Yoshiko

(Weighted) Cluster Editing

Authors: Gunnar Klau, Emanuel Laude, Philipp Spohr

Compilation instructions

Dependencies

• LEMON 1.3
• ILOG CPLEX (>= 12.0)

Compiling

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/ ..

CMake-Flags

-DBUILD_STATIC=ON -> Enables static linking

Make-Targets

executable -> The stand-alone executable of Yoshiko library -> The library (used for instance by the Cytoscape plugin) all -> Builds both

Running Yoshiko (Standalone)

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

Cytoscape App (Graphical User Interface)

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:

https://github.com/AlBi-HHU/YoshikoStandalone