Closed gwaybio closed 6 years ago
I agree with @jaclyn-taroni comments. Just curious as to why a completely new script instead of modifying tybalt_vae.py
?
I have the same question as @danich1, that's what I was trying to get at. I thought it might be for notebook reasons?
Just curious as to why a completely new script instead of modifying tybalt_vae.py?
I thought it might be for notebook reasons?
Precisely. I think it would be best to keep the nbconverted scripts separate from scripts run consistently. If they are not separate, when a notebook changes, it would get messy quick.
Do you think the repo would be better organized with a scripts/nbcovert/
folder storing these scripts instead?
I concur on separating out the nbconverted scripts. Better to separate them off to avoid confusion about which is suppose to be a converted script and what is suppose to be a run-consistent script.
thanks @danich1 and @jaclyn-taroni - I believe b895ece addresses your concerns. I also believe that some portion of concern is regarding redundancy and I definitely agree.
Portions of this code base are getting entirely too redundant, and this realization prompts refactorization (see #74 for more details).
I concur on separating out the nbconverted scripts. Better to separate them off to avoid confusion about which is suppose to be a converted script and what is suppose to be a run-consistent script.
Sounds good. in the next commit, inside this PR (I will also rename the PR). I will reorganize nbconverted scripts.
thanks @danich1 and @jaclyn-taroni - ready for review again
@gwaygenomics - Does your output change when setting kernel_initializer='glorot_uniform'
in your decoder in b895ece
? If so, should probably update those files as well here
Does your output change when setting kernel_initializer='glorot_uniform' in your decoder in b895ece?
Good catch. It does not change since glorot_uniform
is the default. I add it here for consistency and to remove those concerns.
A lot of intermediate files being added in the PR in commit 9997c6d. These files are the result of a parameter sweep of a two hidden layer model (5000 -> 100 -> 100 -> 100 -> 5000). Commit 2b61e96 adds the compiled file with git LFS.
The main file changes include adding options to the parameter sweep script (cd77571) and adding a script that actually trains the models (7abeb7b). This script is very similar to the tybalt notebook.