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resolves #113 #117

Merged
merged 32 commits into from
Jul 9, 2024
Merged

resolves #113 #117

merged 32 commits into from
Jul 9, 2024

Commits on Jun 21, 2024

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  2. results(davis): gvpl_aflow with corrected hparams #90

    Due to logic error in code previous results was just functioning as jus gvpl (no aflow). See 8c89a24.
    jyaacoub committed Jun 21, 2024
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Commits on Jun 25, 2024

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Commits on Jun 26, 2024

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  2. fix(tuned): davis_DG params + loader #90

    To evaluate sequence length vs mse
    jyaacoub committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. refactor(playground): prediction with tuned models moved to its own s…

    …cript #90
    
    For plotting sequence length vs mse
    jyaacoub committed Jun 27, 2024
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Commits on Jun 28, 2024

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Commits on Jul 2, 2024

  1. results(GVPL_ESM): davis GVPL+esm performance #90

    Underwhelming peformance, ESM didnt help at all with GVPL_aflow model
    jyaacoub committed Jul 2, 2024
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  2. results(kiba): updated gvpL_aflow results #90

    Accounting for error in aflow not being used.
    jyaacoub committed Jul 2, 2024
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Commits on Jul 3, 2024

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  5. fix(loader): init_dataset_object and splitting overlap issue #112 #113

    Example usage:
    ```python
    #%% now based on this test set we can create the splits that will be used for all models
    # 5-fold cross validation + test set
    import pandas as pd
    from src import cfg
    from src.train_test.splitting import balanced_kfold_split
    from src.utils.loader import Loader
    
    test_df = pd.read_csv('/home/jean/projects/data/splits/davis_test_genes_oncoG.csv')
    test_prots = set(test_df.prot_id)
    
    db = Loader.load_dataset(f'{cfg.DATA_ROOT}/DavisKibaDataset/davis/nomsa_binary_original_binary/full/')
    
    #%%
    train, val, test = balanced_kfold_split(db,
                    k_folds=5, test_split=0.1, val_split=0.1,
                    test_prots=test_prots, random_seed=0, verbose=True
                    )
    
    #%%
    db.save_subset_folds(train, 'train')
    db.save_subset_folds(val, 'val')
    db.save_subset(test, 'test')
    ```
    jyaacoub committed Jul 3, 2024
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Commits on Jul 4, 2024

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  4. feat: davis splits #112 #113

    jyaacoub committed Jul 4, 2024
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Commits on Jul 5, 2024

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  2. refactor(playground): #113

    jyaacoub committed Jul 5, 2024
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Commits on Jul 6, 2024

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Commits on Jul 8, 2024

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Commits on Jul 9, 2024

  1. results(davis): retrained aflow models #113 due to issue #116

    still need to train esm variants to complete #113 for davis
    jyaacoub committed Jul 9, 2024
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