Skip to content
(Weighted) Cluster Editing
C++ CMake
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.idea/codeStyles Just saving progress. Apr 5, 2018
data
src Merge pull request #29 from mironec/bugfix/jena-input May 2, 2019
.gitignore
CMakeLists.txt Reimplemented heuristic. Apr 4, 2018
CMakeLists.txt.in Added GoogleTesting Mar 19, 2018
LICENSE Initial commit Jan 27, 2014
README.md

README.md

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

You can’t perform that action at this time.