edu.ksu.cis.bnj.bbn.inference.approximate.sampling
Class MCMC

java.lang.Object
  edu.ksu.cis.bnj.bbn.inference.Inference
      edu.ksu.cis.bnj.bbn.inference.ApproximateInference
          edu.ksu.cis.bnj.bbn.inference.approximate.sampling.MCMC

All Implemented Interfaces:

DataGenerator, Optionable

Direct Known Subclasses:

AIS, ChavezMCMC, ForwardSampling, LikelihoodWeighting, LogicSampling, PearlMCMC, SelfImportance

public abstract class MCMC

extends ApproximateInference

implements DataGenerator

Super class for MCMC based approximate inference engine

Author:

Roby Joehanes

Field Summary

protected boolean	abort flag that signals the getMarginals function of subclasses to abort
protected java.util.Timer	abortTimer Timer used to set the abort flag after a given amount of time
static int	defaultMaxIteration
protected boolean	generateSamples
protected java.util.LinkedList	listeners
protected int	maxIteration
static long	NO_TIME_LIMIT
protected static java.lang.String	OPT_GENERATE_DATA
protected static java.lang.String	OPT_MAX_ITERATION
protected static java.lang.String	OPT_RUNNING_TIME_LIMIT
protected static java.lang.String	OPT_USE_MARKOV_BLANKET
protected static MersenneTwisterFast	random
protected long	runningTimeLimit Sets the limit (in milliseconds) for how long the procedure should run
protected Table	tuples
protected boolean	useMarkovBlanketScore

Fields inherited from class edu.ksu.cis.bnj.bbn.inference.ApproximateInference

rmseWriter

Fields inherited from class edu.ksu.cis.bnj.bbn.inference.Inference

graph, inferenceClassName, MAP, MARGINALS, marginalsResult, MPE, OPT_RUN_TYPE, options

Fields inherited from interface edu.ksu.cis.kdd.util.gui.Optionable

OPT_OUTPUT_FILE

Constructor Summary

MCMC()

MCMC(BBNGraph g)

Method Summary

protected void	abort() Sets the abort flag to true, which tells the getMarginals functions to exit at the end of the current iteration.
void	addListener(MCMCListener l)
protected void	cancelAbortTimer() Cancel the abort timer.
void	generateData(boolean d)
Table	generateData(int howmuch) Generate data out of a BBN.
Table	getData()
java.util.Hashtable	getDefaultOptions() TODO: need to read from config file and/or through Settings.java
java.util.Hashtable	getMarkovBlanketScore(BBNNode n, java.util.Hashtable chosen) Get Markov blanket scoring.
int	getMaxIteration()
OptionGUI	getOptionsDialog()
long	getRunningTimeLimit() Gets the Running time limit, which methods can use to abort an inference after a specific amount of time.
boolean	isUseMarkovBlanketScore()
void	removeListener(MCMCListener l)
protected void	sendEvent(MCMCEvent e)
protected void	setAbortTimer() Set a timer to expire in the number of milliseconds specified by runningTimeLimit.
void	setMaxIteration(int maxIteration) Sets the maxIteration.
void	setRunningTimeLimit(long mseconds) Sets the Running time limit, which methods can use to abort an inference after a specific amount of time.
void	setUseMarkovBlanketScore(boolean useMarkovBlanketScore) Sets the useMarkovBlanketScore.

Methods inherited from class edu.ksu.cis.bnj.bbn.inference.ApproximateInference

computeRMSE, getRMSEWriter, setRMSEfile

Methods inherited from class edu.ksu.cis.bnj.bbn.inference.Inference

execute, getCurrentOptions, getGraph, getMAP, getMarginals, getMarginalsResult, getMPE, getName, getOutputFile, getRunType, load, setGraph, setOption, setOptions, setOutputFile, setRunType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface edu.ksu.cis.bnj.bbn.datagen.DataGenerator

getName

Field Detail

OPT_MAX_ITERATION

protected static final java.lang.String OPT_MAX_ITERATION

See Also:

Constant Field Values

OPT_USE_MARKOV_BLANKET

protected static final java.lang.String OPT_USE_MARKOV_BLANKET

See Also:

Constant Field Values

OPT_GENERATE_DATA

protected static final java.lang.String OPT_GENERATE_DATA

See Also:

Constant Field Values

OPT_RUNNING_TIME_LIMIT

protected static final java.lang.String OPT_RUNNING_TIME_LIMIT

See Also:

Constant Field Values

defaultMaxIteration

public static final int defaultMaxIteration

See Also:

Constant Field Values

NO_TIME_LIMIT

public static final long NO_TIME_LIMIT

See Also:

Constant Field Values

random

protected static MersenneTwisterFast random

runningTimeLimit

protected long runningTimeLimit

Sets the limit (in milliseconds) for how long the procedure should run

abort

protected boolean abort

flag that signals the getMarginals function of subclasses to abort

abortTimer

protected java.util.Timer abortTimer

Timer used to set the abort flag after a given amount of time

maxIteration

protected int maxIteration

useMarkovBlanketScore

protected boolean useMarkovBlanketScore

generateSamples

protected boolean generateSamples

tuples

protected Table tuples

listeners

protected java.util.LinkedList listeners

Constructor Detail

MCMC

public MCMC()

MCMC

public MCMC(BBNGraph g)

Parameters:

g -

Method Detail

addListener

public void addListener(MCMCListener l)

sendEvent

protected void sendEvent(MCMCEvent e)

removeListener

public void removeListener(MCMCListener l)

getMarkovBlanketScore

public java.util.Hashtable getMarkovBlanketScore(BBNNode n,
                                                 java.util.Hashtable chosen)

Get Markov blanket scoring.

Parameters:

n - The node we want to have the Markov blanket scored upon

chosen - The chosen values so far

Returns:

Hashtable The table from value -> score

getData

public Table getData()

generateData

public void generateData(boolean d)

generateData

public Table generateData(int howmuch)

Description copied from interface: DataGenerator

Generate data out of a BBN. It uses an inference engine

Specified by:

generateData in interface DataGenerator

Parameters:

howmuch - The number

Returns:

Table

See Also:

DataGenerator.generateData(int)

isUseMarkovBlanketScore

public boolean isUseMarkovBlanketScore()

Returns:

boolean

setUseMarkovBlanketScore

public void setUseMarkovBlanketScore(boolean useMarkovBlanketScore)

Sets the useMarkovBlanketScore.

Parameters:

useMarkovBlanketScore - The useMarkovBlanketScore to set

getMaxIteration

public int getMaxIteration()

Returns:

int

setMaxIteration

public void setMaxIteration(int maxIteration)

Sets the maxIteration.

Parameters:

maxIteration - The maxIteration to set

getDefaultOptions

public java.util.Hashtable getDefaultOptions()

TODO: need to read from config file and/or through Settings.java

Specified by:

getDefaultOptions in interface Optionable

Overrides:

getDefaultOptions in class Inference

See Also:

Optionable.getDefaultOptions()

getOptionsDialog

public OptionGUI getOptionsDialog()

Specified by:

getOptionsDialog in interface Optionable

Overrides:

getOptionsDialog in class Inference

setRunningTimeLimit

public void setRunningTimeLimit(long mseconds)

Sets the Running time limit, which methods can use to abort an inference after a specific amount of time. The procedures do not stop abruptly at the limit; they stop after completing the current iteration

getRunningTimeLimit

public long getRunningTimeLimit()

Gets the Running time limit, which methods can use to abort an inference after a specific amount of time. The procedures do not stop abruptly at the limit; they stop after completing the current iteration

setAbortTimer

protected void setAbortTimer()

Set a timer to expire in the number of milliseconds specified by runningTimeLimit. When the timer expires, it will set the abort flag to true, signaling the getMarginals function to exit before performing all iterations.

cancelAbortTimer

protected void cancelAbortTimer()

Cancel the abort timer. This should be called by subclasses that call setAbortTimer. It is necessary to handle the case where the inference procedure completes all iterations before the timer expires. Currently, not calling this routine will not cause a problem, but later additions may change this.

abort

protected void abort()

Sets the abort flag to true, which tells the getMarginals functions to exit at the end of the current iteration.