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Finding Network Motifs Using MCMC Sampling
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motifMCMC
motifSRW
LICENSE
README.md
check_undirected.py
make_connected_BFS_2.py
make_proper_input_file_for_mcmc_sample.py

README.md

motif-finding

Scientists have shown that network motifs are key building block of various biological networks. Most of the existing exact methods for finding network motifs are inefficient simply due to the inherent complexity of this task. In recent years, researchers are considering approximate methods that save computation by sacrificing exact counting of the frequency of potential motifs. However, these methods are also slow when one considers the motifs of larger size. In this work, we propose two methods for approximate motif finding, namely SRW-rw, and MHRW based on Markov Chain Monte Carlo (MCMC) sampling. Both the methods are significantly faster than the best of the existing methods, with comparable or better accuracy. Further, as the motif size grows the complexity of the proposed methods grows linearly.

Input File Format

Node ids should be between 1 to max number of nodes in the network. Otherwise you will get segmentation fault. So, please format your network file accordingly before your run the script. Please see the yeast-mod file inside motifMCMC for reference.

I have provided three script for making proper file format for the executable to run. To make the right format please execute the script in the following sequence:

python  check_undirected.py dataset/CA-GrQc

Please note that there is no .txt at the end of the file. the script will generate a file with UND appended at the end of the file name.

python make_connected_BFS_2.py  dataset/CA-GrQcUND.txt

The script will create a file with BFSCON appened. Basically, it will create a connected network if the original input graph is not connected.

python     make_proper_input_file_for_mcmc_sample.py  dataset/CA-GrQcUND.txtBFSCON

The above script will rearrage the node ids from 1 to maximum node id.

./motifMiner-mcmc.out  -d dataset/CA-GrQcUND.txtBFSCON-mcmc-format   -i 10000 -s 5 -q 10000 -undir 1

Installation

To make executable, please run the following command under individual folder.

make

You can run the code in following way (In this version -undir should always be 1):

./executablename -d [fileName] -i 100000 [iteration no] -s 4 [size] -q 1000 [queue size] -undir 1 [always expect undir 1]

Reference

If you are using the code for research purposes, please consider citing the following paper:

@inproceedings{saha.hasan:15*2,
  title={Finding Network Motifs Using MCMC Sampling.},
  author={Saha, Tanay Kumar and Al Hasan, Mohammad},
  booktitle={CompleNet},
  pages={13--24},
  year={2015}
}
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