MBEA: Maximal Biclique Enumeration Algorithm

C++ Implementation of the algorithm presented in the paper:

On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types. Y Zhang et al. BMC Bioinformatics 2014 15:110

Usage Instructions

Default usage:

    ./MBEA location/of/graph_file.txt algorithm

• algorithm: either standard for MBEA or improved for iMBEA.

• graph_file.txt is the 0-1 biadjacency matrix of a bipartite graph, where the rows index the left vertex partition and the columns index the right partition. Example: the matrix

0 1
1 1
1 0

encodes the adjacency relations 1->5, 2->4, 2->5, 3->4, where the left vertices have labels {1,2,3} and the right vertices have labels {4,5}.

NOTE: elements must be space separated, one and only one newline should be at the end of the file.

The output to stderr employs this vertex labelling when describing the maximal bicliques.

Build Instructions

Tested on Mac OSX 10.12.2 with clang-802.0.41 and gcc 6.3.0.

Make sure you have CMake 3.6 or higher installed. From the main MBEA directory:

• mdkdir cmake-build-debug; cd cmake-build-debug
• ccmake .. Configure your build options. If you're happy with default, simply do cmake ...
• make After your build completes, move the MBEA executable to wherever is most convenient to you.