repository·master·Indexed 41 days ago
https://github.com/cwtsleiden/networkanalysisA Java package providing algorithms and data structures for undirected network analysis. It features the RunNetworkClustering tool for community detection using Leiden and Louvain algorithms, and the RunNetworkLayout tool for generating layouts using the gradient descent VOS technique. Version 1.3.0 requires Java 8 or higher.
You can include the networkanalysis package in your Java project using Maven or Gradle. The package requires Java 8 or higher.
### Maven
```xml
<dependency>
<groupId>nl.cwts</groupId>
<artifactId>networkanalysis</artifactId>
<version>1.3.0</version>
</dependency>implementation group: 'nl.cwts', name: 'networkanalysis', version: '1.3.0'To compile the source code, you need a Java Development Kit (JDK) version 8 or higher installed. While having Gradle installed is optional because the repository includes the Gradle Wrapper, you must use the wrapper to build the project.
Output Locations:
.class files: build/classes.jar file: build/libsjavadoc files: build/docs# On Windows
gradlew build
# On Linux and MacOS
./gradlew buildThis example demonstrates how to take an edge list, identify clusters using the Leiden algorithm, and then generate a VOS layout for those nodes.
network.txt (tab-separated edge list):0 1
1 2
2 0
2 3
3 5
5 4
4 3clusters.txt):java -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkClustering -r 0.2 -o clusters.txt network.txtlayout.txt):java -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkLayout -o layout.txt network.txtjava -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkClustering -r 0.2 -o clusters.txt network.txt
java -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkLayout -o layout.txt network.txtAfter compiling the source code, you can execute the RunNetworkLayout tool using the generated JAR file. Replace <version> with the actual version number found in the build/libs directory.
java -cp build/libs/networkanalysis-<version>.jar nl.cwts.networkanalysis.run.RunNetworkLayoutAfter compiling the source code, you can execute the RunNetworkClustering tool using the generated JAR file. Replace <version> with the actual version number found in the build/libs directory.
java -cp build/libs/networkanalysis-<version>.jar nl.cwts.networkanalysis.run.RunNetworkClusteringOptions for the RunNetworkClustering CLI tool:
-q --quality-function {CPM|Modularity} (default: CPM)
Quality function to be optimized. Either the CPM (constant Potts model) or
the modularity quality function can be used.
-n --normalization {none|AssociationStrength|Fractionalization} (Default: none)
Method for normalizing edge weights in the CPM quality function.
-r --resolution <resolution> (default: 1.0)
Resolution parameter of the quality function.
-m --min.cluster.size <min. cluster size> (default: 1)
Minimum number of nodes per cluster.
-a --algorithm {Leiden|Louvain} (default: Leiden)
Algorithm for optimizing the quality function. Either the Leiden or the
Louvain algorithm can be used.
-s --random-starts <random starts> (default: 1)
Number of random starts of the algorithm.
-i --iterations <iterations> (default: 10)
Number of iterations of the algorithm.
--randomness <randomness> (default: 0.01)
Randomness parameter of the Leiden algorithm.
--seed <seed> (default: random)
Seed of the random number generator.
-w --weighted-edges
Indicates that the edge list file has a third column containing edge
weights.
--sorted-edge-list
Indicates that the edge list file is sorted. The file should be sorted based
on the nodes in the first column, followed by the nodes in the second
column. Each edge should be included in both directions in the file.
--input-clustering <filename> (default: singleton clustering)
Read the initial clustering from the specified file. The file is expected to
contain two tab-separated columns (without a header line), first a column of
nodes and then a column of clusters. Nodes and clusters are both represented
by zero-index integer numbers. If no file is specified, a singleton
clustering (in which each node has its own cluster) is used as the initial
clustering.
-o --output-clustering <filename> (default: standard output)
Write the final clustering to the specified file. If no file is specified,
the standard output is used.Options for the RunNetworkLayout CLI tool:
-q --quality-function {VOS|LinLog} (default: VOS)
Quality function to be optimized. Either the VOS (visualization of
similarities) or the LinLog quality function can be used.
-n --normalization {none|AssociationStrength|Fractionalization} (Default: none)
Method for normalizing edge weights in the VOS quality function.
-a --attraction <attraction> (Default: 2)
Attraction parameter of the VOS quality function.
-r --repulsion <repulsion> (Default: 1)
Repulsion parameter of the VOS quality function.
-s --random-starts <random starts> (default: 1)
Number of random starts of the gradient descent algorithm.
-i --max-iterations <max. iterations> (default: 1000)
Maximum number of iterations of the gradient descent algorithm.
--initial-step-size <initial step size> (default: 1.0)
Initial step size of the gradient descent algorithm.
--min-step-size <min. step size> (default: 0.001)
Minimum step size of the gradient descent algorithm.
--step-size-reduction <step size reduction> (default: 0.75)
Step size reduction of the gradient descent algorithm.
--required-quality-value-improvements <required quality value improvements>
(default: 5)
Required number of quality value improvements of the gradient descent
algorithm.
--seed <seed> (default: random)
Seed of the random number generator.
-w --weighted-edges
Indicates that the edge list file has a third column containing edge
weights.
--sorted-edge-list
Indicates that the edge list file is sorted. The file should be sorted based
on the nodes in the first column, followed by the nodes in the second
column. Each edge should be included in both directions in the file.
--input-layout <filename> (default: random layout)
Read the initial layout from the specified file. The file is expected to
contain three tab-separated columns (without a header line), first a column
of nodes, then a column of x coordinates, and finally a column of
y coordinates. Nodes are represented by zero-index integer numbers. If no
file is specified, a random layout (in which each node is positioned at
random coordinates) is used as the initial layout.
-o --output-layout <filename> (default: standard output)
Write the final layout to the specified file. If no file is specified,
the standard output is used.The RunNetworkLayout command-line tool determines a layout for an undirected network using the gradient descent VOS layout algorithm.
Input Format:
A tab-separated edge list (without a header). Nodes must be represented by zero-indexed integers. Each edge should appear only once unless using --sorted-edge-list.
java -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkLayout [options] <filename>The RunNetworkClustering command-line tool identifies clusters (communities) in an undirected network using either the Leiden or Louvain algorithm.
Input Format:
A tab-separated edge list (without a header). Nodes must be represented by zero-indexed integers. Each edge should appear only once unless using --sorted-edge-list.
java -cp networkanalysis-1.3.0.jar nl.cwts.networkanalysis.run.RunNetworkClustering [options] <filename>