[scikit-learn] Markov Clustering?
Gael Varoquaux
gael.varoquaux at normalesup.org
Mon Dec 5 08:45:52 EST 2016
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 <avisochek3 at gmail.com> 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 <t3kcit at gmail.com> 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 <t3kcit at gmail.com> 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
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--
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
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