This paper serves as a user guide to the Vienna graph clustering framework. We review our general memetic algorithm, VieClus, to tackle the graph clustering problem. A key component of our contribution are natural recombine operators that employ ensemble clusterings as well as multi-level techniques. Lastly, we combine these techniques with a scalable communication protocol, producing a system that is able to compute high-quality solutions in a short amount of time. After giving a description of the algorithms employed, we establish the connection of the graph clustering problem to protein–protein interaction networks and moreover give a description on how the software can be used, what file formats are expected, and how this can be used to find functional groups in protein–protein interaction networks.
CITATION STYLE
Biedermann, S., Henzinger, M., Schulz, C., & Schuster, B. (2020). Vienna graph clustering. In Methods in Molecular Biology (Vol. 2074, pp. 215–231). Humana Press Inc. https://doi.org/10.1007/978-1-4939-9873-9_16
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