[scikit-learn] Markov Clustering?

[Allan Visochek]

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 <http://micans.org/mcl/>, 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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