protected void calcSamplingValuesPerType(
// FeatureSequence tokenSequence,
int position,
int[] oneDocTopics,
MassValue mass,
double[] topicTermScores,
int[] currentTypeTopicCounts,
int[] localTopicCounts,
// int[] localTopicIndex,
double[] cachedCoefficients,
int[] tokensPerTopic,
double betaSum,
double beta,
int[] typeTotals,
int typeIndex,
double[] typeSkewIndexes,
double skewWeight) {
int oldTopic = oneDocTopics[position];
// Now go over the type/topic counts, decrementing
// where appropriate, and calculating the score
// for each topic at the same time.
int index = 0;
int currentTopic, currentValue;
double prevSkew = typeSkewIndexes[typeIndex];
// typeSkewIndexes[typeIndex] = 0;
double score;
boolean alreadyDecremented = (oldTopic == ParallelTopicModel.UNASSIGNED_TOPIC);
mass.topicTermMass = 0.0;
// int totalCounts = 0;
while (index < currentTypeTopicCounts.length && currentTypeTopicCounts[index] > 0) {
currentTopic = currentTypeTopicCounts[index] & topicMask;
currentValue = currentTypeTopicCounts[index] >> topicBits;
// totalCounts += currentValue;
// if (!ignoreSkewness) {
// typeSkewIndexes[typeIndex] += Math.pow((double) currentValue, 2);
// }
if (!alreadyDecremented && currentTopic == oldTopic) {
// We're decrementing and adding up the
// sampling weights at the same time, but
// decrementing may require us to reorder
// the topics, so after we're done here,
// look at this cell in the array again.
currentValue--;
if (currentValue == 0) {
currentTypeTopicCounts[index] = 0;
} else {
currentTypeTopicCounts[index] = (currentValue << topicBits) + oldTopic;
}
// Shift the reduced value to the right, if necessary.
int subIndex = index;
while (subIndex < currentTypeTopicCounts.length - 1
&& currentTypeTopicCounts[subIndex] < currentTypeTopicCounts[subIndex + 1]) {
int temp = currentTypeTopicCounts[subIndex];
currentTypeTopicCounts[subIndex] = currentTypeTopicCounts[subIndex + 1];
currentTypeTopicCounts[subIndex + 1] = temp;
subIndex++;
}
alreadyDecremented = true;
} else {
// re scale topic term scores (probability mass related to token/label type)
// types having large skew--> not ver discriminative. Thus I decrease their probability mass
// skewWeight is used for normalization. Thus the total probability mass (topic term scores)
// related to types remains almost constant
// but is share based on type skewness promoting types that are discriminative
double skewInx = 1;
if (!ignoreSkewness) {
skewInx = skewWeight * (1 + prevSkew);
}
score = cachedCoefficients[currentTopic] * currentValue * skewInx;
mass.topicTermMass += score;
topicTermScores[index] = score;
index++;
}
}
// skewIndex = skewIndex / Math.pow(typeTotals[typeIndex], 2);
// skewIndex = (double) typeTotals[typeIndex] / (double) avgTypeCount * skewIndex;
/* UPDATE as an optimization step during Summing
if (totalCounts == 0) {
totalCounts = typeTotals[typeIndex];
}
if (!ignoreSkewness && totalCounts>0) {
typeSkewIndexes[typeIndex] = typeSkewIndexes[typeIndex] / Math.pow((double) totalCounts, 2);
}
* */
}
protected void sampleTopicsForOneDoc(TopicAssignment doc // int[][] typeTopicCounts
// ,
// double[] cachedCoefficients,
// int[] tokensPerTopic,
// double betaSum,
// double beta,
// double smoothingOnlyMass,
// int[][] lblTypeTopicCounts,
// double[] cachedLabelCoefficients,
// int[] labelsPerTopic,
// double gammaSum,
// double gamma,
// double smoothingOnlyLblMass
) {
FeatureSequence tokenSequence = (FeatureSequence) doc.instance.getData();
LabelSequence topicSequence = (LabelSequence) doc.topicSequence;
MassValue massValue = new MassValue();
massValue.topicBetaMass = 0.0;
massValue.topicTermMass = 0.0;
massValue.smoothingOnlyMass = smoothingOnlyMass;
int nonZeroTopics = 0;
int[] oneDocTopics = topicSequence.getFeatures();
int[] localTopicCounts = new int[numTopics];
int[] localTopicIndex = new int[numTopics];
// Label Init
LabelSequence lblTopicSequence = (LabelSequence) doc.lblTopicSequence;
FeatureSequence labelSequence = (FeatureSequence) doc.instance.getTarget();
MassValue massLblValue = new MassValue();
massLblValue.topicBetaMass = 0.0;
massLblValue.topicTermMass = 0.0;
massLblValue.smoothingOnlyMass = smoothingOnlyLabelMass;
int[] oneDocLblTopics = lblTopicSequence.getFeatures();
int[] localLblTopicCounts = new int[numTopics];
// initSampling
int docLength = tokenSequence.getLength();
// populate topic counts
for (int position = 0; position < docLength; position++) {
if (oneDocTopics[position] == ParallelTopicModel.UNASSIGNED_TOPIC) {
continue;
}
localTopicCounts[oneDocTopics[position]]++;
}
docLength = labelSequence.getLength();
// populate topic counts
for (int position = 0; position < docLength; position++) {
if (oneDocLblTopics[position] == ParallelTopicModel.UNASSIGNED_TOPIC) {
continue;
}
localLblTopicCounts[oneDocLblTopics[position]]++;
}
// Build an array that densely lists the topics that
// have non-zero counts.
int denseIndex = 0;
for (int topic = 0; topic < numTopics; topic++) {
if (localTopicCounts[topic] != 0 || localLblTopicCounts[topic] != 0) {
localTopicIndex[denseIndex] = topic;
denseIndex++;
}
}
// Record the total number of non-zero topics
nonZeroTopics = denseIndex;
if (nonZeroTopics < 20) {
int a = 1;
}
// Initialize the topic count/beta sampling bucket
// Initialize cached coefficients and the topic/beta
// normalizing constant.
for (denseIndex = 0; denseIndex < nonZeroTopics; denseIndex++) {
int topic = localTopicIndex[denseIndex];
int n = localTopicCounts[topic];
int nl = localLblTopicCounts[topic];
if (ignoreLabels) {
// initialize the normalization constant for the (B * n_{t|d}) term
massValue.topicBetaMass += beta * n / (tokensPerTopic[topic] + betaSum);
// massLblValue.topicBetaMass += gamma * nl / (labelsPerTopic[topic] + gammaSum);
// update the coefficients for the non-zero topics
cachedCoefficients[topic] = (alpha[topic] + n) / (tokensPerTopic[topic] + betaSum);
// cachedLabelCoefficients[topic] = (alpha[topic] + nl) / (labelsPerTopic[topic] +
// gammaSum);
} else {
massValue.topicBetaMass += beta * (n + lblWeight * nl) / (tokensPerTopic[topic] + betaSum);
// massLblValue.topicBetaMass += gamma * (nl + (1 / lblWeight) * n) / (labelsPerTopic[topic]
// + gammaSum);
cachedCoefficients[topic] =
((1 + lblWeight) * alpha[topic] + n + lblWeight * nl)
/ (tokensPerTopic[topic] + betaSum);
// cachedLabelCoefficients[topic] = ((1 + (1 / lblWeight)) * alpha[topic] + nl + (1 /
// lblWeight) * n) / (labelsPerTopic[topic] + gammaSum);
}
}
// end of Init Sampling
double[] topicTermScores = new double[numTopics];
int[] currentTypeTopicCounts;
// Iterate over the positions (words) in the document
docLength = tokenSequence.getLength();
for (int position = 0; position < docLength; position++) {
int type = tokenSequence.getIndexAtPosition(position);
currentTypeTopicCounts = typeTopicCounts[type];
nonZeroTopics =
removeOldTopicContribution(
position,
oneDocTopics,
massValue,
localTopicCounts,
localLblTopicCounts,
localTopicIndex,
cachedCoefficients,
tokensPerTopic,
betaSum,
beta,
lblWeight,
nonZeroTopics);
// calcSamplingValuesPerType
calcSamplingValuesPerType(
// tokenSequence,
position,
oneDocTopics,
massValue,
topicTermScores,
currentTypeTopicCounts,
localTopicCounts,
// localTopicIndex,
cachedCoefficients,
tokensPerTopic,
betaSum,
beta,
typeTotals,
type,
typeSkewIndexes,
skewWeight);
double sample = 0;
sample =
random.nextUniform()
* (massValue.smoothingOnlyMass + massValue.topicBetaMass + massValue.topicTermMass);
double origSample = sample;
// Make sure it actually gets set
int newTopic = -1;
newTopic =
findNewTopic(
sample,
massValue,
topicTermScores,
currentTypeTopicCounts,
localTopicCounts,
localLblTopicCounts,
localTopicIndex,
tokensPerTopic,
betaSum,
beta,
nonZeroTopics,
lblWeight);
if (newTopic == -1) {
System.err.println(
"WorkerRunnable sampling error: "
+ origSample
+ " "
+ sample
+ " "
+ massValue.smoothingOnlyMass
+ " "
+ massValue.topicBetaMass
+ " "
+ massValue.topicTermMass);
newTopic = numTopics - 1; // TODO is this appropriate
// throw new IllegalStateException ("WorkerRunnable: New topic not sampled.");
}
// assert(newTopic != -1);
// Put that new topic into the counts
oneDocTopics[position] = newTopic;
if (ignoreLabels) {
massValue.smoothingOnlyMass -=
alpha[newTopic] * beta / (tokensPerTopic[newTopic] + betaSum);
massValue.topicBetaMass -=
beta * localTopicCounts[newTopic] / (tokensPerTopic[newTopic] + betaSum);
} else {
massValue.smoothingOnlyMass -=
(1 + lblWeight) * alpha[newTopic] * beta / (tokensPerTopic[newTopic] + betaSum);
massValue.topicBetaMass -=
beta
* (localTopicCounts[newTopic] + lblWeight * localLblTopicCounts[newTopic])
/ (tokensPerTopic[newTopic] + betaSum);
}
localTopicCounts[newTopic]++;
// If this is a new topic for this document,
// add the topic to the dense index.
if (localTopicCounts[newTopic] == 1 && localLblTopicCounts[newTopic] == 0) {
// First find the point where we
// should insert the new topic by going to
// the end (which is the only reason we're keeping
// track of the number of non-zero
// topics) and working backwards
denseIndex = nonZeroTopics;
while (denseIndex > 0 && localTopicIndex[denseIndex - 1] > newTopic) {
localTopicIndex[denseIndex] = localTopicIndex[denseIndex - 1];
denseIndex--;
}
localTopicIndex[denseIndex] = newTopic;
nonZeroTopics++;
}
tokensPerTopic[newTopic]++;
if (ignoreLabels) {
// update the coefficients for the non-zero topics
cachedCoefficients[newTopic] =
(alpha[newTopic] + localTopicCounts[newTopic]) / (tokensPerTopic[newTopic] + betaSum);
massValue.smoothingOnlyMass +=
alpha[newTopic] * beta / (tokensPerTopic[newTopic] + betaSum);
massValue.topicBetaMass +=
beta * localTopicCounts[newTopic] / (tokensPerTopic[newTopic] + betaSum);
} else {
massValue.smoothingOnlyMass +=
(1 + lblWeight) * alpha[newTopic] * beta / (tokensPerTopic[newTopic] + betaSum);
massValue.topicBetaMass +=
beta
* (localTopicCounts[newTopic] + lblWeight * localLblTopicCounts[newTopic])
/ (tokensPerTopic[newTopic] + betaSum);
cachedCoefficients[newTopic] =
((1 + lblWeight) * alpha[newTopic]
+ localTopicCounts[newTopic]
+ lblWeight * localLblTopicCounts[newTopic])
/ (tokensPerTopic[newTopic] + betaSum);
}
}
// sample labels
// init labels
for (denseIndex = 0; denseIndex < nonZeroTopics; denseIndex++) {
int topic = localTopicIndex[denseIndex];
int n = localTopicCounts[topic];
int nl = localLblTopicCounts[topic];
if (ignoreLabels) {
// initialize the normalization constant for the (B * n_{t|d}) term
// massValue.topicBetaMass += beta * n / (tokensPerTopic[topic] + betaSum);
massLblValue.topicBetaMass += gamma * nl / (labelsPerTopic[topic] + gammaSum);
// update the coefficients for the non-zero topics
// cachedCoefficients[topic] = (alpha[topic] + n) / (tokensPerTopic[topic] + betaSum);
cachedLabelCoefficients[topic] = (alpha[topic] + nl) / (labelsPerTopic[topic] + gammaSum);
} else {
// massValue.topicBetaMass += beta * (n + lblWeight * nl) / (tokensPerTopic[topic] +
// betaSum);
massLblValue.topicBetaMass +=
gamma * (nl + (1 / lblWeight) * n) / (labelsPerTopic[topic] + gammaSum);
// cachedCoefficients[topic] = ((1 + lblWeight) * alpha[topic] + n + lblWeight * nl) /
// (tokensPerTopic[topic] + betaSum);
cachedLabelCoefficients[topic] =
((1 + (1 / lblWeight)) * alpha[topic] + nl + (1 / lblWeight) * n)
/ (labelsPerTopic[topic] + gammaSum);
}
}
double[] topicLblTermScores = new double[numTopics];
int[] currentLblTypeTopicCounts;
int docLblLength = labelSequence.getLength();
// Iterate over the positions (words) in the document
for (int position = 0; position < docLblLength; position++) {
int type = labelSequence.getIndexAtPosition(position);
currentLblTypeTopicCounts = lbltypeTopicCounts[type];
nonZeroTopics =
removeOldTopicContribution(
position,
oneDocLblTopics,
massLblValue,
localLblTopicCounts,
localTopicCounts,
localTopicIndex,
cachedLabelCoefficients,
labelsPerTopic,
gammaSum,
gamma,
1 / lblWeight,
nonZeroTopics);
// calcSamplingValuesPerType
calcSamplingValuesPerType(
// labelSequence,
position,
oneDocLblTopics,
massLblValue,
topicLblTermScores,
currentLblTypeTopicCounts,
localLblTopicCounts,
// localTopicIndex,
cachedLabelCoefficients,
labelsPerTopic,
gammaSum,
gamma,
lblTypeTotals,
type,
lblTypeSkewIndexes,
lblSkewWeight);
// massLblValue.smoothingOnlyMass = 0; //ignore smoothing mass
double sample =
random.nextUniform()
* (massLblValue.smoothingOnlyMass
+ massLblValue.topicBetaMass
+ massLblValue.topicTermMass);
// double sample = random.nextUniform() * (massValue.smoothingOnlyMass +
// massValue.topicBetaMass + massLblValue.smoothingOnlyMass + massLblValue.topicBetaMass +
// massLblValue.topicTermMass);
double origSample = sample;
// Make sure it actually gets set
int newTopic = -1;
newTopic =
findNewTopic(
sample,
massLblValue,
topicLblTermScores,
currentLblTypeTopicCounts,
localLblTopicCounts,
localTopicCounts,
localTopicIndex,
labelsPerTopic,
gammaSum,
gamma,
nonZeroTopics,
1 / lblWeight);
if (newTopic == -1) {
System.err.println(
"WorkerRunnable sampling labels error: "
+ origSample
+ " "
+ sample
+ " "
+ massLblValue.smoothingOnlyMass
+ " "
+ massLblValue.topicBetaMass
+ " "
+ massLblValue.topicTermMass);
// newTopic = numTopics - 1; // TODO is this appropriate
// throw new IllegalStateException ("WorkerRunnable: New topic not sampled.");
}
assert (newTopic != -1);
// Put that new topic into the counts
oneDocLblTopics[position] = newTopic;
if (ignoreLabels) {
massLblValue.smoothingOnlyMass -=
alpha[newTopic] * gamma / (labelsPerTopic[newTopic] + gammaSum);
massLblValue.topicBetaMass -=
gamma * localLblTopicCounts[newTopic] / (labelsPerTopic[newTopic] + gammaSum);
} else {
massLblValue.smoothingOnlyMass -=
(1 + 1 / lblWeight) * alpha[newTopic] * gamma / (labelsPerTopic[newTopic] + gammaSum);
massLblValue.topicBetaMass -=
gamma
* (localLblTopicCounts[newTopic] + (1 / lblWeight) * localTopicCounts[newTopic])
/ (labelsPerTopic[newTopic] + gammaSum);
}
localLblTopicCounts[newTopic]++;
// If this is a new topic for this document,
// add the topic to the dense index.
if (localLblTopicCounts[newTopic] == 1 && localTopicCounts[newTopic] == 0) {
// First find the point where we
// should insert the new topic by going to
// the end (which is the only reason we're keeping
// track of the number of non-zero
// topics) and working backwards
denseIndex = nonZeroTopics;
while (denseIndex > 0 && localTopicIndex[denseIndex - 1] > newTopic) {
localTopicIndex[denseIndex] = localTopicIndex[denseIndex - 1];
denseIndex--;
}
localTopicIndex[denseIndex] = newTopic;
nonZeroTopics++;
}
labelsPerTopic[newTopic]++;
// update the coefficients for the non-zero topics
if (ignoreLabels) {
cachedLabelCoefficients[newTopic] =
(alpha[newTopic] + localLblTopicCounts[newTopic])
/ (labelsPerTopic[newTopic] + gammaSum);
massLblValue.smoothingOnlyMass +=
alpha[newTopic] * gamma / (labelsPerTopic[newTopic] + gammaSum);
massLblValue.topicBetaMass +=
gamma * localLblTopicCounts[newTopic] / (labelsPerTopic[newTopic] + gammaSum);
} else {
cachedLabelCoefficients[newTopic] =
((1 + 1 / lblWeight) * alpha[newTopic]
+ localLblTopicCounts[newTopic]
+ 1 / lblWeight * localTopicCounts[newTopic])
/ (labelsPerTopic[newTopic] + gammaSum);
massLblValue.smoothingOnlyMass +=
(1 + 1 / lblWeight) * alpha[newTopic] * gamma / (labelsPerTopic[newTopic] + gammaSum);
massLblValue.topicBetaMass +=
gamma
* (localLblTopicCounts[newTopic] + (1 / lblWeight) * localTopicCounts[newTopic])
/ (labelsPerTopic[newTopic] + gammaSum);
}
}
if (shouldSaveState) {
// Update the document-topic count histogram,
// for dirichlet estimation
docLengthCounts[docLength]++;
for (denseIndex = 0; denseIndex < nonZeroTopics; denseIndex++) {
int topic = localTopicIndex[denseIndex];
topicDocCounts[topic][localTopicCounts[topic]]++;
}
docLblLengthCounts[docLblLength]++;
for (denseIndex = 0; denseIndex < nonZeroTopics; denseIndex++) {
int topic = localTopicIndex[denseIndex];
topicLblDocCounts[topic][localLblTopicCounts[topic]]++;
}
}
// Clean up our mess: reset the coefficients to values with only
// smoothing. The next doc will update its own non-zero topics...
for (denseIndex = 0; denseIndex < nonZeroTopics; denseIndex++) {
int topic = localTopicIndex[denseIndex];
if (ignoreLabels) {
cachedCoefficients[topic] = alpha[topic] / (tokensPerTopic[topic] + betaSum);
cachedLabelCoefficients[topic] = alpha[topic] / (labelsPerTopic[topic] + gammaSum);
} else {
cachedCoefficients[topic] =
(1 + lblWeight) * alpha[topic] / (tokensPerTopic[topic] + betaSum);
cachedLabelCoefficients[topic] =
(1 + 1 / lblWeight) * alpha[topic] / (labelsPerTopic[topic] + gammaSum);
}
}
smoothingOnlyMass = massValue.smoothingOnlyMass;
smoothingOnlyLabelMass = massLblValue.smoothingOnlyMass;
}
protected int removeOldTopicContribution(
int position,
int[] oneDocTopics,
MassValue mass,
int[] localTopicCounts,
int[] localLblTopicCounts,
int[] localTopicIndex,
double[] cachedCoefficients,
int[] tokensPerTopic,
double betaSum,
double beta,
double lblWeight,
int nonZeroTopics) {
int oldTopic = oneDocTopics[position];
int denseIndex = 0;
if (oldTopic != ParallelTopicModel.UNASSIGNED_TOPIC) {
// Remove this token from all counts.
// Remove this topic's contribution to the
// normalizing constants
if (ignoreLabels) {
mass.smoothingOnlyMass -= alpha[oldTopic] * beta / (tokensPerTopic[oldTopic] + betaSum);
mass.topicBetaMass -=
beta * localTopicCounts[oldTopic] / (tokensPerTopic[oldTopic] + betaSum);
} else {
mass.smoothingOnlyMass -=
(1 + lblWeight) * alpha[oldTopic] * beta / (tokensPerTopic[oldTopic] + betaSum);
mass.topicBetaMass -=
beta
* (localTopicCounts[oldTopic] + lblWeight * localLblTopicCounts[oldTopic])
/ (tokensPerTopic[oldTopic] + betaSum);
}
// Decrement the local doc/topic counts
localTopicCounts[oldTopic]--;
// Maintain the dense index, if we are deleting
// the old topic
if (localTopicCounts[oldTopic] == 0 && localLblTopicCounts[oldTopic] == 0) {
// First get to the dense location associated with
// the old topic.
denseIndex = 0;
// We know it's in there somewhere, so we don't
// need bounds checking.
while (localTopicIndex[denseIndex] != oldTopic) {
denseIndex++;
}
// shift all remaining dense indices to the left.
while (denseIndex < nonZeroTopics) {
if (denseIndex < localTopicIndex.length - 1) {
localTopicIndex[denseIndex] = localTopicIndex[denseIndex + 1];
}
denseIndex++;
}
nonZeroTopics--;
}
// Decrement the global topic count totals
tokensPerTopic[oldTopic]--;
assert (tokensPerTopic[oldTopic] >= 0) : "old Topic " + oldTopic + " below 0";
// Add the old topic's contribution back into the
// normalizing constants.
if (ignoreLabels) {
mass.smoothingOnlyMass += alpha[oldTopic] * beta / (tokensPerTopic[oldTopic] + betaSum);
mass.topicBetaMass +=
beta * localTopicCounts[oldTopic] / (tokensPerTopic[oldTopic] + betaSum);
// Reset the cached coefficient for this topic
cachedCoefficients[oldTopic] =
(alpha[oldTopic] + localTopicCounts[oldTopic]) / (tokensPerTopic[oldTopic] + betaSum);
} else {
mass.smoothingOnlyMass +=
(1 + lblWeight) * alpha[oldTopic] * beta / (tokensPerTopic[oldTopic] + betaSum);
mass.topicBetaMass +=
beta
* (localTopicCounts[oldTopic] + lblWeight * localLblTopicCounts[oldTopic])
/ (tokensPerTopic[oldTopic] + betaSum);
// Reset the cached coefficient for this topic
cachedCoefficients[oldTopic] =
((1 + lblWeight) * alpha[oldTopic]
+ localTopicCounts[oldTopic]
+ lblWeight * localLblTopicCounts[oldTopic])
/ (tokensPerTopic[oldTopic] + betaSum);
}
}
return nonZeroTopics;
}