UnBBayes Plugin Framework

02/07/201002/07/2010

Contact: Shou Matsumoto (cardialfly@[yahoo|gmail].com)

11

UnBBayesUnBBayes –– PluginPlugin

Feature OverviewFeature Overview

~ ~ Usage and development ofUsage and development of pluginsplugins forfor UnBBayesUnBBayes ~~

Project page: http://sourceforge.net/projects/unbbayes/

22

ContentsContents

��ConceptsConcepts

��Features & BenefitsFeatures & Benefits

��Applications Applications

��Sample Sample Plugins Plugins (you may skip this section)(you may skip this section)

��SpecificationSpecification

��Extension PointsExtension Points’’ Spec. Spec. (you may skip this section)(you may skip this section)

��AvailabilityAvailability

Source: <http://sourceforge.net/projects/unbbayes/>33

What isWhat is UnBBayesUnBBayes??

�� UnBBayesUnBBayes is a probabilistic network is a probabilistic network

framework written in Java. It has both a framework written in Java. It has both a

GUI and an API with inference, GUI and an API with inference,

sampling, learning and evaluation. It sampling, learning and evaluation. It

supports BN, ID, MSBN, OOBN, HBN, supports BN, ID, MSBN, OOBN, HBN,

MEBN/PRMEBN/PR--OWL, structure, parameter OWL, structure, parameter

and incremental learning.and incremental learning.

Co

nce

pts

Co

nce

pts

A plugin descriptor is the main and minimal content of a plugin44

What is aWhat is a pluginplugin??

�� AA pluginplugin consists of a computer program that consists of a computer program that interacts with a host application to provide a interacts with a host application to provide a certain, usually very specific, function "on certain, usually very specific, function "on demand“ [demand“ [wikipediawikipedia].].

�� AnAn UnBBayes’ pluginUnBBayes’ plugin can be a folder, a ZIP or can be a folder, a ZIP or a JAR file located in “a JAR file located in “pluginsplugins” folder.” folder.

�� Content of an ordinalContent of an ordinal UnBBayes’ pluginUnBBayes’ plugin::

–– PluginPlugin descriptor (XML file)descriptor (XML file)

–– Classes (a program)Classes (a program)

–– Resources (e.g. icons, message files...)Resources (e.g. icons, message files...)

Co

nce

pts

Co

nce

pts

Modularization/componentization = organized system55

General Benefits ofGeneral Benefits of PluginsPlugins

�� To enable thirdTo enable third--party developers to create party developers to create

capabilities to extend an applicationcapabilities to extend an application

�� To support features yet unforeseenTo support features yet unforeseen

�� To reduce the size of each applicationTo reduce the size of each application

�� To separate source code from an application To separate source code from an application

because of incompatible software licenses.because of incompatible software licenses.

�� Modularization/Componentization of the Modularization/Componentization of the

softwaresoftware

–– Interfaces are modeled as Interfaces are modeled as extension pointsextension points..

Fea

tures

F

eatu

res

&

& B

enef

its

Ben

efit

s

66

General FeaturesGeneral Features

�� PluginPlugin dependencydependency

�� Plugin’sPlugin’s version controlversion control

�� PluginsPlugins forfor PluginsPlugins

�� HotplugHotplug

�� Flexible I/O handlerFlexible I/O handler

Fea

tures

F

eatu

res

&

& B

enef

its

Ben

efit

s

A dependency is declared in plugin descriptor (XML)77

PluginPlugin dependencydependency

�� We can develop newWe can develop new pluginsplugins reusing a prereusing a pre--existing one.existing one.

–– AA pluginplugin may have some dependency to a premay have some dependency to a pre--existing one.existing one.

�� Pros: Pros:

–– Fast developmentFast development

–– Less redundancy Less redundancy –– smaller programssmaller programs

�� Contras.Contras.

–– Dependency hellDependency hell

•• If myIf my pluginplugin depends on “A” and “A” depends on “B” and depends on “A” and “A” depends on “B” and so on, myso on, my pluginplugin will not work until the user obtains all will not work until the user obtains all the dependencies.the dependencies.

Fea

tures

F

eatu

res

&

& B

enef

its

Ben

efit

s

There is no need to overwrite files in order to overwrite features anymore.88

Plugin’sPlugin’s version controlversion control

�� The application can manage several The application can manage several

different versions of adifferent versions of a pluginplugin..

–– E.g. version 1.0.0, version 5.2.1...E.g. version 1.0.0, version 5.2.1...

�� Usually, the newest version is loaded by Usually, the newest version is loaded by

the application.the application.

–– Except if a givenExcept if a given pluginplugin claims dependency claims dependency

to a unique version.to a unique version.

Fea

tures

& B

enef

its

Fea

tures

& B

enef

its

An extension point is declared in plugin descriptor (XML)99

PluginsPlugins forfor PluginsPlugins

�� ...This application, under the academic ...This application, under the academic world, shall have a new birth of freedom world, shall have a new birth of freedom ---- and that government of theand that government of the pluginplugin, by , by thethe pluginplugin, for the, for the pluginplugin, shall not perish , shall not perish from the earth.from the earth.

–– If aIf a pluginplugin has an has an extension pointextension point, we can , we can add aadd a pluginplugin for it.for it.

–– In another words, we can haveIn another words, we can have pluginspluginsadding functionalities to anotheradding functionalities to another pluginplugin..F

eatu

res

F

eatu

res

&

& B

enef

its

Ben

efit

s

1010

HotplugHotplug

�� Usually, there is no need to restart the Usually, there is no need to restart the

application in order to enable aapplication in order to enable a pluginplugin..

–– Obviously, there are some exceptions.Obviously, there are some exceptions.

�� UnBBayesUnBBayes has a menu item to “reload”has a menu item to “reload”

pluginsplugins at runtime.at runtime.

Fea

tures

F

eatu

res

&

& B

enef

its

Ben

efit

s

File handling is flexible1111

Flexible I/O handlerFlexible I/O handler

�� If more than one moduleIf more than one module pluginplugin can handle a file, can handle a file,

ask for the user.ask for the user.

Fea

tures

F

eatu

res

&

& B

enef

its

Ben

efit

s

�� If more than one If more than one I/O I/O pluginplugin can handle a file, ask can handle a file, ask

for the user.for the user.

1212

ApplicationsApplications

�� Development of a full new functionalityDevelopment of a full new functionality

–– Projects / ModulesProjects / Modules

–– New formalismsNew formalisms

�� Development of a new file format.Development of a new file format.

�� Modeling new node types and/or CPDModeling new node types and/or CPD

�� Usage of new Inference AlgorithmsUsage of new Inference Algorithms

�� LocalizationLocalization

–– E.g. Spanish, JapaneseE.g. Spanish, Japanese

Ap

pli

ca

tio

ns

Ap

pli

ca

tio

ns

1313

Summary of Summary of

extension pointsextension points

I/OI/O

InferenceInference

AlgorithmAlgorithm

NewNew

ModulesModules

LocalizationLocalization

New NodesNew Nodes

andand CPDCPD

Split buttonSplit button for for newnew modulesmodules

A tool with 10 functionalities for massive data handling1414

DataminingDatamining Module Module --

UnBMinerUnBMiner

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

A tool that offers an easy interface for finding entries and analisis. Expert Systems.1515

Metaphor Metaphor –– Medical, Medical,

Human IdentificationHuman Identification

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

Generation of sample data sets from a given network.1616

Sampling Sampling -- Likelihood Likelihood

Weighting, Monte Carlo, GibbsWeighting, Monte Carlo, Gibbs

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

We can select another algorithm to compile a network under the core1717

Inference Algorithms Inference Algorithms ––

Likelihood Weighting, GibbsLikelihood Weighting, Gibbs

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

It is possible to add resource files as plugin1818

OOBN Module’s Japanese OOBN Module’s Japanese

LocalizationLocalization

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

Save or load different network file formats1919

I/O I/O –– DNE, XMLBIF, NETDNE, XMLBIF, NETS

am

ple

Plu

gin

sS

am

ple

Plu

gin

s

It is possible to edit a Conditional Probability Distribution using scripts2020

Conditional Probability Conditional Probability

Distribution Using ScriptsDistribution Using Scripts

Sa

mp

le P

lug

ins

Sa

mp

le P

lug

ins

Everything is configured using plugin descriptors (XML)2121

SpecificationSpecification

�� UnBBayesUnBBayes uses Javauses Java PluginPlugin Framework (JPF) Framework (JPF) forfor pluginplugin support.support.

–– JPF is a openJPF is a open--source, LGPLsource, LGPL licencedlicenced plugplug--in in mechanism adapted from Eclipse's plugmechanism adapted from Eclipse's plug--in in mechanism.mechanism.

�� The “core” ofThe “core” of UnBBayesUnBBayes is the BN module.is the BN module.

–– All other modules/functionalities are beingAll other modules/functionalities are beingrefactoredrefactored asas pluginsplugins..

�� The core has itsThe core has its pluginplugin descriptor to declare descriptor to declare extension points (extension points (unbbayesunbbayes.core)..core).

Sp

ecif

ica

tio

nS

pec

ific

ati

on

2222

Folder StructureFolder StructureS

pec

ific

ati

on

Sp

ecif

ica

tio

n

Place the Place the

plugins hereplugins here

These These areare

default pluginsdefault plugins

thatthat comecome

with thewith the corecore

These XML definitions follow the JPF specification.2323

ModulesModules

�� UnBBayes'UnBBayes' modules are basically swing modules are basically swing

internal frames.internal frames.

Exte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp

ec.

<extension-point id="Module">



<parameter-def id="class"/>



<parameter-def id="builder" multiplicity="none-or-one" />

<parameter-def id="name"/>

<parameter-def id="description" multiplicity="none-or-one" />

<parameter-def id="icon" multiplicity="none-or-one" />



<parameter-def id="category" multiplicity="none-or-one" />

</extension-point>

This is how UnBMiner's plugin descriptor (plugin.xml) looks like2424

Sample ModuleSample Module -- UnBMinerUnBMinerE

xte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp

ec. <?xml version="1.0" ?>

<!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 1.0" "http://jpf.sourceforge.net/plugin_1_0.dtd">

<plugin id="unbbayes.datamining" version="0.0.1">

<requires>

<import plugin-id="unbbayes.util.extension.core"/>

</requires>

<runtime>

<library id="unbminer" path="classes/" type="code">

<export prefix="*" />

</library>

<library type="resources" path="icons/" id="icons" />

</runtime>

<extension plugin-id="unbbayes.util.extension.core" point-id="Module" id="unbminer">

<parameter id="class" value="unbbayes.datamining.gui.extension.UnBMinerJPFModule" />

<parameter id="name" value="Data Mining Project" />

<parameter id="builder" value="unbbayes.datamining.gui.extension.UnBMinerJPFModule" />

<parameter id="description" value="UnBBayes Dataminer - UnBMiner" />

<parameter id="icon" value="mining.png" />

<parameter id="category" value="tool" />

</extension>

</plugin>

Inference Algorithms are usually started when we "compile" a BN2525

Inference AlgorithmInference Algorithm

�� This is basically a panel (for options) This is basically a panel (for options)

–– This panel holds an implementation ofThis panel holds an implementation of

unbbayes.util.extension.bn.inference.IInferenceAlgorithm, ,

which runs a which runs a specificspecific inference algorithm.inference algorithm.

Exte

nsi

on

Poin

ts’

Sp

ecE

xte

nsi

on

Poin

ts’

Sp

ec..

<extension-point id="InferenceAlgorithm">




</extension-point>

A single plugin.xml may implement several extension points2626

Sample AlgorithmSample Algorithm -- GibbsGibbsE

xte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp

ec. <?xml version="1.0" ?> <!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 1.0"

"http://jpf.sourceforge.net/plugin_1_0.dtd">

<plugin id="unbbayes.simulation.sampling.GibbsSampling" version="1.0.0">

<requires><import plugin-id="unbbayes.util.extension.core"/><import plugin-

id="unbbayes.simulation.montecarlo.sampling"/></requires>

<runtime>

<library id="gibbs" path="classes/" type="code"><export prefix="*" /></library>

<library type="resources" path="icons/" id="icons" />

</runtime>

<extension plugin-id="unbbayes.util.extension.core" point-id="Module" id="gibbsSampling">

<parameter id="class" value="unbbayes.gui.GibbsSamplingModule" />

<parameter id="name" value="Gibbs Sampling" />

<parameter id="builder" value="unbbayes.gui.GibbsSamplingModule" />

<parameter id="description" value="Sampling using Gibbs" />

<parameter id="icon" value="sampling.png" />

<parameter id="category" value="sampling" />

</extension>

<extension plugin-id="unbbayes.util.extension.core" point-id="InferenceAlgorithm" id="gibbsAlgorithm">

<parameter id="class" value="unbbayes.gui.option.GibbsSamplingOptionPanel" />

</extension>

</plugin>

A single plugin.xml may specify several extension points - a plugin may expect several plugins2727

I/OI/O

�� This is just a combination of This is just a combination of

unbbayesunbbayes..ioio..BaseIO BaseIO and a nameand a name

–– The name is displayed when a conflict occursThe name is displayed when a conflict occurs

Exte

nsi

on

Poin

ts’

Sp

ecE

xte

nsi

on

Poin

ts’

Sp

ec..

<extension-point id="PNIO">



</extension-point>

This is how DNE's plugin descriptor (plugin.xml) looks like2828

Sample I/OSample I/O -- DNEDNEE

xte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp

ec.

<?xml version="1.0" ?>

<!DOCTYPE plugin PUBLIC "-//JPF//Java Plug-in Manifest 1.0"

"http://jpf.sourceforge.net/plugin_1_0.dtd">

<plugin id="unbbayes.io.DneIO" version="1.0.0">

<requires>

<import plugin-id="unbbayes.util.extension.core"/>

</requires>

<extension plugin-id="unbbayes.util.extension.core" point-id="PNIO"

id="DneIO">

<parameter id="class" value="unbbayes.io.DneIO" />

<parameter id="name" value="DNE" />

</extension>

</plugin>

This extension point is a bridge between JPF mechanism and ResourceBundle mechanism2929

Resources Resources -- LocalizationLocalization

�� This is basically a This is basically a

java.util.ListResourceBundle

–– NamingNaming: <: <ClassNameClassName>>__<<LocaleIDLocaleID>>

•• ResourcesResources_es._es.classclass ((SpanishSpanish) )

•• ResourcesResources_pt._pt.class class ((PortuguesePortuguese))

•• ResourcesResources__jaja..class class ((JapaneseJapanese))

Exte

nsi

on

Poin

ts’

Sp

ecE

xte

nsi

on

Poin

ts’

Sp

ec..

<extension-point id="ResourceBundle">


</extension-point>

Unfortunatelly, most of classes load resources statically, so hotplug is only partial.3030

Sample LocalizationSample LocalizationE

xte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp



<plugin id="unbbayes.oobn.resources.ja" version="1.0.0">

<requires><import plugin-id="unbbayes.util.extension.core"/></requires>

<runtime>

<library id="oobnResource_ja" path="classes/" type="code"><export prefix="*" /></library>

</runtime>

<extension plugin-id="unbbayes.util.extension.core" point-id="ResourceBundle" id="oobn_gui_ja">

<parameter id="class" value="unbbayes.gui.oobn.resources.OOBNGuiResource_ja" />

</extension>

<extension plugin-id="unbbayes.util.extension.core" point-id="ResourceBundle" id="oobn_controller_ja">

<parameter id="class" value="unbbayes.controller.oobn.resources.OOBNControllerResources_ja" />

</extension>

<extension plugin-id="unbbayes.util.extension.core" point-id="ResourceBundle" id="oobn_io_ja">

<parameter id="class" value="unbbayes.io.oobn.resources.OOBNIOResources_ja" />

</extension>

<extension plugin-id="unbbayes.util.extension.core" point-id="ResourceBundle" id="oobn_prs_ja">

<parameter id="class" value="unbbayes.prs.oobn.resources.Resources_ja" />

</extension>

</plugin>

Inference algorithms or I/O must be implemented separately to compile/save these nodes3131

New Types of NodesNew Types of Nodes

�� This is a Node and This is a Node and a set of a set of additional information additional information

to display it within GUI.to display it within GUI.

Exte

nsi

on

Poin

ts’

Sp

ecE

xte

nsi

on

Poin

ts’

Sp

ec..

<extension-point id="PluginNode">






<parameter-def id="shapeClass"/>




<parameter-def id="panelBuilder"/>



<parameter-def id="cursor" multiplicity="none-or-one" />

</extension-point>

This is a sample stub.3232

Sample NodesSample NodesE

xte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp



<plugin id="unbbayes.prs.extension.impl.ProbabilisticNodePluginStub" version="1.0.0">

<requires> <import plugin-id="unbbayes.util.extension.core"/> </requires>

<runtime>

<library id="ProbabilisticNodePluginStub" path="classes/" type="code">


</library>

<library type="resources" path="icons/" id="ProbabilisticNodePluginStub_icons" />

</runtime>

<extension plugin-id="unbbayes.util.extension.core" point-id="PluginNode" id="ProbabilisticNodePluginStub">

<parameter id="class" value="unbbayes.prs.extension.impl.ProbabilisticNodePluginStub" />

<parameter id="shapeClass" value="unbbayes.draw.extension.impl.DefaultPluginUShape" />

<parameter id="name" value="Boolean Node For Plugin Test" />

<parameter id="panelBuilder" value= "unbbayes.gui.table.extension.StubPanelBuilder" />

<parameter id="description" value="This is a stub in order to test plugins" />

<parameter id="icon" value="icon_stub.gif" />

<parameter id="cursor" value="cursor_stub.gif" />

</extension>

</plugin>

See the specs of "New Node Type" plugin for details3333

Probability Distribution Probability Distribution

EditorEditor

�� Identical to Identical to ““New Node TypeNew Node Type” ” pluginplugin

–– Difference: these are for nodes Difference: these are for nodes already already

incorporatedincorporated into into UnBBayes’ UnBBayes’ corecore

•• E.g. E.g. unbbayesunbbayes..prsprs..bnbn..ProbabilisticNodeProbabilisticNode

Exte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp

ec.

<extension-point id="ProbabilityFunctionPanel">

<parameter-def id="class"/> 


<parameter-def id="panelBuilder"/> 



</extension-point>

This is the plugin descriptor (plugin.xml) for CPS plugin3434

Sample Probability Sample Probability

Distribution EditorDistribution Editor

Exte

nsi

on

Poin

ts’

Sp

ec.

Exte

nsi

on

Poin

ts’

Sp



<plugin id="edu.gmu.seor.prognos.unbbayesplugin.cps" version="1.0.0">

<requires> <import plugin-id="unbbayes.util.extension.core"/> </requires>

<runtime>

<library id="cps" path="classes/" type="code">


</library>

<library type="resources" path="icons/" id="cps_icons" />

</runtime>

<extension plugin-id="unbbayes.util.extension.core" point-id="ProbabilityFunctionPanel"

id="cps_ProbabilisticNode">

<parameter id="class" value="unbbayes.prs.bn.ProbabilisticNode" />

<parameter id="name" value="Script edition" />

<parameter id="panelBuilder" value=

"edu.gmu.seor.prognos.unbbayesplugin.cps.gui.extension.CPSPanelBuilder" />

<parameter id="description" value="Edit conditional probability function using scripts" />

<parameter id="icon" value="new_script.png" />

</extension>

</plugin>

A release version for UnBBayes w/ plugin support is yet to come3535

AvailabilityAvailability

�� Currently, these extension points and Currently, these extension points and

samplesample pluginsplugins are only available in theare only available in the

sourceforge’ssourceforge’s SVN (trunk).SVN (trunk).

–– By now, there are no releases supportingBy now, there are no releases supporting

pluginsplugins yet.yet.

�� SVN repository URL:SVN repository URL:

–– https://https://unbbayesunbbayes..svnsvn..sourceforgesourceforge.net/.net/svnrootsvnroot

//unbbayesunbbayes/trunk//trunk/UnBBayesUnBBayes

Av

ail

ab

ilit

yA

va

ilab

ilit

y

Although this is already an open source project, plugins makes it easier to customize3636

FinallyFinally

�� PluginsPlugins can enable thirdcan enable third--party developers to party developers to extendextend UnBBayesUnBBayes

–– Develop features yet unforeseenDevelop features yet unforeseen

•• New formalismsNew formalisms

•• CustomizationCustomization

–– Flexible software licenseFlexible software license

•• Separate sources of incompatible licenses.Separate sources of incompatible licenses.

–– Fast developmentFast development

•• PluginPlugin dependency controldependency control

�� PluginsPlugins reduce the size ofreduce the size of UnBBayesUnBBayes

–– Distribution is easier and application is lightDistribution is easier and application is lightWh

at

Wh

at

plu

gin

sp

lug

ins

can

do

fo

r y

ou

can

do

fo

r y

ou

UnBBayes Plugin Framework

Education

Transcript of UnBBayes Plugin Framework