Anybody have any objection to creating a new IMP.statistics module? Keren's k-means stuff in DOMINO is not specific to DOMINO, and so should probably belong in a more general purpose module. And I'm sure we'll need various other samplers and clustering algorithms in the future.
If no objections, I'll create the module so that Keren move her code there.
Ben
Ben -
Daniel also suggested that I'll move the my PCA stuff there. I have another clustering algorithm implemented that I would like to put there as well.
Keren. On Apr 30, 2009, at 8:15 AM, Ben Webb wrote:
> Anybody have any objection to creating a new IMP.statistics module? > Keren's k-means stuff in DOMINO is not specific to DOMINO, and so > should > probably belong in a more general purpose module. And I'm sure we'll > need various other samplers and clustering algorithms in the future. > > If no objections, I'll create the module so that Keren move her code > there. > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
No, I suggested you make the interfaces look similar (specifically how the computation is triggered). Or at least that us what I meant to suggest :-)
On Apr 30, 2009, at 2:56 PM, Keren Lasker kerenl@salilab.org wrote:
> Ben - > > Daniel also suggested that I'll move the my PCA stuff there. > I have another clustering algorithm implemented that I would like > to put there as well. > > Keren. > On Apr 30, 2009, at 8:15 AM, Ben Webb wrote: > >> Anybody have any objection to creating a new IMP.statistics module? >> Keren's k-means stuff in DOMINO is not specific to DOMINO, and so >> should >> probably belong in a more general purpose module. And I'm sure we'll >> need various other samplers and clustering algorithms in the future. >> >> If no objections, I'll create the module so that Keren move her >> code there. >> >> Ben >> -- >> ben@salilab.org http://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
ok - but it does make sense to be part of statistics. Anyway - how about the following interface for clustering methods (I am going to add another one other then the kmeans stuff) ? feel free to change, no strong opinions here :
class ClusteingData { public: ClusteringData(){} virtual ~ClusteringData(){} virtual void set_data_points(Particles &ps); virtual const Particles &get_data_points() const; virtual void set_number_of_clusters(int k); virtual int get_number_of_clusters() const {return k;} //get all particles that are part of cluster i virtual Particles get_cluster(int i) const; protected: Particles ps_; std::vector<Particles> clusters_; }
void kmeans_clustering(ClusteingData &cd);
On Thu, 30 Apr 2009, Daniel Russel wrote:
> No, I suggested you make the interfaces look similar (specifically how the > computation is triggered). Or at least that us what I meant to suggest :-) > > > > On Apr 30, 2009, at 2:56 PM, Keren Lasker kerenl@salilab.org wrote: > >> Ben - >> >> Daniel also suggested that I'll move the my PCA stuff there. >> I have another clustering algorithm implemented that I would like to put >> there as well. >> >> Keren. >> On Apr 30, 2009, at 8:15 AM, Ben Webb wrote: >> >>> Anybody have any objection to creating a new IMP.statistics module? >>> Keren's k-means stuff in DOMINO is not specific to DOMINO, and so should >>> probably belong in a more general purpose module. And I'm sure we'll >>> need various other samplers and clustering algorithms in the future. >>> >>> If no objections, I'll create the module so that Keren move her code >>> there. >>> >>> Ben >>> -- >>> ben@salilab.org http://salilab.org/~ben/ >>> "It is a capital mistake to theorize before one has data." >>> - Sir Arthur Conan Doyle >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
I've just committed a patch which moves the k-means stuff from IMP.domino to IMP.statistics. Keren, you may want to check to make sure I didn't break any of your code. ;)
I agree that it makes sense to have a common interface for PCA and k-means.
Ben
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Ben Webb -
Daniel Russel -
Keren Lasker