class BayesNetwork extends BayesClassifier
The BayesNetwork
class implements a Bayesian Network Classifier. It
classifies a data vector 'z' by determining which of 'k' classes has the
highest Joint Probability of 'z' and the outcome (i.e., one of the 'k'
classes) of occurring. The Joint Probability calculation is factored
into multiple calculations of Conditional Probability. Conditional
dependencies are specified using a Directed Acyclic Graph 'DAG'. Nodes
are conditionally dependent on their parents only. Conditional probability
are recorded in tables. Training is achieved by ...
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Instance Constructors
-
new
BayesNetwork(x: MatriI, y: VectoI, fn: Array[String], k: Int, cn: Array[String], dag: DAG = null, table: Array[Map[Int, Double]] = null)
- x
the integer-valued training/test data vectors stored as rows of a matrix
- y
the training/test classification vector, where y_i = class for row i of the matrix x
- fn
the names for all factors
- k
the number of classes
- cn
the names for all classes
- dag
the directed acyclic graph specifying conditional dependencies
- table
the array of tables recording conditional probabilities
Value Members
-
final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
- Definition Classes
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def
aic(vc: VectoI, vcp1: VectoI, vcp2: VectoI, popX: HMatrix5[Int], k: Int, me: Int = me_default): Double
Compute the 'AIC' for the given Bayesian Network structure and data.
Compute the 'AIC' for the given Bayesian Network structure and data.
- vc
the value count
- vcp1
the value count for parent 1
- vcp2
the value count for parent 2
- popX
the population counts
- k
the number of classes
- me
the m-estimate value
- Definition Classes
- BayesMetrics
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
buildModel(testStart: Int, testEnd: Int): (Array[Boolean], DAG)
Build a model.
Build a model. FIX - implement
- testStart
the start of the test region
- testEnd
the end of the test region
- Definition Classes
- BayesNetwork → BayesClassifier
-
def
calcCorrelation: MatriD
Calculate the correlation matrix for the feature vectors 'fea'.
Calculate the correlation matrix for the feature vectors 'fea'. If the correlations are too high, the independence assumption may be dubious.
- Definition Classes
- ClassifierInt
-
def
calcCorrelation2(zrg: Range, xrg: Range): MatriD
Calculate the correlation matrix for the feature vectors of Z (Level 3) and those of X (level 2).
Calculate the correlation matrix for the feature vectors of Z (Level 3) and those of X (level 2). If the correlations are too high, the independence assumption may be dubious.
- zrg
the range of Z-columns
- xrg
the range of X-columns
- Definition Classes
- ClassifierInt
-
def
classify(z: VectoI): (Int, String, Double)
Given an integer-valued data vector 'z', classify it returning the class number (0, ..., k-1) with the highest relative posterior probability.
Given an integer-valued data vector 'z', classify it returning the class number (0, ..., k-1) with the highest relative posterior probability. Return the best class, its name and its relative probability
- z
the data vector to classify
- Definition Classes
- BayesNetwork → Classifier
-
def
classify(z: VectoD): (Int, String, Double)
Given a new continuous data vector 'z', determine which class it belongs to, by first rounding it to an integer-valued vector.
Given a new continuous data vector 'z', determine which class it belongs to, by first rounding it to an integer-valued vector. Return the best class, its name and its relative probability
- z
the vector to classify
- Definition Classes
- ClassifierInt → Classifier
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
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def
condMutualInformation(pz: VectorD, ptz: HMatrix3[Double], pxyz: HMatrix5[Double]): MatrixD
Compute conditional mutual information for XY given Z from frequency counts
Compute conditional mutual information for XY given Z from frequency counts
- pz
the probability of Z
- ptz
the probability of X given Z, or Y given Z
- pxyz
the probability of Y and Y given Z
- Definition Classes
- BayesClassifier
- See also
http://www.cs.technion.ac.il/~dang/journal_papers/friedman1997Bayesian.pdf, p.12
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def
cp(i: Int, key: VectorI): Double
Compute the Conditional Probability 'CP' of 'x_i' given its parents' values.
Compute the Conditional Probability 'CP' of 'x_i' given its parents' values.
- i
the 'i'th variable (whose conditional probability is sought)
- key
the values of 'x_i's parents and 'x_i'
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def
crossValidate(nx: Int = 5): Double
Test the accuracy of the classified results by cross-validation, returning the accuracy.
Test the accuracy of the classified results by cross-validation, returning the accuracy. The "test data" starts at 'testStart' and ends at 'testEnd', the rest of the data is "training data'.
- nx
the number of crosses and cross-validations (defaults to 5x).
- Definition Classes
- Classifier
-
def
crossValidateRand(nx: Int = 5): Double
Test the accuracy of the classified results by cross-validation, returning the accuracy.
Test the accuracy of the classified results by cross-validation, returning the accuracy. The "test data" starts at 'testStart' and ends at 'testEnd', the rest of the data is "training data'.
- nx
the number of crosses and cross-validations (defaults to 5x).
- Definition Classes
- Classifier
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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- protected[java.lang]
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final
def
flaw(method: String, message: String): Unit
Show the flaw by printing the error message.
Show the flaw by printing the error message.
- method
the method where the error occurred
- message
the error message
- Definition Classes
- Error
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
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def
hashCode(): Int
- Definition Classes
- AnyRef → Any
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
jp(x: VectorI): Double
Compute the Joint Probability 'JP' of vector 'x' ('z' concatenate outcome).
Compute the Joint Probability 'JP' of vector 'x' ('z' concatenate outcome). as the product of each of its element's conditional probability.
- x
the vector of variables
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def
logLikelihood(vc: VectoI, vcp1: VectoI, vcp2: VectoI, popX: HMatrix5[Int], k: Int, me: Int = me_default): Double
Compute the Log-Likelihood for the given Bayesian Network structure and data.
Compute the Log-Likelihood for the given Bayesian Network structure and data.
- vc
the value count
- vcp1
the value count for parent 1
- vcp2
the value count for parent 2
- popX
the population counts
- k
the number of classes
- me
the m-estimate value
- Definition Classes
- BayesMetrics
-
val
m: Int
the number of data vectors in training/test-set (# rows)
the number of data vectors in training/test-set (# rows)
- Attributes
- protected
- Definition Classes
- ClassifierInt
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val
md: Double
the training-set size as a Double
the training-set size as a Double
- Attributes
- protected
- Definition Classes
- ClassifierInt
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val
n: Int
the number of features/variables (# columns)
the number of features/variables (# columns)
- Attributes
- protected
- Definition Classes
- ClassifierInt
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val
nd: Double
the feature-set size as a Double
the feature-set size as a Double
- Attributes
- protected
- Definition Classes
- ClassifierInt
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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final
def
notify(): Unit
- Definition Classes
- AnyRef
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
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def
reset(): Unit
Reset or re-initialize the frequency tables and the probability tables.
Reset or re-initialize the frequency tables and the probability tables.
- Definition Classes
- BayesNetwork → Classifier
-
def
shiftToZero(): Unit
Shift the 'x' Matrix so that the minimum value for each column equals zero.
Shift the 'x' Matrix so that the minimum value for each column equals zero.
- Definition Classes
- ClassifierInt
-
def
size: Int
Return the number of data vectors in training/test-set (# rows).
Return the number of data vectors in training/test-set (# rows).
- Definition Classes
- ClassifierInt → Classifier
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
test(itest: VectorI): Double
Test the quality of the training with a test-set and return the fraction of correct classifications.
Test the quality of the training with a test-set and return the fraction of correct classifications.
- itest
indices of the instances considered test data
- Definition Classes
- ClassifierInt → Classifier
-
def
test(xx: MatrixI, yy: VectorI): Double
Test the quality of the training with a test-set and return the fraction of correct classifications.
Test the quality of the training with a test-set and return the fraction of correct classifications.
- xx
the integer-valued test vectors stored as rows of a matrix
- yy
the test classification vector, where 'yy_i = class' for row 'i' of 'xx'
- Definition Classes
- ClassifierInt
-
def
test(testStart: Int, testEnd: Int): Double
Test the quality of the training with a test-set and return the fraction of correct classifications.
Test the quality of the training with a test-set and return the fraction of correct classifications.
- testStart
beginning of test region (inclusive)
- testEnd
end of test region (exclusive)
- Definition Classes
- ClassifierInt → Classifier
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
def
train(testStart: Int, testEnd: Int): Unit
Train the classifier, i.e., ...
Train the classifier, i.e., ...
- testStart
starting index of test region (inclusive) used in cross-validation.
- testEnd
ending index of test region (exclusive) used in cross-validation.
- Definition Classes
- BayesNetwork → Classifier
-
def
train(): Unit
Train the classifier, i.e., calculate statistics and create conditional density 'cd' functions.
Train the classifier, i.e., calculate statistics and create conditional density 'cd' functions. Assumes that conditional densities follow the Normal (Gaussian) distribution.
- Definition Classes
- Classifier
-
def
train(itrain: Array[Int]): Unit
Given a set of data vectors and their classifications, build a classifier.
Given a set of data vectors and their classifications, build a classifier.
- itrain
the indices of the instances considered train data
- Definition Classes
- Classifier
-
def
vc_default: VectorI
Return default values for binary input data (value count 'vc' set to 2).
Return default values for binary input data (value count 'vc' set to 2).
- Definition Classes
- ClassifierInt
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def
vc_fromData: VectorI
Return value counts calculated from the input data.
Return value counts calculated from the input data. May wish to call 'shiftToZero' before calling this method.
- Definition Classes
- ClassifierInt
-
def
vc_fromData2(rg: Range): VectorI
Return value counts calculated from the input data.
Return value counts calculated from the input data. May wish to call 'shiftToZero' before calling this method.
- rg
the range of columns to be considered
- Definition Classes
- ClassifierInt
-
final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
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- @throws( ... )