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Development #58

Merged
merged 34 commits into from
Nov 14, 2023
Merged

Development #58

merged 34 commits into from
Nov 14, 2023

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jyaacoub
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@jyaacoub jyaacoub commented Nov 8, 2023

  • ChemGPT results
  • cross-validation results
  • foldseek feature

jyaacoub and others added 30 commits November 6, 2023 11:35
@jyaacoub @papiClafoutis
results: davis-shannon CV #46 (#56)
b56c8e2 
* created ChemEsmDTA class

* results: davis-shannon CV #46 

---------

Co-authored-by: papiClafoutis <[email protected]>
Co-authored-by: Aleem Aamir <[email protected]>
@jyaacoub
results: davis-msa CV #46
06e3b62
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
a89849a 
… development
@jyaacoub
style: Update ChemGPT model name with "CDM" #52
48a5e1d
@jyaacoub
fix: overlap train test issue with new fold change
7a6f7d4
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
ba87123 
… development
@jyaacoub
style(DDP): Update output dir naming convention
27695a6
@jyaacoub
feat(figures): add fig4_pro_feat_violin #46
d90ad99
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
e1198ef 
… development
@jyaacoub
feat: foldseek stub code #53
ca006e9 
Fix target_to_graph function for scalability in features with new foldseek feature
@jyaacoub
Add function to run Foldseek for structural
0481f8c 
sequence extraction
@jyaacoub
results: davis edgeW cross val #46 #25
daa2822
@jyaacoub
feat(DDP): cluster-based configs and SLURM params
e4cd580
@jyaacoub
fix(foldseek): import json
c7bd6a2
@jyaacoub
feat: + fig5_edge_feat_violin plot #46 #25
5ad3c52
@jyaacoub
fix: plt.show in fig4 and fig5
68174dc
@jyaacoub
refactor: new load_datasets fn in loader cls
4c91cd2
@jyaacoub
results: fold 0 and 1 for davis-EDI
86da730
@jyaacoub
refactor: training.py and add train_tune function
5fa65af 
to tuning.py
@jyaacoub
refactor: remove versions from requirements.txt
e25baf9
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
c52bf9a 
… development
@jyaacoub
feat(datasets): feature extraction for foldseek
2e2f924
@jyaacoub
fix(datasets): update sequence to include 3Di
88aa029
@jyaacoub
fix: deprecate self.shannon attribute
0eadb2a
@jyaacoub
fix(config): use path.home to get home dir #53
bfabacf
@jyaacoub
fix: structural info check for DavisKibaDataset
29d7586
@jyaacoub
fix: KeyError in protein feature extraction
6fc396a
@jyaacoub
fix(foldseek): dataset created successfully #53
9dc24c4
@jyaacoub
results: davis-EDI folds 2-4
e9f4be5
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
3f09148 
… development
@jyaacoub jyaacoub merged commit e6077d0 into main Nov 14, 2023
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