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improving jittered surrogates

This commit is contained in:
David Shorten 2022-02-25 18:49:12 +11:00
parent 285c95947a
commit c068c8308d
2 changed files with 41 additions and 12 deletions
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45
java/source/infodynamics/measures/spiking/integration/TransferEntropyCalculatorSpikingIntegration.java
View File

@ -119,6 +119,15 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
*/
protected double noiseLevel = (double) 1e-8;
/**
* Whether to use the jittered sampling approach. Useful for bursty spike trains. Explained in methods section of
* doi.org/10.1101/2021.06.29.450432
*/
protected boolean jitteredSamplesForSurrogates = false;
public static final String DO_JITTERED_SAMPLING_PROP_NAME = "DO_JITTERED_SAMPLING";
protected double jitteredSamplingNoiseLevel = 1;
public static final String JITTERED_SAMPLING_NOISE_LEVEL = "JITTERED_SAMPLING_NOISE_LEVEL";
/**
* Stores whether we are in debug mode
*/
@ -233,6 +242,10 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
}
} else if (propertyName.equalsIgnoreCase(KNNS_PROP_NAME)) {
Knns = Integer.parseInt(propertyValue);
} else if (propertyName.equalsIgnoreCase(DO_JITTERED_SAMPLING_PROP_NAME)) {
jitteredSamplesForSurrogates = Boolean.parseBoolean(propertyValue);
} else if (propertyName.equalsIgnoreCase(JITTERED_SAMPLING_NOISE_LEVEL)) {
jitteredSamplingNoiseLevel = Double.parseDouble(propertyValue);
} else if (propertyName.equalsIgnoreCase(PROP_K_PERM)) {
kPerm = Integer.parseInt(propertyValue);
} else if (propertyName.equalsIgnoreCase(PROP_ADD_NOISE)) {
@ -397,7 +410,7 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
}
processEventsFromSpikingTimeSeries(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes, conditioningEmbeddingsFromSpikes,
jointEmbeddingsFromSpikes, conditioningEmbeddingsFromSamples, jointEmbeddingsFromSamples,
numSamplesMultiplier);
numSamplesMultiplier, false);
}
@ -588,18 +601,18 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
}
protected double[] generateRandomSampleTimes(double[] sourceSpikeTimes, double[] destSpikeTimes, double[][] conditionalSpikeTimes,
double actualNumSamplesMultiplier, int firstTargetIndexOfEmbedding) {
double actualNumSamplesMultiplier, int firstTargetIndexOfEmbedding, boolean doJitteredSampling) {
double sampleLowerBound = destSpikeTimes[firstTargetIndexOfEmbedding];
double sampleUpperBound = destSpikeTimes[destSpikeTimes.length - 1];
int num_samples = (int) Math.round(actualNumSamplesMultiplier * (destSpikeTimes.length - firstTargetIndexOfEmbedding + 1));
double[] randomSampleTimes = new double[num_samples];
Random rand = new Random();
boolean doCellCulture = true;
if (doCellCulture) {
if (doJitteredSampling) {
//System.out.println("jittering " + jitteredSamplingNoiseLevel);
for (int i = 0; i < randomSampleTimes.length; i++) {
randomSampleTimes[i] = destSpikeTimes[firstTargetIndexOfEmbedding + (i % (destSpikeTimes.length - firstTargetIndexOfEmbedding - 1))]
+ 200 * (rand.nextDouble() - 0.5);
+ jitteredSamplingNoiseLevel * (rand.nextDouble() - 0.5);
//randomSampleTimes[i] = -1.0;
if ((randomSampleTimes[i] > sampleUpperBound) || (randomSampleTimes[i] < sampleLowerBound)) {
randomSampleTimes[i] = sampleLowerBound + rand.nextDouble() * (sampleUpperBound - sampleLowerBound);
@ -622,12 +635,13 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
protected void processEventsFromSpikingTimeSeries(double[] sourceSpikeTimes, double[] destSpikeTimes, double[][] conditionalSpikeTimes,
Vector<double[]> conditioningEmbeddingsFromSpikes, Vector<double[]> jointEmbeddingsFromSpikes,
Vector<double[]> conditioningEmbeddingsFromSamples, Vector<double[]> jointEmbeddingsFromSamples,
double actualNumSamplesMultiplier)
double actualNumSamplesMultiplier, boolean doJitteredSampling)
throws Exception {
int firstTargetIndexOfEmbedding = getFirstDestIndex(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes, true);
double[] randomSampleTimes = generateRandomSampleTimes(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
actualNumSamplesMultiplier, firstTargetIndexOfEmbedding);
actualNumSamplesMultiplier, firstTargetIndexOfEmbedding,
doJitteredSampling);
makeEmbeddingsAtPoints(destSpikeTimes, firstTargetIndexOfEmbedding, sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
conditioningEmbeddingsFromSpikes, jointEmbeddingsFromSpikes);
@ -637,12 +651,13 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
protected void processEventsFromSpikingTimeSeries(double[] sourceSpikeTimes, double[] destSpikeTimes, double[][] conditionalSpikeTimes,
Vector<double[]> conditioningEmbeddingsFromSamples, Vector<double[]> jointEmbeddingsFromSamples,
double actualNumSamplesMultiplier)
double actualNumSamplesMultiplier, boolean doJitteredSampling)
throws Exception {
int firstTargetIndexOfEmbedding = getFirstDestIndex(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes, false);
double[] randomSampleTimes = generateRandomSampleTimes(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
actualNumSamplesMultiplier, firstTargetIndexOfEmbedding);
actualNumSamplesMultiplier, firstTargetIndexOfEmbedding,
doJitteredSampling);
makeEmbeddingsAtPoints(randomSampleTimes, 0, sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
conditioningEmbeddingsFromSamples, jointEmbeddingsFromSamples);
}
@ -850,9 +865,15 @@ public class TransferEntropyCalculatorSpikingIntegration implements TransferEntr
} else {
conditionalSpikeTimes = new double[][] {};
}
processEventsFromSpikingTimeSeries(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
resampledConditioningEmbeddingsFromSamples, resampledJointEmbeddingsFromSamples,
surrogateNumSamplesMultiplier);
if (jitteredSamplesForSurrogates) {
processEventsFromSpikingTimeSeries(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
resampledConditioningEmbeddingsFromSamples, resampledJointEmbeddingsFromSamples,
surrogateNumSamplesMultiplier, true);
} else {
processEventsFromSpikingTimeSeries(sourceSpikeTimes, destSpikeTimes, conditionalSpikeTimes,
resampledConditioningEmbeddingsFromSamples, resampledJointEmbeddingsFromSamples,
surrogateNumSamplesMultiplier, false);
}
}
// Convert the vectors to arrays so that they can be put in the trees
double[][] arrayedResampledConditioningEmbeddingsFromSamples = new double[resampledConditioningEmbeddingsFromSamples.size()][numDestPastIntervals];

8
tester.py
View File

@ -83,6 +83,8 @@ teCalc.setProperty("knns", "4")
print("Independent Poisson Processes")
teCalc.setProperty("DEST_PAST_INTERVALS", "1,2")
teCalc.setProperty("SOURCE_PAST_INTERVALS", "1,2")
teCalc.setProperty("DO_JITTERED_SAMPLING", "true")
teCalc.setProperty("JITTERED_SAMPLING_NOISE_LEVEL", "0")
teCalc.appendConditionalIntervals(JArray(JInt, 1)([1, 2]))
teCalc.appendConditionalIntervals(JArray(JInt, 1)([1, 2]))
teCalc.setProperty("NORM_TYPE", "MAX_NORM")
@ -112,6 +114,8 @@ print("Noisy copy zero TE")
#teCalc.appendConditionalIntervals(JArray(JInt, 1)([1]))
teCalc.setProperty("DEST_PAST_INTERVALS", "1")
teCalc.setProperty("SOURCE_PAST_INTERVALS", "1")
teCalc.setProperty("DO_JITTERED_SAMPLING", "true")
teCalc.setProperty("JITTERED_SAMPLING_NOISE_LEVEL", "0")
#teCalc.setProperty("NORM_TYPE", "MAX_NORM")
results_noisy_zero = np.zeros(NUM_REPS)
@ -143,6 +147,8 @@ print("Noisy copy non-zero TE")
teCalc.appendConditionalIntervals(JArray(JInt, 1)([1]))
teCalc.setProperty("DEST_PAST_INTERVALS", "1,2")
teCalc.setProperty("SOURCE_PAST_INTERVALS", "1")
teCalc.setProperty("DO_JITTERED_SAMPLING", "true")
teCalc.setProperty("JITTERED_SAMPLING_NOISE_LEVEL", "0")
#teCalc.setProperty("NORM_TYPE", "MAX_NORM")
results_noisy_non_zero = np.zeros(NUM_REPS)
@ -171,6 +177,8 @@ teCalc = teCalcClass()
teCalc.setProperty("knns", "4")
teCalc.setProperty("DEST_PAST_INTERVALS", "1,2")
teCalc.setProperty("SOURCE_PAST_INTERVALS", "1")
teCalc.setProperty("DO_JITTERED_SAMPLING", "true")
teCalc.setProperty("JITTERED_SAMPLING_NOISE_LEVEL", "0")
#teCalc.setProperty("NUM_SAMPLES_MULTIPLIER", "1")
#teCalc.setProperty("NORM_TYPE", "MAX_NORM")