Example Usage:

>>java findMotifs network.txt bicliques.txt 1 12

finds all 6x6 bicliques in network given by slNetwork.txt, writes each biclique to bicliques.txt, one per line. The network should be given in edge-list format, specifying one edge as a pair of tab-delimited vertices per line.

>>java findMotifs network.txt cliques.txt 0 6

finds all 6-cliques in network given by slNetwork.txt, writes each clique to cliques.txt, one per line.

>>java getConnectedComponents network.txt bicliques.txt bicliqueComponents 10

finds the largest connected components of the subgraph induced by nodes in bicliques.txt, writes (at most) the 10 largest components to bicliqueComponents_1.txt, bicliqueComponents_2.txt, ..., bicliqueComponents_10.txt

>>java partitionDefectiveBiclique network.txt bicliqueComponents_1.txt theBigBiclique

finds a good partition of the biclique given in bicliqueComponents_1.txt into two sets of nodes: s1 and s2; writes s1 to theBigBiclique_1.txt, s2 to theBigBiclique_2.txt.

>>java drawClique network.txt cliqueComponents_1.txt theBigCliqueImage

generates a Pajek file (named theBigCliqueImage.net) from subgraph induced by nodes in clique_Components_1.txt.

>>java drawBiclique network.txt theBigBiclique_1.txt theBigBiclique_2.txt theBigBicliqueImage

generates a Pajek file (named theBigBicliqueImage.net) from subgraph induced by nodes in biclique given by theBigBiclique_1.txt and theBigBiclique_2.txt.

>>java enumerateCliques network.txt 8

executes findMotifs, getConnectedComponents, and drawClique in succession, using the network filename to name the output files.

>>java enumerateBicliques network.txt 12

executes findMotifs, getConnectedComponents, partitionDefectiveBiclique, and drawBiclique in succession, using the network filename to name the output files.


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findMotifs
enumerates motifs in a network

arguments:
networkFile (contains network in edge list format, tab delimited, one edge per line)
outputFile
motifType: 0 for clique, 1 for biclique
motifSize (n)

output: enumerates all motifs of given size (n-cliques or n/2 x n/2 bicliques) writes them one per line to outputFile (for bicliques first n/2 nodes on each line give one component of the biclique)

sample usage:

>>java findMotifs slNetwork.txt bicliques.txt 1 12


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getConnectedComponents
finds the largest connected components among a set of motifs

arguments:
networkFile
motifFile
outputFilePrefix
K

output: finds the largest connected components of the subgraph induced by nodes which are part of a motif, writes the nodes in (at most) k largest connected components to files outputFilePrefix_1.txt,outputFilePrefix_2.txt,...,outputFilePrefix_K.txt

sample usage:

>>java getConnectedComponents slNetwork.txt bicliques.txt bicliqueComponents 10


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partitionDefectiveBiclique
partitions a biclique into two sets of nodes

arguments:
networkFile
nodesFile (file listing nodes in the (likely defective) biclique)
outputFilePrefix

output: finds a reasonable partition of the biclique into two sets of nodes: s1 and s2, writes s1 to outputFilePrefix_1.txt, s2 to outputFilePrefix_2.txt


sample usage:

>>java partitionDefectiveBiclique slNetwork.txt bicliqueComponents_1.txt theBigBiclique


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drawClique
makes a Pajek file from a clique

arguments:
networkFile
nodesFile
outputFilePrefix

output: generates a Pajek file (outputFilePrefix.net) of the given clique

sample usage:

>>java drawClique slNetwork.txt cliqueComponents_1.txt theBigCliqueImage


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drawBiclique
makes a Pajek file from a biclique

arguments:
networkFile
nodesFile1 (specifying one part of the biclique)
nodesFile2 (specifying the other part of the biclique)
outputFilePrefix

output: generates a Pajek file (outputFilePrefix.net) of the given biclique

sample usage:

>>java drawBiclique slNetwork.txt theBigBiclique_1.txt theBigBiclique_2.txt  theBigBicliqueImage


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If you have further questions, please contact Konstantin Voevodski at kvodski@bu.edu.