Dear All,

Our first suggestion is to drop the "[]" in the compound_uris[], ...
parameter names for version 1.2 as they complicate things with URIs.

Second, to include our newly developed algorithms as webservices in
OpenTox, it will be necessary to extend the current API 1.1 a little
bit. For Jörg's multi-label algorithm we would need to change the
prediction_feature parameter in the Algorithm API to
prediction_features[] (or prediction_features, if we drop the brackets).
as there will be more than one feature predicted at the same time. The
model API and model RDF representation can be left unchanged in our
opinion. For validating the multi-label classification there will be new
validation measures. 

Multi Label measures are calculated similar to normal classification
measures. Some are just adapted and micro or macro averaged over the
predictions (Micro or Macro AUC, Precision, Recall, F1...). Others are
introduced for the ranking output of some classifiers (One-error,
coverage, Ranking Loss,...). In the results, we could still use a
similar format as for classification and use the micro and macro
averaged values and the new measures. 

The second algorithm that will need changes (CDE - conditional density
estimation) generates not single prediction values, but prediction
intervals. We propose to just update the dataset with 2 columns
(interval start and end) instead of 1 (predicted value). Here, too, for
validation there will be three additional measures that evaluate the
quality of the predicted intervals. 

Any comments, or suggestions?

Regards,
TUM OpenTox Team

-- 
Dipl.-Bioinf. Tobias Girschick

Technische Universität München
Institut für Informatik
Lehrstuhl I12 - Bioinformatik
Bolzmannstr. 3
85748 Garching b. München, Germany

Room: MI 01.09.042
Phone: +49 (89) 289-18002
Email: tobias.girschick at in.tum.de
Web: http://wwwkramer.in.tum.de/girschick