databionic-esom-user

[Databionic-ESOM-User] automated data clustering?

[Greg D. <gd...@be...>]

Dear ESOM users,

I am using ESOM to cluster DNA sequences from environmental =
microorganisms, based on genome wide signatures (tetranucleotide =
frequency).  Overall I am very happy with the results and it has proven =
to be an extremely valuable tool for our research group.  There are two =
areas that we are hoping to develop further and I am curious if anyone =
has suggestions or comments:

(1) Are there any automated methods for clustering data?  The boundaries =
for our clusters range from obvious to questionable.  While this =
variable strength of clustering is useful information in itself, we =
would like to develop an automated method for defining clusters in order =
to avoid potential errors in where we draw the lines (it is not always =
entirely clear how to do so).

(2) Are there statistical tools that have been developed or applied to =
ESOM to evaluate the robustness of clustering (ideally on a per-cluster =
basis)?  We are interested in such an analysis, which would either be =
based on the U-matrix distance structure and/or an evaluation of the =
accuracy of the clustering (for much of our data we know the true =
cluster affiliations).

Any suggestions or references relevant to these areas would be greatly =
appreciated.

Greg Dick
Postdoctoral Research
University of California, Berkeley     =20

Re: [Databionic-ESOM-User] automated data clustering?

[<fa...@my...>]

Dick,

Prof. Ultsch has developed a method for automated clustering, see

http://www.uni-marburg.de/fb12/datenbionik/pdf/pubs/2005/ultsch05clustering
http://www.uni-marburg.de/fb12/datenbionik/pdf/pubs/2005/ultsch05ustarc

If you contact him directly, he might be willing to share the matlab =20
code with you. I know that a student is working on integrating the =20
method into the ESOM tools but I don't know if and when it would be =20
available.

For the comparison of clusterings or evaluation with know results I =20
recommend to look up measures to compare classifications, for example =20
precision/recall, sensitivity/specificity. you can average these =20
measures over multiple clustering runs. Please be more specific if =20
these general methods do not suffice.

best
fabian

Quoting Greg Dick <gd...@be...>:

> Dear ESOM users,
>
> I am using ESOM to cluster DNA sequences from environmental  =20
> microorganisms, based on genome wide signatures (tetranucleotide  =20
> frequency).  Overall I am very happy with the results and it has  =20
> proven to be an extremely valuable tool for our research group.   =20
> There are two areas that we are hoping to develop further and I am  =20
> curious if anyone has suggestions or comments:
>
> (1) Are there any automated methods for clustering data?  The  =20
> boundaries for our clusters range from obvious to questionable.   =20
> While this variable strength of clustering is useful information in  =20
> itself, we would like to develop an automated method for defining  =20
> clusters in order to avoid potential errors in where we draw the  =20
> lines (it is not always entirely clear how to do so).
>
> (2) Are there statistical tools that have been developed or applied  =20
> to ESOM to evaluate the robustness of clustering (ideally on a  =20
> per-cluster basis)?  We are interested in such an analysis, which  =20
> would either be based on the U-matrix distance structure and/or an  =20
> evaluation of the accuracy of the clustering (for much of our data  =20
> we know the true cluster affiliations).
>
> Any suggestions or references relevant to these areas would be  =20
> greatly appreciated.
>
> Greg Dick
> Postdoctoral Research
> University of California, Berkeley
>
>

[Databionic-ESOM-User] installing ESOM on unix machine

[Greg D. <gd...@um...>]

Hello,

 

We are having trouble installing ESOM on a unix machine. any tips would be
greatly appreciated.

 

It seems the problem may be with maven - we've tried maven 2.2.1, but it
doesn't work and doesn't even have a binary called maven.

We've tried maven 1.1 and it failed with error:
Message: Unrecognised tag: 'license'

We removed the license section from project.xml and got the following error:
Message: Unrecognised tag: 'jars'

We then removed the jars section from project.xml and it did a fair amount
of compiling but ultimately failed:

>> The build cannot continue because of the following unsatisfied
dependencies:
- org.apache.velocity:velocity:1.5:jar
- org.apache.maven.scm:maven-scm-api:1.0-beta-2:jar
- org.apache.maven.scm:maven-scm-provider-cvs:1.0-beta-2:jar
- org.apache.maven.scm:maven-scm-provider-svn:1.0-beta-2:jar
- org.apache.maven.scm:maven-scm-provider-perforce:1.0-beta-2:jar
- org.apache.maven.scm:maven-scm-provider-clearcase:1.0-beta-2:jar
- org.apache.maven.scm:maven-scm-provider-starteam:1.0-beta-2:jar

Does anyone have any suggestions?

 

Thanks,

 

Greg Dick

University of Michigan

 

Re: [Databionic-ESOM-User] installing ESOM on unix machine

[Fabian M. <fa...@my...>]

Greg,

it should work with Maven 1.x as indicated in the manual. Maven 2 is
very different.
Not sure what the problem is you shouldn't have to remove tags.

fabian

Greg Dick wrote:
>
> Hello,
>
>  
>
> We are having trouble installing ESOM on a unix machine… any tips
> would be greatly appreciated.
>
>  
>
> It seems the problem may be with maven – we’ve tried maven 2.2.1, but
> it doesn’t work and doesn’t even have a binary called maven.
>
> We’ve tried maven 1.1 and it failed with error:
> Message: Unrecognised tag: 'license'
>
> We removed the license section from project.xml and got the following
> error:
> Message: Unrecognised tag: 'jars'
>
> We then removed the jars section from project.xml and it did a fair
> amount of compiling but ultimately failed:
>
> >> The build cannot continue because of the following unsatisfied
> dependencies:
> - org.apache.velocity:velocity:1.5:jar
> - org.apache.maven.scm:maven-scm-api:1.0-beta-2:jar
> - org.apache.maven.scm:maven-scm-provider-cvs:1.0-beta-2:jar
> - org.apache.maven.scm:maven-scm-provider-svn:1.0-beta-2:jar
> - org.apache.maven.scm:maven-scm-provider-perforce:1.0-beta-2:jar
> - org.apache.maven.scm:maven-scm-provider-clearcase:1.0-beta-2:jar
> - org.apache.maven.scm:maven-scm-provider-starteam:1.0-beta-2:jar
>
> Does anyone have any suggestions?
>
>  
>
> Thanks,
>
>  
>
> Greg Dick
>
> University of Michigan
>
>  
>
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