Re: [igraph] MCL integration into igraph (was: Community detection with i-graph)

[Stijn van Dongen]

      Hi Tamas,

excellent, thanks very much for the pointers. This is not something I can start
on right away, but I plan to start tackling this hopefully within at most a few
months. Will get back once I am stuck :-) so for now consider it moved onto my
TODO ..

thanks,
Stijn


On Thu, Apr 07, 2011 at 12:06:22PM +0200, Tamas Nepusz wrote:
> Hi Stijn,
> 
> Integrating MCL into igraph has already been on my (admittedly too long)
> to-do list for a while and it would indeed be a very welcome addition.
> Currently we only have some glue code in our wiki to call the external
> MCL executable from igraph:
> 
> http://igraph.wikidot.com/community-detection-in-python
> 
> Obviously a better solution would be to merge the relevant parts of
> mcl's codebase into igraph's source tree and write some conversion
> routines that turn an igraph_t into MCL's internal data structures. This
> is the approach we have followed with other external algorithms such as
> the BLISS and VF2 algorithms and the walktrap community detection
> method. Of course this means that the graph temporarily exists in two
> copies in the memory, but the advantage is that it is much easier to
> merge patches and updates from upstream. Anyway, if you are willing to
> start doing this, let me know and I'll be happy to assist.
> 
> The current focus of development is the 0.6-main branch on Launchpad:
> https://code.launchpad.net/~igraph/igraph/0.6-main. src/walktrap.cpp is
> a good point to start; this file contains a wrapper for the walktrap
> method. The actual conversion code from igraph_t to walktrap's Graph
> data structure is in src/walktrap_graph.cpp (see
> Graph::convert_from_igraph). I think something similar is enough for MCL
> as a first approximation.
> 
> Best regards,
> -- 
> Tamas
> 
> 
> On 04/07/2011 11:54 AM, Stijn van Dongen wrote:
> > 
> >       Hi Tamas, list members,
> > 
> > I think it would be nice if, in addition to the algorithms listed below, it
> > is possible to use the MCL cluster algorithm from within igraph.
> > Do you have suggestions for a prefered way of doing (coding) this?
> > Would someone be willing to assist me?

-- 
Stijn van Dongen         >8<        -o)   O<  forename pronunciation: [Stan]
EMBL-EBI                            /\\   Tel: +44-(0)1223-492675
Hinxton, Cambridge, CB10 1SD, UK   _\_/   http://micans.org/stijn