class SegmentedForwardModel(object):
"""
A forward model that uses dendrite segments. Every cell has a set of segments.
Every segment has a set of synapses. The cell fires when the number of active
synapses on one of its segments reaches a threshold.
"""
def __init__(self, cellCount, inputSize, threshold):
self.proximalConnections = SparseMatrixConnections(cellCount, inputSize)
self.threshold = threshold
self.activeCells = np.empty(0, dtype='uint32')
self.activeSegments = np.empty(0, dtype='uint32')
def associate(self, activeCells, activeInput):
self.activeCells = activeCells
self.activeSegments = self.proximalConnections.createSegments(
activeCells)
self.proximalConnections.matrix.setZerosOnOuter(
self.activeSegments, activeInput, 1.0)
def infer(self, activeInput):
overlaps = self.proximalConnections.computeActivity(activeInput)
self.activeSegments = np.where(overlaps >= self.threshold)[0]
self.activeCells = self.proximalConnections.mapSegmentsToCells(
self.activeSegments)
self.activeCells.sort()
def test_computeActivity_thresholded(self):
for (name, cells, inputs, activeInputs,
initialPermanence, connectedPermanence,
expected) in (("Accepted",
[1, 2, 3], [42, 43, 44],
[42, 44], 0.55, 0.5,
[2, 2, 2]),
("Rejected",
[1, 2, 3], [42, 43, 44],
[42, 44], 0.55, 0.6,
[0, 0, 0]),
("No segments",
[], [42, 43, 44],
[42, 44], 0.55, 0.5,
[]),
("No active inputs",
[1, 2, 3], [42, 43, 44],
[], 0.55, 0.5,
[0, 0, 0])
):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments, inputs, initialPermanence)
overlaps = connections.computeActivity(activeInputs, connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
def __init__(self,
trnCellShape=(32, 32),
relayCellShape=(32, 32),
inputShape=(32, 32),
l6CellCount=1024,
trnThreshold=10,
relayThreshold=1,
seed=42):
"""
:param trnCellShape:
a 2D shape for the TRN
:param relayCellShape:
a 2D shape for the relay cells
:param l6CellCount:
number of L6 cells
:param trnThreshold:
dendritic threshold for TRN cells. This is the min number of active L6
cells on a dendrite for the TRN cell to recognize a pattern on that
dendrite.
:param relayThreshold:
dendritic threshold for relay cells. This is the min number of active TRN
cells on a dendrite for the relay cell to recognize a pattern on that
dendrite.
:param seed:
Seed for the random number generator.
"""
self.trnCellShape = trnCellShape
self.trnWidth = trnCellShape[0]
self.trnHeight = trnCellShape[1]
self.relayCellShape = relayCellShape
self.relayWidth = relayCellShape[0]
self.relayHeight = relayCellShape[1]
self.l6CellCount = l6CellCount
self.trnThreshold = trnThreshold
self.relayThreshold = relayThreshold
self.inputShape = inputShape
self.seed = seed
self.rng = Random(seed)
self.trnActivationThreshold = 5
self.trnConnections = SparseMatrixConnections(
trnCellShape[0]*trnCellShape[1], l6CellCount)
self.relayConnections = SparseMatrixConnections(
relayCellShape[0]*relayCellShape[1],
trnCellShape[0]*trnCellShape[1])
# Initialize/reset variables that are updated with calls to compute
self.reset()
self._initializeTRNToRelayCellConnections()
def __init__(self,
columnDimensions=(2048,),
basalInputDimensions=(),
apicalInputDimensions=(),
cellsPerColumn=32,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
predictedSegmentDecrement=0.0,
maxNewSynapseCount=None,
maxSynapsesPerSegment=-1,
maxSegmentsPerCell=None,
seed=42):
self.columnDimensions = columnDimensions
self.numColumns = self._numPoints(columnDimensions)
self.basalInputDimensions = basalInputDimensions
self.apicalInputDimensions = apicalInputDimensions
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.minThreshold = minThreshold
self.sampleSize = sampleSize
if maxNewSynapseCount is not None:
print "Parameter 'maxNewSynapseCount' is deprecated. Use 'sampleSize'."
self.sampleSize = maxNewSynapseCount
if maxSegmentsPerCell is not None:
print "Warning: ignoring parameter 'maxSegmentsPerCell'"
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.predictedSegmentDecrement = predictedSegmentDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(basalInputDimensions))
self.apicalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(apicalInputDimensions))
self.rng = Random(seed)
self.activeCells = EMPTY_UINT_ARRAY
self.winnerCells = EMPTY_UINT_ARRAY
self.prevPredictedCells = EMPTY_UINT_ARRAY
def test_computeActivity(self):
for (name, cells, inputs, activeInputs,
initialPermanence,
expected) in (("Basic test",
[1, 2, 3], [42, 43, 44],
[42, 44], 0.45,
[2, 2, 2]),
("Small permanence",
[1, 2, 3], [42, 43, 44],
[42, 44], 0.01,
[2, 2, 2]),
("No segments",
[], [42, 43, 44],
[42, 44], 0.45,
[]),
("No active inputs",
[1, 2, 3], [42, 43, 44],
[], 0.45,
[0, 0, 0])
):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments, inputs, initialPermanence)
overlaps = connections.computeActivity(activeInputs)
np.testing.assert_equal(overlaps[segments], expected, name)
def test_mapSegmentsToSynapseCounts(self):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments([1, 2, 3])
connections.growSynapses(segments, [42, 43, 44], 0.5)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[3, 3, 3])
segments2 = connections.createSegments([4, 5])
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments2),
[0, 0])
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts([]),
[])
def __init__(self,
cellCount,
deltaLocationInputSize,
featureLocationInputSize,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
maxSynapsesPerSegment=-1,
seed=42):
# For transition learning, every segment is split into two parts.
# For the segment to be active, both parts must be active.
self.internalConnections = SparseMatrixConnections(
cellCount, cellCount)
self.deltaConnections = SparseMatrixConnections(
cellCount, deltaLocationInputSize)
# Distal segments that receive input from the layer that represents
# feature-locations.
self.featureLocationConnections = SparseMatrixConnections(
cellCount, featureLocationInputSize)
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def test_growSynapses(self):
for (name,
cells, growingSegments,
presynapticInputs, activeInputs,
initialPermanence, connectedPermanence,
expected) in (("Basic test",
[1, 2, 3], [0, 2],
[42, 43, 44], [42, 43],
0.55, 0.5,
[2, 0, 2]),
("No segments selected",
[1, 2, 3], [],
[42, 43, 44], [42, 43],
0.55, 0.5,
[0, 0, 0]),
("No inputs selected",
[1, 2, 3], [0, 2],
[], [42, 43],
0.55, 0.5,
[0, 0, 0])
):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments[growingSegments], presynapticInputs,
initialPermanence)
overlaps = connections.computeActivity(activeInputs, connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
def __init__(self,
cellDimensions,
anchorInputSize,
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (sequence of ints)
@param anchorInputSize (int)
@param activationThreshold (int)
"""
self.activationThreshold = activationThreshold
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
self.cellCount = np.prod(cellDimensions)
cellCountBySource = {
"bodyToSpecificObject": self.cellCount,
"sensorToBody": self.cellCount,
}
self.metricConnections = Multiconnections(self.cellCount,
cellCountBySource)
self.anchorConnections = SparseMatrixConnections(
self.cellCount, anchorInputSize)
def test_adjustSynapses(self):
for (name, cells, inputs,
adjustedSegments, activeInputs,
initialPermanence, activeDelta, inactiveDelta, connectedPermanence,
expected) in (("Basic test",
[1, 2, 3], [42, 43, 44],
[0, 2], [42, 44],
0.45, 0.1, -0.1, 0.5,
[2, 0, 2]),
("Reward inactive",
[1, 2, 3], [42, 43, 44],
[0, 2], [42, 44],
0.45, -0.1, 0.1, 0.5,
[1, 0, 1]),
("No segments",
[1, 2, 3], [42, 43, 44],
[], [42, 44],
0.45, 0.1, -0.1, 0.5,
[0, 0, 0]),
("No active synapses",
[1, 2, 3], [42, 43, 44],
[0, 2], [],
0.45, 0.1, -0.1, 0.5,
[0, 0, 0]),
("Delta of zero",
[1, 2, 3], [42, 43, 44],
[0, 2], [42, 44],
0.55, 0.0, 0.0, 0.5,
[3, 3, 3])
):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments, inputs, initialPermanence)
connections.adjustSynapses(segments[adjustedSegments],
activeInputs, activeDelta, inactiveDelta)
overlaps = connections.computeActivity(inputs, connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
def __init__(self, cellDimensions, anchorInputSize,
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (sequence of ints)
@param anchorInputSize (int)
@param activationThreshold (int)
"""
self.activationThreshold = activationThreshold
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
self.cellCount = np.prod(cellDimensions)
cellCountBySource = {
"bodyToSpecificObject": self.cellCount,
"sensorToBody": self.cellCount,
}
self.metricConnections = Multiconnections(self.cellCount,
cellCountBySource)
self.anchorConnections = SparseMatrixConnections(self.cellCount,
anchorInputSize)
def test_computeActivity_thresholded(self):
for (name, cells, inputs, activeInputs, initialPermanence,
connectedPermanence,
expected) in (("Accepted", [1, 2, 3], [42, 43,
44], [42, 44], 0.55, 0.5,
[2, 2, 2]), ("Rejected", [1, 2, 3], [42, 43, 44],
[42, 44], 0.55, 0.6, [0, 0, 0]),
("No segments", [], [42, 43, 44], [42, 44], 0.55,
0.5, []), ("No active inputs", [1, 2, 3],
[42, 43, 44], [], 0.55, 0.5, [0, 0,
0])):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments, inputs, initialPermanence)
overlaps = connections.computeActivity(activeInputs,
connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
def __init__(self,
cellCount,
deltaLocationInputSize,
featureLocationInputSize,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
maxSynapsesPerSegment=-1,
seed=42):
# For transition learning, every segment is split into two parts.
# For the segment to be active, both parts must be active.
self.internalConnections = SparseMatrixConnections(
cellCount, cellCount)
self.deltaConnections = SparseMatrixConnections(
cellCount, deltaLocationInputSize)
# Distal segments that receive input from the layer that represents
# feature-locations.
self.featureLocationConnections = SparseMatrixConnections(
cellCount, featureLocationInputSize)
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def __init__(self,
columnCount=2048,
basalInputSize=0,
apicalInputSize=0,
cellsPerColumn=32,
activationThreshold=13,
reducedBasalThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
basalPredictedSegmentDecrement=0.0,
apicalPredictedSegmentDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param columnCount (int)
The number of minicolumns
@param basalInputSize (sequence)
The number of bits in the basal input
@param apicalInputSize (int)
The number of bits in the apical input
@param cellsPerColumn (int)
Number of cells per column
@param activationThreshold (int)
If the number of active connected synapses on a segment is at least this
threshold, the segment is said to be active.
@param reducedBasalThreshold (int)
The activation threshold of basal (lateral) segments for cells that have
active apical segments. If equal to activationThreshold (default),
this parameter has no effect.
@param initialPermanence (float)
Initial permanence of a new synapse
@param connectedPermanence (float)
If the permanence value for a synapse is greater than this value, it is said
to be connected.
@param minThreshold (int)
If the number of potential synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param sampleSize (int)
How much of the active SDR to sample with synapses.
@param permanenceIncrement (float)
Amount by which permanences of synapses are incremented during learning.
@param permanenceDecrement (float)
Amount by which permanences of synapses are decremented during learning.
@param basalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param apicalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param maxSynapsesPerSegment
The maximum number of synapses per segment.
@param seed (int)
Seed for the random number generator.
"""
self.columnCount = columnCount
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.minThreshold = minThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
self.activationThreshold = activationThreshold
self.reducedBasalThreshold = reducedBasalThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
basalInputSize)
self.disableApicalDependence = False
self.apicalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
apicalInputSize)
self.rng = Random(seed)
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
def __init__(self, cellCount, inputSize, threshold): self.proximalConnections = SparseMatrixConnections(cellCount, inputSize) self.threshold = threshold self.activeCells = np.empty(0, dtype='uint32') self.activeSegments = np.empty(0, dtype='uint32')
class ApicalDependentTemporalMemory(object):
"""
A generalized Temporal Memory that creates cell SDRs that are specific to both
the basal and apical input.
Prediction requires both basal and apical support. For sequence memory, the
result is that every sequence happens within a "world" which is specified by
the apical input. Sequences are not shared between worlds.
This class is generalized in two ways:
- This class does not specify when a 'timestep' begins and ends. It exposes
two main methods: 'depolarizeCells' and 'activateCells', and callers or
subclasses can introduce the notion of a timestep.
- This class is unaware of whether its 'basalInput' or 'apicalInput' are from
internal or external cells. They are just cell numbers. The caller knows
what these cell numbers mean, but the TemporalMemory doesn't.
"""
def __init__(self,
columnCount=2048,
basalInputSize=0,
apicalInputSize=0,
cellsPerColumn=32,
activationThreshold=13,
reducedBasalThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
basalPredictedSegmentDecrement=0.0,
apicalPredictedSegmentDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param columnCount (int)
The number of minicolumns
@param basalInputSize (sequence)
The number of bits in the basal input
@param apicalInputSize (int)
The number of bits in the apical input
@param cellsPerColumn (int)
Number of cells per column
@param activationThreshold (int)
If the number of active connected synapses on a segment is at least this
threshold, the segment is said to be active.
@param reducedBasalThreshold (int)
The activation threshold of basal (lateral) segments for cells that have
active apical segments. If equal to activationThreshold (default),
this parameter has no effect.
@param initialPermanence (float)
Initial permanence of a new synapse
@param connectedPermanence (float)
If the permanence value for a synapse is greater than this value, it is said
to be connected.
@param minThreshold (int)
If the number of potential synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param sampleSize (int)
How much of the active SDR to sample with synapses.
@param permanenceIncrement (float)
Amount by which permanences of synapses are incremented during learning.
@param permanenceDecrement (float)
Amount by which permanences of synapses are decremented during learning.
@param basalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param apicalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param maxSynapsesPerSegment
The maximum number of synapses per segment.
@param seed (int)
Seed for the random number generator.
"""
self.columnCount = columnCount
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.minThreshold = minThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
self.activationThreshold = activationThreshold
self.reducedBasalThreshold = reducedBasalThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
basalInputSize)
self.disableApicalDependence = False
self.apicalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
apicalInputSize)
self.rng = Random(seed)
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
def reset(self):
"""
Clear all cell and segment activity.
"""
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
def depolarizeCells(self, basalInput, apicalInput, learn):
"""
Calculate predictions.
@param basalInput (numpy array)
List of active input bits for the basal dendrite segments
@param apicalInput (numpy array)
List of active input bits for the apical dendrite segments
@param learn (bool)
Whether learning is enabled. Some TM implementations may depolarize cells
differently or do segment activity bookkeeping when learning is enabled.
"""
# Calculate predictions for this timestep
(activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps) = self._calculateSegmentActivity(
self.apicalConnections, apicalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold, self.reducedBasalThreshold)
apicallySupportedCells = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
if not self.disableApicalDependence:
(activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps) = self._calculateSegmentActivity(
self.basalConnections, basalInput,
self.connectedPermanence, self.activationThreshold,
self.minThreshold, self.reducedBasalThreshold,
reducedThresholdCells = apicallySupportedCells,)
predictedCells = np.intersect1d(
self.basalConnections.mapSegmentsToCells(activeBasalSegments),
apicallySupportedCells)
else:
(activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps) = self._calculateSegmentActivity(
self.basalConnections, basalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold, self.reducedBasalThreshold)
predictedCells = self.basalConnections.mapSegmentsToCells(activeBasalSegments)
self.predictedCells = predictedCells
self.activeBasalSegments = activeBasalSegments
self.activeApicalSegments = activeApicalSegments
self.matchingBasalSegments = matchingBasalSegments
self.matchingApicalSegments = matchingApicalSegments
self.basalPotentialOverlaps = basalPotentialOverlaps
self.apicalPotentialOverlaps = apicalPotentialOverlaps
def activateCells(self,
activeColumns,
basalReinforceCandidates,
apicalReinforceCandidates,
basalGrowthCandidates,
apicalGrowthCandidates,
learn=True):
"""
Activate cells in the specified columns, using the result of the previous
'depolarizeCells' as predictions. Then learn.
@param activeColumns (numpy array)
List of active columns
@param basalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce basal synapses to.
@param apicalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce apical synapses to.
@param basalGrowthCandidates (numpy array or None)
List of bits that the active cells may grow new basal synapses to.
@param apicalGrowthCandidates (numpy array or None)
List of bits that the active cells may grow new apical synapses to
@param learn (bool)
Whether to grow / reinforce / punish synapses
"""
# Calculate active cells
(correctPredictedCells,
burstingColumns) = np2.setCompare(self.predictedCells, activeColumns,
self.predictedCells / self.cellsPerColumn,
rightMinusLeft=True)
newActiveCells = np.concatenate((correctPredictedCells,
np2.getAllCellsInColumns(
burstingColumns, self.cellsPerColumn)))
# Calculate learning
(learningActiveBasalSegments,
learningActiveApicalSegments,
learningMatchingBasalSegments,
learningMatchingApicalSegments,
basalSegmentsToPunish,
apicalSegmentsToPunish,
newSegmentCells,
learningCells) = self._calculateLearning(activeColumns,
burstingColumns,
correctPredictedCells,
self.activeBasalSegments,
self.activeApicalSegments,
self.matchingBasalSegments,
self.matchingApicalSegments,
self.basalPotentialOverlaps,
self.apicalPotentialOverlaps)
if learn:
# Learn on existing segments
for learningSegments in (learningActiveBasalSegments,
learningMatchingBasalSegments):
self._learn(self.basalConnections, self.rng, learningSegments,
basalReinforceCandidates, basalGrowthCandidates,
self.basalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
for learningSegments in (learningActiveApicalSegments,
learningMatchingApicalSegments):
self._learn(self.apicalConnections, self.rng, learningSegments,
apicalReinforceCandidates, apicalGrowthCandidates,
self.apicalPotentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Punish incorrect predictions
if self.basalPredictedSegmentDecrement != 0.0:
self.basalConnections.adjustActiveSynapses(
basalSegmentsToPunish, basalReinforceCandidates,
-self.basalPredictedSegmentDecrement)
if self.apicalPredictedSegmentDecrement != 0.0:
self.apicalConnections.adjustActiveSynapses(
apicalSegmentsToPunish, apicalReinforceCandidates,
-self.apicalPredictedSegmentDecrement)
# Only grow segments if there is basal *and* apical input.
if len(basalGrowthCandidates) > 0 and len(apicalGrowthCandidates) > 0:
self._learnOnNewSegments(self.basalConnections, self.rng,
newSegmentCells, basalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
self._learnOnNewSegments(self.apicalConnections, self.rng,
newSegmentCells, apicalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
# Save the results
newActiveCells.sort()
learningCells.sort()
self.activeCells = newActiveCells
self.winnerCells = learningCells
self.predictedActiveCells = correctPredictedCells
def _calculateLearning(self,
activeColumns,
burstingColumns,
correctPredictedCells,
activeBasalSegments,
activeApicalSegments,
matchingBasalSegments,
matchingApicalSegments,
basalPotentialOverlaps,
apicalPotentialOverlaps):
"""
Learning occurs on pairs of segments. Correctly predicted cells always have
active basal and apical segments, and we learn on these segments. In
bursting columns, we either learn on an existing segment pair, or we grow a
new pair of segments.
@param activeColumns (numpy array)
@param burstingColumns (numpy array)
@param correctPredictedCells (numpy array)
@param activeBasalSegments (numpy array)
@param activeApicalSegments (numpy array)
@param matchingBasalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveBasalSegments (numpy array)
Active basal segments on correct predicted cells
- learningActiveApicalSegments (numpy array)
Active apical segments on correct predicted cells
- learningMatchingBasalSegments (numpy array)
Matching basal segments selected for learning in bursting columns
- learningMatchingApicalSegments (numpy array)
Matching apical segments selected for learning in bursting columns
- basalSegmentsToPunish (numpy array)
Basal segments that should be punished for predicting an inactive column
- apicalSegmentsToPunish (numpy array)
Apical segments that should be punished for predicting an inactive column
- newSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new segments
- learningCells (numpy array)
Every cell that has a learning segment or was selected to grow a segment
"""
# Correctly predicted columns
learningActiveBasalSegments = self.basalConnections.filterSegmentsByCell(
activeBasalSegments, correctPredictedCells)
learningActiveApicalSegments = self.apicalConnections.filterSegmentsByCell(
activeApicalSegments, correctPredictedCells)
# Bursting columns
cellsForMatchingBasal = self.basalConnections.mapSegmentsToCells(
matchingBasalSegments)
cellsForMatchingApical = self.apicalConnections.mapSegmentsToCells(
matchingApicalSegments)
matchingCells = np.intersect1d(
cellsForMatchingBasal, cellsForMatchingApical)
(matchingCellsInBurstingColumns,
burstingColumnsWithNoMatch) = np2.setCompare(
matchingCells, burstingColumns, matchingCells / self.cellsPerColumn,
rightMinusLeft=True)
(learningMatchingBasalSegments,
learningMatchingApicalSegments) = self._chooseBestSegmentPairPerColumn(
matchingCellsInBurstingColumns, matchingBasalSegments,
matchingApicalSegments, basalPotentialOverlaps, apicalPotentialOverlaps)
newSegmentCells = self._getCellsWithFewestSegments(
burstingColumnsWithNoMatch)
# Incorrectly predicted columns
if self.basalPredictedSegmentDecrement > 0.0:
correctMatchingBasalMask = np.in1d(
cellsForMatchingBasal / self.cellsPerColumn, activeColumns)
basalSegmentsToPunish = matchingBasalSegments[~correctMatchingBasalMask]
else:
basalSegmentsToPunish = ()
if self.apicalPredictedSegmentDecrement > 0.0:
correctMatchingApicalMask = np.in1d(
cellsForMatchingApical / self.cellsPerColumn, activeColumns)
apicalSegmentsToPunish = matchingApicalSegments[~correctMatchingApicalMask]
else:
apicalSegmentsToPunish = ()
# Make a list of every cell that is learning
learningCells = np.concatenate(
(correctPredictedCells,
self.basalConnections.mapSegmentsToCells(learningMatchingBasalSegments),
newSegmentCells))
return (learningActiveBasalSegments,
learningActiveApicalSegments,
learningMatchingBasalSegments,
learningMatchingApicalSegments,
basalSegmentsToPunish,
apicalSegmentsToPunish,
newSegmentCells,
learningCells)
@staticmethod
def _calculateSegmentActivity(connections, activeInput, connectedPermanence,
activationThreshold, minThreshold,
reducedThreshold,
reducedThresholdCells = ()):
"""
Calculate the active and matching basal segments for this timestep.
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active apical segments lower the activation threshold for basal segments
overlaps = connections.computeActivity(activeInput, connectedPermanence)
outrightActiveSegments = np.flatnonzero(overlaps >= activationThreshold)
if (reducedThreshold != activationThreshold and
len(reducedThresholdCells) > 0):
potentiallyActiveSegments = np.flatnonzero(
(overlaps < activationThreshold) & (overlaps >= reducedThreshold))
cellsOfCASegments = connections.mapSegmentsToCells(
potentiallyActiveSegments)
# apically active segments are condit. active segments from apically
# active cells
conditionallyActiveSegments = potentiallyActiveSegments[
np.in1d(cellsOfCASegments, reducedThresholdCells)]
activeSegments = np.concatenate((outrightActiveSegments,
conditionallyActiveSegments))
else:
activeSegments = outrightActiveSegments
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments,
matchingSegments,
potentialOverlaps)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput, growthCandidates,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, and grow new synapses.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
@staticmethod
def _learnOnNewSegments(connections, rng, newSegmentCells, growthCandidates,
initialPermanence, sampleSize, maxSynapsesPerSegment):
"""
Create new segments, and grow synapses on them.
@param connections (SparseMatrixConnections)
@param rng (Random)
@param newSegmentCells (numpy array)
@param growthCandidates (numpy array)
"""
numNewSynapses = len(growthCandidates)
if sampleSize != -1:
numNewSynapses = min(numNewSynapses, sampleSize)
if maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, maxSynapsesPerSegment)
newSegments = connections.createSegments(newSegmentCells)
connections.growSynapsesToSample(newSegments, growthCandidates,
numNewSynapses, initialPermanence,
rng)
def _chooseBestSegmentPairPerColumn(self,
matchingCellsInBurstingColumns,
matchingBasalSegments,
matchingApicalSegments,
basalPotentialOverlaps,
apicalPotentialOverlaps):
"""
Choose the best pair of matching segments - one basal and one apical - for
each column. Pairs are ranked by the sum of their potential overlaps.
When there's a tie, the first pair wins.
@param matchingCellsInBurstingColumns (numpy array)
Cells in bursting columns that have at least one matching basal segment and
at least one matching apical segment
@param matchingBasalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningBasalSegments (numpy array)
The selected basal segments
- learningApicalSegments (numpy array)
The selected apical segments
"""
basalCandidateSegments = self.basalConnections.filterSegmentsByCell(
matchingBasalSegments, matchingCellsInBurstingColumns)
apicalCandidateSegments = self.apicalConnections.filterSegmentsByCell(
matchingApicalSegments, matchingCellsInBurstingColumns)
# Sort everything once rather than inside of each call to argmaxMulti.
self.basalConnections.sortSegmentsByCell(basalCandidateSegments)
self.apicalConnections.sortSegmentsByCell(apicalCandidateSegments)
# Narrow it down to one pair per cell.
oneBasalPerCellFilter = np2.argmaxMulti(
basalPotentialOverlaps[basalCandidateSegments],
self.basalConnections.mapSegmentsToCells(basalCandidateSegments),
assumeSorted=True)
basalCandidateSegments = basalCandidateSegments[oneBasalPerCellFilter]
oneApicalPerCellFilter = np2.argmaxMulti(
apicalPotentialOverlaps[apicalCandidateSegments],
self.apicalConnections.mapSegmentsToCells(apicalCandidateSegments),
assumeSorted=True)
apicalCandidateSegments = apicalCandidateSegments[oneApicalPerCellFilter]
# Narrow it down to one pair per column.
cellScores = (basalPotentialOverlaps[basalCandidateSegments] +
apicalPotentialOverlaps[apicalCandidateSegments])
columnsForCandidates = (
self.basalConnections.mapSegmentsToCells(basalCandidateSegments) /
self.cellsPerColumn)
onePerColumnFilter = np2.argmaxMulti(cellScores, columnsForCandidates,
assumeSorted=True)
learningBasalSegments = basalCandidateSegments[onePerColumnFilter]
learningApicalSegments = apicalCandidateSegments[onePerColumnFilter]
return (learningBasalSegments,
learningApicalSegments)
def _getCellsWithFewestSegments(self, columns):
"""
For each column, get the cell that has the fewest total segments (basal or
apical). Break ties randomly.
@param columns (numpy array)
Columns to check
@return (numpy array)
One cell for each of the provided columns
"""
candidateCells = np2.getAllCellsInColumns(columns, self.cellsPerColumn)
# Arrange the segment counts into one row per minicolumn.
segmentCounts = np.reshape(
self.basalConnections.getSegmentCounts(candidateCells) +
self.apicalConnections.getSegmentCounts(candidateCells),
newshape=(len(columns),
self.cellsPerColumn))
# Filter to just the cells that are tied for fewest in their minicolumn.
minSegmentCounts = np.amin(segmentCounts, axis=1, keepdims=True)
candidateCells = candidateCells[np.flatnonzero(segmentCounts ==
minSegmentCounts)]
# Filter to one cell per column, choosing randomly from the minimums.
# To do the random choice, add a random offset to each index in-place, using
# casting to floor the result.
(_,
onePerColumnFilter,
numCandidatesInColumns) = np.unique(candidateCells / self.cellsPerColumn,
return_index=True, return_counts=True)
offsetPercents = np.empty(len(columns), dtype="float32")
self.rng.initializeReal32Array(offsetPercents)
np.add(onePerColumnFilter,
offsetPercents*numCandidatesInColumns,
out=onePerColumnFilter,
casting="unsafe")
return candidateCells[onePerColumnFilter]
def getActiveCells(self):
"""
@return (numpy array)
Active cells
"""
return self.activeCells
def getPredictedActiveCells(self):
"""
@return (numpy array)
Active cells that were correctly predicted
"""
return np.intersect1d(self.activeCells, self.predictedCells)
def getWinnerCells(self):
"""
@return (numpy array)
Cells that were selected for learning
"""
return self.winnerCells
def getPredictedCells(self):
"""
@return (numpy array)
Cells that were predicted for this timestep
"""
return self.predictedCells
def getActiveBasalSegments(self):
"""
@return (numpy array)
Active basal segments for this timestep
"""
return self.activeBasalSegments
def getActiveApicalSegments(self):
"""
@return (numpy array)
Matching basal segments for this timestep
"""
return self.activeApicalSegments
def numberOfColumns(self):
""" Returns the number of columns in this layer.
@return (int) Number of columns
"""
return self.columnCount
def numberOfCells(self):
"""
Returns the number of cells in this layer.
@return (int) Number of cells
"""
return self.numberOfColumns() * self.cellsPerColumn
def getCellsPerColumn(self):
"""
Returns the number of cells per column.
@return (int) The number of cells per column.
"""
return self.cellsPerColumn
def getActivationThreshold(self):
"""
Returns the activation threshold.
@return (int) The activation threshold.
"""
return self.activationThreshold
def setActivationThreshold(self, activationThreshold):
"""
Sets the activation threshold.
@param activationThreshold (int) activation threshold.
"""
self.activationThreshold = activationThreshold
def getInitialPermanence(self):
"""
Get the initial permanence.
@return (float) The initial permanence.
"""
return self.initialPermanence
def setInitialPermanence(self, initialPermanence):
"""
Sets the initial permanence.
@param initialPermanence (float) The initial permanence.
"""
self.initialPermanence = initialPermanence
def getMinThreshold(self):
"""
Returns the min threshold.
@return (int) The min threshold.
"""
return self.minThreshold
def setMinThreshold(self, minThreshold):
"""
Sets the min threshold.
@param minThreshold (int) min threshold.
"""
self.minThreshold = minThreshold
def getSampleSize(self):
"""
Gets the sampleSize.
@return (int)
"""
return self.sampleSize
def setSampleSize(self, sampleSize):
"""
Sets the sampleSize.
@param sampleSize (int)
"""
self.sampleSize = sampleSize
def getPermanenceIncrement(self):
"""
Get the permanence increment.
@return (float) The permanence increment.
"""
return self.permanenceIncrement
def setPermanenceIncrement(self, permanenceIncrement):
"""
Sets the permanence increment.
@param permanenceIncrement (float) The permanence increment.
"""
self.permanenceIncrement = permanenceIncrement
def getPermanenceDecrement(self):
"""
Get the permanence decrement.
@return (float) The permanence decrement.
"""
return self.permanenceDecrement
def setPermanenceDecrement(self, permanenceDecrement):
"""
Sets the permanence decrement.
@param permanenceDecrement (float) The permanence decrement.
"""
self.permanenceDecrement = permanenceDecrement
def getBasalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.basalPredictedSegmentDecrement
def setBasalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
def getApicalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.apicalPredictedSegmentDecrement
def setApicalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
def getConnectedPermanence(self):
"""
Get the connected permanence.
@return (float) The connected permanence.
"""
return self.connectedPermanence
def setConnectedPermanence(self, connectedPermanence):
"""
Sets the connected permanence.
@param connectedPermanence (float) The connected permanence.
"""
self.connectedPermanence = connectedPermanence
class ApicalTiebreakTemporalMemory(object):
"""
A generalized Temporal Memory with apical dendrites that add a "tiebreak".
Basal connections are used to implement traditional Temporal Memory.
The apical connections are used for further disambiguation. If multiple cells
in a minicolumn have active basal segments, each of those cells is predicted,
unless one of them also has an active apical segment, in which case only the
cells with active basal and apical segments are predicted.
In other words, the apical connections have no effect unless the basal input
is a union of SDRs (e.g. from bursting minicolumns).
This class is generalized in two ways:
- This class does not specify when a 'timestep' begins and ends. It exposes
two main methods: 'depolarizeCells' and 'activateCells', and callers or
subclasses can introduce the notion of a timestep.
- This class is unaware of whether its 'basalInput' or 'apicalInput' are from
internal or external cells. They are just cell numbers. The caller knows
what these cell numbers mean, but the TemporalMemory doesn't.
"""
def __init__(self,
columnCount=2048,
basalInputSize=0,
apicalInputSize=0,
cellsPerColumn=32,
activationThreshold=13,
reducedBasalThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
basalPredictedSegmentDecrement=0.0,
apicalPredictedSegmentDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param columnCount (int)
The number of minicolumns
@param basalInputSize (sequence)
The number of bits in the basal input
@param apicalInputSize (int)
The number of bits in the apical input
@param cellsPerColumn (int)
Number of cells per column
@param activationThreshold (int)
If the number of active connected synapses on a segment is at least this
threshold, the segment is said to be active.
@param reducedBasalThreshold (int)
The activation threshold of basal (lateral) segments for cells that have
active apical segments. If equal to activationThreshold (default),
this parameter has no effect.
@param initialPermanence (float)
Initial permanence of a new synapse
@param connectedPermanence (float)
If the permanence value for a synapse is greater than this value, it is said
to be connected.
@param minThreshold (int)
If the number of potential synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param sampleSize (int)
How much of the active SDR to sample with synapses.
@param permanenceIncrement (float)
Amount by which permanences of synapses are incremented during learning.
@param permanenceDecrement (float)
Amount by which permanences of synapses are decremented during learning.
@param basalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param apicalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param maxSynapsesPerSegment
The maximum number of synapses per segment.
@param seed (int)
Seed for the random number generator.
"""
self.columnCount = columnCount
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.reducedBasalThreshold = reducedBasalThreshold
self.minThreshold = minThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(
columnCount * cellsPerColumn, basalInputSize)
self.apicalConnections = SparseMatrixConnections(
columnCount * cellsPerColumn, apicalInputSize)
self.rng = Random(seed)
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
self.useApicalTiebreak = True
self.useApicalModulationBasalThreshold = True
def reset(self):
"""
Clear all cell and segment activity.
"""
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
def depolarizeCells(self, basalInput, apicalInput, learn):
"""
Calculate predictions.
@param basalInput (numpy array)
List of active input bits for the basal dendrite segments
@param apicalInput (numpy array)
List of active input bits for the apical dendrite segments
@param learn (bool)
Whether learning is enabled. Some TM implementations may depolarize cells
differently or do segment activity bookkeeping when learning is enabled.
"""
(activeApicalSegments, matchingApicalSegments,
apicalPotentialOverlaps) = self._calculateApicalSegmentActivity(
self.apicalConnections, apicalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
if learn or self.useApicalModulationBasalThreshold == False:
reducedBasalThresholdCells = ()
else:
reducedBasalThresholdCells = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
(activeBasalSegments, matchingBasalSegments,
basalPotentialOverlaps) = self._calculateBasalSegmentActivity(
self.basalConnections, basalInput, reducedBasalThresholdCells,
self.connectedPermanence, self.activationThreshold,
self.minThreshold, self.reducedBasalThreshold)
predictedCells = self._calculatePredictedCells(activeBasalSegments,
activeApicalSegments)
self.predictedCells = predictedCells
self.activeBasalSegments = activeBasalSegments
self.activeApicalSegments = activeApicalSegments
self.matchingBasalSegments = matchingBasalSegments
self.matchingApicalSegments = matchingApicalSegments
self.basalPotentialOverlaps = basalPotentialOverlaps
self.apicalPotentialOverlaps = apicalPotentialOverlaps
def activateCells(self,
activeColumns,
basalReinforceCandidates,
apicalReinforceCandidates,
basalGrowthCandidates,
apicalGrowthCandidates,
learn=True):
"""
Activate cells in the specified columns, using the result of the previous
'depolarizeCells' as predictions. Then learn.
@param activeColumns (numpy array)
List of active columns
@param basalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce basal synapses to.
@param apicalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce apical synapses to.
@param basalGrowthCandidates (numpy array)
List of bits that the active cells may grow new basal synapses to.
@param apicalGrowthCandidates (numpy array)
List of bits that the active cells may grow new apical synapses to
@param learn (bool)
Whether to grow / reinforce / punish synapses
"""
# Calculate active cells
(correctPredictedCells, burstingColumns) = np2.setCompare(
self.predictedCells,
activeColumns,
self.predictedCells / self.cellsPerColumn,
rightMinusLeft=True)
newActiveCells = np.concatenate(
(correctPredictedCells,
np2.getAllCellsInColumns(burstingColumns, self.cellsPerColumn)))
# Calculate learning
(learningActiveBasalSegments, learningMatchingBasalSegments,
basalSegmentsToPunish, newBasalSegmentCells,
learningCells) = self._calculateBasalLearning(
activeColumns, burstingColumns, correctPredictedCells,
self.activeBasalSegments, self.matchingBasalSegments,
self.basalPotentialOverlaps)
(learningActiveApicalSegments, learningMatchingApicalSegments,
apicalSegmentsToPunish,
newApicalSegmentCells) = self._calculateApicalLearning(
learningCells, activeColumns, self.activeApicalSegments,
self.matchingApicalSegments, self.apicalPotentialOverlaps)
# Learn
if learn:
# Learn on existing segments
for learningSegments in (learningActiveBasalSegments,
learningMatchingBasalSegments):
self._learn(self.basalConnections, self.rng, learningSegments,
basalReinforceCandidates, basalGrowthCandidates,
self.basalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
for learningSegments in (learningActiveApicalSegments,
learningMatchingApicalSegments):
self._learn(self.apicalConnections, self.rng, learningSegments,
apicalReinforceCandidates, apicalGrowthCandidates,
self.apicalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
# Punish incorrect predictions
if self.basalPredictedSegmentDecrement != 0.0:
self.basalConnections.adjustActiveSynapses(
basalSegmentsToPunish, basalReinforceCandidates,
-self.basalPredictedSegmentDecrement)
if self.apicalPredictedSegmentDecrement != 0.0:
self.apicalConnections.adjustActiveSynapses(
apicalSegmentsToPunish, apicalReinforceCandidates,
-self.apicalPredictedSegmentDecrement)
# Grow new segments
if len(basalGrowthCandidates) > 0:
self._learnOnNewSegments(self.basalConnections, self.rng,
newBasalSegmentCells,
basalGrowthCandidates,
self.initialPermanence,
self.sampleSize,
self.maxSynapsesPerSegment)
if len(apicalGrowthCandidates) > 0:
self._learnOnNewSegments(self.apicalConnections, self.rng,
newApicalSegmentCells,
apicalGrowthCandidates,
self.initialPermanence,
self.sampleSize,
self.maxSynapsesPerSegment)
# Save the results
newActiveCells.sort()
learningCells.sort()
self.activeCells = newActiveCells
self.winnerCells = learningCells
self.predictedActiveCells = correctPredictedCells
def _calculateBasalLearning(self, activeColumns, burstingColumns,
correctPredictedCells, activeBasalSegments,
matchingBasalSegments, basalPotentialOverlaps):
"""
Basic Temporal Memory learning. Correctly predicted cells always have
active basal segments, and we learn on these segments. In bursting
columns, we either learn on an existing basal segment, or we grow a new one.
The only influence apical dendrites have on basal learning is: the apical
dendrites influence which cells are considered "predicted". So an active
apical dendrite can prevent some basal segments in active columns from
learning.
@param correctPredictedCells (numpy array)
@param burstingColumns (numpy array)
@param activeBasalSegments (numpy array)
@param matchingBasalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveBasalSegments (numpy array)
Active basal segments on correct predicted cells
- learningMatchingBasalSegments (numpy array)
Matching basal segments selected for learning in bursting columns
- basalSegmentsToPunish (numpy array)
Basal segments that should be punished for predicting an inactive column
- newBasalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new basal segments
- learningCells (numpy array)
Cells that have learning basal segments or are selected to grow a basal
segment
"""
# Correctly predicted columns
learningActiveBasalSegments = self.basalConnections.filterSegmentsByCell(
activeBasalSegments, correctPredictedCells)
cellsForMatchingBasal = self.basalConnections.mapSegmentsToCells(
matchingBasalSegments)
matchingCells = np.unique(cellsForMatchingBasal)
(matchingCellsInBurstingColumns,
burstingColumnsWithNoMatch) = np2.setCompare(matchingCells,
burstingColumns,
matchingCells /
self.cellsPerColumn,
rightMinusLeft=True)
learningMatchingBasalSegments = self._chooseBestSegmentPerColumn(
self.basalConnections, matchingCellsInBurstingColumns,
matchingBasalSegments, basalPotentialOverlaps, self.cellsPerColumn)
newBasalSegmentCells = self._getCellsWithFewestSegments(
self.basalConnections, self.rng, burstingColumnsWithNoMatch,
self.cellsPerColumn)
learningCells = np.concatenate(
(correctPredictedCells,
self.basalConnections.mapSegmentsToCells(
learningMatchingBasalSegments), newBasalSegmentCells))
# Incorrectly predicted columns
correctMatchingBasalMask = np.in1d(
cellsForMatchingBasal / self.cellsPerColumn, activeColumns)
basalSegmentsToPunish = matchingBasalSegments[
~correctMatchingBasalMask]
return (learningActiveBasalSegments, learningMatchingBasalSegments,
basalSegmentsToPunish, newBasalSegmentCells, learningCells)
def _calculateApicalLearning(self, learningCells, activeColumns,
activeApicalSegments, matchingApicalSegments,
apicalPotentialOverlaps):
"""
Calculate apical learning for each learning cell.
The set of learning cells was determined completely from basal segments.
Do all apical learning on the same cells.
Learn on any active segments on learning cells. For cells without active
segments, learn on the best matching segment. For cells without a matching
segment, grow a new segment.
@param learningCells (numpy array)
@param correctPredictedCells (numpy array)
@param activeApicalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveApicalSegments (numpy array)
Active apical segments on correct predicted cells
- learningMatchingApicalSegments (numpy array)
Matching apical segments selected for learning in bursting columns
- apicalSegmentsToPunish (numpy array)
Apical segments that should be punished for predicting an inactive column
- newApicalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new apical segments
"""
# Cells with active apical segments
learningActiveApicalSegments = self.apicalConnections.filterSegmentsByCell(
activeApicalSegments, learningCells)
# Cells with matching apical segments
learningCellsWithoutActiveApical = np.setdiff1d(
learningCells,
self.apicalConnections.mapSegmentsToCells(
learningActiveApicalSegments))
cellsForMatchingApical = self.apicalConnections.mapSegmentsToCells(
matchingApicalSegments)
learningCellsWithMatchingApical = np.intersect1d(
learningCellsWithoutActiveApical, cellsForMatchingApical)
learningMatchingApicalSegments = self._chooseBestSegmentPerCell(
self.apicalConnections, learningCellsWithMatchingApical,
matchingApicalSegments, apicalPotentialOverlaps)
# Cells that need to grow an apical segment
newApicalSegmentCells = np.setdiff1d(learningCellsWithoutActiveApical,
learningCellsWithMatchingApical)
# Incorrectly predicted columns
correctMatchingApicalMask = np.in1d(
cellsForMatchingApical / self.cellsPerColumn, activeColumns)
apicalSegmentsToPunish = matchingApicalSegments[
~correctMatchingApicalMask]
return (learningActiveApicalSegments, learningMatchingApicalSegments,
apicalSegmentsToPunish, newApicalSegmentCells)
@staticmethod
def _calculateApicalSegmentActivity(connections, activeInput,
connectedPermanence,
activationThreshold, minThreshold):
"""
Calculate the active and matching apical segments for this timestep.
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active
overlaps = connections.computeActivity(activeInput,
connectedPermanence)
activeSegments = np.flatnonzero(overlaps >= activationThreshold)
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments, matchingSegments, potentialOverlaps)
@staticmethod
def _calculateBasalSegmentActivity(connections, activeInput,
reducedBasalThresholdCells,
connectedPermanence,
activationThreshold, minThreshold,
reducedBasalThreshold):
"""
Calculate the active and matching basal segments for this timestep.
The difference with _calculateApicalSegmentActivity is that cells
with active apical segments (collected in reducedBasalThresholdCells) have
a lower activation threshold for their basal segments (set by
reducedBasalThreshold parameter).
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active apical segments lower the activation threshold for basal (lateral) segments
overlaps = connections.computeActivity(activeInput,
connectedPermanence)
outrightActiveSegments = np.flatnonzero(
overlaps >= activationThreshold)
if reducedBasalThreshold != activationThreshold and len(
reducedBasalThresholdCells) > 0:
potentiallyActiveSegments = np.flatnonzero(
(overlaps < activationThreshold)
& (overlaps >= reducedBasalThreshold))
cellsOfCASegments = connections.mapSegmentsToCells(
potentiallyActiveSegments)
# apically active segments are condit. active segments from apically active cells
conditionallyActiveSegments = potentiallyActiveSegments[np.in1d(
cellsOfCASegments, reducedBasalThresholdCells)]
activeSegments = np.concatenate(
(outrightActiveSegments, conditionallyActiveSegments))
else:
activeSegments = outrightActiveSegments
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments, matchingSegments, potentialOverlaps)
def _calculatePredictedCells(self, activeBasalSegments,
activeApicalSegments):
"""
Calculate the predicted cells, given the set of active segments.
An active basal segment is enough to predict a cell.
An active apical segment is *not* enough to predict a cell.
When a cell has both types of segments active, other cells in its minicolumn
must also have both types of segments to be considered predictive.
@param activeBasalSegments (numpy array)
@param activeApicalSegments (numpy array)
@return (numpy array)
"""
cellsForBasalSegments = self.basalConnections.mapSegmentsToCells(
activeBasalSegments)
cellsForApicalSegments = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
fullyDepolarizedCells = np.intersect1d(cellsForBasalSegments,
cellsForApicalSegments)
partlyDepolarizedCells = np.setdiff1d(cellsForBasalSegments,
fullyDepolarizedCells)
inhibitedMask = np.in1d(partlyDepolarizedCells / self.cellsPerColumn,
fullyDepolarizedCells / self.cellsPerColumn)
predictedCells = np.append(fullyDepolarizedCells,
partlyDepolarizedCells[~inhibitedMask])
if self.useApicalTiebreak == False:
predictedCells = cellsForBasalSegments
return predictedCells
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
growthCandidates, potentialOverlaps, initialPermanence,
sampleSize, permanenceIncrement, permanenceDecrement,
maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax, maxNew,
numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
@staticmethod
def _learnOnNewSegments(connections, rng, newSegmentCells,
growthCandidates, initialPermanence, sampleSize,
maxSynapsesPerSegment):
numNewSynapses = len(growthCandidates)
if sampleSize != -1:
numNewSynapses = min(numNewSynapses, sampleSize)
if maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, maxSynapsesPerSegment)
newSegments = connections.createSegments(newSegmentCells)
connections.growSynapsesToSample(newSegments, growthCandidates,
numNewSynapses, initialPermanence,
rng)
@classmethod
def _chooseBestSegmentPerCell(cls, connections, cells, allMatchingSegments,
potentialOverlaps):
"""
For each specified cell, choose its matching segment with largest number
of active potential synapses. When there's a tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param cells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
@return (numpy array)
One segment per cell
"""
candidateSegments = connections.filterSegmentsByCell(
allMatchingSegments, cells)
# Narrow it down to one pair per cell.
onePerCellFilter = np2.argmaxMulti(
potentialOverlaps[candidateSegments],
connections.mapSegmentsToCells(candidateSegments))
learningSegments = candidateSegments[onePerCellFilter]
return learningSegments
@classmethod
def _chooseBestSegmentPerColumn(cls, connections, matchingCells,
allMatchingSegments, potentialOverlaps,
cellsPerColumn):
"""
For all the columns covered by 'matchingCells', choose the column's matching
segment with largest number of active potential synapses. When there's a
tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param matchingCells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
"""
candidateSegments = connections.filterSegmentsByCell(
allMatchingSegments, matchingCells)
# Narrow it down to one segment per column.
cellScores = potentialOverlaps[candidateSegments]
columnsForCandidates = (
connections.mapSegmentsToCells(candidateSegments) / cellsPerColumn)
onePerColumnFilter = np2.argmaxMulti(cellScores, columnsForCandidates)
learningSegments = candidateSegments[onePerColumnFilter]
return learningSegments
@classmethod
def _getCellsWithFewestSegments(cls, connections, rng, columns,
cellsPerColumn):
"""
For each column, get the cell that has the fewest total basal segments.
Break ties randomly.
@param connections (SparseMatrixConnections)
@param rng (Random)
@param columns (numpy array) Columns to check
@return (numpy array)
One cell for each of the provided columns
"""
candidateCells = np2.getAllCellsInColumns(columns, cellsPerColumn)
# Arrange the segment counts into one row per minicolumn.
segmentCounts = np.reshape(
connections.getSegmentCounts(candidateCells),
newshape=(len(columns), cellsPerColumn))
# Filter to just the cells that are tied for fewest in their minicolumn.
minSegmentCounts = np.amin(segmentCounts, axis=1, keepdims=True)
candidateCells = candidateCells[np.flatnonzero(
segmentCounts == minSegmentCounts)]
# Filter to one cell per column, choosing randomly from the minimums.
# To do the random choice, add a random offset to each index in-place, using
# casting to floor the result.
(_, onePerColumnFilter,
numCandidatesInColumns) = np.unique(candidateCells / cellsPerColumn,
return_index=True,
return_counts=True)
offsetPercents = np.empty(len(columns), dtype="float32")
rng.initializeReal32Array(offsetPercents)
np.add(onePerColumnFilter,
offsetPercents * numCandidatesInColumns,
out=onePerColumnFilter,
casting="unsafe")
return candidateCells[onePerColumnFilter]
def getActiveCells(self):
"""
@return (numpy array)
Active cells
"""
return self.activeCells
def getPredictedActiveCells(self):
"""
@return (numpy array)
Active cells that were correctly predicted
"""
return self.predictedActiveCells
def getWinnerCells(self):
"""
@return (numpy array)
Cells that were selected for learning
"""
return self.winnerCells
def getActiveBasalSegments(self):
"""
@return (numpy array)
Active basal segments for this timestep
"""
return self.activeBasalSegments
def getActiveApicalSegments(self):
"""
@return (numpy array)
Matching basal segments for this timestep
"""
return self.activeApicalSegments
def numberOfColumns(self):
""" Returns the number of columns in this layer.
@return (int) Number of columns
"""
return self.columnCount
def numberOfCells(self):
"""
Returns the number of cells in this layer.
@return (int) Number of cells
"""
return self.numberOfColumns() * self.cellsPerColumn
def getCellsPerColumn(self):
"""
Returns the number of cells per column.
@return (int) The number of cells per column.
"""
return self.cellsPerColumn
def getActivationThreshold(self):
"""
Returns the activation threshold.
@return (int) The activation threshold.
"""
return self.activationThreshold
def setActivationThreshold(self, activationThreshold):
"""
Sets the activation threshold.
@param activationThreshold (int) activation threshold.
"""
self.activationThreshold = activationThreshold
def getReducedBasalThreshold(self):
"""
Returns the reduced basal activation threshold for apically active cells.
@return (int) The activation threshold.
"""
return self.reducedBasalThreshold
def setReducedBasalThreshold(self, reducedBasalThreshold):
"""
Sets the reduced basal activation threshold for apically active cells.
@param reducedBasalThreshold (int) activation threshold.
"""
self.reducedBasalThreshold = reducedBasalThreshold
def getInitialPermanence(self):
"""
Get the initial permanence.
@return (float) The initial permanence.
"""
return self.initialPermanence
def setInitialPermanence(self, initialPermanence):
"""
Sets the initial permanence.
@param initialPermanence (float) The initial permanence.
"""
self.initialPermanence = initialPermanence
def getMinThreshold(self):
"""
Returns the min threshold.
@return (int) The min threshold.
"""
return self.minThreshold
def setMinThreshold(self, minThreshold):
"""
Sets the min threshold.
@param minThreshold (int) min threshold.
"""
self.minThreshold = minThreshold
def getSampleSize(self):
"""
Gets the sampleSize.
@return (int)
"""
return self.sampleSize
def setSampleSize(self, sampleSize):
"""
Sets the sampleSize.
@param sampleSize (int)
"""
self.sampleSize = sampleSize
def getPermanenceIncrement(self):
"""
Get the permanence increment.
@return (float) The permanence increment.
"""
return self.permanenceIncrement
def setPermanenceIncrement(self, permanenceIncrement):
"""
Sets the permanence increment.
@param permanenceIncrement (float) The permanence increment.
"""
self.permanenceIncrement = permanenceIncrement
def getPermanenceDecrement(self):
"""
Get the permanence decrement.
@return (float) The permanence decrement.
"""
return self.permanenceDecrement
def setPermanenceDecrement(self, permanenceDecrement):
"""
Sets the permanence decrement.
@param permanenceDecrement (float) The permanence decrement.
"""
self.permanenceDecrement = permanenceDecrement
def getBasalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.basalPredictedSegmentDecrement
def setBasalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
def getApicalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.apicalPredictedSegmentDecrement
def setApicalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
def getConnectedPermanence(self):
"""
Get the connected permanence.
@return (float) The connected permanence.
"""
return self.connectedPermanence
def setConnectedPermanence(self, connectedPermanence):
"""
Sets the connected permanence.
@param connectedPermanence (float) The connected permanence.
"""
self.connectedPermanence = connectedPermanence
def getUseApicalTieBreak(self):
"""
Get whether we actually use apical tie-break.
@return (Bool) Whether apical tie-break is used.
"""
return self.useApicalTiebreak
def setUseApicalTiebreak(self, useApicalTiebreak):
"""
Sets whether we actually use apical tie-break.
@param useApicalTiebreak (Bool) Whether apical tie-break is used.
"""
self.useApicalTiebreak = useApicalTiebreak
def getUseApicalModulationBasalThreshold(self):
"""
Get whether we actually use apical modulation of basal threshold.
@return (Bool) Whether apical modulation is used.
"""
return self.useApicalModulationBasalThreshold
def setUseApicalModulationBasalThreshold(
self, useApicalModulationBasalThreshold):
"""
Sets whether we actually use apical modulation of basal threshold.
@param useApicalModulationBasalThreshold (Bool) Whether apical modulation is used.
"""
self.useApicalModulationBasalThreshold = useApicalModulationBasalThreshold
class SuperficialLocationModule2D(object):
"""
A model of a location module. It's similar to a grid cell module, but it uses
squares rather than triangles.
The cells are arranged into a m*n rectangle which is tiled onto 2D space.
Each cell represents a small rectangle in each tile.
+------+------+------++------+------+------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #1 | #2 | #3 || #1 | #2 | #3 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #4 | #5 | #6 || #4 | #5 | #6 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #7 | #8 | #9 || #7 | #8 | #9 |
| | | || | | |
+------+------+------++------+------+------+
We assume that path integration works *somehow*. This model receives a "delta
location" vector, and it shifts the active cells accordingly. The model stores
intermediate coordinates of active cells. Whenever sensory cues activate a
cell, the model adds this cell to the list of coordinates being shifted.
Whenever sensory cues cause a cell to become inactive, that cell is removed
from the list of coordinates.
(This model doesn't attempt to propose how "path integration" works. It
attempts to show how locations are anchored to sensory cues.)
When orientation is set to 0 degrees, the deltaLocation is a [di, dj],
moving di cells "down" and dj cells "right".
When orientation is set to 90 degrees, the deltaLocation is essentially a
[dx, dy], applied in typical x,y coordinates with the origin on the bottom
left.
Usage:
Adjust the location in response to motor input:
lm.shift([di, dj])
Adjust the location in response to sensory input:
lm.anchor(anchorInput)
Learn an anchor input for the current location:
lm.learn(anchorInput)
The "anchor input" is typically a feature-location pair SDR.
During inference, you'll typically call:
lm.shift(...)
# Consume lm.getActiveCells()
# ...
lm.anchor(...)
During learning, you'll do the same, but you'll call lm.learn() instead of
lm.anchor().
"""
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
pointOffsets=(0.5,),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param pointOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "point" which is shifted in subsequent
motions. By default, this point is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, With value [0.2, 0.8], it will place 4 points:
[0.2, 0.2], [0.2, 0.8], [0.8, 0.2], [0.8, 0.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions, dtype="float")
self.cellFieldsPerUnitDistance = self.cellDimensions / self.moduleMapDimensions
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation), math.cos(orientation)]])
self.pointOffsets = pointOffsets
# These coordinates are in units of "cell fields".
self.activePoints = np.empty((0,2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def reset(self):
"""
Clear the active cells.
"""
self.activePoints = np.empty((0,2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
def _computeActiveCells(self):
# Round each coordinate to the nearest cell.
flooredActivePoints = np.floor(self.activePoints).astype("int")
# Convert coordinates to cell numbers.
self.cellsForActivePoints = (
np.ravel_multi_index(flooredActivePoints.T, self.cellDimensions))
self.activeCells = np.unique(self.cellsForActivePoints)
def activateRandomLocation(self):
"""
Set the location to a random point.
"""
self.activePoints = np.array([np.random.random(2) * self.cellDimensions])
self._computeActiveCells()
def shift(self, deltaLocation):
"""
Shift the current active cells by a vector.
@param deltaLocation (pair of floats)
A translation vector [di, dj].
"""
# Calculate delta in the module's coordinates.
deltaLocationInCellFields = (np.matmul(self.rotationMatrix, deltaLocation) *
self.cellFieldsPerUnitDistance)
# Shift the active coordinates.
np.add(self.activePoints, deltaLocationInCellFields, out=self.activePoints)
np.mod(self.activePoints, self.cellDimensions, out=self.activePoints)
self._computeActiveCells()
def anchor(self, anchorInput):
"""
Infer the location from sensory input. Activate any cells with enough active
synapses to this sensory input. Deactivate all other cells.
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
if len(anchorInput) == 0:
return
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
sensorySupportedCells = np.unique(
self.connections.mapSegmentsToCells(activeSegments))
inactivated = np.setdiff1d(self.activeCells, sensorySupportedCells)
inactivatedIndices = np.in1d(self.cellsForActivePoints,
inactivated).nonzero()[0]
if inactivatedIndices.size > 0:
self.activePoints = np.delete(self.activePoints, inactivatedIndices,
axis=0)
activated = np.setdiff1d(sensorySupportedCells, self.activeCells)
activatedCoordsBase = np.transpose(
np.unravel_index(activated, self.cellDimensions)).astype('float')
activatedCoords = np.concatenate(
[activatedCoordsBase + [iOffset, jOffset]
for iOffset in self.pointOffsets
for jOffset in self.pointOffsets]
)
if activatedCoords.size > 0:
self.activePoints = np.append(self.activePoints, activatedCoords, axis=0)
self._computeActiveCells()
self.activeSegments = activeSegments
def learn(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.connections.computeActivity(anchorInput)
matchingSegments = np.where(potentialOverlaps >=
self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.connections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[
np.in1d(cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.connections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.connections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[
np.in1d(cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells, cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.connections, self.rng, learningSegments,
anchorInput, potentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.connections.createSegments(newSegmentCells)
self.connections.growSynapsesToSample(
newSegments, anchorInput, numNewSynapses,
self.initialPermanence, self.rng)
self.activeSegments = activeSegments
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput,
maxNew, initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
def numberOfCells(self):
return np.prod(self.cellDimensions)
def test_growSynapsesToSample_multi(self):
rng = Random()
for (name,
cells, growingSegments,
initialConnectedInputs, presynapticInputs, activeInputs,
initialPermanence, connectedPermanence, sampleSizes,
expected) in (("Basic test",
[1, 2, 3], [0, 2],
[], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5,
[2, 3],
[2, 0, 3]),
("One already connected",
[1, 2, 3], [0, 2],
[42], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5,
[1, 2],
[2, 0, 3]),
("Higher sample size than axon count",
[1, 2, 3], [0, 2],
[], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5,
[5, 10],
[4, 0, 4]),
("Higher sample size than available axon count",
[1, 2, 3], [0, 2],
[42, 43], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5,
[3, 3],
[4, 0, 4])
):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(
segments[growingSegments], initialConnectedInputs, initialPermanence)
connections.growSynapsesToSample(
segments[growingSegments], presynapticInputs,
sampleSizes, initialPermanence, rng)
overlaps = connections.computeActivity(activeInputs, connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
for (name,
cells, growingSegments,
initialConnectedInputs, presynapticInputs, activeInputs,
initialPermanence, connectedPermanence,
sampleSizes) in (("Basic randomness test",
[1, 2, 3], [0, 2],
[], [42, 43, 44, 45],
[42, 43], 0.55, 0.5, [2, 3]),
):
# Activate a subset of the inputs. The resulting overlaps should
# differ on various trials.
firstResult = None
differingResults = False
for _ in xrange(20):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(
segments[growingSegments], initialConnectedInputs, initialPermanence)
connections.growSynapsesToSample(
segments[growingSegments], presynapticInputs,
sampleSizes, initialPermanence, rng)
overlaps = connections.computeActivity(activeInputs,
connectedPermanence)
if firstResult is None:
firstResult = overlaps[segments]
else:
differingResults = not np.array_equal(overlaps[segments], firstResult)
if differingResults:
break
self.assertTrue(differingResults, name)
def __init__(self,
columnCount=2048,
basalInputSize=0,
apicalInputSize=0,
cellsPerColumn=32,
initialPermanence=0.21,
connectedPermanence=0.50,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
activationThresholdBasal=13,
minThresholdBasal=10,
activationThresholdApical=2,
minThresholdApical=1,
basalPredictedSegmentDecrement=0.0,
apicalPredictedSegmentDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param columnCount (int)
The number of minicolumns
@param basalInputSize (sequence)
The number of bits in the basal input
@param apicalInputSize (int)
The number of bits in the apical input
@param cellsPerColumn (int)
Number of cells per column
@param initialPermanence (float)
Initial permanence of a new synapse
@param connectedPermanence (float)
If the permanence value for a synapse is greater than this value, it is said
to be connected.
@param activationThresholdBasal (int)
If the number of active connected basal synapses on a segment is at least this
threshold, the segment is said to be active.
@param activationThresholdApical (int)
If the number of active connected apical synapses on a segment is at least this
threshold, the segment is said to be active.
@param minThresholdBasal (int)
If the number of potential basal synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param minThresholdApical (int)
If the number of potential apical synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param sampleSize (int)
How much of the active SDR to sample with synapses.
@param permanenceIncrement (float)
Amount by which permanences of synapses are incremented during learning.
@param permanenceDecrement (float)
Amount by which permanences of synapses are decremented during learning.
@param basalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param apicalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param maxSynapsesPerSegment
The maximum number of synapses per segment.
@param seed (int)
Seed for the random number generator.
"""
self.columnCount = columnCount
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.maxSynapsesPerSegment = maxSynapsesPerSegment
# weighted basal/apical params
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
self.minThresholdBasal = minThresholdBasal
self.minThresholdApical = minThresholdApical
self.activationThresholdBasal = activationThresholdBasal
self.activationThresholdApical = activationThresholdApical
self.basalConnections = SparseMatrixConnections(
columnCount * cellsPerColumn, basalInputSize)
self.apicalConnections = SparseMatrixConnections(
columnCount * cellsPerColumn, apicalInputSize)
self.rng = Random(seed)
self.activeCells = ()
self.winnerCells = ()
self.predictedCells = ()
self.activeBasalSegments = ()
self.activeApicalSegments = ()
class SingleLayerLocationMemory(object):
"""
A layer of cells which learns how to take a "delta location" (e.g. a motor
command or a proprioceptive delta) and update its active cells to represent
the new location.
Its active cells might represent a union of locations.
As the location changes, the featureLocationInput causes this union to narrow
down until the location is inferred.
This layer receives absolute proprioceptive info as proximal input.
For now, we assume that there's a one-to-one mapping between absolute
proprioceptive input and the location SDR. So rather than modeling
proximal synapses, we'll just relay the proprioceptive SDR. In the future
we might want to consider a many-to-one mapping of proprioceptive inputs
to location SDRs.
After this layer is trained, it no longer needs the proprioceptive input.
The delta location will drive the layer. The current active cells and the
other distal connections will work together with this delta location to
activate a new set of cells.
When no cells are active, activate a large union of possible locations.
With subsequent inputs, the union will narrow down to a single location SDR.
"""
def __init__(self,
cellCount,
deltaLocationInputSize,
featureLocationInputSize,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
maxSynapsesPerSegment=-1,
seed=42):
# For transition learning, every segment is split into two parts.
# For the segment to be active, both parts must be active.
self.internalConnections = SparseMatrixConnections(
cellCount, cellCount)
self.deltaConnections = SparseMatrixConnections(
cellCount, deltaLocationInputSize)
# Distal segments that receive input from the layer that represents
# feature-locations.
self.featureLocationConnections = SparseMatrixConnections(
cellCount, featureLocationInputSize)
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def reset(self):
"""
Deactivate all cells.
"""
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
def compute(self, deltaLocation=(), newLocation=(),
featureLocationInput=(), featureLocationGrowthCandidates=(),
learn=True):
"""
Run one time step of the Location Memory algorithm.
@param deltaLocation (sorted numpy array)
@param newLocation (sorted numpy array)
@param featureLocationInput (sorted numpy array)
@param featureLocationGrowthCandidates (sorted numpy array)
"""
prevActiveCells = self.activeCells
self.activeDeltaSegments = np.where(
(self.internalConnections.computeActivity(
prevActiveCells, self.connectedPermanence
) >= self.activationThreshold)
&
(self.deltaConnections.computeActivity(
deltaLocation, self.connectedPermanence
) >= self.activationThreshold))[0]
# When we're moving, the feature-location input has no effect.
if len(deltaLocation) == 0:
self.activeFeatureLocationSegments = np.where(
self.featureLocationConnections.computeActivity(
featureLocationInput, self.connectedPermanence
) >= self.activationThreshold)[0]
else:
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
if len(newLocation) > 0:
# Drive activations by relaying this location SDR.
self.activeCells = newLocation
if learn:
# Learn the delta.
self._learnTransition(prevActiveCells, deltaLocation, newLocation)
# Learn the featureLocationInput.
self._learnFeatureLocationPair(newLocation, featureLocationInput,
featureLocationGrowthCandidates)
elif len(prevActiveCells) > 0:
if len(deltaLocation) > 0:
# Drive activations by applying the deltaLocation to the current location.
# Completely ignore the featureLocationInput. It's outdated, associated
# with the previous location.
cellsForDeltaSegments = self.internalConnections.mapSegmentsToCells(
self.activeDeltaSegments)
self.activeCells = np.unique(cellsForDeltaSegments)
else:
# Keep previous active cells active.
# Modulate with the featureLocationInput.
if len(self.activeFeatureLocationSegments) > 0:
cellsForFeatureLocationSegments = (
self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments))
self.activeCells = np.intersect1d(prevActiveCells,
cellsForFeatureLocationSegments)
else:
self.activeCells = prevActiveCells
elif len(featureLocationInput) > 0:
# Drive activations with the featureLocationInput.
cellsForFeatureLocationSegments = (
self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments))
self.activeCells = np.unique(cellsForFeatureLocationSegments)
def _learnTransition(self, prevActiveCells, deltaLocation, newLocation):
"""
For each cell in the newLocation SDR, learn the transition of prevLocation
(i.e. prevActiveCells) + deltaLocation.
The transition might be already known. In that case, just reinforce the
existing segments.
"""
prevLocationPotentialOverlaps = self.internalConnections.computeActivity(
prevActiveCells)
deltaPotentialOverlaps = self.deltaConnections.computeActivity(
deltaLocation)
matchingDeltaSegments = np.where(
(prevLocationPotentialOverlaps >= self.learningThreshold) &
(deltaPotentialOverlaps >= self.learningThreshold))[0]
# Cells with a active segment pair: reinforce the segment
cellsForActiveSegments = self.internalConnections.mapSegmentsToCells(
self.activeDeltaSegments)
learningActiveDeltaSegments = self.activeDeltaSegments[
np.in1d(cellsForActiveSegments, newLocation)]
remainingCells = np.setdiff1d(newLocation, cellsForActiveSegments)
# Remaining cells with a matching segment pair: reinforce the best matching
# segment pair.
candidateSegments = self.internalConnections.filterSegmentsByCell(
matchingDeltaSegments, remainingCells)
cellsForCandidateSegments = self.internalConnections.mapSegmentsToCells(
candidateSegments)
candidateSegments = matchingDeltaSegments[
np.in1d(cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
prevLocationPotentialOverlaps[candidateSegments] +
deltaPotentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingDeltaSegments = candidateSegments[onePerCellFilter]
newDeltaSegmentCells = np.setdiff1d(remainingCells, cellsForCandidateSegments)
for learningSegments in (learningActiveDeltaSegments,
learningMatchingDeltaSegments):
self._learn(self.internalConnections, self.rng, learningSegments,
prevActiveCells, prevActiveCells,
prevLocationPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
self._learn(self.deltaConnections, self.rng, learningSegments,
deltaLocation, deltaLocation, deltaPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
numNewLocationSynapses = len(prevActiveCells)
numNewDeltaSynapses = len(deltaLocation)
if self.sampleSize != -1:
numNewLocationSynapses = min(numNewLocationSynapses, self.sampleSize)
numNewDeltaSynapses = min(numNewDeltaSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewLocationSynapses = min(numNewLocationSynapses,
self.maxSynapsesPerSegment)
numNewDeltaSynapses = min(numNewLocationSynapses,
self.maxSynapsesPerSegment)
newPrevLocationSegments = self.internalConnections.createSegments(
newDeltaSegmentCells)
newDeltaSegments = self.deltaConnections.createSegments(
newDeltaSegmentCells)
assert np.array_equal(newPrevLocationSegments, newDeltaSegments)
self.internalConnections.growSynapsesToSample(
newPrevLocationSegments, prevActiveCells, numNewLocationSynapses,
self.initialPermanence, self.rng)
self.deltaConnections.growSynapsesToSample(
newDeltaSegments, deltaLocation, numNewDeltaSynapses,
self.initialPermanence, self.rng)
def _learnFeatureLocationPair(self, newLocation, featureLocationInput,
featureLocationGrowthCandidates):
"""
Grow / reinforce synapses between the location layer's dendrites and the
input layer's active cells.
"""
potentialOverlaps = self.featureLocationConnections.computeActivity(
featureLocationInput)
matchingSegments = np.where(potentialOverlaps > self.learningThreshold)[0]
# Cells with a active segment pair: reinforce the segment
cellsForActiveSegments = self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments)
learningActiveSegments = self.activeFeatureLocationSegments[
np.in1d(cellsForActiveSegments, newLocation)]
remainingCells = np.setdiff1d(newLocation, cellsForActiveSegments)
# Remaining cells with a matching segment pair: reinforce the best matching
# segment pair.
candidateSegments = self.featureLocationConnections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.featureLocationConnections.mapSegmentsToCells(
candidateSegments))
candidateSegments = candidateSegments[
np.in1d(cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells, cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.featureLocationConnections, self.rng, learningSegments,
featureLocationInput, featureLocationGrowthCandidates,
potentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
numNewSynapses = len(featureLocationInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.featureLocationConnections.createSegments(
newSegmentCells)
self.featureLocationConnections.growSynapsesToSample(
newSegments, featureLocationGrowthCandidates, numNewSynapses,
self.initialPermanence, self.rng)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput, growthCandidates,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
class Superficial2DLocationModule(object):
"""
A model of a location module. It's similar to a grid cell module, but it uses
squares rather than triangles.
The cells are arranged into a m*n rectangle which is tiled onto 2D space.
Each cell represents a small rectangle in each tile.
+------+------+------++------+------+------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #1 | #2 | #3 || #1 | #2 | #3 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #4 | #5 | #6 || #4 | #5 | #6 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #7 | #8 | #9 || #7 | #8 | #9 |
| | | || | | |
+------+------+------++------+------+------+
We assume that path integration works *somehow*. This model receives a "delta
location" vector, and it shifts the active cells accordingly. The model stores
intermediate coordinates of active cells. Whenever sensory cues activate a
cell, the model adds this cell to the list of coordinates being shifted.
Whenever sensory cues cause a cell to become inactive, that cell is removed
from the list of coordinates.
(This model doesn't attempt to propose how "path integration" works. It
attempts to show how locations are anchored to sensory cues.)
When orientation is set to 0 degrees, the displacement is a [di, dj],
moving di cells "down" and dj cells "right".
When orientation is set to 90 degrees, the displacement is essentially a
[dx, dy], applied in typical x,y coordinates with the origin on the bottom
left.
Usage:
- When the sensor moves, call movementCompute.
- When the sensor senses something, call sensoryCompute.
The "anchor input" is typically a feature-location pair SDR.
To specify how points are tracked, pass anchoringMethod = "corners",
"narrowing" or "discrete". "discrete" will cause the network to operate in a
fully discrete space, where uncertainty is impossible as long as movements are
integers. "narrowing" is designed to narrow down uncertainty of initial
locations of sensory stimuli. "corners" is designed for noise-tolerance, and
will activate all cells that are possible outcomes of path integration.
"""
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
cellCoordinateOffsets=(0.5, ),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
anchoringMethod="narrowing",
rotationMatrix=None,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param cellCoordinateOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "phase" which is shifted in subsequent
motions. By default, this phase is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, with value [0.2, 0.8], when cell [2, 3] is activated
it will place 4 phases, corresponding to the following points in cell
coordinates: [2.2, 3.2], [2.2, 3.8], [2.8, 3.2], [2.8, 3.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions,
dtype="float")
self.phasesPerUnitDistance = 1.0 / self.moduleMapDimensions
if rotationMatrix is None:
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation),
math.cos(orientation)]])
if anchoringMethod == "discrete":
# Need to convert matrix to have integer values
nonzeros = self.rotationMatrix[np.where(
np.abs(self.rotationMatrix) > 0)]
smallestValue = np.amin(nonzeros)
self.rotationMatrix /= smallestValue
self.rotationMatrix = np.ceil(self.rotationMatrix)
else:
self.rotationMatrix = rotationMatrix
self.cellCoordinateOffsets = cellCoordinateOffsets
# Phase is measured as a number in the range [0.0, 1.0)
self.activePhases = np.empty((0, 2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.phaseDisplacement = np.empty((0, 2), dtype="float")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.anchoringMethod = anchoringMethod
self.rng = Random(seed)
def reset(self):
"""
Clear the active cells.
"""
self.activePhases = np.empty((0, 2), dtype="float")
self.phaseDisplacement = np.empty((0, 2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
def _computeActiveCells(self):
# Round each coordinate to the nearest cell.
activeCellCoordinates = np.floor(self.activePhases *
self.cellDimensions).astype("int")
# Convert coordinates to cell numbers.
self.cellsForActivePhases = (np.ravel_multi_index(
activeCellCoordinates.T, self.cellDimensions))
self.activeCells = np.unique(self.cellsForActivePhases)
def activateRandomLocation(self):
"""
Set the location to a random point.
"""
self.activePhases = np.array([np.random.random(2)])
if self.anchoringMethod == "discrete":
# Need to place the phase in the middle of a cell
self.activePhases = np.floor(
self.activePhases * self.cellDimensions) / self.cellDimensions
self._computeActiveCells()
def movementCompute(self, displacement, noiseFactor=0):
"""
Shift the current active cells by a vector.
@param displacement (pair of floats)
A translation vector [di, dj].
"""
if noiseFactor != 0:
displacement = copy.deepcopy(displacement)
xnoise = np.random.normal(0, noiseFactor)
ynoise = np.random.normal(0, noiseFactor)
displacement[0] += xnoise
displacement[1] += ynoise
# Calculate delta in the module's coordinates.
phaseDisplacement = (np.matmul(self.rotationMatrix, displacement) *
self.phasesPerUnitDistance)
# Shift the active coordinates.
np.add(self.activePhases, phaseDisplacement, out=self.activePhases)
# In Python, (x % 1.0) can return 1.0 because of floating point goofiness.
# Generally this doesn't cause problems, it's just confusing when you're
# debugging.
np.round(self.activePhases, decimals=9, out=self.activePhases)
np.mod(self.activePhases, 1.0, out=self.activePhases)
self._computeActiveCells()
self.phaseDisplacement = phaseDisplacement
def _sensoryComputeInferenceMode(self, anchorInput):
"""
Infer the location from sensory input. Activate any cells with enough active
synapses to this sensory input. Deactivate all other cells.
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
if len(anchorInput) == 0:
return
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
sensorySupportedCells = np.unique(
self.connections.mapSegmentsToCells(activeSegments))
inactivated = np.setdiff1d(self.activeCells, sensorySupportedCells)
inactivatedIndices = np.in1d(self.cellsForActivePhases,
inactivated).nonzero()[0]
if inactivatedIndices.size > 0:
self.activePhases = np.delete(self.activePhases,
inactivatedIndices,
axis=0)
activated = np.setdiff1d(sensorySupportedCells, self.activeCells)
# Find centers of point clouds
if "corners" in self.anchoringMethod:
activatedCoordsBase = np.transpose(
np.unravel_index(sensorySupportedCells,
self.cellDimensions)).astype('float')
else:
activatedCoordsBase = np.transpose(
np.unravel_index(activated,
self.cellDimensions)).astype('float')
# Generate points to add
activatedCoords = np.concatenate([
activatedCoordsBase + [iOffset, jOffset]
for iOffset in self.cellCoordinateOffsets
for jOffset in self.cellCoordinateOffsets
])
if "corners" in self.anchoringMethod:
self.activePhases = activatedCoords / self.cellDimensions
else:
if activatedCoords.size > 0:
self.activePhases = np.append(self.activePhases,
activatedCoords /
self.cellDimensions,
axis=0)
self._computeActiveCells()
self.activeSegments = activeSegments
def _sensoryComputeLearningMode(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.connections.computeActivity(anchorInput)
matchingSegments = np.where(
potentialOverlaps >= self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.connections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[np.in1d(
cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.connections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.connections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[np.in1d(
cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
potentialOverlaps[candidateSegments], cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells,
cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.connections, self.rng, learningSegments,
anchorInput, potentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.connections.createSegments(newSegmentCells)
self.connections.growSynapsesToSample(newSegments, anchorInput,
numNewSynapses,
self.initialPermanence, self.rng)
self.activeSegments = activeSegments
def sensoryCompute(self, anchorInput, anchorGrowthCandidates, learn):
if learn:
self._sensoryComputeLearningMode(anchorGrowthCandidates)
else:
self._sensoryComputeInferenceMode(anchorInput)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement,
maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax, maxNew,
numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput, maxNew,
initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
def numberOfCells(self):
return np.prod(self.cellDimensions)
class Superficial2DLocationModule(object):
"""
A model of a location module. It's similar to a grid cell module, but it uses
squares rather than triangles.
The cells are arranged into a m*n rectangle which is tiled onto 2D space.
Each cell represents a small rectangle in each tile.
+------+------+------++------+------+------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #1 | #2 | #3 || #1 | #2 | #3 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #4 | #5 | #6 || #4 | #5 | #6 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #7 | #8 | #9 || #7 | #8 | #9 |
| | | || | | |
+------+------+------++------+------+------+
We assume that path integration works *somehow*. This model receives a "delta
location" vector, and it shifts the active cells accordingly. The model stores
intermediate coordinates of active cells. Whenever sensory cues activate a
cell, the model adds this cell to the list of coordinates being shifted.
Whenever sensory cues cause a cell to become inactive, that cell is removed
from the list of coordinates.
(This model doesn't attempt to propose how "path integration" works. It
attempts to show how locations are anchored to sensory cues.)
When orientation is set to 0 degrees, the displacement is a [di, dj],
moving di cells "down" and dj cells "right".
When orientation is set to 90 degrees, the displacement is essentially a
[dx, dy], applied in typical x,y coordinates with the origin on the bottom
left.
Usage:
- When the sensor moves, call movementCompute.
- When the sensor senses something, call sensoryCompute.
The "anchor input" is typically a feature-location pair SDR.
To specify how points are tracked, pass anchoringMethod = "corners",
"narrowing" or "discrete". "discrete" will cause the network to operate in a
fully discrete space, where uncertainty is impossible as long as movements are
integers. "narrowing" is designed to narrow down uncertainty of initial
locations of sensory stimuli. "corners" is designed for noise-tolerance, and
will activate all cells that are possible outcomes of path integration.
"""
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
cellCoordinateOffsets=(0.5,),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
anchoringMethod="narrowing",
rotationMatrix = None,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param cellCoordinateOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "phase" which is shifted in subsequent
motions. By default, this phase is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, with value [0.2, 0.8], when cell [2, 3] is activated
it will place 4 phases, corresponding to the following points in cell
coordinates: [2.2, 3.2], [2.2, 3.8], [2.8, 3.2], [2.8, 3.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions, dtype="float")
self.phasesPerUnitDistance = 1.0 / self.moduleMapDimensions
if rotationMatrix is None:
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation), math.cos(orientation)]])
if anchoringMethod == "discrete":
# Need to convert matrix to have integer values
nonzeros = self.rotationMatrix[np.where(np.abs(self.rotationMatrix)>0)]
smallestValue = np.amin(nonzeros)
self.rotationMatrix /= smallestValue
self.rotationMatrix = np.ceil(self.rotationMatrix)
else:
self.rotationMatrix = rotationMatrix
self.cellCoordinateOffsets = cellCoordinateOffsets
# Phase is measured as a number in the range [0.0, 1.0)
self.activePhases = np.empty((0,2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.phaseDisplacement = np.empty((0,2), dtype="float")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.anchoringMethod = anchoringMethod
self.rng = Random(seed)
def reset(self):
"""
Clear the active cells.
"""
self.activePhases = np.empty((0,2), dtype="float")
self.phaseDisplacement = np.empty((0,2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
def _computeActiveCells(self):
# Round each coordinate to the nearest cell.
activeCellCoordinates = np.floor(
self.activePhases * self.cellDimensions).astype("int")
# Convert coordinates to cell numbers.
self.cellsForActivePhases = (
np.ravel_multi_index(activeCellCoordinates.T, self.cellDimensions))
self.activeCells = np.unique(self.cellsForActivePhases)
def activateRandomLocation(self):
"""
Set the location to a random point.
"""
self.activePhases = np.array([np.random.random(2)])
if self.anchoringMethod == "discrete":
# Need to place the phase in the middle of a cell
self.activePhases = np.floor(
self.activePhases * self.cellDimensions)/self.cellDimensions
self._computeActiveCells()
def movementCompute(self, displacement, noiseFactor = 0):
"""
Shift the current active cells by a vector.
@param displacement (pair of floats)
A translation vector [di, dj].
"""
if noiseFactor != 0:
displacement = copy.deepcopy(displacement)
xnoise = np.random.normal(0, noiseFactor)
ynoise = np.random.normal(0, noiseFactor)
displacement[0] += xnoise
displacement[1] += ynoise
# Calculate delta in the module's coordinates.
phaseDisplacement = (np.matmul(self.rotationMatrix, displacement) *
self.phasesPerUnitDistance)
# Shift the active coordinates.
np.add(self.activePhases, phaseDisplacement, out=self.activePhases)
# In Python, (x % 1.0) can return 1.0 because of floating point goofiness.
# Generally this doesn't cause problems, it's just confusing when you're
# debugging.
np.round(self.activePhases, decimals=9, out=self.activePhases)
np.mod(self.activePhases, 1.0, out=self.activePhases)
self._computeActiveCells()
self.phaseDisplacement = phaseDisplacement
def _sensoryComputeInferenceMode(self, anchorInput):
"""
Infer the location from sensory input. Activate any cells with enough active
synapses to this sensory input. Deactivate all other cells.
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
if len(anchorInput) == 0:
return
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
sensorySupportedCells = np.unique(
self.connections.mapSegmentsToCells(activeSegments))
inactivated = np.setdiff1d(self.activeCells, sensorySupportedCells)
inactivatedIndices = np.in1d(self.cellsForActivePhases,
inactivated).nonzero()[0]
if inactivatedIndices.size > 0:
self.activePhases = np.delete(self.activePhases, inactivatedIndices,
axis=0)
activated = np.setdiff1d(sensorySupportedCells, self.activeCells)
# Find centers of point clouds
if "corners" in self.anchoringMethod:
activatedCoordsBase = np.transpose(
np.unravel_index(sensorySupportedCells,
self.cellDimensions)).astype('float')
else:
activatedCoordsBase = np.transpose(
np.unravel_index(activated, self.cellDimensions)).astype('float')
# Generate points to add
activatedCoords = np.concatenate(
[activatedCoordsBase + [iOffset, jOffset]
for iOffset in self.cellCoordinateOffsets
for jOffset in self.cellCoordinateOffsets]
)
if "corners" in self.anchoringMethod:
self.activePhases = activatedCoords / self.cellDimensions
else:
if activatedCoords.size > 0:
self.activePhases = np.append(self.activePhases,
activatedCoords / self.cellDimensions,
axis=0)
self._computeActiveCells()
self.activeSegments = activeSegments
def _sensoryComputeLearningMode(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.connections.computeActivity(anchorInput)
matchingSegments = np.where(potentialOverlaps >=
self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.connections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[
np.in1d(cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.connections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.connections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[
np.in1d(cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells, cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.connections, self.rng, learningSegments,
anchorInput, potentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.connections.createSegments(newSegmentCells)
self.connections.growSynapsesToSample(
newSegments, anchorInput, numNewSynapses,
self.initialPermanence, self.rng)
self.activeSegments = activeSegments
def sensoryCompute(self, anchorInput, anchorGrowthCandidates, learn):
if learn:
self._sensoryComputeLearningMode(anchorGrowthCandidates)
else:
self._sensoryComputeInferenceMode(anchorInput)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput,
maxNew, initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
def numberOfCells(self):
return np.prod(self.cellDimensions)
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
pointOffsets=(0.5, ),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param pointOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "point" which is shifted in subsequent
motions. By default, this point is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, With value [0.2, 0.8], it will place 4 points:
[0.2, 0.2], [0.2, 0.8], [0.8, 0.2], [0.8, 0.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions,
dtype="float")
self.cellFieldsPerUnitDistance = self.cellDimensions / self.moduleMapDimensions
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation),
math.cos(orientation)]])
self.pointOffsets = pointOffsets
# These coordinates are in units of "cell fields".
self.activePoints = np.empty((0, 2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
pointOffsets=(0.5,),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param pointOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "point" which is shifted in subsequent
motions. By default, this point is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, With value [0.2, 0.8], it will place 4 points:
[0.2, 0.2], [0.2, 0.8], [0.8, 0.2], [0.8, 0.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions, dtype="float")
self.cellFieldsPerUnitDistance = self.cellDimensions / self.moduleMapDimensions
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation), math.cos(orientation)]])
self.pointOffsets = pointOffsets
# These coordinates are in units of "cell fields".
self.activePoints = np.empty((0,2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
class Thalamus(object):
"""
A simple discrete time thalamus. This thalamus has a 2D TRN layer and a 2D
relay cell layer. L6 cells project to the dendrites of TRN cells - these
connections are learned. TRN cells project to the dendrites of relay cells in
a fixed fan-out pattern. A 2D feed forward input source projects to the relay
cells in a fixed fan-out pattern.
The output of the thalamus is the activity of each relay cell. This activity
can be in one of three states: inactive, active (tonic), and active (burst).
TRN cells control whether the relay cells will burst. If any dendrite on a TRN
cell recognizes the current L6 pattern, it de-inactivates the T-type CA2+
channels on the dendrites of any relay cell it projects to. These relay cells
are then in "burst-ready mode".
Feed forward activity is in the form of a binary vector corresponding to
active/spiking axons (e.g. from ganglion cells). Any relay cells that receive
input from an axon will either output tonic or burst activity depending on the
state of the T-type CA2+ channels on their dendrites. Relay cells that don't
receive input will remain inactive, regardless of their dendritic state.
Usage:
1. Train the TRN cells on a bunch of L6 patterns: learnL6Pattern()
2. De-inactivate relay cells by sending in an L6 pattern: deInactivateCells()
3. Compute feed forward activity for an input: computeFeedForwardActivity()
4. reset()
5. Goto 2
"""
def __init__(self,
trnCellShape=(32, 32),
relayCellShape=(32, 32),
inputShape=(32, 32),
l6CellCount=1024,
trnThreshold=10,
relayThreshold=1,
seed=42):
"""
:param trnCellShape:
a 2D shape for the TRN
:param relayCellShape:
a 2D shape for the relay cells
:param l6CellCount:
number of L6 cells
:param trnThreshold:
dendritic threshold for TRN cells. This is the min number of active L6
cells on a dendrite for the TRN cell to recognize a pattern on that
dendrite.
:param relayThreshold:
dendritic threshold for relay cells. This is the min number of active TRN
cells on a dendrite for the relay cell to recognize a pattern on that
dendrite.
:param seed:
Seed for the random number generator.
"""
self.trnCellShape = trnCellShape
self.trnWidth = trnCellShape[0]
self.trnHeight = trnCellShape[1]
self.relayCellShape = relayCellShape
self.relayWidth = relayCellShape[0]
self.relayHeight = relayCellShape[1]
self.l6CellCount = l6CellCount
self.trnThreshold = trnThreshold
self.relayThreshold = relayThreshold
self.inputShape = inputShape
self.seed = seed
self.rng = Random(seed)
self.trnActivationThreshold = 5
self.trnConnections = SparseMatrixConnections(
trnCellShape[0]*trnCellShape[1], l6CellCount)
self.relayConnections = SparseMatrixConnections(
relayCellShape[0]*relayCellShape[1],
trnCellShape[0]*trnCellShape[1])
# Initialize/reset variables that are updated with calls to compute
self.reset()
self._initializeTRNToRelayCellConnections()
def learnL6Pattern(self, l6Pattern, cellsToLearnOn):
"""
Learn the given l6Pattern on TRN cell dendrites. The TRN cells to learn
are given in cellsTeLearnOn. Each of these cells will learn this pattern on
a single dendritic segment.
:param l6Pattern:
An SDR from L6. List of indices corresponding to L6 cells.
:param cellsToLearnOn:
Each cell index is (x,y) corresponding to the TRN cells that should learn
this pattern. For each cell, create a new dendrite that stores this
pattern. The SDR is stored on this dendrite
"""
cellIndices = [self.trnCellIndex(x) for x in cellsToLearnOn]
newSegments = self.trnConnections.createSegments(cellIndices)
self.trnConnections.growSynapses(newSegments, l6Pattern, 1.0)
# print("Learning L6 SDR:", l6Pattern,
# "new segments: ", newSegments,
# "cells:", self.trnConnections.mapSegmentsToCells(newSegments))
def deInactivateCells(self, l6Input):
"""
Activate trnCells according to the l6Input. These in turn will impact
bursting mode in relay cells that are connected to these trnCells.
Given the feedForwardInput, compute which cells will be silent, tonic,
or bursting.
:param l6Input:
:return: nothing
"""
# Figure out which TRN cells recognize the L6 pattern.
self.trnOverlaps = self.trnConnections.computeActivity(l6Input, 0.5)
self.activeTRNSegments = np.flatnonzero(
self.trnOverlaps >= self.trnActivationThreshold)
self.activeTRNCellIndices = self.trnConnections.mapSegmentsToCells(
self.activeTRNSegments)
# print("trnOverlaps:", self.trnOverlaps,
# "active segments:", self.activeTRNSegments)
for s, idx in zip(self.activeTRNSegments, self.activeTRNCellIndices):
print(self.trnOverlaps[s], idx, self.trnIndextoCoord(idx))
# Figure out which relay cells have dendrites in de-inactivated state
self.relayOverlaps = self.relayConnections.computeActivity(
self.activeTRNCellIndices, 0.5
)
self.activeRelaySegments = np.flatnonzero(
self.relayOverlaps >= self.relayThreshold)
self.burstReadyCellIndices = self.relayConnections.mapSegmentsToCells(
self.activeRelaySegments)
self.burstReadyCells.reshape(-1)[self.burstReadyCellIndices] = 1
def computeFeedForwardActivity(self, feedForwardInput):
"""
Activate trnCells according to the l6Input. These in turn will impact
bursting mode in relay cells that are connected to these trnCells.
Given the feedForwardInput, compute which cells will be silent, tonic,
or bursting.
:param feedForwardInput:
a numpy matrix of shape relayCellShape containing 0's and 1's
:return:
feedForwardInput is modified to contain 0, 1, or 2. A "2" indicates
bursting cells.
"""
feedForwardInput += self.burstReadyCells * feedForwardInput
def reset(self):
"""
Set everything back to zero
"""
self.trnOverlaps = []
self.activeTRNSegments = []
self.activeTRNCellIndices = []
self.relayOverlaps = []
self.activeRelaySegments = []
self.burstReadyCellIndices = []
self.burstReadyCells = np.zeros((self.relayWidth, self.relayHeight))
def trnCellIndex(self, coord):
"""
Map a 2D coordinate to 1D cell index.
:param coord: a 2D coordinate
:return: integer index
"""
return coord[1] * self.trnWidth + coord[0]
def trnIndextoCoord(self, i):
"""
Map 1D cell index to a 2D coordinate
:param i: integer 1D cell index
:return: (x, y), a 2D coordinate
"""
x = i % self.trnWidth
y = i / self.trnWidth
return x, y
def relayCellIndex(self, coord):
"""
Map a 2D coordinate to 1D cell index.
:param coord: a 2D coordinate
:return: integer index
"""
return coord[1] * self.relayWidth + coord[0]
def relayIndextoCoord(self, i):
"""
Map 1D cell index to a 2D coordinate
:param i: integer 1D cell index
:return: (x, y), a 2D coordinate
"""
x = i % self.relayWidth
y = i / self.relayWidth
return x, y
def _initializeTRNToRelayCellConnections(self):
"""
Initialize TRN to relay cell connectivity. For each relay cell, create a
dendritic segment for each TRN cell it connects to.
"""
for x in range(self.relayWidth):
for y in range(self.relayHeight):
# Create one dendrite for each trn cell that projects to this relay cell
# This dendrite contains one synapse corresponding to this TRN->relay
# connection.
relayCellIndex = self.relayCellIndex((x,y))
trnCells = self._preSynapticTRNCells(x, y)
for trnCell in trnCells:
newSegment = self.relayConnections.createSegments([relayCellIndex])
self.relayConnections.growSynapses(newSegment,
[self.trnCellIndex(trnCell)], 1.0)
def _preSynapticTRNCells(self, i, j):
"""
Given a relay cell at the given coordinate, return a list of the (x,y)
coordinates of all TRN cells that project to it.
:param relayCellCoordinate:
:return:
"""
xmin = max(i - 1, 0)
xmax = min(i + 2, self.trnWidth)
ymin = max(j - 1, 0)
ymax = min(j + 2, self.trnHeight)
trnCells = [
(x, y) for x in range(xmin, xmax) for y in range(ymin, ymax)
]
return trnCells
def test_clipPermanences(self):
connections = SparseMatrixConnections(2048, 2048)
# Destroy synapses with permanences <= 0.0
segments = connections.createSegments([1, 2, 3])
connections.growSynapses(segments, [42, 43, 44], 0.05)
connections.growSynapses(segments, [45, 46], 0.1)
connections.adjustInactiveSynapses(segments, [], -0.1)
connections.clipPermanences(segments)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[0, 0, 0])
# Clip permanences to 1.0
connections.growSynapses(segments, [42, 43, 44], 0.95)
connections.adjustInactiveSynapses(segments, [], 0.50)
connections.clipPermanences(segments)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[3, 3, 3])
connections.adjustInactiveSynapses(segments, [], -0.5)
overlaps1 = connections.computeActivity([42, 43, 44], 0.49)
overlaps2 = connections.computeActivity([42, 43, 44], 0.51)
np.testing.assert_equal(overlaps1, [3, 3, 3])
np.testing.assert_equal(overlaps2, [0, 0, 0])
class TemporalMemory(object):
"""
TemporalMemory with basal and apical connections, and with the ability to
connect to external cells.
Basal connections are used to implement traditional Temporal Memory.
The apical connections are used for further disambiguation. If multiple cells
in a minicolumn have active basal segments, each of those cells is predicted,
unless one of them also has an active apical segment, in which case only the
cells with active basal and apical segments are predicted.
In other words, the apical connections have no effect unless the basal input
is a union of SDRs (e.g. from bursting minicolumns).
This TemporalMemory is unaware of whether its basalInput or apicalInput are
from internal or external cells. They are just cell numbers. The caller knows
what these cell numbers mean, but the TemporalMemory doesn't. This allows the
same code to work for various algorithms.
To implement sequence memory, use
basalInputDimensions=(numColumns*cellsPerColumn,)
and call compute like this:
tm.compute(activeColumns, tm.getActiveCells(), tm.getWinnerCells())
"""
def __init__(self,
columnDimensions=(2048,),
basalInputDimensions=(),
apicalInputDimensions=(),
cellsPerColumn=32,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
predictedSegmentDecrement=0.0,
maxNewSynapseCount=None,
maxSynapsesPerSegment=-1,
maxSegmentsPerCell=None,
seed=42):
self.columnDimensions = columnDimensions
self.numColumns = self._numPoints(columnDimensions)
self.basalInputDimensions = basalInputDimensions
self.apicalInputDimensions = apicalInputDimensions
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.minThreshold = minThreshold
self.sampleSize = sampleSize
if maxNewSynapseCount is not None:
print "Parameter 'maxNewSynapseCount' is deprecated. Use 'sampleSize'."
self.sampleSize = maxNewSynapseCount
if maxSegmentsPerCell is not None:
print "Warning: ignoring parameter 'maxSegmentsPerCell'"
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.predictedSegmentDecrement = predictedSegmentDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(basalInputDimensions))
self.apicalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(apicalInputDimensions))
self.rng = Random(seed)
self.activeCells = EMPTY_UINT_ARRAY
self.winnerCells = EMPTY_UINT_ARRAY
self.prevPredictedCells = EMPTY_UINT_ARRAY
def reset(self):
self.activeCells = EMPTY_UINT_ARRAY
self.winnerCells = EMPTY_UINT_ARRAY
self.prevPredictedCells = EMPTY_UINT_ARRAY
def compute(self,
activeColumns,
basalInput,
basalGrowthCandidates,
apicalInput=EMPTY_UINT_ARRAY,
apicalGrowthCandidates=EMPTY_UINT_ARRAY,
learn=True):
"""
@param activeColumns (numpy array)
@param basalInput (numpy array)
@param basalGrowthCandidates (numpy array)
@param apicalInput (numpy array)
@param apicalGrowthCandidates (numpy array)
@param learn (bool)
"""
# Calculate predictions for this timestep
(activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps) = self._calculateSegmentActivity(
self.basalConnections, basalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
(activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps) = self._calculateSegmentActivity(
self.apicalConnections, apicalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
predictedCells = self._calculatePredictedCells(activeBasalSegments,
activeApicalSegments)
# Calculate active cells
(correctPredictedCells,
burstingColumns) = np2.setCompare(predictedCells, activeColumns,
predictedCells / self.cellsPerColumn,
rightMinusLeft=True)
newActiveCells = np.concatenate((correctPredictedCells,
np2.getAllCellsInColumns(
burstingColumns, self.cellsPerColumn)))
# Calculate learning
(learningActiveBasalSegments,
learningMatchingBasalSegments,
basalSegmentsToPunish,
newBasalSegmentCells,
learningCells) = self._calculateBasalLearning(
activeColumns, burstingColumns, correctPredictedCells,
activeBasalSegments, matchingBasalSegments, basalPotentialOverlaps)
(learningActiveApicalSegments,
learningMatchingApicalSegments,
apicalSegmentsToPunish,
newApicalSegmentCells) = self._calculateApicalLearning(
learningCells, activeColumns, activeApicalSegments,
matchingApicalSegments, apicalPotentialOverlaps)
# Learn
if learn:
# Learn on existing segments
for learningSegments in (learningActiveBasalSegments,
learningMatchingBasalSegments):
self._learn(self.basalConnections, self.rng, learningSegments,
basalInput, basalGrowthCandidates, basalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
for learningSegments in (learningActiveApicalSegments,
learningMatchingApicalSegments):
self._learn(self.apicalConnections, self.rng, learningSegments,
apicalInput, apicalGrowthCandidates,
apicalPotentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Punish incorrect predictions
if self.predictedSegmentDecrement != 0.0:
self.basalConnections.adjustActiveSynapses(
basalSegmentsToPunish, basalInput, -self.predictedSegmentDecrement)
self.apicalConnections.adjustActiveSynapses(
apicalSegmentsToPunish, apicalInput, -self.predictedSegmentDecrement)
# Grow new segments
if len(basalGrowthCandidates) > 0:
self._learnOnNewSegments(self.basalConnections, self.rng,
newBasalSegmentCells, basalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
if len(apicalGrowthCandidates) > 0:
self._learnOnNewSegments(self.apicalConnections, self.rng,
newApicalSegmentCells, apicalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
# Save the results
self.activeCells = newActiveCells
self.winnerCells = learningCells
self.prevPredictedCells = predictedCells
def _calculateBasalLearning(self,
activeColumns,
burstingColumns,
correctPredictedCells,
activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps):
"""
Basic Temporal Memory learning. Correctly predicted cells always have
active basal segments, and we learn on these segments. In bursting
columns, we either learn on an existing basal segment, or we grow a new one.
The only influence apical dendrites have on basal learning is: the apical
dendrites influence which cells are considered "predicted". So an active
apical dendrite can keep some basal segments in active columns from
learning.
@param correctPredictedCells (numpy array)
@param burstingColumns (numpy array)
@param activeBasalSegments (numpy array)
@param matchingBasalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveBasalSegments (numpy array)
Active basal segments on correct predicted cells
- learningMatchingBasalSegments (numpy array)
Matching basal segments selected for learning in bursting columns
- basalSegmentsToPunish (numpy array)
Basal segments that should be punished for predicting an inactive column
- newBasalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new basal segments
- learningCells (numpy array)
Cells that have learning basal segments or are selected to grow a basal
segment
"""
# Correctly predicted columns
learningActiveBasalSegments = self.basalConnections.filterSegmentsByCell(
activeBasalSegments, correctPredictedCells)
cellsForMatchingBasal = self.basalConnections.mapSegmentsToCells(
matchingBasalSegments)
matchingCells = np.unique(cellsForMatchingBasal)
(matchingCellsInBurstingColumns,
burstingColumnsWithNoMatch) = np2.setCompare(
matchingCells, burstingColumns, matchingCells / self.cellsPerColumn,
rightMinusLeft=True)
learningMatchingBasalSegments = self._chooseBestSegmentPerColumn(
self.basalConnections, matchingCellsInBurstingColumns,
matchingBasalSegments, basalPotentialOverlaps, self.cellsPerColumn)
newBasalSegmentCells = self._getCellsWithFewestSegments(
self.basalConnections, self.rng, burstingColumnsWithNoMatch,
self.cellsPerColumn)
learningCells = np.concatenate(
(correctPredictedCells,
self.basalConnections.mapSegmentsToCells(learningMatchingBasalSegments),
newBasalSegmentCells))
# Incorrectly predicted columns
correctMatchingBasalMask = np.in1d(
cellsForMatchingBasal / self.cellsPerColumn, activeColumns)
basalSegmentsToPunish = matchingBasalSegments[~correctMatchingBasalMask]
return (learningActiveBasalSegments,
learningMatchingBasalSegments,
basalSegmentsToPunish,
newBasalSegmentCells,
learningCells)
def _calculateApicalLearning(self,
learningCells,
activeColumns,
activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps):
"""
Calculate apical learning for each learning cell.
The set of learning cells was determined completely from basal segments.
Do all apical learning on the same cells.
Learn on any active segments on learning cells. For cells without active
segments, learn on the best matching segment. For cells without a matching
segment, grow a new segment.
@param learningCells (numpy array)
@param correctPredictedCells (numpy array)
@param activeApicalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveApicalSegments (numpy array)
Active apical segments on correct predicted cells
- learningMatchingApicalSegments (numpy array)
Matching apical segments selected for learning in bursting columns
- apicalSegmentsToPunish (numpy array)
Apical segments that should be punished for predicting an inactive column
- newApicalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new apical segments
"""
# Cells with active apical segments
learningActiveApicalSegments = self.apicalConnections.filterSegmentsByCell(
activeApicalSegments, learningCells)
# Cells with matching apical segments
learningCellsWithoutActiveApical = np.setdiff1d(
learningCells,
self.apicalConnections.mapSegmentsToCells(learningActiveApicalSegments))
cellsForMatchingApical = self.apicalConnections.mapSegmentsToCells(
matchingApicalSegments)
learningCellsWithMatchingApical = np.intersect1d(
learningCellsWithoutActiveApical, cellsForMatchingApical)
learningMatchingApicalSegments = self._chooseBestSegmentPerCell(
self.apicalConnections, learningCellsWithMatchingApical,
matchingApicalSegments, apicalPotentialOverlaps)
# Cells that need to grow an apical segment
newApicalSegmentCells = np.setdiff1d(learningCellsWithoutActiveApical,
learningCellsWithMatchingApical)
# Incorrectly predicted columns
correctMatchingApicalMask = np.in1d(
cellsForMatchingApical / self.cellsPerColumn, activeColumns)
apicalSegmentsToPunish = matchingApicalSegments[~correctMatchingApicalMask]
return (learningActiveApicalSegments,
learningMatchingApicalSegments,
apicalSegmentsToPunish,
newApicalSegmentCells)
@staticmethod
def _calculateSegmentActivity(connections, activeInput, connectedPermanence,
activationThreshold, minThreshold):
"""
Calculate the active and matching segments for this timestep.
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active
overlaps = connections.computeActivity(activeInput, connectedPermanence)
activeSegments = np.flatnonzero(overlaps >= activationThreshold)
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments,
matchingSegments,
potentialOverlaps)
def _calculatePredictedCells(self, activeBasalSegments, activeApicalSegments):
"""
Calculate the predicted cells, given the set of active segments.
An active basal segment is enough to predict a cell.
An active apical segment is *not* enough to predict a cell.
When a cell has both types of segments active, other cells in its minicolumn
must also have both types of segments to be considered predictive.
@param activeBasalSegments (numpy array)
@param activeApicalSegments (numpy array)
@return (numpy array)
"""
cellsForBasalSegments = self.basalConnections.mapSegmentsToCells(
activeBasalSegments)
cellsForApicalSegments = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
fullyDepolarizedCells = np.intersect1d(cellsForBasalSegments,
cellsForApicalSegments)
partlyDepolarizedCells = np.setdiff1d(cellsForBasalSegments,
fullyDepolarizedCells)
inhibitedMask = np.in1d(partlyDepolarizedCells / self.cellsPerColumn,
fullyDepolarizedCells / self.cellsPerColumn)
predictedCells = np.append(fullyDepolarizedCells,
partlyDepolarizedCells[~inhibitedMask])
return predictedCells
@staticmethod
def _learn(connections, rng, learningSegments, activeInput, growthCandidates,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param newSegmentCells (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
@staticmethod
def _learnOnNewSegments(connections, rng, newSegmentCells, growthCandidates,
initialPermanence, sampleSize, maxSynapsesPerSegment):
numNewSynapses = len(growthCandidates)
if sampleSize != -1:
numNewSynapses = min(numNewSynapses, sampleSize)
if maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, maxSynapsesPerSegment)
newSegments = connections.createSegments(newSegmentCells)
connections.growSynapsesToSample(newSegments, growthCandidates,
numNewSynapses, initialPermanence,
rng)
@classmethod
def _chooseBestSegmentPerCell(cls,
connections,
cells,
allMatchingSegments,
potentialOverlaps):
"""
For each specified cell, choose its matching segment with largest number
of active potential synapses. When there's a tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param cells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
@return (numpy array)
One segment per cell
"""
candidateSegments = connections.filterSegmentsByCell(allMatchingSegments,
cells)
# Narrow it down to one pair per cell.
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
connections.mapSegmentsToCells(
candidateSegments))
learningSegments = candidateSegments[onePerCellFilter]
return learningSegments
@classmethod
def _chooseBestSegmentPerColumn(cls, connections, matchingCells,
allMatchingSegments, potentialOverlaps,
cellsPerColumn):
"""
For all the columns covered by 'matchingCells', choose the column's matching
segment with largest number of active potential synapses. When there's a
tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param matchingCells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
"""
candidateSegments = connections.filterSegmentsByCell(allMatchingSegments,
matchingCells)
# Narrow it down to one segment per column.
cellScores = potentialOverlaps[candidateSegments]
columnsForCandidates = (connections.mapSegmentsToCells(candidateSegments) /
cellsPerColumn)
onePerColumnFilter = np2.argmaxMulti(cellScores, columnsForCandidates)
learningSegments = candidateSegments[onePerColumnFilter]
return learningSegments
@classmethod
def _getCellsWithFewestSegments(cls, connections, rng, columns,
cellsPerColumn):
"""
For each column, get the cell that has the fewest total basal segments.
Break ties randomly.
@param connections (SparseMatrixConnections)
@param rng (Random)
@param columns (numpy array) Columns to check
@return (numpy array)
One cell for each of the provided columns
"""
candidateCells = np2.getAllCellsInColumns(columns, cellsPerColumn)
# Arrange the segment counts into one row per minicolumn.
segmentCounts = np.reshape(connections.getSegmentCounts(candidateCells),
newshape=(len(columns),
cellsPerColumn))
# Filter to just the cells that are tied for fewest in their minicolumn.
minSegmentCounts = np.amin(segmentCounts, axis=1, keepdims=True)
candidateCells = candidateCells[np.flatnonzero(segmentCounts ==
minSegmentCounts)]
# Filter to one cell per column, choosing randomly from the minimums.
# To do the random choice, add a random offset to each index in-place, using
# casting to floor the result.
(_,
onePerColumnFilter,
numCandidatesInColumns) = np.unique(candidateCells / cellsPerColumn,
return_index=True, return_counts=True)
offsetPercents = np.empty(len(columns), dtype="float32")
rng.initializeReal32Array(offsetPercents)
np.add(onePerColumnFilter,
offsetPercents*numCandidatesInColumns,
out=onePerColumnFilter,
casting="unsafe")
return candidateCells[onePerColumnFilter]
@staticmethod
def _numPoints(dimensions):
"""
Get the number of discrete points in a set of dimensions.
@param dimensions (sequence of integers)
@return (int)
"""
if len(dimensions) == 0:
return 0
else:
return reduce(operator.mul, dimensions, 1)
def getActiveCells(self):
return self.activeCells
def getWinnerCells(self):
return self.winnerCells
def getPreviouslyPredictedCells(self):
return self.prevPredictedCells
def test_whenPermanenceFallsBelowZero(self):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments([1, 2, 3])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustSynapses(segments, [42, 43], -0.06, 0.0)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustSynapses(segments, [], 0.0, -0.06)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustActiveSynapses(segments, [42, 43], -0.06)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustInactiveSynapses(segments, [], -0.06)
np.testing.assert_equal(connections.mapSegmentsToSynapseCounts(segments),
[0, 0, 0])
def __init__(self,
trnCellShape=(32, 32),
relayCellShape=(32, 32),
inputShape=(32, 32),
l6CellCount=1024,
trnThreshold=10,
relayThreshold=1,
seed=42):
"""
:param trnCellShape:
a 2D shape for the TRN
:param relayCellShape:
a 2D shape for the relay cells
:param l6CellCount:
number of L6 cells
:param trnThreshold:
dendritic threshold for TRN cells. This is the min number of active L6
cells on a dendrite for the TRN cell to recognize a pattern on that
dendrite.
:param relayThreshold:
dendritic threshold for relay cells. This is the min number of active TRN
cells on a dendrite for the relay cell to recognize a pattern on that
dendrite.
:param seed:
Seed for the random number generator.
"""
# Shapes of TRN cell layer, relay cell layer, and feed forward input layer
self.trnCellShape = trnCellShape
self.trnWidth = trnCellShape[0]
self.trnHeight = trnCellShape[1]
self.relayCellShape = relayCellShape
self.relayWidth = relayCellShape[0]
self.relayHeight = relayCellShape[1]
self.inputShape = inputShape
self.inputWidth = inputShape[0]
self.inputHeight = inputShape[1]
self.l6CellCount = l6CellCount
self.relayThreshold = relayThreshold
self.seed = seed
self.rng = Random(seed)
self.trnActivationThreshold = trnThreshold
self.trnConnections = SparseMatrixConnections(
trnCellShape[0] * trnCellShape[1], l6CellCount)
self.relayConnections = SparseMatrixConnections(
relayCellShape[0] * relayCellShape[1],
trnCellShape[0] * trnCellShape[1])
# Initialize/reset variables that are updated with calls to compute
self.reset()
self._initializeTRNToRelayCellConnections()
class SuperficialLocationModule2D(object):
"""
A model of a location module. It's similar to a grid cell module, but it uses
squares rather than triangles.
The cells are arranged into a m*n rectangle which is tiled onto 2D space.
Each cell represents a small rectangle in each tile.
+------+------+------++------+------+------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #1 | #2 | #3 || #1 | #2 | #3 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #4 | #5 | #6 || #4 | #5 | #6 |
| | | || | | |
+--------------------++--------------------+
| Cell | Cell | Cell || Cell | Cell | Cell |
| #7 | #8 | #9 || #7 | #8 | #9 |
| | | || | | |
+------+------+------++------+------+------+
We assume that path integration works *somehow*. This model receives a "delta
location" vector, and it shifts the active cells accordingly. The model stores
intermediate coordinates of active cells. Whenever sensory cues activate a
cell, the model adds this cell to the list of coordinates being shifted.
Whenever sensory cues cause a cell to become inactive, that cell is removed
from the list of coordinates.
(This model doesn't attempt to propose how "path integration" works. It
attempts to show how locations are anchored to sensory cues.)
When orientation is set to 0 degrees, the deltaLocation is a [di, dj],
moving di cells "down" and dj cells "right".
When orientation is set to 90 degrees, the deltaLocation is essentially a
[dx, dy], applied in typical x,y coordinates with the origin on the bottom
left.
Usage:
Adjust the location in response to motor input:
lm.shift([di, dj])
Adjust the location in response to sensory input:
lm.anchor(anchorInput)
Learn an anchor input for the current location:
lm.learn(anchorInput)
The "anchor input" is typically a feature-location pair SDR.
During inference, you'll typically call:
lm.shift(...)
# Consume lm.getActiveCells()
# ...
lm.anchor(...)
During learning, you'll do the same, but you'll call lm.learn() instead of
lm.anchor().
"""
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
pointOffsets=(0.5, ),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param pointOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "point" which is shifted in subsequent
motions. By default, this point is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, With value [0.2, 0.8], it will place 4 points:
[0.2, 0.2], [0.2, 0.8], [0.8, 0.2], [0.8, 0.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions,
dtype="float")
self.cellFieldsPerUnitDistance = self.cellDimensions / self.moduleMapDimensions
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation),
math.cos(orientation)]])
self.pointOffsets = pointOffsets
# These coordinates are in units of "cell fields".
self.activePoints = np.empty((0, 2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def reset(self):
"""
Clear the active cells.
"""
self.activePoints = np.empty((0, 2), dtype="float")
self.cellsForActivePoints = np.empty(0, dtype="int")
self.activeCells = np.empty(0, dtype="int")
def _computeActiveCells(self):
# Round each coordinate to the nearest cell.
flooredActivePoints = np.floor(self.activePoints).astype("int")
# Convert coordinates to cell numbers.
self.cellsForActivePoints = (np.ravel_multi_index(
flooredActivePoints.T, self.cellDimensions))
self.activeCells = np.unique(self.cellsForActivePoints)
def activateRandomLocation(self):
"""
Set the location to a random point.
"""
self.activePoints = np.array(
[np.random.random(2) * self.cellDimensions])
self._computeActiveCells()
def shift(self, deltaLocation):
"""
Shift the current active cells by a vector.
@param deltaLocation (pair of floats)
A translation vector [di, dj].
"""
# Calculate delta in the module's coordinates.
deltaLocationInCellFields = (
np.matmul(self.rotationMatrix, deltaLocation) *
self.cellFieldsPerUnitDistance)
# Shift the active coordinates.
np.add(self.activePoints,
deltaLocationInCellFields,
out=self.activePoints)
np.mod(self.activePoints, self.cellDimensions, out=self.activePoints)
self._computeActiveCells()
def anchor(self, anchorInput):
"""
Infer the location from sensory input. Activate any cells with enough active
synapses to this sensory input. Deactivate all other cells.
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
if len(anchorInput) == 0:
return
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
sensorySupportedCells = np.unique(
self.connections.mapSegmentsToCells(activeSegments))
inactivated = np.setdiff1d(self.activeCells, sensorySupportedCells)
inactivatedIndices = np.in1d(self.cellsForActivePoints,
inactivated).nonzero()[0]
if inactivatedIndices.size > 0:
self.activePoints = np.delete(self.activePoints,
inactivatedIndices,
axis=0)
activated = np.setdiff1d(sensorySupportedCells, self.activeCells)
activatedCoordsBase = np.transpose(
np.unravel_index(activated, self.cellDimensions)).astype('float')
activatedCoords = np.concatenate([
activatedCoordsBase + [iOffset, jOffset]
for iOffset in self.pointOffsets for jOffset in self.pointOffsets
])
if activatedCoords.size > 0:
self.activePoints = np.append(self.activePoints,
activatedCoords,
axis=0)
self._computeActiveCells()
self.activeSegments = activeSegments
def learn(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.connections.computeActivity(anchorInput,
self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.connections.computeActivity(anchorInput)
matchingSegments = np.where(
potentialOverlaps >= self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.connections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[np.in1d(
cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.connections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.connections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[np.in1d(
cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
potentialOverlaps[candidateSegments], cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells,
cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.connections, self.rng, learningSegments,
anchorInput, potentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.connections.createSegments(newSegmentCells)
self.connections.growSynapsesToSample(newSegments, anchorInput,
numNewSynapses,
self.initialPermanence, self.rng)
self.activeSegments = activeSegments
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement,
maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax, maxNew,
numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput, maxNew,
initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
def numberOfCells(self):
return np.prod(self.cellDimensions)
class ApicalTiebreakTemporalMemory(object):
"""
A generalized Temporal Memory with apical dendrites that add a "tiebreak".
Basal connections are used to implement traditional Temporal Memory.
The apical connections are used for further disambiguation. If multiple cells
in a minicolumn have active basal segments, each of those cells is predicted,
unless one of them also has an active apical segment, in which case only the
cells with active basal and apical segments are predicted.
In other words, the apical connections have no effect unless the basal input
is a union of SDRs (e.g. from bursting minicolumns).
This class is generalized in two ways:
- This class does not specify when a 'timestep' begins and ends. It exposes
two main methods: 'depolarizeCells' and 'activateCells', and callers or
subclasses can introduce the notion of a timestep.
- This class is unaware of whether its 'basalInput' or 'apicalInput' are from
internal or external cells. They are just cell numbers. The caller knows
what these cell numbers mean, but the TemporalMemory doesn't.
"""
def __init__(self,
columnCount=2048,
basalInputSize=0,
apicalInputSize=0,
cellsPerColumn=32,
activationThreshold=13,
reducedBasalThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
basalPredictedSegmentDecrement=0.0,
apicalPredictedSegmentDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param columnCount (int)
The number of minicolumns
@param basalInputSize (sequence)
The number of bits in the basal input
@param apicalInputSize (int)
The number of bits in the apical input
@param cellsPerColumn (int)
Number of cells per column
@param activationThreshold (int)
If the number of active connected synapses on a segment is at least this
threshold, the segment is said to be active.
@param reducedBasalThreshold (int)
The activation threshold of basal (lateral) segments for cells that have
active apical segments. If equal to activationThreshold (default),
this parameter has no effect.
@param initialPermanence (float)
Initial permanence of a new synapse
@param connectedPermanence (float)
If the permanence value for a synapse is greater than this value, it is said
to be connected.
@param minThreshold (int)
If the number of potential synapses active on a segment is at least this
threshold, it is said to be "matching" and is eligible for learning.
@param sampleSize (int)
How much of the active SDR to sample with synapses.
@param permanenceIncrement (float)
Amount by which permanences of synapses are incremented during learning.
@param permanenceDecrement (float)
Amount by which permanences of synapses are decremented during learning.
@param basalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param apicalPredictedSegmentDecrement (float)
Amount by which segments are punished for incorrect predictions.
@param maxSynapsesPerSegment
The maximum number of synapses per segment.
@param seed (int)
Seed for the random number generator.
"""
self.columnCount = columnCount
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.reducedBasalThreshold = reducedBasalThreshold
self.minThreshold = minThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
basalInputSize)
self.apicalConnections = SparseMatrixConnections(columnCount*cellsPerColumn,
apicalInputSize)
self.rng = Random(seed)
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
self.useApicalTiebreak=True
self.useApicalModulationBasalThreshold=True
def reset(self):
"""
Clear all cell and segment activity.
"""
self.activeCells = np.empty(0, dtype="uint32")
self.winnerCells = np.empty(0, dtype="uint32")
self.predictedCells = np.empty(0, dtype="uint32")
self.predictedActiveCells = np.empty(0, dtype="uint32")
self.activeBasalSegments = np.empty(0, dtype="uint32")
self.activeApicalSegments = np.empty(0, dtype="uint32")
self.matchingBasalSegments = np.empty(0, dtype="uint32")
self.matchingApicalSegments = np.empty(0, dtype="uint32")
self.basalPotentialOverlaps = np.empty(0, dtype="int32")
self.apicalPotentialOverlaps = np.empty(0, dtype="int32")
def depolarizeCells(self, basalInput, apicalInput, learn):
"""
Calculate predictions.
@param basalInput (numpy array)
List of active input bits for the basal dendrite segments
@param apicalInput (numpy array)
List of active input bits for the apical dendrite segments
@param learn (bool)
Whether learning is enabled. Some TM implementations may depolarize cells
differently or do segment activity bookkeeping when learning is enabled.
"""
(activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps) = self._calculateApicalSegmentActivity(
self.apicalConnections, apicalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
if learn or self.useApicalModulationBasalThreshold==False:
reducedBasalThresholdCells = ()
else:
reducedBasalThresholdCells = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
(activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps) = self._calculateBasalSegmentActivity(
self.basalConnections, basalInput, reducedBasalThresholdCells,
self.connectedPermanence,
self.activationThreshold, self.minThreshold, self.reducedBasalThreshold)
predictedCells = self._calculatePredictedCells(activeBasalSegments,
activeApicalSegments)
self.predictedCells = predictedCells
self.activeBasalSegments = activeBasalSegments
self.activeApicalSegments = activeApicalSegments
self.matchingBasalSegments = matchingBasalSegments
self.matchingApicalSegments = matchingApicalSegments
self.basalPotentialOverlaps = basalPotentialOverlaps
self.apicalPotentialOverlaps = apicalPotentialOverlaps
def activateCells(self,
activeColumns,
basalReinforceCandidates,
apicalReinforceCandidates,
basalGrowthCandidates,
apicalGrowthCandidates,
learn=True):
"""
Activate cells in the specified columns, using the result of the previous
'depolarizeCells' as predictions. Then learn.
@param activeColumns (numpy array)
List of active columns
@param basalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce basal synapses to.
@param apicalReinforceCandidates (numpy array)
List of bits that the active cells may reinforce apical synapses to.
@param basalGrowthCandidates (numpy array)
List of bits that the active cells may grow new basal synapses to.
@param apicalGrowthCandidates (numpy array)
List of bits that the active cells may grow new apical synapses to
@param learn (bool)
Whether to grow / reinforce / punish synapses
"""
# Calculate active cells
(correctPredictedCells,
burstingColumns) = np2.setCompare(self.predictedCells, activeColumns,
self.predictedCells / self.cellsPerColumn,
rightMinusLeft=True)
newActiveCells = np.concatenate((correctPredictedCells,
np2.getAllCellsInColumns(
burstingColumns, self.cellsPerColumn)))
# Calculate learning
(learningActiveBasalSegments,
learningMatchingBasalSegments,
basalSegmentsToPunish,
newBasalSegmentCells,
learningCells) = self._calculateBasalLearning(
activeColumns, burstingColumns, correctPredictedCells,
self.activeBasalSegments, self.matchingBasalSegments,
self.basalPotentialOverlaps)
(learningActiveApicalSegments,
learningMatchingApicalSegments,
apicalSegmentsToPunish,
newApicalSegmentCells) = self._calculateApicalLearning(
learningCells, activeColumns, self.activeApicalSegments,
self.matchingApicalSegments, self.apicalPotentialOverlaps)
# Learn
if learn:
# Learn on existing segments
for learningSegments in (learningActiveBasalSegments,
learningMatchingBasalSegments):
self._learn(self.basalConnections, self.rng, learningSegments,
basalReinforceCandidates, basalGrowthCandidates,
self.basalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
for learningSegments in (learningActiveApicalSegments,
learningMatchingApicalSegments):
self._learn(self.apicalConnections, self.rng, learningSegments,
apicalReinforceCandidates, apicalGrowthCandidates,
self.apicalPotentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Punish incorrect predictions
if self.basalPredictedSegmentDecrement != 0.0:
self.basalConnections.adjustActiveSynapses(
basalSegmentsToPunish, basalReinforceCandidates,
-self.basalPredictedSegmentDecrement)
if self.apicalPredictedSegmentDecrement != 0.0:
self.apicalConnections.adjustActiveSynapses(
apicalSegmentsToPunish, apicalReinforceCandidates,
-self.apicalPredictedSegmentDecrement)
# Grow new segments
if len(basalGrowthCandidates) > 0:
self._learnOnNewSegments(self.basalConnections, self.rng,
newBasalSegmentCells, basalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
if len(apicalGrowthCandidates) > 0:
self._learnOnNewSegments(self.apicalConnections, self.rng,
newApicalSegmentCells, apicalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
# Save the results
newActiveCells.sort()
learningCells.sort()
self.activeCells = newActiveCells
self.winnerCells = learningCells
self.predictedActiveCells = correctPredictedCells
def _calculateBasalLearning(self,
activeColumns,
burstingColumns,
correctPredictedCells,
activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps):
"""
Basic Temporal Memory learning. Correctly predicted cells always have
active basal segments, and we learn on these segments. In bursting
columns, we either learn on an existing basal segment, or we grow a new one.
The only influence apical dendrites have on basal learning is: the apical
dendrites influence which cells are considered "predicted". So an active
apical dendrite can prevent some basal segments in active columns from
learning.
@param correctPredictedCells (numpy array)
@param burstingColumns (numpy array)
@param activeBasalSegments (numpy array)
@param matchingBasalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveBasalSegments (numpy array)
Active basal segments on correct predicted cells
- learningMatchingBasalSegments (numpy array)
Matching basal segments selected for learning in bursting columns
- basalSegmentsToPunish (numpy array)
Basal segments that should be punished for predicting an inactive column
- newBasalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new basal segments
- learningCells (numpy array)
Cells that have learning basal segments or are selected to grow a basal
segment
"""
# Correctly predicted columns
learningActiveBasalSegments = self.basalConnections.filterSegmentsByCell(
activeBasalSegments, correctPredictedCells)
cellsForMatchingBasal = self.basalConnections.mapSegmentsToCells(
matchingBasalSegments)
matchingCells = np.unique(cellsForMatchingBasal)
(matchingCellsInBurstingColumns,
burstingColumnsWithNoMatch) = np2.setCompare(
matchingCells, burstingColumns, matchingCells / self.cellsPerColumn,
rightMinusLeft=True)
learningMatchingBasalSegments = self._chooseBestSegmentPerColumn(
self.basalConnections, matchingCellsInBurstingColumns,
matchingBasalSegments, basalPotentialOverlaps, self.cellsPerColumn)
newBasalSegmentCells = self._getCellsWithFewestSegments(
self.basalConnections, self.rng, burstingColumnsWithNoMatch,
self.cellsPerColumn)
learningCells = np.concatenate(
(correctPredictedCells,
self.basalConnections.mapSegmentsToCells(learningMatchingBasalSegments),
newBasalSegmentCells))
# Incorrectly predicted columns
correctMatchingBasalMask = np.in1d(
cellsForMatchingBasal / self.cellsPerColumn, activeColumns)
basalSegmentsToPunish = matchingBasalSegments[~correctMatchingBasalMask]
return (learningActiveBasalSegments,
learningMatchingBasalSegments,
basalSegmentsToPunish,
newBasalSegmentCells,
learningCells)
def _calculateApicalLearning(self,
learningCells,
activeColumns,
activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps):
"""
Calculate apical learning for each learning cell.
The set of learning cells was determined completely from basal segments.
Do all apical learning on the same cells.
Learn on any active segments on learning cells. For cells without active
segments, learn on the best matching segment. For cells without a matching
segment, grow a new segment.
@param learningCells (numpy array)
@param correctPredictedCells (numpy array)
@param activeApicalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveApicalSegments (numpy array)
Active apical segments on correct predicted cells
- learningMatchingApicalSegments (numpy array)
Matching apical segments selected for learning in bursting columns
- apicalSegmentsToPunish (numpy array)
Apical segments that should be punished for predicting an inactive column
- newApicalSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new apical segments
"""
# Cells with active apical segments
learningActiveApicalSegments = self.apicalConnections.filterSegmentsByCell(
activeApicalSegments, learningCells)
# Cells with matching apical segments
learningCellsWithoutActiveApical = np.setdiff1d(
learningCells,
self.apicalConnections.mapSegmentsToCells(learningActiveApicalSegments))
cellsForMatchingApical = self.apicalConnections.mapSegmentsToCells(
matchingApicalSegments)
learningCellsWithMatchingApical = np.intersect1d(
learningCellsWithoutActiveApical, cellsForMatchingApical)
learningMatchingApicalSegments = self._chooseBestSegmentPerCell(
self.apicalConnections, learningCellsWithMatchingApical,
matchingApicalSegments, apicalPotentialOverlaps)
# Cells that need to grow an apical segment
newApicalSegmentCells = np.setdiff1d(learningCellsWithoutActiveApical,
learningCellsWithMatchingApical)
# Incorrectly predicted columns
correctMatchingApicalMask = np.in1d(
cellsForMatchingApical / self.cellsPerColumn, activeColumns)
apicalSegmentsToPunish = matchingApicalSegments[~correctMatchingApicalMask]
return (learningActiveApicalSegments,
learningMatchingApicalSegments,
apicalSegmentsToPunish,
newApicalSegmentCells)
@staticmethod
def _calculateApicalSegmentActivity(connections, activeInput, connectedPermanence,
activationThreshold, minThreshold):
"""
Calculate the active and matching apical segments for this timestep.
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active
overlaps = connections.computeActivity(activeInput, connectedPermanence)
activeSegments = np.flatnonzero(overlaps >= activationThreshold)
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments,
matchingSegments,
potentialOverlaps)
@staticmethod
def _calculateBasalSegmentActivity(connections, activeInput,
reducedBasalThresholdCells, connectedPermanence,
activationThreshold, minThreshold, reducedBasalThreshold):
"""
Calculate the active and matching basal segments for this timestep.
The difference with _calculateApicalSegmentActivity is that cells
with active apical segments (collected in reducedBasalThresholdCells) have
a lower activation threshold for their basal segments (set by
reducedBasalThreshold parameter).
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active apical segments lower the activation threshold for basal (lateral) segments
overlaps = connections.computeActivity(activeInput, connectedPermanence)
outrightActiveSegments = np.flatnonzero(overlaps >= activationThreshold)
if reducedBasalThreshold != activationThreshold and len(reducedBasalThresholdCells) > 0:
potentiallyActiveSegments = np.flatnonzero((overlaps < activationThreshold)
& (overlaps >= reducedBasalThreshold))
cellsOfCASegments = connections.mapSegmentsToCells(potentiallyActiveSegments)
# apically active segments are condit. active segments from apically active cells
conditionallyActiveSegments = potentiallyActiveSegments[np.in1d(cellsOfCASegments,
reducedBasalThresholdCells)]
activeSegments = np.concatenate((outrightActiveSegments, conditionallyActiveSegments))
else:
activeSegments = outrightActiveSegments
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments,
matchingSegments,
potentialOverlaps)
def _calculatePredictedCells(self, activeBasalSegments, activeApicalSegments):
"""
Calculate the predicted cells, given the set of active segments.
An active basal segment is enough to predict a cell.
An active apical segment is *not* enough to predict a cell.
When a cell has both types of segments active, other cells in its minicolumn
must also have both types of segments to be considered predictive.
@param activeBasalSegments (numpy array)
@param activeApicalSegments (numpy array)
@return (numpy array)
"""
cellsForBasalSegments = self.basalConnections.mapSegmentsToCells(
activeBasalSegments)
cellsForApicalSegments = self.apicalConnections.mapSegmentsToCells(
activeApicalSegments)
fullyDepolarizedCells = np.intersect1d(cellsForBasalSegments,
cellsForApicalSegments)
partlyDepolarizedCells = np.setdiff1d(cellsForBasalSegments,
fullyDepolarizedCells)
inhibitedMask = np.in1d(partlyDepolarizedCells / self.cellsPerColumn,
fullyDepolarizedCells / self.cellsPerColumn)
predictedCells = np.append(fullyDepolarizedCells,
partlyDepolarizedCells[~inhibitedMask])
if self.useApicalTiebreak == False:
predictedCells = cellsForBasalSegments
return predictedCells
@staticmethod
def _learn(connections, rng, learningSegments, activeInput, growthCandidates,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
@staticmethod
def _learnOnNewSegments(connections, rng, newSegmentCells, growthCandidates,
initialPermanence, sampleSize, maxSynapsesPerSegment):
numNewSynapses = len(growthCandidates)
if sampleSize != -1:
numNewSynapses = min(numNewSynapses, sampleSize)
if maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, maxSynapsesPerSegment)
newSegments = connections.createSegments(newSegmentCells)
connections.growSynapsesToSample(newSegments, growthCandidates,
numNewSynapses, initialPermanence,
rng)
@classmethod
def _chooseBestSegmentPerCell(cls,
connections,
cells,
allMatchingSegments,
potentialOverlaps):
"""
For each specified cell, choose its matching segment with largest number
of active potential synapses. When there's a tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param cells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
@return (numpy array)
One segment per cell
"""
candidateSegments = connections.filterSegmentsByCell(allMatchingSegments,
cells)
# Narrow it down to one pair per cell.
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
connections.mapSegmentsToCells(
candidateSegments))
learningSegments = candidateSegments[onePerCellFilter]
return learningSegments
@classmethod
def _chooseBestSegmentPerColumn(cls, connections, matchingCells,
allMatchingSegments, potentialOverlaps,
cellsPerColumn):
"""
For all the columns covered by 'matchingCells', choose the column's matching
segment with largest number of active potential synapses. When there's a
tie, the first segment wins.
@param connections (SparseMatrixConnections)
@param matchingCells (numpy array)
@param allMatchingSegments (numpy array)
@param potentialOverlaps (numpy array)
"""
candidateSegments = connections.filterSegmentsByCell(allMatchingSegments,
matchingCells)
# Narrow it down to one segment per column.
cellScores = potentialOverlaps[candidateSegments]
columnsForCandidates = (connections.mapSegmentsToCells(candidateSegments) /
cellsPerColumn)
onePerColumnFilter = np2.argmaxMulti(cellScores, columnsForCandidates)
learningSegments = candidateSegments[onePerColumnFilter]
return learningSegments
@classmethod
def _getCellsWithFewestSegments(cls, connections, rng, columns,
cellsPerColumn):
"""
For each column, get the cell that has the fewest total basal segments.
Break ties randomly.
@param connections (SparseMatrixConnections)
@param rng (Random)
@param columns (numpy array) Columns to check
@return (numpy array)
One cell for each of the provided columns
"""
candidateCells = np2.getAllCellsInColumns(columns, cellsPerColumn)
# Arrange the segment counts into one row per minicolumn.
segmentCounts = np.reshape(connections.getSegmentCounts(candidateCells),
newshape=(len(columns),
cellsPerColumn))
# Filter to just the cells that are tied for fewest in their minicolumn.
minSegmentCounts = np.amin(segmentCounts, axis=1, keepdims=True)
candidateCells = candidateCells[np.flatnonzero(segmentCounts ==
minSegmentCounts)]
# Filter to one cell per column, choosing randomly from the minimums.
# To do the random choice, add a random offset to each index in-place, using
# casting to floor the result.
(_,
onePerColumnFilter,
numCandidatesInColumns) = np.unique(candidateCells / cellsPerColumn,
return_index=True, return_counts=True)
offsetPercents = np.empty(len(columns), dtype="float32")
rng.initializeReal32Array(offsetPercents)
np.add(onePerColumnFilter,
offsetPercents*numCandidatesInColumns,
out=onePerColumnFilter,
casting="unsafe")
return candidateCells[onePerColumnFilter]
def getActiveCells(self):
"""
@return (numpy array)
Active cells
"""
return self.activeCells
def getPredictedActiveCells(self):
"""
@return (numpy array)
Active cells that were correctly predicted
"""
return self.predictedActiveCells
def getWinnerCells(self):
"""
@return (numpy array)
Cells that were selected for learning
"""
return self.winnerCells
def getActiveBasalSegments(self):
"""
@return (numpy array)
Active basal segments for this timestep
"""
return self.activeBasalSegments
def getActiveApicalSegments(self):
"""
@return (numpy array)
Matching basal segments for this timestep
"""
return self.activeApicalSegments
def numberOfColumns(self):
""" Returns the number of columns in this layer.
@return (int) Number of columns
"""
return self.columnCount
def numberOfCells(self):
"""
Returns the number of cells in this layer.
@return (int) Number of cells
"""
return self.numberOfColumns() * self.cellsPerColumn
def getCellsPerColumn(self):
"""
Returns the number of cells per column.
@return (int) The number of cells per column.
"""
return self.cellsPerColumn
def getActivationThreshold(self):
"""
Returns the activation threshold.
@return (int) The activation threshold.
"""
return self.activationThreshold
def setActivationThreshold(self, activationThreshold):
"""
Sets the activation threshold.
@param activationThreshold (int) activation threshold.
"""
self.activationThreshold = activationThreshold
def getReducedBasalThreshold(self):
"""
Returns the reduced basal activation threshold for apically active cells.
@return (int) The activation threshold.
"""
return self.reducedBasalThreshold
def setReducedBasalThreshold(self, reducedBasalThreshold):
"""
Sets the reduced basal activation threshold for apically active cells.
@param reducedBasalThreshold (int) activation threshold.
"""
self.reducedBasalThreshold = reducedBasalThreshold
def getInitialPermanence(self):
"""
Get the initial permanence.
@return (float) The initial permanence.
"""
return self.initialPermanence
def setInitialPermanence(self, initialPermanence):
"""
Sets the initial permanence.
@param initialPermanence (float) The initial permanence.
"""
self.initialPermanence = initialPermanence
def getMinThreshold(self):
"""
Returns the min threshold.
@return (int) The min threshold.
"""
return self.minThreshold
def setMinThreshold(self, minThreshold):
"""
Sets the min threshold.
@param minThreshold (int) min threshold.
"""
self.minThreshold = minThreshold
def getSampleSize(self):
"""
Gets the sampleSize.
@return (int)
"""
return self.sampleSize
def setSampleSize(self, sampleSize):
"""
Sets the sampleSize.
@param sampleSize (int)
"""
self.sampleSize = sampleSize
def getPermanenceIncrement(self):
"""
Get the permanence increment.
@return (float) The permanence increment.
"""
return self.permanenceIncrement
def setPermanenceIncrement(self, permanenceIncrement):
"""
Sets the permanence increment.
@param permanenceIncrement (float) The permanence increment.
"""
self.permanenceIncrement = permanenceIncrement
def getPermanenceDecrement(self):
"""
Get the permanence decrement.
@return (float) The permanence decrement.
"""
return self.permanenceDecrement
def setPermanenceDecrement(self, permanenceDecrement):
"""
Sets the permanence decrement.
@param permanenceDecrement (float) The permanence decrement.
"""
self.permanenceDecrement = permanenceDecrement
def getBasalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.basalPredictedSegmentDecrement
def setBasalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.basalPredictedSegmentDecrement = basalPredictedSegmentDecrement
def getApicalPredictedSegmentDecrement(self):
"""
Get the predicted segment decrement.
@return (float) The predicted segment decrement.
"""
return self.apicalPredictedSegmentDecrement
def setApicalPredictedSegmentDecrement(self, predictedSegmentDecrement):
"""
Sets the predicted segment decrement.
@param predictedSegmentDecrement (float) The predicted segment decrement.
"""
self.apicalPredictedSegmentDecrement = apicalPredictedSegmentDecrement
def getConnectedPermanence(self):
"""
Get the connected permanence.
@return (float) The connected permanence.
"""
return self.connectedPermanence
def setConnectedPermanence(self, connectedPermanence):
"""
Sets the connected permanence.
@param connectedPermanence (float) The connected permanence.
"""
self.connectedPermanence = connectedPermanence
def getUseApicalTieBreak(self):
"""
Get whether we actually use apical tie-break.
@return (Bool) Whether apical tie-break is used.
"""
return self.useApicalTiebreak
def setUseApicalTiebreak(self, useApicalTiebreak):
"""
Sets whether we actually use apical tie-break.
@param useApicalTiebreak (Bool) Whether apical tie-break is used.
"""
self.useApicalTiebreak = useApicalTiebreak
def getUseApicalModulationBasalThreshold(self):
"""
Get whether we actually use apical modulation of basal threshold.
@return (Bool) Whether apical modulation is used.
"""
return self.useApicalModulationBasalThreshold
def setUseApicalModulationBasalThreshold(self, useApicalModulationBasalThreshold):
"""
Sets whether we actually use apical modulation of basal threshold.
@param useApicalModulationBasalThreshold (Bool) Whether apical modulation is used.
"""
self.useApicalModulationBasalThreshold = useApicalModulationBasalThreshold
def test_clipPermanences(self):
connections = SparseMatrixConnections(2048, 2048)
# Destroy synapses with permanences <= 0.0
segments = connections.createSegments([1, 2, 3])
connections.growSynapses(segments, [42, 43, 44], 0.05)
connections.growSynapses(segments, [45, 46], 0.1)
connections.adjustInactiveSynapses(segments, [], -0.1)
connections.clipPermanences(segments)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [0, 0, 0])
# Clip permanences to 1.0
connections.growSynapses(segments, [42, 43, 44], 0.95)
connections.adjustInactiveSynapses(segments, [], 0.50)
connections.clipPermanences(segments)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [3, 3, 3])
connections.adjustInactiveSynapses(segments, [], -0.5)
overlaps1 = connections.computeActivity([42, 43, 44], 0.49)
overlaps2 = connections.computeActivity([42, 43, 44], 0.51)
np.testing.assert_equal(overlaps1, [3, 3, 3])
np.testing.assert_equal(overlaps2, [0, 0, 0])
class SensorToSpecificObjectModule(object):
"""
Represents the sensor location relative to a specific object. Typically
these modules are arranged in an array, and the combined population SDR is
used to predict a feature-location pair.
This class has two sets of connections. Both of them compute the "sensor's
location relative to a specific object" in different ways.
The "metric connections" compute it from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
These connections are learned once and then never need to be updated. They
might be genetically hardcoded. They're initialized externally, e.g. in
BodyToSpecificObjectModule2D.
The "anchor connections" compute it from the sensory input. Whenever a
cortical column learns a feature-location pair, this layer forms reciprocal
connections with the feature-location pair layer.
These segments receive input at different times. The metric connections
receive input first, and they activate a set of cells. This set of cells is
used externally to predict a feature-location pair. Then this feature-location
pair is the input to the anchor connections.
"""
def __init__(self,
cellDimensions,
anchorInputSize,
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (sequence of ints)
@param anchorInputSize (int)
@param activationThreshold (int)
"""
self.activationThreshold = activationThreshold
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
self.cellCount = np.prod(cellDimensions)
cellCountBySource = {
"bodyToSpecificObject": self.cellCount,
"sensorToBody": self.cellCount,
}
self.metricConnections = Multiconnections(self.cellCount,
cellCountBySource)
self.anchorConnections = SparseMatrixConnections(
self.cellCount, anchorInputSize)
def reset(self):
self.activeCells = np.empty(0, dtype="int")
def metricCompute(self, sensorToBody, bodyToSpecificObject):
"""
Compute the
"sensor's location relative to a specific object"
from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
@param sensorToBody (numpy array)
Active cells of a single module that represents the sensor's location
relative to the body
@param bodyToSpecificObject (numpy array)
Active cells of a single module that represents the body's location relative
to a specific object
"""
overlaps = self.metricConnections.computeActivity({
"bodyToSpecificObject":
bodyToSpecificObject,
"sensorToBody":
sensorToBody,
})
self.activeMetricSegments = np.where(overlaps >= 2)[0]
self.activeCells = np.unique(
self.metricConnections.mapSegmentsToCells(
self.activeMetricSegments))
def anchorCompute(self, anchorInput, learn):
"""
Compute the
"sensor's location relative to a specific object"
from the feature-location pair.
@param anchorInput (numpy array)
Active cells in the feature-location pair layer
@param learn (bool)
If true, maintain current cell activity and learn this input on the
currently active cells
"""
if learn:
self._anchorComputeLearningMode(anchorInput)
else:
overlaps = self.anchorConnections.computeActivity(
anchorInput, self.connectedPermanence)
self.activeSegments = np.where(
overlaps >= self.activationThreshold)[0]
self.activeCells = np.unique(
self.anchorConnections.mapSegmentsToCells(self.activeSegments))
def _anchorComputeLearningMode(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.anchorConnections.computeActivity(
anchorInput, self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.anchorConnections.computeActivity(anchorInput)
matchingSegments = np.where(
potentialOverlaps >= self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.anchorConnections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[np.in1d(
cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.anchorConnections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.anchorConnections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[np.in1d(
cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
potentialOverlaps[candidateSegments], cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells,
cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.anchorConnections, self.rng, learningSegments,
anchorInput, potentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.anchorConnections.createSegments(newSegmentCells)
self.anchorConnections.growSynapsesToSample(newSegments, anchorInput,
numNewSynapses,
self.initialPermanence,
self.rng)
self.activeSegments = activeSegments
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement,
maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax, maxNew,
numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput, maxNew,
initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
class ApicalDependentTemporalMemory(object):
"""
An alternate approach to apical dendrites. Every cell SDR is specific to both
the basal the apical input. Prediction requires both basal and apical support.
A normal TemporalMemory trained on the sequences "A B C D" and "A B C E" will
not assign "B" and "C" SDRs specific to their full sequence. These two
sequences will use the same B' and C' SDRs. When the sequence reaches D/E,
the SDRs finally diverge.
With this algorithm, the SDRs diverge immediately, because the SDRs are
specific to the apical input. But if there's never any apical input, there
will never be predictions.
"""
def __init__(self,
columnDimensions=(2048,),
basalInputDimensions=(),
apicalInputDimensions=(),
cellsPerColumn=32,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
minThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
predictedSegmentDecrement=0.0,
maxNewSynapseCount=None,
maxSynapsesPerSegment=-1,
maxSegmentsPerCell=None,
seed=42):
self.columnDimensions = columnDimensions
self.numColumns = self._numPoints(columnDimensions)
self.basalInputDimensions = basalInputDimensions
self.apicalInputDimensions = apicalInputDimensions
self.cellsPerColumn = cellsPerColumn
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.minThreshold = minThreshold
self.sampleSize = sampleSize
if maxNewSynapseCount is not None:
print "Parameter 'maxNewSynapseCount' is deprecated. Use 'sampleSize'."
self.sampleSize = maxNewSynapseCount
if maxSegmentsPerCell is not None:
print "Warning: ignoring parameter 'maxSegmentsPerCell'"
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.predictedSegmentDecrement = predictedSegmentDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.basalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(basalInputDimensions))
self.apicalConnections = SparseMatrixConnections(
self.numColumns*cellsPerColumn, self._numPoints(apicalInputDimensions))
self.rng = Random(seed)
self.activeCells = EMPTY_UINT_ARRAY
self.winnerCells = EMPTY_UINT_ARRAY
self.prevPredictedCells = EMPTY_UINT_ARRAY
def reset(self):
self.activeCells = EMPTY_UINT_ARRAY
self.winnerCells = EMPTY_UINT_ARRAY
self.prevPredictedCells = EMPTY_UINT_ARRAY
def compute(self,
activeColumns,
basalInput,
basalGrowthCandidates,
apicalInput,
apicalGrowthCandidates,
learn=True):
"""
@param activeColumns (numpy array)
@param basalInput (numpy array)
@param basalGrowthCandidates (numpy array)
@param apicalInput (numpy array)
@param apicalGrowthCandidates (numpy array)
@param learn (bool)
"""
# Calculate predictions for this timestep
(activeBasalSegments,
matchingBasalSegments,
basalPotentialOverlaps) = self._calculateSegmentActivity(
self.basalConnections, basalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
(activeApicalSegments,
matchingApicalSegments,
apicalPotentialOverlaps) = self._calculateSegmentActivity(
self.apicalConnections, apicalInput, self.connectedPermanence,
self.activationThreshold, self.minThreshold)
predictedCells = np.intersect1d(
self.basalConnections.mapSegmentsToCells(activeBasalSegments),
self.apicalConnections.mapSegmentsToCells(activeApicalSegments))
# Calculate active cells
(correctPredictedCells,
burstingColumns) = np2.setCompare(predictedCells, activeColumns,
predictedCells / self.cellsPerColumn,
rightMinusLeft=True)
newActiveCells = np.concatenate((correctPredictedCells,
np2.getAllCellsInColumns(
burstingColumns, self.cellsPerColumn)))
# Calculate learning
(learningActiveBasalSegments,
learningActiveApicalSegments,
learningMatchingBasalSegments,
learningMatchingApicalSegments,
basalSegmentsToPunish,
apicalSegmentsToPunish,
newSegmentCells,
learningCells) = self._calculateLearning(activeColumns,
burstingColumns,
correctPredictedCells,
activeBasalSegments,
activeApicalSegments,
matchingBasalSegments,
matchingApicalSegments,
basalPotentialOverlaps,
apicalPotentialOverlaps)
if learn:
# Learn on existing segments
for learningSegments in (learningActiveBasalSegments,
learningMatchingBasalSegments):
self._learn(self.basalConnections, self.rng, learningSegments,
basalInput, basalGrowthCandidates, basalPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
for learningSegments in (learningActiveApicalSegments,
learningMatchingApicalSegments):
self._learn(self.apicalConnections, self.rng, learningSegments,
apicalInput, apicalGrowthCandidates,
apicalPotentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
# Punish incorrect predictions
if self.predictedSegmentDecrement != 0.0:
self.basalConnections.adjustActiveSynapses(
basalSegmentsToPunish, basalInput, -self.predictedSegmentDecrement)
self.apicalConnections.adjustActiveSynapses(
apicalSegmentsToPunish, apicalInput, -self.predictedSegmentDecrement)
# Only grow segments if there is basal *and* apical input.
if len(basalGrowthCandidates) > 0 and len(apicalGrowthCandidates) > 0:
self._learnOnNewSegments(self.basalConnections, self.rng,
newSegmentCells, basalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
self._learnOnNewSegments(self.apicalConnections, self.rng,
newSegmentCells, apicalGrowthCandidates,
self.initialPermanence, self.sampleSize,
self.maxSynapsesPerSegment)
# Save the results
self.prevPredictedCells = predictedCells
self.activeCells = newActiveCells
self.winnerCells = learningCells
def _calculateLearning(self,
activeColumns,
burstingColumns,
correctPredictedCells,
activeBasalSegments,
activeApicalSegments,
matchingBasalSegments,
matchingApicalSegments,
basalPotentialOverlaps,
apicalPotentialOverlaps):
"""
Learning occurs on pairs of segments. Correctly predicted cells always have
active basal and apical segments, and we learn on these segments. In
bursting columns, we either learn on an existing segment pair, or we grow a
new pair of segments.
@param activeColumns (numpy array)
@param burstingColumns (numpy array)
@param correctPredictedCells (numpy array)
@param activeBasalSegments (numpy array)
@param activeApicalSegments (numpy array)
@param matchingBasalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningActiveBasalSegments (numpy array)
Active basal segments on correct predicted cells
- learningActiveApicalSegments (numpy array)
Active apical segments on correct predicted cells
- learningMatchingBasalSegments (numpy array)
Matching basal segments selected for learning in bursting columns
- learningMatchingApicalSegments (numpy array)
Matching apical segments selected for learning in bursting columns
- basalSegmentsToPunish (numpy array)
Basal segments that should be punished for predicting an inactive column
- apicalSegmentsToPunish (numpy array)
Apical segments that should be punished for predicting an inactive column
- newSegmentCells (numpy array)
Cells in bursting columns that were selected to grow new segments
- learningCells (numpy array)
Every cell that has a learning segment or was selected to grow a segment
"""
# Correctly predicted columns
learningActiveBasalSegments = self.basalConnections.filterSegmentsByCell(
activeBasalSegments, correctPredictedCells)
learningActiveApicalSegments = self.apicalConnections.filterSegmentsByCell(
activeApicalSegments, correctPredictedCells)
# Bursting columns
cellsForMatchingBasal = self.basalConnections.mapSegmentsToCells(
matchingBasalSegments)
cellsForMatchingApical = self.apicalConnections.mapSegmentsToCells(
matchingApicalSegments)
matchingCells = np.intersect1d(
cellsForMatchingBasal, cellsForMatchingApical)
(matchingCellsInBurstingColumns,
burstingColumnsWithNoMatch) = np2.setCompare(
matchingCells, burstingColumns, matchingCells / self.cellsPerColumn,
rightMinusLeft=True)
(learningMatchingBasalSegments,
learningMatchingApicalSegments) = self._chooseBestSegmentPairPerColumn(
matchingCellsInBurstingColumns, matchingBasalSegments,
matchingApicalSegments, basalPotentialOverlaps, apicalPotentialOverlaps)
newSegmentCells = self._getCellsWithFewestSegments(
burstingColumnsWithNoMatch)
# Incorrectly predicted columns
if self.predictedSegmentDecrement > 0.0:
correctMatchingBasalMask = np.in1d(
cellsForMatchingBasal / self.cellsPerColumn, activeColumns)
correctMatchingApicalMask = np.in1d(
cellsForMatchingApical / self.cellsPerColumn, activeColumns)
basalSegmentsToPunish = matchingBasalSegments[~correctMatchingBasalMask]
apicalSegmentsToPunish = matchingApicalSegments[~correctMatchingApicalMask]
else:
basalSegmentsToPunish = ()
apicalSegmentsToPunish = ()
# Make a list of every cell that is learning
learningCells = np.concatenate(
(correctPredictedCells,
self.basalConnections.mapSegmentsToCells(learningMatchingBasalSegments),
newSegmentCells))
return (learningActiveBasalSegments,
learningActiveApicalSegments,
learningMatchingBasalSegments,
learningMatchingApicalSegments,
basalSegmentsToPunish,
apicalSegmentsToPunish,
newSegmentCells,
learningCells)
@staticmethod
def _calculateSegmentActivity(connections, activeInput, connectedPermanence,
activationThreshold, minThreshold):
"""
Calculate the active and matching segments for this timestep.
@param connections (SparseMatrixConnections)
@param activeInput (numpy array)
@return (tuple)
- activeSegments (numpy array)
Dendrite segments with enough active connected synapses to cause a
dendritic spike
- matchingSegments (numpy array)
Dendrite segments with enough active potential synapses to be selected for
learning in a bursting column
- potentialOverlaps (numpy array)
The number of active potential synapses for each segment.
Includes counts for active, matching, and nonmatching segments.
"""
# Active
overlaps = connections.computeActivity(activeInput, connectedPermanence)
activeSegments = np.flatnonzero(overlaps >= activationThreshold)
# Matching
potentialOverlaps = connections.computeActivity(activeInput)
matchingSegments = np.flatnonzero(potentialOverlaps >= minThreshold)
return (activeSegments,
matchingSegments,
potentialOverlaps)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput, growthCandidates,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, and grow new synapses.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param newSegmentCells (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
@staticmethod
def _learnOnNewSegments(connections, rng, newSegmentCells, growthCandidates,
initialPermanence, sampleSize, maxSynapsesPerSegment):
"""
Create new segments, and grow synapses on them.
@param connections (SparseMatrixConnections)
@param rng (Random)
@param newSegmentCells (numpy array)
@param growthCandidates (numpy array)
"""
numNewSynapses = len(growthCandidates)
if sampleSize != -1:
numNewSynapses = min(numNewSynapses, sampleSize)
if maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, maxSynapsesPerSegment)
newSegments = connections.createSegments(newSegmentCells)
connections.growSynapsesToSample(newSegments, growthCandidates,
numNewSynapses, initialPermanence,
rng)
def _chooseBestSegmentPairPerColumn(self,
matchingCellsInBurstingColumns,
matchingBasalSegments,
matchingApicalSegments,
basalPotentialOverlaps,
apicalPotentialOverlaps):
"""
Choose the best pair of matching segments - one basal and one apical - for
each column. Pairs are ranked by the sum of their potential overlaps.
When there's a tie, the first pair wins.
@param matchingCellsInBurstingColumns (numpy array)
Cells in bursting columns that have at least one matching basal segment and
at least one matching apical segment
@param matchingBasalSegments (numpy array)
@param matchingApicalSegments (numpy array)
@param basalPotentialOverlaps (numpy array)
@param apicalPotentialOverlaps (numpy array)
@return (tuple)
- learningBasalSegments (numpy array)
The selected basal segments
- learningApicalSegments (numpy array)
The selected apical segments
"""
basalCandidateSegments = self.basalConnections.filterSegmentsByCell(
matchingBasalSegments, matchingCellsInBurstingColumns)
apicalCandidateSegments = self.apicalConnections.filterSegmentsByCell(
matchingApicalSegments, matchingCellsInBurstingColumns)
# Sort everything once rather than inside of each call to argmaxMulti.
self.basalConnections.sortSegmentsByCell(basalCandidateSegments)
self.apicalConnections.sortSegmentsByCell(apicalCandidateSegments)
# Narrow it down to one pair per cell.
oneBasalPerCellFilter = np2.argmaxMulti(
basalPotentialOverlaps[basalCandidateSegments],
self.basalConnections.mapSegmentsToCells(basalCandidateSegments),
assumeSorted=True)
basalCandidateSegments = basalCandidateSegments[oneBasalPerCellFilter]
oneApicalPerCellFilter = np2.argmaxMulti(
apicalPotentialOverlaps[apicalCandidateSegments],
self.apicalConnections.mapSegmentsToCells(apicalCandidateSegments),
assumeSorted=True)
apicalCandidateSegments = apicalCandidateSegments[oneApicalPerCellFilter]
# Narrow it down to one pair per column.
cellScores = (basalPotentialOverlaps[basalCandidateSegments] +
apicalPotentialOverlaps[apicalCandidateSegments])
columnsForCandidates = (
self.basalConnections.mapSegmentsToCells(basalCandidateSegments) /
self.cellsPerColumn)
onePerColumnFilter = np2.argmaxMulti(cellScores, columnsForCandidates,
assumeSorted=True)
learningBasalSegments = basalCandidateSegments[onePerColumnFilter]
learningApicalSegments = apicalCandidateSegments[onePerColumnFilter]
return (learningBasalSegments,
learningApicalSegments)
def _getCellsWithFewestSegments(self, columns):
"""
For each column, get the cell that has the fewest total segments (basal or
apical). Break ties randomly.
@param columns (numpy array)
Columns to check
@return (numpy array)
One cell for each of the provided columns
"""
candidateCells = np2.getAllCellsInColumns(columns, self.cellsPerColumn)
# Arrange the segment counts into one row per minicolumn.
segmentCounts = np.reshape(
self.basalConnections.getSegmentCounts(candidateCells) +
self.apicalConnections.getSegmentCounts(candidateCells),
newshape=(len(columns),
self.cellsPerColumn))
# Filter to just the cells that are tied for fewest in their minicolumn.
minSegmentCounts = np.amin(segmentCounts, axis=1, keepdims=True)
candidateCells = candidateCells[np.flatnonzero(segmentCounts ==
minSegmentCounts)]
# Filter to one cell per column, choosing randomly from the minimums.
# To do the random choice, add a random offset to each index in-place, using
# casting to floor the result.
(_,
onePerColumnFilter,
numCandidatesInColumns) = np.unique(candidateCells / self.cellsPerColumn,
return_index=True, return_counts=True)
offsetPercents = np.empty(len(columns), dtype="float32")
self.rng.initializeReal32Array(offsetPercents)
np.add(onePerColumnFilter,
offsetPercents*numCandidatesInColumns,
out=onePerColumnFilter,
casting="unsafe")
return candidateCells[onePerColumnFilter]
@staticmethod
def _numPoints(dimensions):
"""
Get the number of discrete points in a set of dimensions.
@param dimensions (sequence of integers)
@return (int)
"""
if len(dimensions) == 0:
return 0
else:
return reduce(operator.mul, dimensions, 1)
def getActiveCells(self):
return self.activeCells
def getWinnerCells(self):
return self.winnerCells
def getPreviouslyPredictedCells(self):
return self.prevPredictedCells
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
cellCoordinateOffsets=(0.5, ),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
anchoringMethod="narrowing",
rotationMatrix=None,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param cellCoordinateOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "phase" which is shifted in subsequent
motions. By default, this phase is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, with value [0.2, 0.8], when cell [2, 3] is activated
it will place 4 phases, corresponding to the following points in cell
coordinates: [2.2, 3.2], [2.2, 3.8], [2.8, 3.2], [2.8, 3.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions,
dtype="float")
self.phasesPerUnitDistance = 1.0 / self.moduleMapDimensions
if rotationMatrix is None:
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation),
math.cos(orientation)]])
if anchoringMethod == "discrete":
# Need to convert matrix to have integer values
nonzeros = self.rotationMatrix[np.where(
np.abs(self.rotationMatrix) > 0)]
smallestValue = np.amin(nonzeros)
self.rotationMatrix /= smallestValue
self.rotationMatrix = np.ceil(self.rotationMatrix)
else:
self.rotationMatrix = rotationMatrix
self.cellCoordinateOffsets = cellCoordinateOffsets
# Phase is measured as a number in the range [0.0, 1.0)
self.activePhases = np.empty((0, 2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.phaseDisplacement = np.empty((0, 2), dtype="float")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.anchoringMethod = anchoringMethod
self.rng = Random(seed)
def test_whenPermanenceFallsBelowZero(self):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments([1, 2, 3])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustSynapses(segments, [42, 43], -0.06, 0.0)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustSynapses(segments, [], 0.0, -0.06)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustActiveSynapses(segments, [42, 43], -0.06)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [0, 0, 0])
connections.growSynapses(segments, [42, 43], 0.05)
connections.adjustInactiveSynapses(segments, [], -0.06)
np.testing.assert_equal(
connections.mapSegmentsToSynapseCounts(segments), [0, 0, 0])
class SensorToSpecificObjectModule(object):
"""
Represents the sensor location relative to a specific object. Typically
these modules are arranged in an array, and the combined population SDR is
used to predict a feature-location pair.
This class has two sets of connections. Both of them compute the "sensor's
location relative to a specific object" in different ways.
The "metric connections" compute it from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
These connections are learned once and then never need to be updated. They
might be genetically hardcoded. They're initialized externally, e.g. in
BodyToSpecificObjectModule2D.
The "anchor connections" compute it from the sensory input. Whenever a
cortical column learns a feature-location pair, this layer forms reciprocal
connections with the feature-location pair layer.
These segments receive input at different times. The metric connections
receive input first, and they activate a set of cells. This set of cells is
used externally to predict a feature-location pair. Then this feature-location
pair is the input to the anchor connections.
"""
def __init__(self, cellDimensions, anchorInputSize,
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
seed=42):
"""
@param cellDimensions (sequence of ints)
@param anchorInputSize (int)
@param activationThreshold (int)
"""
self.activationThreshold = activationThreshold
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
self.cellCount = np.prod(cellDimensions)
cellCountBySource = {
"bodyToSpecificObject": self.cellCount,
"sensorToBody": self.cellCount,
}
self.metricConnections = Multiconnections(self.cellCount,
cellCountBySource)
self.anchorConnections = SparseMatrixConnections(self.cellCount,
anchorInputSize)
def reset(self):
self.activeCells = np.empty(0, dtype="int")
def metricCompute(self, sensorToBody, bodyToSpecificObject):
"""
Compute the
"sensor's location relative to a specific object"
from the
"body's location relative to a specific object"
and the
"sensor's location relative to body"
@param sensorToBody (numpy array)
Active cells of a single module that represents the sensor's location
relative to the body
@param bodyToSpecificObject (numpy array)
Active cells of a single module that represents the body's location relative
to a specific object
"""
overlaps = self.metricConnections.computeActivity({
"bodyToSpecificObject": bodyToSpecificObject,
"sensorToBody": sensorToBody,
})
self.activeMetricSegments = np.where(overlaps >= 2)[0]
self.activeCells = np.unique(
self.metricConnections.mapSegmentsToCells(
self.activeMetricSegments))
def anchorCompute(self, anchorInput, learn):
"""
Compute the
"sensor's location relative to a specific object"
from the feature-location pair.
@param anchorInput (numpy array)
Active cells in the feature-location pair layer
@param learn (bool)
If true, maintain current cell activity and learn this input on the
currently active cells
"""
if learn:
self._anchorComputeLearningMode(anchorInput)
else:
overlaps = self.anchorConnections.computeActivity(
anchorInput, self.connectedPermanence)
self.activeSegments = np.where(overlaps >= self.activationThreshold)[0]
self.activeCells = np.unique(
self.anchorConnections.mapSegmentsToCells(self.activeSegments))
def _anchorComputeLearningMode(self, anchorInput):
"""
Associate this location with a sensory input. Subsequently, anchorInput will
activate the current location during anchor().
@param anchorInput (numpy array)
A sensory input. This will often come from a feature-location pair layer.
"""
overlaps = self.anchorConnections.computeActivity(
anchorInput, self.connectedPermanence)
activeSegments = np.where(overlaps >= self.activationThreshold)[0]
potentialOverlaps = self.anchorConnections.computeActivity(anchorInput)
matchingSegments = np.where(potentialOverlaps >=
self.learningThreshold)[0]
# Cells with a active segment: reinforce the segment
cellsForActiveSegments = self.anchorConnections.mapSegmentsToCells(
activeSegments)
learningActiveSegments = activeSegments[
np.in1d(cellsForActiveSegments, self.activeCells)]
remainingCells = np.setdiff1d(self.activeCells, cellsForActiveSegments)
# Remaining cells with a matching segment: reinforce the best
# matching segment.
candidateSegments = self.anchorConnections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (
self.anchorConnections.mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[
np.in1d(cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(potentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells, cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.anchorConnections, self.rng, learningSegments,
anchorInput, potentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
# Remaining cells without a matching segment: grow one.
numNewSynapses = len(anchorInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.anchorConnections.createSegments(newSegmentCells)
self.anchorConnections.growSynapsesToSample(
newSegments, anchorInput, numNewSynapses,
self.initialPermanence, self.rng)
self.activeSegments = activeSegments
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
potentialOverlaps, initialPermanence, sampleSize,
permanenceIncrement, permanenceDecrement, maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(activeInput)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax,
maxNew, numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, activeInput,
maxNew, initialPermanence, rng)
def getActiveCells(self):
return self.activeCells
def test_growSynapsesToSample_multi(self):
rng = Random()
for (name, cells, growingSegments, initialConnectedInputs,
presynapticInputs, activeInputs, initialPermanence,
connectedPermanence, sampleSizes,
expected) in (("Basic test", [1, 2, 3], [0,
2], [], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5, [2, 3], [2, 0, 3]),
("One already connected", [1, 2, 3], [0, 2], [42],
[42, 43, 44, 45], [42, 43, 44,
45], 0.55, 0.5, [1,
2], [2, 0, 3]),
("Higher sample size than axon count", [1, 2,
3], [0, 2],
[], [42, 43, 44,
45], [42, 43, 44,
45], 0.55, 0.5, [5, 10], [4, 0, 4]),
("Higher sample size than available axon count",
[1, 2, 3], [0, 2], [42, 43], [42, 43, 44, 45],
[42, 43, 44, 45], 0.55, 0.5, [3, 3], [4, 0, 4])):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments[growingSegments],
initialConnectedInputs, initialPermanence)
connections.growSynapsesToSample(segments[growingSegments],
presynapticInputs, sampleSizes,
initialPermanence, rng)
overlaps = connections.computeActivity(activeInputs,
connectedPermanence)
np.testing.assert_equal(overlaps[segments], expected, name)
for (name, cells, growingSegments, initialConnectedInputs,
presynapticInputs, activeInputs, initialPermanence,
connectedPermanence,
sampleSizes) in (("Basic randomness test", [1, 2, 3], [0, 2], [],
[42, 43, 44, 45], [42, 43], 0.55, 0.5, [2,
3]), ):
# Activate a subset of the inputs. The resulting overlaps should
# differ on various trials.
firstResult = None
differingResults = False
for _ in range(20):
connections = SparseMatrixConnections(2048, 2048)
segments = connections.createSegments(cells)
connections.growSynapses(segments[growingSegments],
initialConnectedInputs,
initialPermanence)
connections.growSynapsesToSample(segments[growingSegments],
presynapticInputs,
sampleSizes,
initialPermanence, rng)
overlaps = connections.computeActivity(activeInputs,
connectedPermanence)
if firstResult is None:
firstResult = overlaps[segments]
else:
differingResults = not np.array_equal(
overlaps[segments], firstResult)
if differingResults:
break
self.assertTrue(differingResults, name)
def __init__(self,
cellDimensions,
moduleMapDimensions,
orientation,
anchorInputSize,
cellCoordinateOffsets=(0.5,),
activationThreshold=10,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.0,
maxSynapsesPerSegment=-1,
anchoringMethod="narrowing",
rotationMatrix = None,
seed=42):
"""
@param cellDimensions (tuple(int, int))
Determines the number of cells. Determines how space is divided between the
cells.
@param moduleMapDimensions (tuple(float, float))
Determines the amount of world space covered by all of the cells combined.
In grid cell terminology, this is equivalent to the "scale" of a module.
A module with a scale of "5cm" would have moduleMapDimensions=(5.0, 5.0).
@param orientation (float)
The rotation of this map, measured in radians.
@param anchorInputSize (int)
The number of input bits in the anchor input.
@param cellCoordinateOffsets (list of floats)
These must each be between 0.0 and 1.0. Every time a cell is activated by
anchor input, this class adds a "phase" which is shifted in subsequent
motions. By default, this phase is placed at the center of the cell. This
parameter allows you to control where the point is placed and whether multiple
are placed. For example, with value [0.2, 0.8], when cell [2, 3] is activated
it will place 4 phases, corresponding to the following points in cell
coordinates: [2.2, 3.2], [2.2, 3.8], [2.8, 3.2], [2.8, 3.8]
"""
self.cellDimensions = np.asarray(cellDimensions, dtype="int")
self.moduleMapDimensions = np.asarray(moduleMapDimensions, dtype="float")
self.phasesPerUnitDistance = 1.0 / self.moduleMapDimensions
if rotationMatrix is None:
self.orientation = orientation
self.rotationMatrix = np.array(
[[math.cos(orientation), -math.sin(orientation)],
[math.sin(orientation), math.cos(orientation)]])
if anchoringMethod == "discrete":
# Need to convert matrix to have integer values
nonzeros = self.rotationMatrix[np.where(np.abs(self.rotationMatrix)>0)]
smallestValue = np.amin(nonzeros)
self.rotationMatrix /= smallestValue
self.rotationMatrix = np.ceil(self.rotationMatrix)
else:
self.rotationMatrix = rotationMatrix
self.cellCoordinateOffsets = cellCoordinateOffsets
# Phase is measured as a number in the range [0.0, 1.0)
self.activePhases = np.empty((0,2), dtype="float")
self.cellsForActivePhases = np.empty(0, dtype="int")
self.phaseDisplacement = np.empty((0,2), dtype="float")
self.activeCells = np.empty(0, dtype="int")
self.activeSegments = np.empty(0, dtype="uint32")
self.connections = SparseMatrixConnections(np.prod(cellDimensions),
anchorInputSize)
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.anchoringMethod = anchoringMethod
self.rng = Random(seed)
class SingleLayerLocationMemory(object):
"""
A layer of cells which learns how to take a "delta location" (e.g. a motor
command or a proprioceptive delta) and update its active cells to represent
the new location.
Its active cells might represent a union of locations.
As the location changes, the featureLocationInput causes this union to narrow
down until the location is inferred.
This layer receives absolute proprioceptive info as proximal input.
For now, we assume that there's a one-to-one mapping between absolute
proprioceptive input and the location SDR. So rather than modeling
proximal synapses, we'll just relay the proprioceptive SDR. In the future
we might want to consider a many-to-one mapping of proprioceptive inputs
to location SDRs.
After this layer is trained, it no longer needs the proprioceptive input.
The delta location will drive the layer. The current active cells and the
other distal connections will work together with this delta location to
activate a new set of cells.
When no cells are active, activate a large union of possible locations.
With subsequent inputs, the union will narrow down to a single location SDR.
"""
def __init__(self,
cellCount,
deltaLocationInputSize,
featureLocationInputSize,
activationThreshold=13,
initialPermanence=0.21,
connectedPermanence=0.50,
learningThreshold=10,
sampleSize=20,
permanenceIncrement=0.1,
permanenceDecrement=0.1,
maxSynapsesPerSegment=-1,
seed=42):
# For transition learning, every segment is split into two parts.
# For the segment to be active, both parts must be active.
self.internalConnections = SparseMatrixConnections(
cellCount, cellCount)
self.deltaConnections = SparseMatrixConnections(
cellCount, deltaLocationInputSize)
# Distal segments that receive input from the layer that represents
# feature-locations.
self.featureLocationConnections = SparseMatrixConnections(
cellCount, featureLocationInputSize)
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
self.initialPermanence = initialPermanence
self.connectedPermanence = connectedPermanence
self.learningThreshold = learningThreshold
self.sampleSize = sampleSize
self.permanenceIncrement = permanenceIncrement
self.permanenceDecrement = permanenceDecrement
self.activationThreshold = activationThreshold
self.maxSynapsesPerSegment = maxSynapsesPerSegment
self.rng = Random(seed)
def reset(self):
"""
Deactivate all cells.
"""
self.activeCells = np.empty(0, dtype="uint32")
self.activeDeltaSegments = np.empty(0, dtype="uint32")
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
def compute(self,
deltaLocation=(),
newLocation=(),
featureLocationInput=(),
featureLocationGrowthCandidates=(),
learn=True):
"""
Run one time step of the Location Memory algorithm.
@param deltaLocation (sorted numpy array)
@param newLocation (sorted numpy array)
@param featureLocationInput (sorted numpy array)
@param featureLocationGrowthCandidates (sorted numpy array)
"""
prevActiveCells = self.activeCells
self.activeDeltaSegments = np.where(
(self.internalConnections.computeActivity(
prevActiveCells, self.connectedPermanence) >=
self.activationThreshold)
& (self.deltaConnections.computeActivity(
deltaLocation, self.connectedPermanence) >=
self.activationThreshold))[0]
# When we're moving, the feature-location input has no effect.
if len(deltaLocation) == 0:
self.activeFeatureLocationSegments = np.where(
self.featureLocationConnections.computeActivity(
featureLocationInput, self.connectedPermanence) >=
self.activationThreshold)[0]
else:
self.activeFeatureLocationSegments = np.empty(0, dtype="uint32")
if len(newLocation) > 0:
# Drive activations by relaying this location SDR.
self.activeCells = newLocation
if learn:
# Learn the delta.
self._learnTransition(prevActiveCells, deltaLocation,
newLocation)
# Learn the featureLocationInput.
self._learnFeatureLocationPair(
newLocation, featureLocationInput,
featureLocationGrowthCandidates)
elif len(prevActiveCells) > 0:
if len(deltaLocation) > 0:
# Drive activations by applying the deltaLocation to the current location.
# Completely ignore the featureLocationInput. It's outdated, associated
# with the previous location.
cellsForDeltaSegments = self.internalConnections.mapSegmentsToCells(
self.activeDeltaSegments)
self.activeCells = np.unique(cellsForDeltaSegments)
else:
# Keep previous active cells active.
# Modulate with the featureLocationInput.
if len(self.activeFeatureLocationSegments) > 0:
cellsForFeatureLocationSegments = (
self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments))
self.activeCells = np.intersect1d(
prevActiveCells, cellsForFeatureLocationSegments)
else:
self.activeCells = prevActiveCells
elif len(featureLocationInput) > 0:
# Drive activations with the featureLocationInput.
cellsForFeatureLocationSegments = (
self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments))
self.activeCells = np.unique(cellsForFeatureLocationSegments)
def _learnTransition(self, prevActiveCells, deltaLocation, newLocation):
"""
For each cell in the newLocation SDR, learn the transition of prevLocation
(i.e. prevActiveCells) + deltaLocation.
The transition might be already known. In that case, just reinforce the
existing segments.
"""
prevLocationPotentialOverlaps = self.internalConnections.computeActivity(
prevActiveCells)
deltaPotentialOverlaps = self.deltaConnections.computeActivity(
deltaLocation)
matchingDeltaSegments = np.where(
(prevLocationPotentialOverlaps >= self.learningThreshold)
& (deltaPotentialOverlaps >= self.learningThreshold))[0]
# Cells with a active segment pair: reinforce the segment
cellsForActiveSegments = self.internalConnections.mapSegmentsToCells(
self.activeDeltaSegments)
learningActiveDeltaSegments = self.activeDeltaSegments[np.in1d(
cellsForActiveSegments, newLocation)]
remainingCells = np.setdiff1d(newLocation, cellsForActiveSegments)
# Remaining cells with a matching segment pair: reinforce the best matching
# segment pair.
candidateSegments = self.internalConnections.filterSegmentsByCell(
matchingDeltaSegments, remainingCells)
cellsForCandidateSegments = self.internalConnections.mapSegmentsToCells(
candidateSegments)
candidateSegments = matchingDeltaSegments[np.in1d(
cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
prevLocationPotentialOverlaps[candidateSegments] +
deltaPotentialOverlaps[candidateSegments],
cellsForCandidateSegments)
learningMatchingDeltaSegments = candidateSegments[onePerCellFilter]
newDeltaSegmentCells = np.setdiff1d(remainingCells,
cellsForCandidateSegments)
for learningSegments in (learningActiveDeltaSegments,
learningMatchingDeltaSegments):
self._learn(self.internalConnections, self.rng, learningSegments,
prevActiveCells, prevActiveCells,
prevLocationPotentialOverlaps, self.initialPermanence,
self.sampleSize, self.permanenceIncrement,
self.permanenceDecrement, self.maxSynapsesPerSegment)
self._learn(self.deltaConnections, self.rng, learningSegments,
deltaLocation, deltaLocation, deltaPotentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
numNewLocationSynapses = len(prevActiveCells)
numNewDeltaSynapses = len(deltaLocation)
if self.sampleSize != -1:
numNewLocationSynapses = min(numNewLocationSynapses,
self.sampleSize)
numNewDeltaSynapses = min(numNewDeltaSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewLocationSynapses = min(numNewLocationSynapses,
self.maxSynapsesPerSegment)
numNewDeltaSynapses = min(numNewLocationSynapses,
self.maxSynapsesPerSegment)
newPrevLocationSegments = self.internalConnections.createSegments(
newDeltaSegmentCells)
newDeltaSegments = self.deltaConnections.createSegments(
newDeltaSegmentCells)
assert np.array_equal(newPrevLocationSegments, newDeltaSegments)
self.internalConnections.growSynapsesToSample(newPrevLocationSegments,
prevActiveCells,
numNewLocationSynapses,
self.initialPermanence,
self.rng)
self.deltaConnections.growSynapsesToSample(newDeltaSegments,
deltaLocation,
numNewDeltaSynapses,
self.initialPermanence,
self.rng)
def _learnFeatureLocationPair(self, newLocation, featureLocationInput,
featureLocationGrowthCandidates):
"""
Grow / reinforce synapses between the location layer's dendrites and the
input layer's active cells.
"""
potentialOverlaps = self.featureLocationConnections.computeActivity(
featureLocationInput)
matchingSegments = np.where(
potentialOverlaps > self.learningThreshold)[0]
# Cells with a active segment pair: reinforce the segment
cellsForActiveSegments = self.featureLocationConnections.mapSegmentsToCells(
self.activeFeatureLocationSegments)
learningActiveSegments = self.activeFeatureLocationSegments[np.in1d(
cellsForActiveSegments, newLocation)]
remainingCells = np.setdiff1d(newLocation, cellsForActiveSegments)
# Remaining cells with a matching segment pair: reinforce the best matching
# segment pair.
candidateSegments = self.featureLocationConnections.filterSegmentsByCell(
matchingSegments, remainingCells)
cellsForCandidateSegments = (self.featureLocationConnections.
mapSegmentsToCells(candidateSegments))
candidateSegments = candidateSegments[np.in1d(
cellsForCandidateSegments, remainingCells)]
onePerCellFilter = np2.argmaxMulti(
potentialOverlaps[candidateSegments], cellsForCandidateSegments)
learningMatchingSegments = candidateSegments[onePerCellFilter]
newSegmentCells = np.setdiff1d(remainingCells,
cellsForCandidateSegments)
for learningSegments in (learningActiveSegments,
learningMatchingSegments):
self._learn(self.featureLocationConnections, self.rng,
learningSegments, featureLocationInput,
featureLocationGrowthCandidates, potentialOverlaps,
self.initialPermanence, self.sampleSize,
self.permanenceIncrement, self.permanenceDecrement,
self.maxSynapsesPerSegment)
numNewSynapses = len(featureLocationInput)
if self.sampleSize != -1:
numNewSynapses = min(numNewSynapses, self.sampleSize)
if self.maxSynapsesPerSegment != -1:
numNewSynapses = min(numNewSynapses, self.maxSynapsesPerSegment)
newSegments = self.featureLocationConnections.createSegments(
newSegmentCells)
self.featureLocationConnections.growSynapsesToSample(
newSegments, featureLocationGrowthCandidates, numNewSynapses,
self.initialPermanence, self.rng)
@staticmethod
def _learn(connections, rng, learningSegments, activeInput,
growthCandidates, potentialOverlaps, initialPermanence,
sampleSize, permanenceIncrement, permanenceDecrement,
maxSynapsesPerSegment):
"""
Adjust synapse permanences, grow new synapses, and grow new segments.
@param learningActiveSegments (numpy array)
@param learningMatchingSegments (numpy array)
@param segmentsToPunish (numpy array)
@param activeInput (numpy array)
@param growthCandidates (numpy array)
@param potentialOverlaps (numpy array)
"""
# Learn on existing segments
connections.adjustSynapses(learningSegments, activeInput,
permanenceIncrement, -permanenceDecrement)
# Grow new synapses. Calculate "maxNew", the maximum number of synapses to
# grow per segment. "maxNew" might be a number or it might be a list of
# numbers.
if sampleSize == -1:
maxNew = len(growthCandidates)
else:
maxNew = sampleSize - potentialOverlaps[learningSegments]
if maxSynapsesPerSegment != -1:
synapseCounts = connections.mapSegmentsToSynapseCounts(
learningSegments)
numSynapsesToReachMax = maxSynapsesPerSegment - synapseCounts
maxNew = np.where(maxNew <= numSynapsesToReachMax, maxNew,
numSynapsesToReachMax)
connections.growSynapsesToSample(learningSegments, growthCandidates,
maxNew, initialPermanence, rng)
def getActiveCells(self):
return self.activeCells