Dirichlet

Documentation of 'cc.mallet.types.Dirichlet' Java class Dirichlet

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java.lang.Object
- cc.mallet.types.Dirichlet

```
public class Dirichlet
extends java.lang.Object
```
Various useful functions related to Dirichlet distributions.

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class Dirichlet.Estimator

static class Dirichlet.MethodOfMomentsEstimator

Nested Classes
Modifier and Type	Class and Description
`static class`	`Dirichlet.Estimator`
`static class`	`Dirichlet.MethodOfMomentsEstimator`

Field Summary

Fields
Modifier and Type	Field and Description
`static double`	`DIGAMMA_COEF_1`
`static double`	`DIGAMMA_COEF_10`
`static double`	`DIGAMMA_COEF_2`
`static double`	`DIGAMMA_COEF_3`
`static double`	`DIGAMMA_COEF_4`
`static double`	`DIGAMMA_COEF_5`
`static double`	`DIGAMMA_COEF_6`
`static double`	`DIGAMMA_COEF_7`
`static double`	`DIGAMMA_COEF_8`
`static double`	`DIGAMMA_COEF_9`
`static double`	`DIGAMMA_LARGE`
`static double`	`DIGAMMA_SMALL`
`static double`	`EULER_MASCHERONI` Actually the negative Euler-Mascheroni constant
`static double`	`HALF_LOG_TWO_PI`
`static double`	`PI_SQUARED_OVER_SIX`

Constructor Summary

Constructors
Constructor and Description
`Dirichlet(Alphabet dict)` A symmetric Dirichlet with alpha_i = 1.0 and the number of dimensions of the given alphabet.
`Dirichlet(Alphabet dict, double alpha)` A symmetric Dirichlet with alpha_i = `alpha` and the number of dimensions of the given alphabet.
`Dirichlet(double[] p)` A dirichlet parameterized with a single vector of positive reals
`Dirichlet(double[] alphas, Alphabet dict)` Constructor that takes an alphabet representing the meaning of each dimension
`Dirichlet(double m, double[] p)` A dirichlet parameterized by a distribution and a magnitude
`Dirichlet(int size)` A symmetric Dirichlet with alpha_i = 1.0 and `size` dimensions
`Dirichlet(int size, double alpha)` A symmetric dirichlet: E(X_i) = E(X_j) for all i, j

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`absoluteDifference(Dirichlet other)` Compute the L1 residual between two dirichlets
`double`	`alpha(int featureIndex)`
`void`	`checkBreakeven(double x)`
`static java.lang.String`	`compare(double sum, int k, int n, int w)`
`static double`	`digamma(double z)` Calculate digamma using an asymptotic expansion involving Bernoulli numbers.
`static double`	`digammaDifference(double x, int n)`
`double`	`dirichletMultinomialLikelihoodRatio(int[] countsX, int[] countsY)` This version uses a non-symmetric Dirichlet prior
`static double`	`dirichletMultinomialLikelihoodRatio(int[] countsX, int[] countsY, double alpha, double alphaSum)` What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
`static double`	`dirichletMultinomialLikelihoodRatio(IntIntHashMap countsX, IntIntHashMap countsY, double alpha, double alphaSum)` What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
`static java.lang.String`	`distributionToString(double magnitude, double[] distribution)` Create a printable list of alpha_i parameters
`int[]`	`drawObservation(int n)` Dirichlet-multinomial: draw a distribution from the dirichlet, then draw n samples from that multinomial.
`int[]`	`drawObservation(int n, double[] distribution)` Draw a count vector from the probability distribution provided.
`java.lang.Object[]`	`drawObservations(int d, int n)` Create a set of d draws from a dirichlet-multinomial, each with an average of n observations.
`static double`	`ewensLikelihoodRatio(int[] countsX, int[] countsY, double lambda)` Similar to the Dirichlet-multinomial test,s this is a likelihood ratio based on the Ewens Sampling Formula, which can be considered the distribution of partitions of integers generated by the Chinese restaurant process.
`Alphabet`	`getAlphabet()`
`static double`	`learnParameters(double[] parameters, int[][] observations, int[] observationLengths)` Learn Dirichlet parameters using frequency histograms
`static double`	`learnParameters(double[] parameters, int[][] observations, int[] observationLengths, double shape, double scale, int numIterations)` Learn Dirichlet parameters using frequency histograms
`long`	`learnParametersWithDigamma(int[][] binCounts, int[] observationLengths)`
`long`	`learnParametersWithDigamma(java.lang.Object[] observations)` Use the fixed point iteration described by Tom Minka.
`long`	`learnParametersWithHistogram(int[][] binCountHistograms, int[] lengthHistogram)`
`long`	`learnParametersWithHistogram(java.lang.Object[] observations)` Use the fixed point iteration described by Tom Minka.
`long`	`learnParametersWithLeaveOneOut(int[][] binCounts, int[] observationLengths)` Learn parameters using Minka's Leave-One-Out (LOO) likelihood
`long`	`learnParametersWithLeaveOneOut(java.lang.Object[] observations)`
`long`	`learnParametersWithMoments(java.lang.Object[] observations)` Estimate a dirichlet with the moment matching method described by Ronning.
`static double`	`learnSymmetricConcentration(int[] countHistogram, int[] observationLengths, int numDimensions, double currentValue)` Learn the concentration parameter of a symmetric Dirichlet using frequency histograms.
`static double`	`logGamma(double z)` Currently aliased to `logGammaStirling`
`static double`	`logGammaDefinition(double z)` This calculates a log gamma function exactly.
`static double`	`logGammaDifference(double z, int n)` This directly calculates the difference between two log gamma functions using a recursive formula.
`static double`	`logGammaNemes(double z)` Gergo Nemes' approximation
`static double`	`logGammaStirling(double z)` Use a fifth order Stirling's approximation.
`static void`	`main(java.lang.String[] args)`
`double[]`	`nextDistribution()`
`void`	`print()`
`Dirichlet`	`randomDirichlet(Randoms r, double averageAlpha)`
`FeatureSequence`	`randomFeatureSequence(Randoms r, int length)`
`FeatureVector`	`randomFeatureVector(Randoms r, int size)`
`Multinomial`	`randomMultinomial(Randoms r)`
`TokenSequence`	`randomTokenSequence(Randoms r, int length)`
`double[]`	`randomVector(Randoms r)`
`static void`	`runComparison()`
`int`	`size()`
`double`	`squaredDifference(Dirichlet other)` Compute the L2 residual between two dirichlets
`static void`	`testSymmetricConcentration(int numDimensions, int numObservations, int observationMeanLength)`
`void`	`toFile(java.lang.String filename)` Write the parameters alpha_i to the specified file, one per line
`static double`	`trigamma(double z)`

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - EULER_MASCHERONI
```
public static final double EULER_MASCHERONI
```
    Actually the negative Euler-Mascheroni constant
    
    See Also:
    
    Constant Field Values
  - PI_SQUARED_OVER_SIX
```
public static final double PI_SQUARED_OVER_SIX
```
    See Also:
    
    Constant Field Values
  - HALF_LOG_TWO_PI
```
public static final double HALF_LOG_TWO_PI
```
  - DIGAMMA_COEF_1
```
public static final double DIGAMMA_COEF_1
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_2
```
public static final double DIGAMMA_COEF_2
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_3
```
public static final double DIGAMMA_COEF_3
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_4
```
public static final double DIGAMMA_COEF_4
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_5
```
public static final double DIGAMMA_COEF_5
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_6
```
public static final double DIGAMMA_COEF_6
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_7
```
public static final double DIGAMMA_COEF_7
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_8
```
public static final double DIGAMMA_COEF_8
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_9
```
public static final double DIGAMMA_COEF_9
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_COEF_10
```
public static final double DIGAMMA_COEF_10
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_LARGE
```
public static final double DIGAMMA_LARGE
```
    See Also:
    
    Constant Field Values
  - DIGAMMA_SMALL
```
public static final double DIGAMMA_SMALL
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Dirichlet
```
public Dirichlet(double m,
                 double[] p)
```
    A dirichlet parameterized by a distribution and a magnitude
    
    Parameters:
    
    m - The magnitude of the Dirichlet: sum_i alpha_i
    
    p - A probability distribution: p_i = alpha_i / m
  - Dirichlet
```
public Dirichlet(double[] p)
```
    A dirichlet parameterized with a single vector of positive reals
  - Dirichlet
```
public Dirichlet(double[] alphas,
                 Alphabet dict)
```
    Constructor that takes an alphabet representing the meaning of each dimension
  - Dirichlet
```
public Dirichlet(Alphabet dict)
```
    A symmetric Dirichlet with alpha_i = 1.0 and the number of dimensions of the given alphabet.
  - Dirichlet
```
public Dirichlet(Alphabet dict,
                 double alpha)
```
    A symmetric Dirichlet with alpha_i = alpha and the number of dimensions of the given alphabet.
  - Dirichlet
```
public Dirichlet(int size)
```
    A symmetric Dirichlet with alpha_i = 1.0 and size dimensions
  - Dirichlet
```
public Dirichlet(int size,
                 double alpha)
```
    A symmetric dirichlet: E(X_i) = E(X_j) for all i, j
    
    Parameters:
    
    n - The number of dimensions
    
    alpha - The parameter for each dimension
- Method Detail
  - nextDistribution
```
public double[] nextDistribution()
```
  - distributionToString
```
public static java.lang.String distributionToString(double magnitude,
                                                    double[] distribution)
```
    Create a printable list of alpha_i parameters
  - toFile
```
public void toFile(java.lang.String filename)
            throws java.io.IOException
```
    Write the parameters alpha_i to the specified file, one per line
    
    Throws:
    
    java.io.IOException
  - drawObservation
```
public int[] drawObservation(int n)
```
    Dirichlet-multinomial: draw a distribution from the dirichlet, then draw n samples from that multinomial.
  - drawObservation
```
public int[] drawObservation(int n,
                             double[] distribution)
```
    Draw a count vector from the probability distribution provided.
    
    Parameters:
    
    n - The expected total number of counts in the returned vector. The actual number is ~ Poisson(n)
  - drawObservations
```
public java.lang.Object[] drawObservations(int d,
                                           int n)
```
    Create a set of d draws from a dirichlet-multinomial, each with an average of n observations.
  - logGammaDefinition
```
public static double logGammaDefinition(double z)
```
    This calculates a log gamma function exactly. It's extremely inefficient -- use this for comparison only.
  - logGammaDifference
```
public static double logGammaDifference(double z,
                                        int n)
```
    This directly calculates the difference between two log gamma functions using a recursive formula. The break-even with the Stirling approximation is about n=2, so it's not necessarily worth using this.
  - logGamma
```
public static double logGamma(double z)
```
    Currently aliased to logGammaStirling
  - logGammaStirling
```
public static double logGammaStirling(double z)
```
    Use a fifth order Stirling's approximation.
    
    Parameters:
    
    z - Note that Stirling's approximation is increasingly unstable as z approaches 0. If z is less than 2, we shift it up, calculate the approximation, and then shift the answer back down.
  - logGammaNemes
```
public static double logGammaNemes(double z)
```
    Gergo Nemes' approximation
  - digamma
```
public static double digamma(double z)
```
    Calculate digamma using an asymptotic expansion involving Bernoulli numbers.
  - digammaDifference
```
public static double digammaDifference(double x,
                                       int n)
```
  - trigamma
```
public static double trigamma(double z)
```
  - learnSymmetricConcentration
```
public static double learnSymmetricConcentration(int[] countHistogram,
                                                 int[] observationLengths,
                                                 int numDimensions,
                                                 double currentValue)
```
    Learn the concentration parameter of a symmetric Dirichlet using frequency histograms. Since all parameters are the same, we only need to keep track of the number of observation/dimension pairs with count N
    
    Parameters:
    
    countHistogram - An array of frequencies. If the matrix X represents observations such that x_dt is how many times word t occurs in document d, countHistogram[3] is the total number of cells in any column that equal 3.
    
    observationLengths - A histogram of sample lengths, for example observationLengths[20] could be the number of documents that are exactly 20 tokens long.
    
    numDimensions - The total number of dimensions.
    
    currentValue - An initial starting value.
  - testSymmetricConcentration
```
public static void testSymmetricConcentration(int numDimensions,
                                              int numObservations,
                                              int observationMeanLength)
```
  - learnParameters
```
public static double learnParameters(double[] parameters,
                                     int[][] observations,
                                     int[] observationLengths)
```
    Learn Dirichlet parameters using frequency histograms
    
    Parameters:
    
    parameters - A reference to the current values of the parameters, which will be updated in place
    
    observations - An array of count histograms. observations[10][3] could be the number of documents that contain exactly 3 tokens of word type 10.
    
    observationLengths - A histogram of sample lengths, for example observationLengths[20] could be the number of documents that are exactly 20 tokens long.
  - learnParameters
```
public static double learnParameters(double[] parameters,
                                     int[][] observations,
                                     int[] observationLengths,
                                     double shape,
                                     double scale,
                                     int numIterations)
```
    Learn Dirichlet parameters using frequency histograms
    
    Parameters:
    
    parameters - A reference to the current values of the parameters, which will be updated in place
    
    observations - An array of count histograms. observations[10][3] could be the number of documents that contain exactly 3 tokens of word type 10.
    
    observationLengths - A histogram of sample lengths, for example observationLengths[20] could be the number of documents that are exactly 20 tokens long.
    
    shape - Gamma prior E(X) = shape * scale, var(X) = shape * scale²
    
    scale -
    
    numIterations - 200 to 1000 generally insures convergence, but 1-5 is often enough to step in the right direction
  - learnParametersWithHistogram
```
public long learnParametersWithHistogram(java.lang.Object[] observations)
```
    Use the fixed point iteration described by Tom Minka.
  - learnParametersWithHistogram
```
public long learnParametersWithHistogram(int[][] binCountHistograms,
                                         int[] lengthHistogram)
```
  - learnParametersWithDigamma
```
public long learnParametersWithDigamma(java.lang.Object[] observations)
```
    Use the fixed point iteration described by Tom Minka.
  - learnParametersWithDigamma
```
public long learnParametersWithDigamma(int[][] binCounts,
                                       int[] observationLengths)
```
  - learnParametersWithMoments
```
public long learnParametersWithMoments(java.lang.Object[] observations)
```
    Estimate a dirichlet with the moment matching method described by Ronning.
  - learnParametersWithLeaveOneOut
```
public long learnParametersWithLeaveOneOut(java.lang.Object[] observations)
```
  - learnParametersWithLeaveOneOut
```
public long learnParametersWithLeaveOneOut(int[][] binCounts,
                                           int[] observationLengths)
```
    Learn parameters using Minka's Leave-One-Out (LOO) likelihood
  - absoluteDifference
```
public double absoluteDifference(Dirichlet other)
```
    Compute the L1 residual between two dirichlets
  - squaredDifference
```
public double squaredDifference(Dirichlet other)
```
    Compute the L2 residual between two dirichlets
  - checkBreakeven
```
public void checkBreakeven(double x)
```
  - compare
```
public static java.lang.String compare(double sum,
                                       int k,
                                       int n,
                                       int w)
```
  - dirichletMultinomialLikelihoodRatio
```
public static double dirichletMultinomialLikelihoodRatio(IntIntHashMap countsX,
                                                         IntIntHashMap countsY,
                                                         double alpha,
                                                         double alphaSum)
```
    What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
  - dirichletMultinomialLikelihoodRatio
```
public static double dirichletMultinomialLikelihoodRatio(int[] countsX,
                                                         int[] countsY,
                                                         double alpha,
                                                         double alphaSum)
```
    What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
  - dirichletMultinomialLikelihoodRatio
```
public double dirichletMultinomialLikelihoodRatio(int[] countsX,
                                                  int[] countsY)
```
    This version uses a non-symmetric Dirichlet prior
  - ewensLikelihoodRatio
```
public static double ewensLikelihoodRatio(int[] countsX,
                                          int[] countsY,
                                          double lambda)
```
    Similar to the Dirichlet-multinomial test,s this is a likelihood ratio based on the Ewens Sampling Formula, which can be considered the distribution of partitions of integers generated by the Chinese restaurant process.
  - runComparison
```
public static void runComparison()
```
  - main
```
public static void main(java.lang.String[] args)
```
  - getAlphabet
```
public Alphabet getAlphabet()
```
  - size
```
public int size()
```
  - alpha
```
public double alpha(int featureIndex)
```
  - print
```
public void print()
```
  - randomMultinomial
```
public Multinomial randomMultinomial(Randoms r)
```
  - randomDirichlet
```
public Dirichlet randomDirichlet(Randoms r,
                                 double averageAlpha)
```
  - randomFeatureSequence
```
public FeatureSequence randomFeatureSequence(Randoms r,
                                             int length)
```
  - randomFeatureVector
```
public FeatureVector randomFeatureVector(Randoms r,
                                         int size)
```
  - randomTokenSequence
```
public TokenSequence randomTokenSequence(Randoms r,
                                         int length)
```
  - randomVector
```
public double[] randomVector(Randoms r)
```

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Class Dirichlet

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

EULER_MASCHERONI

PI_SQUARED_OVER_SIX

HALF_LOG_TWO_PI

DIGAMMA_COEF_1

DIGAMMA_COEF_2

DIGAMMA_COEF_3

DIGAMMA_COEF_4

DIGAMMA_COEF_5

DIGAMMA_COEF_6

DIGAMMA_COEF_7

DIGAMMA_COEF_8

DIGAMMA_COEF_9

DIGAMMA_COEF_10

DIGAMMA_LARGE

DIGAMMA_SMALL

Constructor Detail

Dirichlet

Dirichlet

Dirichlet

Dirichlet

Dirichlet

Dirichlet

Dirichlet

Method Detail

nextDistribution

distributionToString

toFile

drawObservation

drawObservation

drawObservations

logGammaDefinition

logGammaDifference

logGamma

logGammaStirling

logGammaNemes

digamma

digammaDifference

trigamma

learnSymmetricConcentration

testSymmetricConcentration

learnParameters

learnParameters

learnParametersWithHistogram

learnParametersWithHistogram

learnParametersWithDigamma

learnParametersWithDigamma

learnParametersWithMoments

learnParametersWithLeaveOneOut

learnParametersWithLeaveOneOut

absoluteDifference

squaredDifference

checkBreakeven

compare

dirichletMultinomialLikelihoodRatio

dirichletMultinomialLikelihoodRatio

dirichletMultinomialLikelihoodRatio

ewensLikelihoodRatio

runComparison

main

getAlphabet

size

alpha

print

randomMultinomial

randomDirichlet

randomFeatureSequence

randomFeatureVector

randomTokenSequence

randomVector