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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

Commits on Nov 6, 2023

  1. results: davis-shannon CV #46 (#56) 

    * created ChemEsmDTA class

* results: davis-shannon CV #46 

---------

Co-authored-by: papiClafoutis <[email protected]>
Co-authored-by: Aleem Aamir <[email protected]>
    @jyaacoub @papiClafoutis
    3 people authored Nov 6, 2023
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  2. results: davis-msa CV #46

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    jyaacoub committed Nov 6, 2023
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  3. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
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Commits on Nov 7, 2023

  1. style: Update ChemGPT model name with "CDM" #52

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  2. fix: overlap train test issue with new fold change

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    jyaacoub committed Nov 7, 2023
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  3. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 7, 2023
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  4. style(DDP): Update output dir naming convention

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    jyaacoub committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. feat(figures): add fig4_pro_feat_violin #46

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  2. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
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  3. feat: foldseek stub code #53 

    Fix target_to_graph function for scalability in features with new foldseek feature
    @jyaacoub
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Commits on Nov 9, 2023

  1. Add function to run Foldseek for structural 

    sequence extraction
    @jyaacoub
    jyaacoub committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. results: davis edgeW cross val #46 #25

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  2. feat(DDP): cluster-based configs and SLURM params

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  3. fix(foldseek): import json

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  4. feat: + fig5_edge_feat_violin plot #46 #25

    @jyaacoub
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Commits on Nov 12, 2023

  1. fix: plt.show in fig4 and fig5

    @jyaacoub
    jyaacoub committed Nov 12, 2023
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  2. refactor: new load_datasets fn in loader cls

    @jyaacoub
    jyaacoub committed Nov 12, 2023
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Commits on Nov 13, 2023

  1. results: fold 0 and 1 for davis-EDI

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  2. refactor: training.py and add train_tune function 

    to tuning.py
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    jyaacoub committed Nov 13, 2023
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  3. refactor: remove versions from requirements.txt

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  4. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
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  5. feat(datasets): feature extraction for foldseek

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  6. fix(datasets): update sequence to include 3Di

    @jyaacoub
    jyaacoub committed Nov 13, 2023
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  7. fix: deprecate self.shannon attribute

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  8. fix(config): use path.home to get home dir #53

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  9. fix: structural info check for DavisKibaDataset

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  10. fix: KeyError in protein feature extraction

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  11. fix(foldseek): dataset created successfully #53

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    jyaacoub committed Nov 13, 2023
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  12. results: davis-EDI folds 2-4

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    jyaacoub committed Nov 13, 2023
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  13. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
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  14. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 13, 2023
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  15. fix: added ESM to fig4 violin #46

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    jyaacoub committed Nov 13, 2023
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  16. feat(Loader): added SaProt option 'SPD'

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    jyaacoub committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. feat: protein stratification analysis for Davis#57

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    jyaacoub committed Nov 14, 2023
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