And... [1] Stijn van Dongen. Graph Clustering by Flow Simulation. PhD thesis, University of Utrecht, May 2000. http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm
has 1201 citations. I think it's fair to say the method is very widely known and used. Raphael On 5 December 2016 at 13:45, Gael Varoquaux <[email protected]> wrote: > Interestingly, a couple of days before this thread was started a > researcher in a top lab of a huge private-sector company had mentionned > to me that they found this algorithm very useful in practice (sorry for > taking time to point this out, I just needed to check with him that > indeed it was this specific algorithm). > > G > > On Sun, Dec 04, 2016 at 08:18:54AM +0000, Raphael C wrote: >> I think you get a better view of the importance of Markov Clustering in >> academia from https://scholar.google.co.uk/scholar?hl=en&as_sdt=0,5&q= >> Markov+clustering . > >> Raphael > >> On Sat, 3 Dec 2016 at 22:43 Allan Visochek <[email protected]> wrote: > >> Thanks for pointing that out, I sort of picked it up by word of mouth so >> I'd assumed it had a bit more precedence in the academic world. > >> I'll look into it a little more, but I'd definitely be interested in >> contributing something else if that doesn't work out. > >> -Allan > >> On Sat, Dec 3, 2016 at 4:45 PM, Andy <[email protected]> wrote: > >> Hey Allan. > >> None of the references apart from the last one seems to be published >> in >> a peer-reviewed place, is that right? >> And "A stochastic uncoupling process for graphs" has 13 citations >> since >> 2000. Unless there is a more prominent >> publication or evidence of heavy use, I think it's disqualified. >> Academia is certainly not the only metric for evaluation, so if you >> have others, that's good, too ;) > >> Best, >> Andy > >> On 12/03/2016 04:33 PM, Allan Visochek wrote: > >> Hey Andy, > >> This algorithm does operate on sparse graphs so it may be beyond >> the scope of sci-kit learn, let me know what you think. >> The website is here, it includes a brief description of how the >> algorithm operates under Documentation -> Overview1 and >> Overview2. >> The references listed on the website are included below. > >> Best, >> -Allan > > >> [1] Stijn van Dongen. Graph Clustering by Flow Simulation. PhD >> thesis, University of Utrecht, May 2000. >> http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm > >> [2] Stijn van Dongen. A cluster algorithm for graphs. Technical >> Report INS-R0010, National Research Institute for Mathematics and >> Computer Science in the Netherlands, Amsterdam, May 2000. >> http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z > >> [3] Stijn van Dongen. A stochastic uncoupling process for graphs. >> Technical Report INS-R0011, National Research Institute for >> Mathematics and Computer Science in the Netherlands, Amsterdam, >> May >> 2000. >> http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z > >> [4] Stijn van Dongen. Performance criteria for graph clustering >> and >> Markov cluster experiments. Technical Report INS-R0012, National >> Research Institute for Mathematics and Computer Science in the >> Netherlands, Amsterdam, May 2000. >> http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z > >> [5] Enright A.J., Van Dongen S., Ouzounis C.A. An efficient >> algorithm for large-scale detection of protein families, Nucleic >> Acids Research 30(7):1575-1584 (2002). > > >> On Sat, Dec 3, 2016 at 3:34 PM, Andy <[email protected]> wrote: > >> Hi Allan. >> Can you provide the original paper? >> It this something usually used on sparse graphs? We do have >> algorithms that operate on data-induced >> graphs, like SpectralClustering, but we don't really >> implement >> general graph algorithms (there's no PageRank or community >> detection). > >> Andy > > >> On 12/03/2016 12:19 PM, Allan Visochek wrote: > >> Hi there, > >> My name is Allan Visochek, I'm a data scientist and web >> developer and I love scikit-learn so first of all, thanks >> so much for the work that you do. > >> I'm reaching out because I've found the markov clustering >> algorithm to be quite useful for me in some of my work >> and >> noticed that there is no implementation in scikit-learn, >> is >> anybody working on this? If not, id be happy to take this >> on. I'm new to open source, but I've been working with >> python for a few years now. > >> Best, >> -Allan > > > >> _______________________________________________ >> scikit-learn mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/scikit-learn > >> _______________________________________________ scikit-learn >> mailing list [email protected] https://mail.python.org/ >> mailman/listinfo/scikit-learn > >> _______________________________________________ >> scikit-learn mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/scikit-learn > > >> _______________________________________________ >> scikit-learn mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/scikit-learn > > > >> _______________________________________________ >> scikit-learn mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/scikit-learn > > >> _______________________________________________ >> scikit-learn mailing list >> [email protected] >> https://mail.python.org/mailman/listinfo/scikit-learn > > > -- > Gael Varoquaux > Researcher, INRIA Parietal > NeuroSpin/CEA Saclay , Bat 145, 91191 Gif-sur-Yvette France > Phone: ++ 33-1-69-08-79-68 > http://gael-varoquaux.info http://twitter.com/GaelVaroquaux > _______________________________________________ > scikit-learn mailing list > [email protected] > https://mail.python.org/mailman/listinfo/scikit-learn _______________________________________________ scikit-learn mailing list [email protected] https://mail.python.org/mailman/listinfo/scikit-learn
