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Cross-val results for kiba and PDBbind #62

Merged
merged 34 commits into from
Nov 22, 2023
Merged

Cross-val results for kiba and PDBbind #62

merged 34 commits into from
Nov 22, 2023

Commits on Nov 3, 2023

  1. created ChemEsmDTA class

    @papiClafoutis
    papiClafoutis committed Nov 3, 2023
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Commits on Nov 6, 2023

  1. results: davis-shannon CV

    Aleem Aamir committed Nov 6, 2023
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  2. Merge branch 'ligand-dev' of https://github.com/jyaacoub/MutDTA into … 

    …ligand-dev
    Aleem Aamir committed Nov 6, 2023
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  3. added two more layers

    @papiClafoutis
    papiClafoutis committed Nov 6, 2023
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  4. Merge branch 'ligand-dev' of https://github.com/jyaacoub/MutDTA into … 

    …ligand-dev
    @papiClafoutis
    papiClafoutis committed Nov 6, 2023
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Commits on Nov 14, 2023

  1. results: davis-shannon CV

    @jyaacoub
    Aleem Aamir authored and jyaacoub committed Nov 14, 2023
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  2. added two more layers

    @papiClafoutis @jyaacoub
    papiClafoutis authored and jyaacoub committed Nov 14, 2023
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  3. Merge branch 'ligand-dev' of https://github.com/jyaacoub/MutDTA into … 

    …ligand-dev
    @jyaacoub
    jyaacoub committed Nov 14, 2023
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  4. Merge pull request #59 from jyaacoub/ligand-dev 

    Ligand dev
    @jyaacoub
    jyaacoub authored Nov 14, 2023
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  5. feat: grouped cc #60

    @jyaacoub
    jyaacoub committed Nov 14, 2023
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Commits on Nov 15, 2023

  1. feat(training): balanced_kfold_split #60

    @jyaacoub
    jyaacoub committed Nov 15, 2023
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  2. fix: using new kfold fn in init_data #60 

    Also playground contains plots for analysis of distributions.
    @jyaacoub
    jyaacoub committed Nov 15, 2023
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  3. fix(PDBbind): af2 and aln dir path 

    + update af2 file path for PDBbind
+ update aln_p to point to new PDBbind_aln dir instead in the init_dataset.py file.
+ Check to ensure aln file is not empty

Also recleaned aln files with MSARunner that were not cleaned before.
    @jyaacoub
    jyaacoub committed Nov 15, 2023
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  4. feat: support for Narval cluster with A100 GPUs

    @jyaacoub
    jyaacoub committed Nov 15, 2023
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Commits on Nov 16, 2023

  1. fix(figures): pearson and spearman is max

    @jyaacoub
    jyaacoub committed Nov 16, 2023
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  2. results: kiba af2 and anm0-3

    @jyaacoub
    jyaacoub committed Nov 16, 2023
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  3. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 16, 2023
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Commits on Nov 17, 2023

  1. results: PDBbind msa shannon cc

    @jyaacoub
    jyaacoub committed Nov 17, 2023
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  2. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 17, 2023
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  3. results: PDBbind ESM cv

    @jyaacoub
    jyaacoub committed Nov 17, 2023
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  4. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
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  5. results: PDBbind_nomsa & kiba_msa-shannon

    @jyaacoub
    jyaacoub committed Nov 17, 2023
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  6. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development

Conflicts:
	results/model_media/model_stats.csv
	results/model_media/model_stats_val.csv
    @jyaacoub
    jyaacoub committed Nov 17, 2023
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Commits on Nov 21, 2023

  1. results: kiba nomsa and simple crossval

    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  2. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  3. results: PDBbind anm and af2 crossval

    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  4. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development
    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  5. results: PDBbind simple crossval

    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  6. Merge branch 'development' of https://github.com/jyaacoub/MutDTA into… 

    … development

Conflicts:
	results/model_media/model_stats_val.csv
    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  7. fix(figs): set add_stats default to True

    @jyaacoub
    jyaacoub committed Nov 21, 2023
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  8. fix(figures): add check for esm results

    @jyaacoub
    jyaacoub committed Nov 21, 2023
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Commits on Nov 22, 2023

  1. feat(test): no_rename option 

    Useful for when the model is currently being trained and we dont want to update the state dict and we just want to see results.
    @jyaacoub
    jyaacoub committed Nov 22, 2023
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  2. results: kiba EDI cross val

    @jyaacoub
    jyaacoub committed Nov 22, 2023
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  3. fix(figures): resolves #61

    @jyaacoub
    jyaacoub committed Nov 22, 2023
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