[scikit-learn] Markov Clustering?

[Andy]

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 <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 
> <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 
> <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 
> <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 
> <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 
> <mailto: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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