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O2vae integration rebase theirs #76

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O2vae integration rebase theirs #76

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ctr26
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@ctr26 ctr26 commented Oct 1, 2024

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ctr26 and others added 30 commits October 1, 2024 17:00
@ctr26
Early stopping on val loss to stop overfitting
e63ae25
@ctr26
Attempt at cli
04676b9
@ctr26
First attempt as arg hashing for checkpoints
0c9fe71
@afoix @ctr26
local changes to run
1cfc8e8
@afoix @ctr26
command line arguments
27c8a0f
@afoix @ctr26
enable testing + uncomment dataset
9ac9348
@afoix @ctr26
added a slurm python script
7d4e34a
@afoix @ctr26
fix cli type
1467975
@afoix @ctr26
add correct name for the jobs
5dfcb5f
@afoix @ctr26
Log f1 score mean and std in wandb
f2b8bec
@afoix @ctr26
choose memory allocation base on latent space size
d356a51
@afoix @ctr26
dynamically chose n gpus based on latent space size + fix mem allocat…
b5fdc99 
…ion as well
@afoix @ctr26
fix gpu allocation typo
97168a3
@afoix @ctr26
comment out all the mean and std login for f1
5fe27f9
@afoix @ctr26
added a --clear-checkpoints clarg
6834d9e
@afoix @ctr26
use wandblogger to log info (mean, std dev...)
a022b00
@afoix @ctr26
run individual jobs in own folder to work around checkpoints
c12ad1b
@afoix @ctr26
modification for slurm
57ab2f1
@afoix @ctr26
changes in the shape embed script
c0dc332
@afoix @ctr26
fix merge commit + add command line args for dataset (name and path) …
519c2f0 
…and wandb project
@afoix @ctr26
duplicated slurm script + specify dataset
7f9284b
@afoix @ctr26
Fix wandb logger
f9c2588
@afoix @ctr26
Add helakyoto dataset to the slurm script
5409eaf
@afoix @ctr26
Added allen dataset
efad1ed
@afoix @ctr26
Limit time per job increased to 24h
1c4483b
@afoix @ctr26
change back to use dataset name from clarg + change default wandb job…
df09279 
…name and latent space size
@afoix @ctr26
Added a tiny dataset for quick debugging (commented out in the slurm …
bc65954 
…script)
@afoix @ctr26
use specific gpu resource
e4d9c14
@afoix @ctr26
put back frobenius norm false
e4ca0f7
@ctr26
Probably should stratify
d85c59b
@afoix @ctr26
keep exploring potential plots
3538d1d
@afoix @ctr26
more graphs
558a33c
@afoix @ctr26
fix model name in shapeembed output csv
0b96ccc
@afoix @ctr26
Added loss / mse to shapeembed's generated csv
3c9c73f
@afoix @ctr26
updated slurm script with regex filtering of squeue output
23f4a3e
@afoix @ctr26
added a simple latex table to the gather_run_results script
0529483
@afoix @ctr26
minor refactor in efd
8a83f2a
@afoix @ctr26
minor refactor in regionprops
00f2ea8
@afoix @ctr26
generated plots and more tables in gather_run_results
c26bf23
@afoix @ctr26
added regionprops and efd to gather results script
c120280
@afoix @ctr26
Updated graphs titles
3f536bf
@afoix @ctr26
fake beta column if necessary and filter out regionprops and efd for …
0dba64d 
…f1 Vs Mse comparison
@afoix @ctr26
updated datasets + only find jobs and scores if corresponding filter …
d6e5d67 
…active
@afoix @ctr26
bugfix overwriting loop dataframe
1b0d180
@afoix @ctr26
dded a clarg to control region prop properties
c58b863
@afoix @ctr26
Added random order to efd and regionprops
f13364e
@afoix @ctr26
force different markers for scatter plot F1vMSE
0169334
@afoix @ctr26
updated scatterplot
51b2ccc
@afoix @ctr26
add standard deviation to the report for regions props and efd
c3d6578
@afoix @ctr26
modification slurm script
6e625b5
@afoix @ctr26
changes to test o2vae integration XXX relies on an adapted o2vae repo…
7ae6643 
… present in bioimage_embed/modles/o2vae
@afoix @ctr26
off-by-one in square recrop
3674971
@afoix @ctr26
added drop_last for uneven dataset sizes
5f0c02e
@afoix @ctr26
specialized slurm script
4b07568
@afoix @ctr26
added o2vae repo patch
e15c2c5
@ctr26 ctr26 force-pushed the master branch 5 times, most recently from 74b7ffc to 90a566a Compare October 9, 2024 09:20
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2 participants
@ctr26 @afoix