What is GEDEVO-M?

GEDEVO-M is an extension of the idea implemented in GEDEVO to multiple input networks. GEDEVO-M aims to minimize the sum of GEDs between every pair of input networks.

Download

README.txt
gedevo-m (linux64)
gedevo-m (win32)
data
test scripts

How to run GEDEVO

• Start ./gedevo-m (or gedevo-m.exe for Windows) with no parameters for a short description of the command line parameters.
• See README file for details.
• Run test_net.sh or test_viral.sh on Linux (test_net.bat or test_viral.bat for Windows) an example of GEDEVO-M.
• Command line example for Linux:

   
  ./gedevo-m\
     --grnum    5  \
     --groups   EBV  HSV-1  KSHV  mCMV  VZV\
     --edgelist EBV    data/EBV.rawEL\
     --edgelist HSV-1  data/HSV-1.rawEL\
     --edgelist KSHV   data/KSHV.rawEL\
     --edgelist mCMV   data/mCMV.rawEL\
     --edgelist VZV    data/VZV.rawEL\
  \
     --grsig    EBV     data/EBV.sigs \
     --grsig    HSV-1   data/HSV-1.sigs \
     --grsig    KSHV    data/KSHV.sigs \
     --grsig    mCMV    data/mCMV.sigs \
     --grsig    VZV     data/VZV.sigs \
     --pop       500\
     --maxsame   3000\
     --maxiter   100000\
     --create    --no-prematch --no-workfiles --undirected \
     --logfile   ./er0_VIRAL_P0500.log \
     --autosave 21600 \
     --prefix   ./er0_VIRAL_P0500 \
     --threads   50  
  

Citation

Rashid Ibragimov, Maximilian Malek, Jiong Guo, Jan Baumbach: Multiple Graph Edit Distance - Simultaneous Topological Alignment of Multiple Protein-Protein Interaction Networks with an Evolutionary Algorithm. GECCO 2014 (accepted).