First Commit

First Commit

Author: myhome98304

MCL

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+#!/bin/bash
+
+cd $(dirname $(readlink -f $0))
+
+#help message
+help()
+{
+    echo "MCL - Markov Clustering"
+    echo " "
+    echo "Usage: $0 [INPUT (Graph File)] [OutputPath] [epsilon] [rand_seed]"
+    echo "epsilon			: run until the error is under epsilon"
+	echo "rand_seed			: random seed number"
+}
+
+QUERY="java -jar bin/PS-MCL.jar $1 $2 -hem 0 0 -basic 1 $3"
+		
+echo $QUERY
+echo =====================
+$QUERY

Makefile

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+all: install demo
+
+demo:
+	./do_PS-MCL.sh
+
+install:
+	chmod +x ./*.sh
+	chmod +x PS-MCL R-MCL B-MCL MCL

PS-MCL.sh

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+#!/bin/bash
+
+cd $(dirname $(readlink -f $0))
+
+#help message
+help()
+{
+    echo "PS-MCL - Parallel Shotgun Coarsening Markov Clustering"
+    echo " "
+    echo "Usage: $0 [INPUT (Graph File)] [OutputPath] [CoarseMode] [Coarse Level] [Balance Factor] [MCL Mode] [Number of Thread] [epsilon] [rand_seed] [skip rate]"
+    echo "CoarseMode        : -sc or -hem"
+    echo "Coarse Level      : non-negative Integer"
+    echo "Balance Factor    : non-negative Double"
+    echo "MCL Mode          : -reg or -basic"
+    echo "Number of Thread  : positive Integer"
+	echo "epsilon			: run until the error is under epsilon"
+	echo "rand_seed			: random seed number"
+	echo "skip rate			: skip rate of nodes in shotgun coarsening"
+}
+
+if [ $# -lt 6 ];then
+    echo "Error: Please provide parameters"
+    echo "========================================="
+    help
+    exit 127
+fi
+
+
+
+
+QUERY="java -jar bin/PS-MCL.jar"
+for arg in "$@"; do 
+    QUERY="$QUERY ${arg}"
+done
+
+		
+echo $QUERY
+echo =====================
+$QUERY

README.md

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+################################################################################
+# PS-MCL : Parallel Shotgun Coarsening Markov Clustering.
+#
+# Author: InJae Yu ([email protected]), KAIST
+#		  YongSub Lim([email protected]), KAIST
+#         U Kang ([email protected]), KAIST 
+#
+# Version : 1.0
+# Date : August 17, 2015
+# Main Contact: U Kang
+#
+#
+################################################################################
+
+1. General information
+
+This is an implementation of PS-MCL (Parallel Shotgun Coarsening MCL)
+This also includes implementations for the original MCL, R-MCL and MLR-MCL.
+
+
+2. Minimal Environment
+
+This tool needs
+	(a) Java 1.8 or higher
+
+This software was tested on Ubuntu.
+	
+
+3. How to run PS-MCL
+
+IMPORTANT!
+- Before you use it, please check that the script files are executable. If not,
+you may manually modify the permission of scripts or you may type "make install"
+to do the same work.
+- You may type "make demo" if you want to just try PS-MCL.
+
+
+To run MCL, you need to do the followings:
+- prepare an undirected edge file.
+  The format should be "node_index DELIMITER node_index". 
+  
+
+PS-MCL.jar is located in /bin
+
+Command : ./PS-MCL [INPUT (Graph File Path)] [Output Directory] [CoarseMode] [Coarse Level] [Balance Factor] [MCL Mode] [Number of Thread] [epsilon] [rand_seed]
+
+You should provide following arguments.
+
+	(a) INPUT 	: path of input data
+	(b) Output Directory : directory for output data
+	(c) CoarseMode		: -sc or -hem. "-sc" for Shotgun Coarsening which is proposed method, and "-hem" for Heavy Edge Matching.
+	(d) Coarse Level		: The number of coarsening step. Should be an non-negative integer.
+	(e) Balance Factor		: Balance factor for B-MCL. If this is 0, R-MCL will be executed.
+	(f) MCL Mode		: -basic or -reg. Run MCL with "-basic". Run R,B-MCL with "-reg"(B-MCL is specialized by R-MCL with balance factor larger than 0).
+	(g) Number of Thread		: the number of threads to be used
+	(h) epsilon		: run until the error is under epsilon
+	(i) rand_seed		: random seed number
+	(i) skip rate		: Float number from 0~1 when using "-sc" mode. 
+
+
+
+4. Demo Run
+Type "make" in the source folder. The MCL will start a demo run B-MCL for "dataset/ETC/Yeast-2/Yeast-2" with 3 coarsening step.
+File "Yeast-2" contains 7,049 edges between 2,223 nodes. If the application runs well, you will see the cluster size distribution as
+"size of cluster \t # of clusters \t # of nodes contained in such size of cluster" and detailed result in the console.
+
+
+5. Output Explanation
+The output will consist of following files.
+"Data, MCL Mode, Coarsen Info, Thread Info".result
+"Data, MCL Mode, Coarsen Info, Thread Info".assign
+"Data, MCL Mode, Coarsen Info, Thread Info".dist
+
+ex) ./PS-MCL dataset/SUNY/DIP/DIP ./ -sc 4 1.5 -reg 4 1 
+makes 3 outputs
+==================================================================================================================================================
+DIP_B-MCL-1.5_SC_Level-5_numT-4_conv-norm.result		: records time, NCut, # of clusters
+
+coarsen_mode   coarseLevel    b_Factor       mcl_mode       time           NCut           AVG_Ncut       ClusterNum     #ofThread      ofIteration    
+SC             5              1.500000       Regularized    5.109000       647.902975     0.398710       1625           4              50      
+==================================================================================================================================================
+DIP_B-MCL-1.5_SC_Level-5_numT-4_conv-norm.assign 	: cluster assignment of each node
+
+cluster        index          
+0              128            
+0              144            
+0              129            
+==================================================================================================================================================
+DIP_B-MCL-1.5_SC_Level-5_numT-4_conv-norm.dist		: distribution of size of clusters
+
+size           #of Clusters   #of Nodes      
+1              6              6              
+2              17             34             
+3              32             96             
+4              27             108            
+5              51             255            
+6              50             300           
+==================================================================================================================================================
+.result and .dist files' contents will be also printed in console.
+
+
+
+6. Scripts for existing MCL based methods
+
+To use MCL, R-MCL, B-MCL, use provided scripts MCL, R-MCL(Multi-Level), and B-MCL(Multi-Level).
+MCL : ./MCL [INPUT (Graph File Path)] [Output Directory] [epsilon]
+R-MCL : ./R-MCL [INPUT (Graph File Path)] [Output Directory] [Coarse Level] [epsilon]
+B-MCL : ./B-MCL [INPUT (Graph File Path)] [Output Directory] [Coarse Level] [Balance Factor] [epsilon]
+
+
+7. Rebuilding source codes
+
+MCL distribution includes the source code. You can modify the code and rebuild
+the code. The source codes are in 'src' directory.
+Since the binary file PS-MCL.jar already exists in 'bin' directory, normally you
+don't need to build the code again. Thus, this is the instruction when you 
+modify the source code and build it.
+To build the source code, use the script 'compile_PS-MCL.sh'. When you
+execute the script, it automatically compile the source codes in 'src' and make
+a jar file PS-MCL.jar in 'bin' directory. 

bin/MCL.jar

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+cd $(dirname $(readlink -f $0))
+
+echo compiling java sources...
+rm -rf class
+mkdir class
+javac -d class $(find ./src -name *.java)
+
+echo make jar archive...
+cd class
+echo Main-Class: mcl.MCL > manifest.mf
+jar cmvf manifest.mf PS-MCL.jar ./
+rm ../bin/PS-MCL.jar
+mv PS-MCL.jar ../bin/ 
+cd ..
+rm -rf class
+
+echo done.