[scikit-learn] Markov Clustering?

Allan Visochek avisochek3 at gmail.com
Sat Dec 3 17:43:30 EST 2016


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 <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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