How to use ELKI for DBSCAN with precomputed distance matrix

Question

I've a precomputed distance matrix for all the points in my database. I'm trying to invoke ELKI gui with following command:

            /usr/share/java/elki.jar 
            -dbc.in xml_files.1000 
            -dbc.filter FixedDBIDsFilter 
            -dbc.startid 0 
            -algorithm clustering.DBSCAN 
            -algorithm.distancefunction external.FileBasedDoubleDistanceFunction 
            -distance.matrix Distance.txt 
            -dbscan.epsilon 1 
            -dbscan.minpts 10

But I keep getting following error message :

Wrong parameter format! Parameter "dbscan.epsilon" requires a distance value, but the distance was not set!

I can't figure out what am I doing wrong here...

Answer 1

Which version of ELKI are you using?

This error message usually indicates an issue with the distance parser used by the matrix reader.

Since ELKI supports different valued distance functions, DBSCAN cannot parse the epsilon parameter until the actual distance value type is known (which will provide the value parsing function).

Any earlier error message? If you have any earlier error (including missing required parameters), it will prevent DBSCAN from being able to parse the value.

Try setting the epsilon value last, and also try the command line. In the MiniGUI, due to the incremental way the parameters are set, these dynamic-typed parameters unfortunately can be flaky. Any patch to improve the handling of such parameters is appreciated.