pctwass
commented
1 month ago Hi Michael. These hyperparameter may be added to a specific hyperparameter file used by (approx) aligned UMAP (as is configured in the config file (see the dict [hyperparameter-config-files] in config/config.toml). I have updated the UMAP hyperparameter file to reflect this (see configs/hyperparameters/hyperparameters_umap.toml).
This behaviour should be explained in the user guide. Have you checked the Configuration File section of the guide? It is described in the second paragraph, just above the General Settings subsection. Perhaps I did not explain it clearly in the guide.
I rather not move these into the general config, because these hyperparameters are specific to aligned UMAP
Peter, I could not locate the hyperparameter settings for the alignment. Would it make sense to include them into the "configs" folder somewhere? Overall, as you managed to identify those hyperparameters which virtually have no / minimal influence, and those (regularization strength) that have an influence, please consider adding comments to each of them about this. For those with an influence, provide approx. suitable ranges would be very useful to have.