(Weighted) Cluster Editing
Authors: Gunnar Klau, Emanuel Laude, Philipp Spohr
- LEMON 1.3
- ILOG CPLEX (>= 12.0)
Get yoshiko from github:
git clone <HTTPS clone URL (see on the right side of this page)>
First, LEMON 1.3 needs to be installed:
wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.tar.gz
tar xvzf lemon-1.3.tar.gz
cd lemon-1.3
cmake -DCMAKE_INSTALL_PREFIX=~/lemon
make install
You can remove the LEMON sources now, i.e., rm -rf lemon-1.3.
CPLEX is a commercial product owned by IBM. For academic purposes it can be obtained at no charge via IBM's Academic Initiative programme:
http://www-03.ibm.com/ibm/university/academic/pub/page/membership
Next, Yoshiko can be compiled:
mkdir build
cd build
cmake ..
make all
In case auto-detection of LEMON or CPLEX fails, do
cmake \
-DLIBLEMON_ROOT=~/lemon \
-DCPLEX_INC_DIR=~/ILOG/cplex/include/ \
-DCPLEX_LIB_DIR=~/ILOG/cplex/lib/x86-64_osx/static_pic \
-DCONCERT_LIB_DIR=~/ILOG/concert/lib/x86-64_osx/static_pic \
-DCONCERT_INC_DIR=~/ILOG/concert/include/ ..
-DBUILD_STATIC=ON -> Enables static linking
executable -> The stand-alone executable of Yoshiko library -> The library (used for instance by the Cytoscape plugin) all -> Builds both
Requires you to build Yoshiko as a standalone program (see Make-Targets)\
To run yoshiko on the test instance (without producing any output):
./yoshiko -f ../data/test/fusarium.txt -v 4
Get a list of options:
./yoshiko -h
If you are looking for a graphical user interface, you can find a Cytoscape implementation building on this software at:
https://gitlab.cs.uni-duesseldorf.de/spohr/YoshikoWrapper
Another stand-alone implementation (that does not require CPLEX) utilizing only the heuristic, is available here: