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README.md


-------- Welcome to the readme.txt of SGPursuit Algorithm. --------

------------------------------------------ General Information ----------------------------------------

This section contains the general information about our code and dataset. This folder contains our proposed algorithm, SGPursuit, which is under review of ICDM-2017.

In this folder, there are three sub-folders:

  1. code: contains our SGPursuit algorithm and the baseline methods used in our paper.
  2. dataset: has 3 datasets that we used in our experiments.
  3. dataProcessing: contains the code and data for preprocessing of the real data.

!!!Important: Before you go, make sure that these 3 folders are in the same parent folder. I assume that your put these three sub-folders into {your/root/path} directory.


-------- How to run our SGPursuit Algorithm? --------

Firstly, go to {your/root/path}/code/SGPursuit/ directory. There are 2 ways to run SGPursuit.

  1. use mvn exec:java command: mvn exec:java -Dexec.mainClass="edu.albany.cs.SGPursuit.TestOnCrimesOfChicago" for Crimes of chicago mvn exec:java -Dexec.mainClass="edu.albany.cs.SGPursuit.TestOnYelp" for Yelp data mvn exec:java -Dexec.mainClass="edu.albany.cs.DenseSubGraph.DenseSubGraphUnitTest" for simulation data mvn exec:java -Dexec.mainClass="edu.albany.cs.DenseSubGraph.MultiClusterSGPursuit.RealdataSetsExperiment" for Real dataset data !!!Important: You should install maven and Java-1.8 before you run this program.

[Datasets]: [Simualtion Dataset Main Folder] data/DenseGraph/DenseSubgraph_APDM/ [Real world Dataset(GraphML files and apdm files) ] data/DenseGraph/Realdata/apdm/

  1. use Intellij IDE: You can use Intellij IDE to import our code as a maven project. After you set up the project, then you can find TestOnCrimesOfChicago.java, TestOnYelp.java, and DenseSubGraphUnitTest.java. Finally, you can run it.

-------- How to run the baseline methods? --------

Baseline methods are FocusCO,GAMer,SODA,AMEN. SODA and AMEN are in code main folder. FocusCO and GAMer are in "{SGPursuit project}/edu/albany/cs/baselines/".

  1. AMEN: go to the folder {your/root/path}/code/AMEN. Make sure you have matlab environment. Then just type the following command to go to maltab environment: >>matlab -nodesktop >>test_amen_on_crimes_of_chicago
  2. SODA: go to {your/root/path}/code/SODA. Make sure you have python and cvxopt (and solvers). >>python soda_crimesOfchicago.py
  3. FocusCO: [Simualtion Dataset Main Folder] /SG-Pursuit/data/DenseGraph/DenseSubgraph_APDM/ [Sub foldors] 1)VaryingNumOfAttributes 2)VaryingNumOfClusters 3)VaryingClusterSizes
    Requirements: 1. A recent version of Matlab 2.Java 6+ There are two programs in this baseline method. The first is a matlab script which learns a distance metric and reweighs the input graph. The second is a java program which extracts communities & outliers from the reweighted graph. We use a matlab proxy tool to call matlab code from the java project.

To run FocusCO use maven: "mvn exec:java -Dexec.mainClass="edu.albany.cs.baselines.FocusCO.FocusCOMatlab.TestFocusCO.focusCOTest1VaryNumOfAtt" this expeiment function coressponding to the Figure 4 in our paper.(or you can test other experiment function in same class: focusCOTest1VaryNumOfAtt(),focusCOTest2VaryNumOfCluster(), focusCOTest3VaryClusterSize(). Note*: you can download the original code from github: https://github.com/phanein/focused-clustering.

  1. GAMer: This method provided by the authors in page: "http://dme.rwth-aachen.de/en/gamer". They provided a executable jar file. You can find our test code in "edu.albany.cs.baselines.GAMer". 4.1 Simualtion dataset experiment [Simualtion Dataset Main Folder] /SG-Pursuit/data/DenseGraph/DenseSubgraph_APDM/ [Sub foldors] 1)VaryingNumOfAttributes 2)VaryingNumOfClusters 3)VaryingClusterSizes To run GAMer test code use maven: "mvn exec:java -Dexec.mainClass="edu.albany.cs.baselines.GAMer.TestGAMer.test1VaryNumOfAtt" this expeiment resutls coressponding to the Figure 4 in our paper.(or you can test other experiment function in same class: test2VaryNumOfCluster(),test3VaryClusterSize() 4.2 Real dataset experiemnt [Real world Dataset(GraphML files) ] /SG-Pursuit/data/DenseGraph/Realdata/. this expeiment resutls coressponding to the Table 4 in our paper. To run GAMer realdata test code use maven: "mvn exec:java -Dexec.mainClass="edu.albany.cs.baselines.GAMer.TestGAMerRealDataset.testRealdatasets"

--------- Data processing ---------

In case that you are interested in our data preprocessing. The folder dataProcessing contains the raw data and the pre-processing code. The pre-processing code is not documented very well. However, you can email me (bzhou6@albany.edu / aalimu@albany.edu) if you have any questions.

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