<div style="white-space:pre-wrap">I think you get a better view of the importance of Markov Clustering in academia from <a href="https://scholar.google.co.uk/scholar?hl=en&as_sdt=0,5&q=Markov+clustering">https://scholar.google.co.uk/scholar?hl=en&as_sdt=0,5&q=Markov+clustering</a> .<br><br>Raphael</div><br><div class="gmail_quote"><div dir="ltr">On Sat, 3 Dec 2016 at 22:43 Allan Visochek <<a href="mailto:avisochek3@gmail.com">avisochek3@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="gmail_msg">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. <div class="gmail_msg"><br class="gmail_msg"><div class="gmail_msg"><div class="gmail_msg">I'll look into it a little more, but I'd definitely be interested in contributing something else if that doesn't work out.</div></div></div></div><div dir="ltr" class="gmail_msg"><div class="gmail_msg"><br class="gmail_msg"></div><div class="gmail_msg">-Allan</div></div><div class="gmail_extra gmail_msg"><br class="gmail_msg"><div class="gmail_quote gmail_msg">On Sat, Dec 3, 2016 at 4:45 PM, Andy <span dir="ltr" class="gmail_msg"><<a href="mailto:t3kcit@gmail.com" class="gmail_msg" target="_blank">t3kcit@gmail.com</a>></span> wrote:<br class="gmail_msg"><blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000" class="gmail_msg">
Hey Allan.<br class="gmail_msg">
<br class="gmail_msg">
None of the references apart from the last one seems to be published
in a peer-reviewed place, is that right?<br class="gmail_msg">
And "A stochastic uncoupling process for graphs" has 13 citations
since 2000. Unless there is a more prominent<br class="gmail_msg">
publication or evidence of heavy use, I think it's disqualified.<br class="gmail_msg">
Academia is certainly not the only metric for evaluation, so if you
have others, that's good, too ;)<br class="gmail_msg">
<br class="gmail_msg">
Best,<br class="gmail_msg">
Andy<br class="gmail_msg">
<br class="gmail_msg">
<div class="m_8677542748461967555m_8192344549692176098moz-cite-prefix gmail_msg">On 12/03/2016 04:33 PM, Allan Visochek
wrote:<br class="gmail_msg">
</div>
<blockquote type="cite" class="gmail_msg">
<div dir="ltr" class="gmail_msg">Hey Andy,
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">This algorithm does operate on sparse graphs so it may be
beyond the scope of sci-kit learn, let me know what you
think. </div>
<div class="gmail_msg">The website is <a href="http://micans.org/mcl/" class="gmail_msg" target="_blank">here</a>, it
includes a brief description of how the algorithm operates
under Documentation -> Overview1 and Overview2. </div>
<div class="gmail_msg">The references listed on the website are included below.</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Best,</div>
<div class="gmail_msg">-Allan</div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">
<p class="m_8677542748461967555m_8192344549692176098m_3662110346703346319gmail-asd_par gmail_msg"><a name="m_8677542748461967555_m_8192344549692176098_m_3662110346703346319_gcbfs" class="gmail_msg">[1]</a> Stijn
van Dongen. <i class="gmail_msg">Graph Clustering by Flow Simulation</i>. PhD
thesis, University of Utrecht, May 2000.<br class="gmail_msg">
<a href="http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm" class="gmail_msg" target="_blank">http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm</a></p>
<p class="m_8677542748461967555m_8192344549692176098m_3662110346703346319gmail-asd_par gmail_msg"><a name="m_8677542748461967555_m_8192344549692176098_m_3662110346703346319_cafg" class="gmail_msg">[2]</a> Stijn
van Dongen. <i class="gmail_msg">A cluster algorithm for graphs</i>. Technical
Report INS-R0010, National Research Institute for
Mathematics and Computer Science in the Netherlands,
Amsterdam, May 2000.<br class="gmail_msg">
<a href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z" class="gmail_msg" target="_blank">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z</a></p>
<p class="m_8677542748461967555m_8192344549692176098m_3662110346703346319gmail-asd_par gmail_msg"><a name="m_8677542748461967555_m_8192344549692176098_m_3662110346703346319_supfg" class="gmail_msg">[3]</a> Stijn
van Dongen. <i class="gmail_msg">A stochastic uncoupling process for graphs</i>.
Technical Report INS-R0011, National Research Institute for
Mathematics and Computer Science in the Netherlands,
Amsterdam, May 2000.<br class="gmail_msg">
<a href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z" class="gmail_msg" target="_blank">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0011.ps.Z</a></p>
<p class="m_8677542748461967555m_8192344549692176098m_3662110346703346319gmail-asd_par gmail_msg"><a name="m_8677542748461967555_m_8192344549692176098_m_3662110346703346319_pcfgcmce" class="gmail_msg">[4]</a> Stijn van
Dongen. <i class="gmail_msg">Performance criteria for graph clustering and
Markov cluster experiments</i>. Technical Report
INS-R0012, National Research Institute for Mathematics and
Computer Science in the Netherlands, Amsterdam, May 2000.<br class="gmail_msg">
<a href="http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z" class="gmail_msg" target="_blank">http://www.cwi.nl/ftp/CWIreports/INS/INS-R0012.ps.Z</a></p>
<p class="m_8677542748461967555m_8192344549692176098m_3662110346703346319gmail-asd_par gmail_msg"><a name="m_8677542748461967555_m_8192344549692176098_m_3662110346703346319_eaflsdopf" class="gmail_msg">[5]</a> Enright
A.J., Van Dongen S., Ouzounis C.A. <i class="gmail_msg">An efficient algorithm
for large-scale detection of protein families</i>, Nucleic
Acids Research 30(7):1575-1584 (2002).</p>
</div>
</div>
<div class="gmail_extra gmail_msg"><br class="gmail_msg">
<div class="gmail_quote gmail_msg">On Sat, Dec 3, 2016 at 3:34 PM, Andy <span dir="ltr" class="gmail_msg"><<a href="mailto:t3kcit@gmail.com" class="gmail_msg" target="_blank">t3kcit@gmail.com</a>></span>
wrote:<br class="gmail_msg">
<blockquote class="gmail_quote gmail_msg" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000" class="gmail_msg"> Hi Allan.<br class="gmail_msg">
Can you provide the original paper?<br class="gmail_msg">
It this something usually used on sparse graphs? We do
have algorithms that operate on data-induced<br class="gmail_msg">
graphs, like SpectralClustering, but we don't really
implement general graph algorithms (there's no PageRank or
community detection).<br class="gmail_msg">
<br class="gmail_msg">
Andy<br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
<div class="m_8677542748461967555m_8192344549692176098m_-5298880587644186335moz-cite-prefix gmail_msg">On
12/03/2016 12:19 PM, Allan Visochek wrote:<br class="gmail_msg">
</div>
<blockquote type="cite" class="gmail_msg">
<div dir="ltr" class="gmail_msg">Hi there,
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">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. </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">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. </div>
<div class="gmail_msg"><br class="gmail_msg">
</div>
<div class="gmail_msg">Best,</div>
<div class="gmail_msg">-Allan</div>
</div>
<br class="gmail_msg">
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