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
