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| *.class | ||
| *.swp | ||
| *.swo | ||
| build/ | ||
| build.xml | ||
| manifest.mf | ||
| nbproject/ | ||
| test/ | ||
| src/PublicationClustering.java | ||
| /dist/ | ||
| test_network.ser | ||
| test* | ||
| *.txt |
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| MIT License | ||
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| Copyright (c) 2018 Centre for Science and Technology Studies (CWTS), Leiden University | ||
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| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
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| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
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| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
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| ## Introduction | ||
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| This package provides data structures and algorithms for network analysis in `java`. | ||
| Currently, the focus of the package is restricted to clustering (or community detection) in networks. | ||
| In particular, the package contains an implementation of the [Leiden algorithm](https://arxiv.org/abs/xxx.xxxx) and the [Louvain algorithm](https://arxiv.org/abs/0803.0476). | ||
| Only undirected networks are supported. | ||
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| ## Usage | ||
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| To run the clustering algorithms, the command-line tool `RunNetworkClustering` is provided. | ||
| The latest version of the tool is available as a pre-compiled `jar` file in the GitHub [release](https://github.com/CWTSLeiden/networkanalysis/releases/latest). | ||
| The source code is also available in this repository. | ||
| You can use it to [compile](#compilation) the code yourself. | ||
| The `.jar` file can be executed as follows: | ||
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| ``` | ||
| java -jar RunNetworkClustering.jar | ||
| ``` | ||
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| If no further arguments are provided, the following usage notice will be displayed: | ||
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| ``` | ||
| Usage: RunNetworkClustering [options] <filename> | ||
| Identify clusters (also known as communities) in a network, using either the | ||
| Leiden or the Louvain algorithm. | ||
| The file in <filename> is expected to contain a tab-separated edge list | ||
| (without a header line). Nodes are represented by zero-index integer numbers. | ||
| Only undirected networks are supported. Each edge should be included only once | ||
| in the file. | ||
| Options: | ||
| -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. | ||
| -r --resolution <resolution> (default: 1.0) | ||
| Resolution parameter of the quality function. | ||
| -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. | ||
| ``` | ||
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| To run the clustering algorithms, you need `java 1.8.0` or higher. | ||
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| ### Example | ||
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| The following example illustrates the use of the `RunNetworkClustering` tool. | ||
| Consider this network: | ||
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| ```text | ||
| 0-----1 | ||
| \ / | ||
| \ / | ||
| 2 | ||
| | | ||
| 3 | ||
| / \ | ||
| / \ | ||
| 4-----5 | ||
| ``` | ||
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| The network is encoded as an edge list that is saved in a tab-separated text file: | ||
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| ```text | ||
| 0 1 | ||
| 1 2 | ||
| 2 0 | ||
| 2 3 | ||
| 3 5 | ||
| 5 4 | ||
| 4 3 | ||
| ``` | ||
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| Nodes must be represented by integer numbers starting from 0. | ||
| Assuming that the edge list has been saved in the file `network.txt`, the `RunNetworkClustering` tool can be run as follows: | ||
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| ``` | ||
| java -jar RunNetworkClustering.jar -r 0.2 -o clusters.txt network.txt | ||
| ``` | ||
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| In this case, clusters are identified using the Leiden algorithm based on the CPM quality function with a value of `0.2` for the resolution parameter. | ||
| The resulting clustering is saved in the text file `clusters.txt`: | ||
|
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| ```text | ||
| 0 | ||
| 0 | ||
| 0 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| ``` | ||
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| The file `clusters.txt` shows that two clusters have been identified. | ||
| Cluster 0 includes nodes 0, 1, and 2. | ||
| Cluster 1 includes nodes 3, 4, and 5. | ||
| In the above example, the edges in the file `network.txt` have not been sorted. | ||
| To provide a sorted edge list as input, include the edges in both directions and use the option ``--sorted-edge-list``. | ||
| Furthermore, edge weights can be provided by adding a third column to the file `network.txt` and by using the option ``--weighted-edges``. | ||
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| ## Compilation | ||
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| The source code can be compiled as follows: | ||
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| ``` | ||
| javac -d build src/cwts/networkanalysis/*.java src/cwts/networkanalysis/run/*.java src/cwts/util/*.java | ||
| ``` | ||
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| The compiled `class` files will be output to the directory `build`. | ||
| There are no external dependencies. | ||
| The `main` method is provided in the class `cwts.networkanalysis.run.RunNetworkClustering`. | ||
| After the code has been compiled, the `RunNetworkClustering` tool can be run as follows: | ||
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| ``` | ||
| java -cp build cwts.networkanalysis.run.RunNetworkClustering | ||
| ``` | ||
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| The latest stable version of the code is available from the [`master`](https://github.com/CWTSLeiden/networkanalysis/tree/master) branch on GitHub. | ||
| The most recent code, which may be under development, is available from the [`develop`](https://github.com/CWTSLeiden/networkanalysis/tree/develop) branch. | ||
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| ## Issues | ||
|
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| If you encounter any issues, please report them using the [issue tracker](https://github.com/CWTSLeiden/networkanalysis/issues). | ||
| Before submitting, please examine whether issues have not yet been reported before. | ||
|
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| ## Documentation | ||
|
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| Documentation of the source code is provided in the code in `javadoc` format. | ||
| The documentation is also available in a [compiled format](https://CWTSLeiden.github.io/networkanalysis). | ||
|
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| ## Contribution | ||
|
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| You are welcome to contribute to this package. | ||
| Please follow the typical GitHub workflow: fork from this repository and make a pull request to submit your changes. | ||
| At the moment, we have not yet set up any continuous integration, so please make sure that any proposed pull request compiles and functions correctly. | ||
|
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| ## License | ||
|
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| This package is distributed under the MIT License. | ||
| Please refer to the [`LICENSE`](LICENSE) file for further details. |
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| <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> | ||
| <!-- NewPage --> | ||
| <html lang="en"> | ||
| <head> | ||
| <!-- Generated by javadoc (9-ea) on Fri Oct 19 10:50:05 CEST 2018 --> | ||
| <title>All Classes</title> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> | ||
| <meta name="date" content="2018-10-19"> | ||
| <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style"> | ||
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| <h1 class="bar">All Classes</h1> | ||
| <div class="indexContainer"> | ||
| <ul> | ||
| <li><a href="cwts/util/Arrays.html" title="class in cwts.util" target="classFrame">Arrays</a></li> | ||
| <li><a href="cwts/networkanalysis/Clustering.html" title="class in cwts.networkanalysis" target="classFrame">Clustering</a></li> | ||
| <li><a href="cwts/networkanalysis/ClusteringAlgorithm.html" title="interface in cwts.networkanalysis" target="classFrame"><span class="interfaceName">ClusteringAlgorithm</span></a></li> | ||
| <li><a href="cwts/networkanalysis/ComponentsAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">ComponentsAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/CPMClusteringAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">CPMClusteringAlgorithm</a></li> | ||
| <li><a href="cwts/util/DynamicDoubleArray.html" title="class in cwts.util" target="classFrame">DynamicDoubleArray</a></li> | ||
| <li><a href="cwts/util/DynamicIntArray.html" title="class in cwts.util" target="classFrame">DynamicIntArray</a></li> | ||
| <li><a href="cwts/networkanalysis/FastLocalMovingAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">FastLocalMovingAlgorithm</a></li> | ||
| <li><a href="cwts/util/FastMath.html" title="class in cwts.util" target="classFrame">FastMath</a></li> | ||
| <li><a href="cwts/networkanalysis/IncrementalClusteringAlgorithm.html" title="interface in cwts.networkanalysis" target="classFrame"><span class="interfaceName">IncrementalClusteringAlgorithm</span></a></li> | ||
| <li><a href="cwts/networkanalysis/IncrementalCPMClusteringAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">IncrementalCPMClusteringAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/IterativeCPMClusteringAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">IterativeCPMClusteringAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/LeidenAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">LeidenAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/LocalMergingAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">LocalMergingAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/LouvainAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">LouvainAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/Network.html" title="class in cwts.networkanalysis" target="classFrame">Network</a></li> | ||
| <li><a href="cwts/networkanalysis/QualityClusteringAlgorithm.html" title="interface in cwts.networkanalysis" target="classFrame"><span class="interfaceName">QualityClusteringAlgorithm</span></a></li> | ||
| <li><a href="cwts/networkanalysis/StandardLocalMovingAlgorithm.html" title="class in cwts.networkanalysis" target="classFrame">StandardLocalMovingAlgorithm</a></li> | ||
| </ul> | ||
| </div> | ||
| </body> | ||
| </html> |
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| <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> | ||
| <!-- NewPage --> | ||
| <html lang="en"> | ||
| <head> | ||
| <!-- Generated by javadoc (9-ea) on Fri Oct 19 10:50:05 CEST 2018 --> | ||
| <title>All Classes</title> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> | ||
| <meta name="date" content="2018-10-19"> | ||
| <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style"> | ||
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| </head> | ||
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| <h1 class="bar">All Classes</h1> | ||
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| <li><a href="cwts/networkanalysis/Clustering.html" title="class in cwts.networkanalysis">Clustering</a></li> | ||
| <li><a href="cwts/networkanalysis/ClusteringAlgorithm.html" title="interface in cwts.networkanalysis"><span class="interfaceName">ClusteringAlgorithm</span></a></li> | ||
| <li><a href="cwts/networkanalysis/ComponentsAlgorithm.html" title="class in cwts.networkanalysis">ComponentsAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/CPMClusteringAlgorithm.html" title="class in cwts.networkanalysis">CPMClusteringAlgorithm</a></li> | ||
| <li><a href="cwts/util/DynamicDoubleArray.html" title="class in cwts.util">DynamicDoubleArray</a></li> | ||
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| <li><a href="cwts/networkanalysis/IncrementalCPMClusteringAlgorithm.html" title="class in cwts.networkanalysis">IncrementalCPMClusteringAlgorithm</a></li> | ||
| <li><a href="cwts/networkanalysis/IterativeCPMClusteringAlgorithm.html" title="class in cwts.networkanalysis">IterativeCPMClusteringAlgorithm</a></li> | ||
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| <li><a href="cwts/networkanalysis/StandardLocalMovingAlgorithm.html" title="class in cwts.networkanalysis">StandardLocalMovingAlgorithm</a></li> | ||
| </ul> | ||
| </div> | ||
| </body> | ||
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