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[Databionic-ESOM-User] Re : Databionic-ESOM-User Digest, Vol 12, Issue 3
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From: rimet f. <rim...@ya...> - 2008-05-22 19:26:35
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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... 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... You can reach the person managing the list at 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...> Subject: Re: [Databionic-ESOM-User] Bray-Curtis distances To: dat...@li... Message-ID: <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... > 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... 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 |
