Feature_perc

[amissarova]

Hi!

I was wondering about the rationale for feature_perc = 0.5 and not 1? Are any particular reasons to randomly select features (besides computational complexity)?

Thanks!

[skinnider]

Nope, just a way to reduce the runtime.

[amissarova]

cool, thanks

[amissarova]

related q: I just tried running augur with feature_perc = 1. I would have expected that for each gene, each subsampling and each fold I will now get importance score - but it is not the case (there are some subsampling where I dont have an input for this gene). Why?
Thanks!

[skinnider]

By default 50% of genes will be filtered out with select_variance - are they there when setting var_quantile=0?

[amissarova]

Hey,
I now set feature_perc = 1 and var_quantile = 0 --> for some genes, I still dont have an importance score entry for some of the subsamplings.

[amissarova]

Guess that possibly happens coz of the initial hard-coded filtering of genes with no variance (for given downsampling)? Or are there some other reasons?

[skinnider]

That seems plausible, yes.