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modified create splits and data processing script, and created splits… #1

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modified create splits and data processing script, and created splits… #1

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kimele2003
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… for different property sets

kevingreenman and others added 30 commits February 4, 2022 21:59
@kevingreenman
Update README with journal citation
28a8078
@kevingreenman
Add Zenodo model files link
04eb1f8
@kevingreenman
Fix typo
3d51622
@kevingreenman
Update citation with more info
01775e0
@kevingreenman
Update citation cff file with new doi
9706fd2
@kevingreenman
added Colab examples notebook
1bc4dac
@kimele2003
modified create splits and data processing script, and created splits…
7890c7e 
… for different property sets
@kimele2003
modified create splits and data processing script, and created splits…
fe6d75f 
… for different property sets
@kimele2003
made scripts and notebook for training/predicting
e0d5c41
@kimele2003
made scripts and notebook for training/predicting
6f7f0dc
@kimele2003
made bash scripts and ran predictions for all property combos
b67adb1
@kimele2003
made bash scripts and ran predictions for all property combos
2a9a19e
@kimele2003
created prediction plots table and modified data cleaning, splits, an…
ea99203 
…d predict scripts for same test set
@kimele2003
created prediction plots table and modified data cleaning, splits, an…
ce7535c 
…d predict scripts for same test set
@kimele2003
same test set csvs for absPeak and emiPeak
fa91a5b
@kimele2003
same test set csvs for absPeak and emiPeak
7c54840
@kimele2003
removed test scripts and notebooks
aedc92c
@kimele2003
removed test scripts and notebooks
3cc63e2
@kimele2003
absolute paths in predict2 script and made batch scripts for same tes…
75e1bb9 
…t set
@kimele2003
absolute paths in predict2 script and made batch scripts for same tes…
3dbc76f 
…t set
@kimele2003
ran batch scripts for same test set
565d533
@kimele2003
ran batch scripts for same test set
0496f3f
@kimele2003
created table for comparing same test set prediction plots
03c6068
@kimele2003
created table for comparing same test set prediction plots
1e5f4d3
added chemprop_sigopt_engaging.py script
b8e6cba
added chemprop_sigopt_engaging.py script
12e84ce
@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
c048aae 
merging for first time
@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
d2bb9d4 
merging for first time
@kimele2003
added bash script
18328fe
@kimele2003
added bash script
6a7a61f
@kimele2003
added relative paths to all bash scripts
466e54a
@kimele2003
added relative paths to all bash scripts
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@kimele2003
changed relative paths in bash scripts
cd9bc7d
@kimele2003
changed relative paths in bash scripts
2d25b22
@kimele2003
updated gen_bash2
e51e937
@kimele2003
updated gen_bash2
656a9f7
@kimele2003
corrected prop_split_args
f5bdf89
@kimele2003
corrected prop_split_args
292b19e
@kimele2003
corrected hyperparam opt template bash script
06439a6
@kimele2003
corrected hyperparam opt template bash script
eabec8b
@kimele2003
activate uvvisml instead of chemprop
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@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
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@kimele2003
changed location of hyperparam opt py script
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@kimele2003
changed location of hyperparam opt py script
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@kimele2003
added epoch args
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@kimele2003
added epoch args
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@kimele2003
first sbatch runs of all combos
a224b2d
@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
8e024d5
@kimele2003
updated hyperparam opt py script
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@kimele2003
updated hyperparam opt py script
7fdc4af
@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
d0bc4f1 
pull updated hyperparam opt py script
@kimele2003
modified gitignore
ae5d525
@kimele2003
Merge branch 'main' of github.com:kimele2003/uvvisml into main
8be1a86 
commiting merge for chemprop

Conflicts:
	uvvisml/chemprop
@kimele2003
uvvisml/chemprop directory
9ab6fea
@kimele2003
renamed and removed duplicate files
8ef48ab
@kimele2003
moved and renamed documentation file
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@kimele2003
reorganized files in bash_scripts and pred_plots_metrics dirs
ba74cdc
@kimele2003
recovered pred_plots_same_test_set notebook and updated docs
55737e9
@kevingreenman
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Hey, great job on the UVVisML PR! I have a few suggestions:

  • remove Miniconda3-latest-Linux-x86_64.sh file and add to .gitignore
  • remove uvvisml/Miniconda3-py37_4.8.3-Linux-x86_64.sh file and add to .gitignore
  • in the .gitignore, should the last line be "models.tar.gz.1" or "models.tar.gz"?
  • the documentation.md looks great! One suggestion for making it a bit more readable: I recommend using the `` quotes for any file or directory names in the paragraphs. It looks like you used those for file names already, but I think also using them for directories is a good idea. Eventually I think we'll want to combine this file with README.md, but it's okay in the separate file for now.
  • In each subdirectory of bash_scripts/, you have a symbolic link to either predict2.py or chemprop_sigopt_engaging.py. But I'm not sure these links are pointing to the correct places (they all point one directory up, but I the scripts they point to are not one directory up)
  • Could you move predict2.py and predict2.ipynb into the uvvisml/ directory so they'd be in the same place as uvvisml/predict.py? You'll have to change the code in these a bit to account for the new location, so run a few tests to make sure that it works like it did before from the new location

After you make these changes, I think we can merge it into a new branch on the public repo

@kevingreenman kevingreenman changed the base branch from main to multi-property May 17, 2022 16:07
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2 participants
@kimele2003 @kevingreenman