revise the way of computing probability

.classpath

@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="src" output="tests/bin-test" path="tests/src-test"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
+		<attributes>
+			<attribute name="module" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.apache.ivyde.eclipse.cpcontainer.IVYDE_CONTAINER/?project=SLPNMiner&amp;ivyXmlPath=ivy.xml&amp;confs=*&amp;ivySettingsPath=ivysettings.xml&amp;loadSettingsOnDemand=false&amp;ivyUserDir=&amp;propertyFiles="/>
+	<classpathentry kind="lib" path="eclipse-collections-9.2.0.jar"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.github/workflows/ant.yml

@@ -0,0 +1,46 @@
+# This workflow will build a Java project with Ant
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-ant
+
+name: Java CI
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+    - name: Set up JDK 11
+      uses: actions/setup-java@v3
+      with:
+        java-version: '11'
+        distribution: 'temurin'
+    - name: Build with Ant
+      run: ant -noinput -buildfile build.xml buildHudson
+      env:
+        bytecode_format: ${{ vars.BYTECODE_FORMAT }}
+        major_minor: ${{ vars.MAJOR_MINOR }}
+    - name: Upload build result
+      uses: actions/upload-artifact@v3
+      with:
+        name: release
+        path: latestrelease/
+    - name: Commit files
+      run: |
+        git config --local user.email "41898282+github-actions[bot]@users.noreply.github.com"
+        git config --local user.name "github-actions[bot]"
+        git add latestrelease/
+        git commit -m "Add changes"
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: ${{ github.ref }}

.gitignore

@@ -0,0 +1,3 @@
+/bin/
+/tests/
+/.idea/

.project

@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>SLPNMiner</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.apache.ivyde.eclipse.ivynature</nature>
+	</natures>
+</projectDescription>

NewPackageIvy.iml

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="EclipseModuleManager">
+    <conelement value="org.apache.ivyde.eclipse.cpcontainer.IVYDE_CONTAINER/?project=NewPackageIvy&amp;ivyXmlPath=ivy.xml&amp;confs=*&amp;ivySettingsPath=ivysettings.xml&amp;loadSettingsOnDemand=false&amp;ivyUserDir=&amp;propertyFiles=" />
+    <src_description expected_position="0">
+      <src_folder value="file://$MODULE_DIR$/src" expected_position="0" />
+      <src_folder value="file://$MODULE_DIR$/tests/src-test" expected_position="1" />
+    </src_description>
+  </component>
+  <component name="NewModuleRootManager">
+    <output url="file://$MODULE_DIR$/bin" />
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/tests/src-test" isTestSource="false" />
+    </content>
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="library" name="org.apache.ivyde.eclipse.cpcontainer.IVYDE_CONTAINER/?project=NewPackageIvy&amp;ivyXmlPath=ivy.xml&amp;confs=*&amp;ivySettingsPath=ivysettings.xml&amp;loadSettingsOnDemand=false&amp;ivyUserDir=&amp;propertyFiles=" level="application" />
+  </component>
+</module>

ProM Package Manager (SLPNMiner).launch

@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+    <booleanAttribute key="org.eclipse.debug.core.ATTR_FORCE_SYSTEM_CONSOLE_ENCODING" value="false"/>
+    <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+        <listEntry value="/SLPNMiner"/>
+    </listAttribute>
+    <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+        <listEntry value="4"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+    <listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+        <listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
+        <listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
+    <listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+        <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER&quot; javaProject=&quot;SLPNMiner&quot; path=&quot;1&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
+        <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry id=&quot;org.eclipse.jdt.launching.classpathentry.defaultClasspath&quot;&gt;&#13;&#10;&lt;memento exportedEntriesOnly=&quot;false&quot; project=&quot;SLPNMiner&quot;/&gt;&#13;&#10;&lt;/runtimeClasspathEntry&gt;&#13;&#10;"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+    <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.processmining.contexts.uitopia.packagemanager.PMFrame"/>
+    <stringAttribute key="org.eclipse.jdt.launching.MODULE_NAME" value="SLPNMiner"/>
+    <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="SLPNMiner"/>
+    <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-ea -Xmx1G -Djava.library.path=."/>
+    <stringAttribute key="yk-options" value="&#13;&#10;additional-options=&#13;&#10;snapshots-dir=&#13;&#10;"/>
+</launchConfiguration>

ProM with UITopia (SLPNMiner).launch

@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+    <booleanAttribute key="org.eclipse.debug.core.ATTR_FORCE_SYSTEM_CONSOLE_ENCODING" value="false"/>
+    <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+        <listEntry value="/SLPNMiner"/>
+    </listAttribute>
+    <listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+        <listEntry value="4"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+    <listAttribute key="org.eclipse.debug.ui.favoriteGroups">
+        <listEntry value="org.eclipse.debug.ui.launchGroup.debug"/>
+        <listEntry value="org.eclipse.debug.ui.launchGroup.run"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_ATTR_USE_ARGFILE" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_SHOW_CODEDETAILS_IN_EXCEPTION_MESSAGES" value="true"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_CLASSPATH_ONLY_JAR" value="false"/>
+    <booleanAttribute key="org.eclipse.jdt.launching.ATTR_USE_START_ON_FIRST_THREAD" value="true"/>
+    <listAttribute key="org.eclipse.jdt.launching.CLASSPATH">
+        <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry containerPath=&quot;org.eclipse.jdt.launching.JRE_CONTAINER&quot; javaProject=&quot;SLPNMiner&quot; path=&quot;1&quot; type=&quot;4&quot;/&gt;&#13;&#10;"/>
+        <listEntry value="&lt;?xml version=&quot;1.0&quot; encoding=&quot;UTF-8&quot; standalone=&quot;no&quot;?&gt;&#13;&#10;&lt;runtimeClasspathEntry id=&quot;org.eclipse.jdt.launching.classpathentry.defaultClasspath&quot;&gt;&#13;&#10;&lt;memento exportedEntriesOnly=&quot;false&quot; project=&quot;SLPNMiner&quot;/&gt;&#13;&#10;&lt;/runtimeClasspathEntry&gt;&#13;&#10;"/>
+    </listAttribute>
+    <booleanAttribute key="org.eclipse.jdt.launching.DEFAULT_CLASSPATH" value="false"/>
+    <stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.processmining.contexts.uitopia.UI"/>
+    <stringAttribute key="org.eclipse.jdt.launching.MODULE_NAME" value="SLPNMiner"/>
+    <stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="SLPNMiner"/>
+    <stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-Djava.library.path=. -Djava.util.Arrays.useLegacyMergeSort=true -Djava.system.class.loader=org.processmining.framework.util.ProMClassLoader&#10;-Xms12288M -Xmx24576M"/>
+    <stringAttribute key="yk-options" value="&#13;&#10;additional-options=&#13;&#10;snapshots-dir=&#13;&#10;"/>
+</launchConfiguration>

ProM.ini

@@ -0,0 +1,47 @@
+# This file contains information about this ProM release
+# it points ProM to the right packages and keeps version
+# information
+#
+# Folders should be separated using "/" (forward slash). 
+# This will be replaced with File.Separator().
+#
+# Specifies the ProM release version
+PROM_VERSION = NightlyBuild
+#
+# Specifies which package should be installed
+RELEASE_PACKAGE = RunnerUpPackages
+#
+# Specifies the URL to the default package repository
+# (default is "http://prom.win.tue.nl/ProM/packages/packages.xml")
+PACKAGE_URL = http://www.promtools.org/prom6/packages/packages.xml
+#
+# Specifies whether ProM is Verbose 
+# (possible: "ALL" / "ERROR" / "NONE", defaults to "ALL")
+VERBOSE = ALL
+#
+# The library folder is relative to the prom installation
+# folder (default is "lib")
+LIB_FOLDER = lib
+#
+# The images folder is relative to the prom library
+# folder (default is "=images")
+IMAGES_FOLDER = images
+#
+# The macro folder is relative to the prom library
+# folder (default is "macros")
+MACRO_FOLDER = macros
+#
+# The prom user folder is NOT relative to the 
+# prom installation folder. The (default is empty, in
+# which case the OS handles the location)
+PROM_USER_FOLDER =
+#
+# The package folder is relative to the 
+# prom user folder. The (default is "packages")
+PACKAGE_FOLDER = packages
+#
+# The workspace folder is relative to the 
+# prom user folder. The (default is "workspace")
+WORKSPACE_FOLDER = workspace
+
+

ReadMe.md

@@ -0,0 +1,40 @@
+# SLPNMiner
+
+SLPNMiner is a ProM package for the discovery of Stochastic Labelled Petri net, which provides plugin-ins for stochastic process discovery. The input are an event log and a Petri net model, and the output is a stochastic labelled petri net. The two current implemented plugins adopt the techniques introduced in the following to assist weight estimation. 
+
+* Entropic relevance:
+[Hanan Alkhammash, Artem Polyvyanyy, Alistair Moffat, Luciano García-Bañuelos: Entropic relevance: A mechanism for measuring stochastic process models discovered from event data. Inf. Syst. 107: 101922 (2022)](https://www.sciencedirect.com/science/article/pii/S0306437921001277)
+
+* Unit Earth Mover Stochastic Conformance:
+[Sander J. J. Leemans, Wil M. P. van der Aalst, Tobias Brockhoff, Artem Polyvyanyy: Stochastic process mining: Earth movers' stochastic conformance. Inf. Syst. 102: 101724 (2021)](https://www.sciencedirect.com/science/article/pii/S0306437921001277)
+
+## Installation
+*  If you have not yet installed or run ProM6 before, follow the installation tutorial: https://promtools.org/prom-6-getting-started/installation/
+
+* Although the majority of ProM developers use jdk 8, I have to use jdk 17 for this project, so that some third-party libraries (requires jdk 11+) can run. Therefore, **jdk 8 is not going to work** for this project*. The following VM argument should be added to make sure ProM GUI can launch with jdk 17: 
+    ```python 
+    -Djava.system.class.loader=org.processmining.framework.util.ProMClassLoader     
+    ```
+   <img src="https://github.com/promworkbench/SLPNMiner/blob/main/img/VM_parameter.jpg" style="width:600px; height:250px"/>
+
+## Usage
+*  After starting ProM plugin, import the event log and a Petri net model to the GUI.
+
+   <img src="https://github.com/promworkbench/SLPNMiner/blob/main/img/step1.jpg" style="width:600px; height:220px"/>
+
+*  Then, select the plugin-in *Discover SLPN with uEMSC* or *Discover SLPN with Enropic Relevance*.
+
+   <img src="https://github.com/promworkbench/SLPNMiner/blob/main/img/step2.jpg" style="width:600px; height:220px"/>
+
+* The output is a SLPN, which shows the probability value for each transition.
+   <img src="https://github.com/promworkbench/SLPNMiner/blob/main/img/step3.jpg" style="width:470px; height:250px"/>
+
+## Contributing
+
+Pull requests are welcome. For major changes, please open an issue first
+to discuss what you would like to change.
+
+Please make sure to update tests as appropriate.
+
+## License
+L-GPL (https://www.gnu.org/licenses/lgpl-3.0.en.html)