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Training new pocket representation #135

Merged
merged 11 commits into from
Sep 15, 2024
Merged

Training new pocket representation #135

merged 11 commits into from
Sep 15, 2024

Commits on Aug 2, 2024

  1. refactor(config): update issue number for pockets #103

    @jyaacoub
    jyaacoub committed Aug 2, 2024
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  2. Merge branch 'main' into v103

    @jyaacoub
    jyaacoub authored Aug 2, 2024
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Commits on Aug 6, 2024

  1. fix(splitting): checks that split worked

    @jyaacoub
    jyaacoub committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. fix(pocket_alignment): in place modification, offline setup, and edge… 

    … index renumbering #103

- Had to make some modifications since edge index needs to be updated after applying the mask so that it still points to the right nodes and we dont get something like an "IndexError" for being out of bounds

- Also error due to not removing all proteins without pocket sequences (line 216 saved the old dataset instead of the new one).

- Successfully built pocket datasets for davis and kiba

#131 #103
    @jyaacoub
    jyaacoub committed Aug 7, 2024
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  2. Merge branch 'pocket-training-v103' into v103

    @jyaacoub
    jyaacoub authored Aug 7, 2024
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  3. Merge pull request #134 from jyaacoub/v103 

    Merging two branches for #103
    @jyaacoub
    jyaacoub authored Aug 7, 2024
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Commits on Aug 12, 2024

  1. results(davis): pocket version on DG and aflow #103 

    Aflow still underperforms here...
    @jyaacoub
    jyaacoub committed Aug 12, 2024
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Commits on Aug 16, 2024

  1. fix(esm): apply pocket mask to ESM embeddings #103

    @jyaacoub
    jyaacoub committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. fix(loader): no support for shuffle with DDP

    @jyaacoub
    jyaacoub committed Aug 19, 2024
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Commits on Aug 20, 2024

  1. results(kiba): DG and aflow pocket #103

    @jyaacoub
    jyaacoub committed Aug 20, 2024
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Commits on Sep 15, 2024

  1. Merge branch 'main' into pocket-training-v103

    @jyaacoub
    jyaacoub authored Sep 15, 2024
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