOverlapScore)
if expConfig.classification:
# classify SDRs with noise
noiseLevelList = np.linspace(0, 1.0, 21)
classification_accuracy = classificationAccuracyVsNoise(
sp, testInputs, noiseLevelList)
metrics['classification'].append(
np.trapz(classification_accuracy, noiseLevelList))
np.savez('./results/classification/{}/epoch_{}'.format(expName, epoch),
noiseLevelList, classification_accuracy)
# train SP here,
# Learn is turned off at the first epoch to gather stats of untrained SP
learn = False if epoch == 0 else True
# randomize the presentation order of input vectors
sdrOrders = np.random.permutation(np.arange(numInputVector))
activeColumnsTrain, meanBoostFactors = runSPOnBatch(sp, inputVectors, learn, sdrOrders)
# run SP on test dataset and compute metrics
activeColumnsPreviousEpoch = copy.copy(activeColumnsCurrentEpoch)
activeColumnsCurrentEpoch, dum = runSPOnBatch(sp, testInputs, learn=False)
stability = calculateStability(activeColumnsCurrentEpoch,
activeColumnsPreviousEpoch)
if (expConfig.changeDataSetContinuously or
epoch == expConfig.changeDataSetAt):
stability = float('nan')
metrics['stability'].append(stability)
metrics['sparsity'].append(np.mean(np.mean(activeColumnsCurrentEpoch, 1)))
metrics['entropy'].append(calculateEntropy(activeColumnsCurrentEpoch))
# generate ideal SP outputs where all columns have the same activation prob.
activeColumnsIdeal = np.random.rand(numInputVector, numColumns) > metrics['sparsity'][-1]
metrics['maxEntropy'].append(calculateEntropy(activeColumnsIdeal))
connectedSynsPreviousEpoch = copy.copy(connectedSyns)
sp.getConnectedCounts(connectedCounts)
connectedSyns = getConnectedSyns(sp)
metrics['meanBoostFactor'].append(np.mean(meanBoostFactors))
sp.getActiveDutyCycles(activeDutyCycle)
metrics['numConnectedSyn'].append(np.sum(connectedCounts))
numNewSynapses = connectedSyns - connectedSynsPreviousEpoch
numNewSynapses[numNewSynapses < 0] = 0
metrics['numNewSyn'].append(np.sum(numNewSynapses))
numEliminatedSynapses = connectedSynsPreviousEpoch - connectedSyns
numEliminatedSynapses[numEliminatedSynapses < 0] = 0
metrics['numRemoveSyn'].append(np.sum(numEliminatedSynapses))
metrics['reconstructionError'].append(
reconstructionError(sp, testInputs, activeColumnsCurrentEpoch))
metrics['witnessError'].append(
witnessError(sp, testInputs, activeColumnsCurrentEpoch))
print tabulate(metrics, headers="keys")
if expConfig.checkRFCenters:
# check distribution of RF centers, useful to monitor recovery from trauma
RFcenters, avgDistToCenter = getRFCenters(sp, params, type='connected')
if expConfig.spatialImp == 'faulty_sp':
aliveColumns = sp.getAliveColumns()
else:
aliveColumns = np.arange(numColumns)
fig = plotReceptiveFieldCenter(RFcenters[aliveColumns, :],
connectedCounts[aliveColumns],
(params['nX'], params['nY']))
plt.savefig('figures/RFcenters/{}/epoch_{}.png'.format(expName, epoch))
plt.close(fig)
np.savez('results/RFcenters/{}/epoch_{}'.format(expName, epoch),
RFcenters, avgDistToCenter)
if expConfig.checkInputSpaceCoverage:
# check coverage of input space, useful to monitor recovery from trauma
inputSpaceCoverage = calculateInputSpaceCoverage(sp)
np.savez('results/InputCoverage/{}/epoch_{}'.format(expName, epoch),
inputSpaceCoverage, connectedCounts)
plt.figure(2)
plt.clf()
plt.imshow(inputSpaceCoverage, interpolation='nearest', cmap="jet")
plt.colorbar()
plt.savefig(
'figures/InputCoverage/{}/epoch_{}.png'.format(expName, epoch))
if expConfig.checkTestInput:
RFcenters, avgDistToCenter = getRFCenters(sp, params, type='connected')
inputIdx = 0
outputColumns = np.zeros((numColumns, 1), dtype=uintType)
sp.compute(testInputs[inputIdx, :], False, outputColumns)
activeColumns = np.where(outputColumns > 0)[0]
fig = plotReceptiveFieldCenter(RFcenters[aliveColumns, :],
connectedCounts[aliveColumns],
(params['nX'], params['nY']))
plt.scatter(RFcenters[activeColumns, 0], RFcenters[activeColumns, 1],
color='r')
plt.savefig(
'figures/ResponseToTestInputs/{}/epoch_{}.png'.format(expName, epoch))
if expConfig.saveBoostFactors:
np.savez('results/boostFactors/{}/epoch_{}'.format(expName, epoch),
meanBoostFactors)
if expConfig.showExampleRFs:
fig = plotReceptiveFields2D(sp, params['nX'], params['nY'])
plt.savefig('figures/exampleRFs/{}/epoch_{}'.format(expName, epoch))
plt.close(fig)
if epoch in checkPoints:
# inspect SP again
inspectSpatialPoolerStats(sp, inputVectors, expName+"epoch{}".format(epoch))
epoch += 1
# plot stats over training
fileName = 'figures/network_stats_over_training_{}.pdf'.format(expName)
plotSPstatsOverTime(metrics, fileName)
metrics['expName'] = expName
pickle.dump(metrics, open('results/traces/{}/trace'.format(expName), 'wb'))
plotReceptiveFields2D(sp, params['nX'], params['nY'])
inspectSpatialPoolerStats(sp, inputVectors, inputVectorType + "afterTraining")
plotExampleInputOutput(sp, inputVectors, expName + "final")
return metrics, expName