{"abstract":[{"lang":"eng","text":"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."}],"publication_status":"published","publication":"Protein-Protein Interaction Networks","alternative_title":["Methods in Molecular Biology"],"_id":"11847","doi":"10.1007/978-1-4939-9873-9_16","author":[{"last_name":"Biedermann","first_name":"Sonja","full_name":"Biedermann, Sonja"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Schulz","first_name":"Christian","full_name":"Schulz, Christian"},{"last_name":"Schuster","full_name":"Schuster, Bernhard","first_name":"Bernhard"}],"publication_identifier":{"isbn":["9781493998722"],"eissn":["1940-6029"],"eisbn":["9781493998739"],"issn":["1064-3745"]},"extern":"1","type":"book_chapter","date_updated":"2023-02-17T09:34:26Z","volume":2074,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["31583641"]},"status":"public","page":"215–231","month":"10","date_created":"2022-08-16T06:54:48Z","citation":{"ieee":"S. Biedermann, M. H. Henzinger, C. Schulz, and B. Schuster, “Vienna Graph Clustering,” in <i>Protein-Protein Interaction Networks</i>, vol. 2074, S. Canzar and F. Rojas Ringeling, Eds. Springer Nature, 2019, pp. 215–231.","short":"S. Biedermann, M.H. Henzinger, C. Schulz, B. Schuster, in:, S. Canzar, F. Rojas Ringeling (Eds.), Protein-Protein Interaction Networks, Springer Nature, 2019, pp. 215–231.","ama":"Biedermann S, Henzinger MH, Schulz C, Schuster B. Vienna Graph Clustering. In: Canzar S, Rojas Ringeling F, eds. <i>Protein-Protein Interaction Networks</i>. Vol 2074. MIMB. Springer Nature; 2019:215–231. doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>","mla":"Biedermann, Sonja, et al. “Vienna Graph Clustering.” <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, vol. 2074, Springer Nature, 2019, pp. 215–231, doi:<a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">10.1007/978-1-4939-9873-9_16</a>.","apa":"Biedermann, S., Henzinger, M. H., Schulz, C., &#38; Schuster, B. (2019). Vienna Graph Clustering. In S. Canzar &#38; F. Rojas Ringeling (Eds.), <i>Protein-Protein Interaction Networks</i> (Vol. 2074, pp. 215–231). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>","chicago":"Biedermann, Sonja, Monika H Henzinger, Christian Schulz, and Bernhard Schuster. “Vienna Graph Clustering.” In <i>Protein-Protein Interaction Networks</i>, edited by Stefan Canzar and Francisca Rojas Ringeling, 2074:215–231. MIMB. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-1-4939-9873-9_16\">https://doi.org/10.1007/978-1-4939-9873-9_16</a>.","ista":"Biedermann S, Henzinger MH, Schulz C, Schuster B. 2019.Vienna Graph Clustering. In: Protein-Protein Interaction Networks. Methods in Molecular Biology, vol. 2074, 215–231."},"article_processing_charge":"No","oa_version":"None","scopus_import":"1","series_title":"MIMB","quality_controlled":"1","title":"Vienna Graph Clustering","language":[{"iso":"eng"}],"intvolume":"      2074","editor":[{"last_name":"Canzar","first_name":"Stefan","full_name":"Canzar, Stefan"},{"last_name":"Rojas Ringeling","first_name":"Francisca","full_name":"Rojas Ringeling, Francisca"}],"date_published":"2019-10-04T00:00:00Z","day":"04","year":"2019","publisher":"Springer Nature","pmid":1}