News

Aug 2013
yoshiko version 2.0

We have released yoshiko version 2.0, a mature version of our cluster editing algorithm. It has been implemented mostly by Emanuel Laude and contains a lot of helpful redcution rules from fixed parameter algorithmics and a powerful heuristic for large data sets.

24 Aug 2011
natalie version 2.0

We have released natalie version 2.0, a mature version of our network alignment algorithm.

27 Jun 2011
side chain placement

scp is a package that contains our code for exact side chain placement as used in a recent paper in Optimization Letters.

5 Mar 2010
heinz and BioNet

heinz now works together with the BioNet package.

17 Dec 2008
yoshiko/charles

The yoshiko/charles code is now online. The tool solves the cluster editing problem as well as its directed "cousin", the transitivity editing problem, to provable optimality.

1 Sep 2008
planet lisa moves to Amsterdam

The planet lisa project is now based at the Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands.

20 Jul 2008
ISMB 2008

Our paper Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach has won the oustanding paper award at ISMB 2008 in Toronto, Canada. See the heinz section for more information on our software to discover optimal subnetworks with respect to our signal-based scoring scheme of p-values.

Jul 2008
ISMB 2008

We will give a presentation at ISMB 2008 on Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach. Our software is available as the heinz package.

Oct 07
Algorithmic Operations Research

Our theoretical lara paper has been accepted for publication in Algorithmic Operations Research.

27 Jul 07
BMC Bioinformatics

The paper describing the lara program has been accepted for publication in BMC Bioinformatics.

28 Jun 07
4SALE support for lara

lara has been integrated into the RNA alignment and editing framework 4SALE. Get the latest lara version that is compatible with 4SALE.

yoshiko and charles

The planet LiSA library is now hosted in "Amsterdam"

https://github.com/ls-cwi

yoshiko computes exact solutions to the Cluster Editing problem.

A note on version 2.0

Emanuel Laude did a great job in his Computer Science Bachelor's thesis at the University of Würzburg. Thanks to him, we now have a tool (yoshiko 2.0) that directly combines the redcution rules from fixed parameter algorithmics with the integer linear programming approach as described in S. Böcker, S. Briesemeister, G. W. Klau. Exact algorithms for cluster editing: evaluation and experiments. Algorithmica 60(2):316-334, 2011. Furthermore, yoshiko 2.0 runs on different platforms (Linux, MacOS and Windows) and comes with a powerful heuristic mode.

A note on version 1.5 (yoshiko/charles)

Version 1.5 of our tool also supports transitivity editing in directed graphs, and a previous version of this tool was called charles. Version 2.0 only supports the undirected case (cluster editing), but is much more powerful because of integrated reduction rules from fixed parameter algorithmics. The directed case is described in the paper "On optimal comparability editing with applications to molecular diagnostics" (BMC Bioinformatics, 2009) with Sebastian Böcker from Jena and Sebastian Briesemeister from Tübingen. Note that the title is misleading as a better name for these problems is Transitivity Editing. The Transitivity Editing problem appears, for example, in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgroups. The task is to identify the minimum number of edge insertions or deletions to transform G into a transitive graph, that is, if edges (u, v) and (v, w) are present then edge (u, w) must be present, too.

The data we used in our paper will be provided upon request.

warning Please note that you need a CPLEX license to run charles. However, the tool based on fixed-parameter algorithmics does not need such a license and can be found here.


Download

version date link description comments
2.0 Aug 13 yoshiko 2.0 reimplementation by Emanuel Laude 64 bit linux executable
2.0 Aug 13 yoshiko 2.0 reimplementation by Emanuel Laude 64 bit MacOS executable
2.0 Aug 13 yoshiko 2.0 reimplementation by Emanuel Laude 64 bit Windows executable
1.5 Dec 08 yoshiko/charles 1.5 version used for computations in our APBC paper (BMC Bioinformatics) This is a 64 bit linux executable.
  Dec 08   data used in our APBC paper The file exceeds the 10MB limit of this TWiki system. It is available upon request.
Topic revision: r8 - 08 Mar 2017, BodoRiedigerKlaus
 
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