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Re: [Databionic-ESOM-User] Re : Databionic-ESOM-User Digest, Vol 12, Issue 3
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From: Fabian M. <fa...@my...> - 2008-05-22 22:44:11
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Frederic, so you have 30-60 dimensional vectors with counts, similar to a histogram. in this case I would say that the used method to interpolate vectors makes sense and can be used together with sorensen. Do you think you are able to add this with some guidance? fabian rimet frederic wrote: > > Dear Fabian, > > My data are botanical data (counts of phytoplanctonic species in a > lake). Each sample of water is characterised by several algae species > (about 30 to 60 species) and for each species correspond a number of > cells. > > I'm not sure that Hamming distances can be used for my data (never > seen an example in litterature using the kind of distance), usually > Sorensen distances are used. > > It would be really nice to add Sorensen distances in the Databionics > ESOM analyser (when using the training tool in the data space distance > function menu). > > Thanks for your help, > > Frederic > > > > ----- Message d'origine ---- > De : "dat...@li..." > <dat...@li...> > À : dat...@li... > Envoyé le : Dimanche, 18 Mai 2008, 21h20mn 43s > Objet : Databionic-ESOM-User Digest, Vol 12, Issue 3 > > Send Databionic-ESOM-User mailing list submissions to > dat...@li... > <mailto:dat...@li...> > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > or, via email, send a message with subject or body 'help' to > dat...@li... > <mailto:dat...@li...> > > You can reach the person managing the list at > dat...@li... > <mailto:dat...@li...> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Databionic-ESOM-User digest..." > > > Today's Topics: > > 1. Re: Bray-Curtis distances (Fabian M?rchen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 17 May 2008 21:40:44 -0400 > From: Fabian M?rchen <fa...@my... <mailto:fa...@my...>> > Subject: Re: [Databionic-ESOM-User] Bray-Curtis distances > To: dat...@li... > <mailto:dat...@li...> > Message-ID: <482...@my... > <mailto:482...@my...>> > Content-Type: text/plain; charset=ISO-8859-1 > > Frederic, > > Bray Curtis could be added very easily as it is already implemented in > colt. > > The Jaccard distance measures the difference between sets whereas the > ESOM works with numeric vectors. what does your input look like? do you > have categoric vectors represented as real numbers? > > Please note that for a meaningful ESOM training you need a distance > function for your vectors and the (weighted) mean of you input vectors > must represent an 'average' of the examples. This might not be the case > for categoric data depending on the encoding. A binary encoding might > work. > > A little while ago I added the hamming distance per special request. > Hamming is defined for binary vectors. The ESOM training generated > vectors using the default weighted mean but the distance function > rounds each entry to the nearest integer and counts the number of > identical entries in the two vectors. > > best > fabian > > Niko Efthymiou wrote: > > On Wednesday 14 May 2008, rimet frederic wrote: > > > >> Hello, > >> I've tried your eSOM program on ecological data (phytoplancton counts > >> of a french lake). It produces interesting maps and groups. > >> Nevertheless I wanted to know if you plan to add in the data space > >> distance function other distances more adapted to ecological data, as > >> for instance Sorensen (Bray & Curtis) Distance or Jaccard Distance ? > >> Thanks for your answer, > >> Fr?d?ric RIMET > >> > > > > Hello, > > > > as far as I know there are no such plans. However adding this metrics > > should not be wery hard. You just have to implement them as > > > > cern.colt.function.ThresholdVectorVectorFunction > > cern.colt.function.VectorVectorFunction > > > > objects and add them to > > > > databionics.math.DistanceFactory > > databionics.esom.Train > > > > and that schould be about it (my crystal ball reads ~100 lines of > code). > > Please consider submiting a patch if you do add them. > > > > > > Greats Niko > > > > > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > _______________________________________________ > > Databionic-ESOM-User mailing list > > Dat...@li... > <mailto:Dat...@li...> > > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > > > > > > > > > ------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > ------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > <mailto:Dat...@li...> > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > > > End of Databionic-ESOM-User Digest, Vol 12, Issue 3 > *************************************************** > > __________________________________________________ > Do You Yahoo!? > En finir avec le spam? Yahoo! Mail vous offre la meilleure protection > possible contre les messages non sollicités > http://mail.yahoo.fr Yahoo! Mail > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > ------------------------------------------------------------------------ > > _______________________________________________ > Databionic-ESOM-User mailing list > Dat...@li... > https://lists.sourceforge.net/lists/listinfo/databionic-esom-user > |
