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Protein function prediction with GO - Part 3 #64

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Protein function prediction with GO - Part 3 #64

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Commits on Nov 4, 2024

  1. script to evaluate go predictions

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  2. Merge branch 'dev' into protein_prediction

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    aditya0by0 committed Nov 4, 2024
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  3. add fmax to evaluation script

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    aditya0by0 committed Nov 4, 2024
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  4. Merge branch 'dev' into protein_prediction

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    aditya0by0 committed Nov 4, 2024
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Commits on Nov 5, 2024

  1. add base code for deep_go data migration 

    - migration from deep go format to chebai->go_uniprot format
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    aditya0by0 committed Nov 5, 2024
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  2. varry fmax threshold as per paper

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    aditya0by0 committed Nov 5, 2024
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  3. go_uniprot: add sequence len to docstring

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    aditya0by0 committed Nov 5, 2024
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Commits on Nov 6, 2024

  1. update experiment evidence codes as per DeepGo SE 

    - #36 (comment)
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    aditya0by0 committed Nov 6, 2024
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  2. Merge branch 'dev' into protein_prediction

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    aditya0by0 committed Nov 6, 2024
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  3. consIder X as a valid amino acid as per DeepGO-SE 

    - #36 (comment)
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    aditya0by0 committed Nov 6, 2024
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  4. deepgo se mirgration : add class to migrate

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    aditya0by0 committed Nov 6, 2024
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  5. Merge branch 'dev' into protein_prediction

    @aditya0by0
    aditya0by0 committed Nov 6, 2024
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Commits on Nov 7, 2024

  1. migration: rectify errors

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    aditya0by0 committed Nov 7, 2024
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  2. protein trigram containing tokenS with X 

    - #36 (comment)
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    aditya0by0 committed Nov 7, 2024
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  3. protein token unigram contain X 

    - #36 (comment)
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    aditya0by0 committed Nov 7, 2024
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Commits on Nov 11, 2024

  1. add migration for deepgo1 - 2018 paper

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    aditya0by0 committed Nov 11, 2024
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Commits on Nov 12, 2024

  1. deepgo1: create non-exclusive val set as a placeholder

    @aditya0by0
    aditya0by0 committed Nov 12, 2024
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Commits on Nov 13, 2024

  1. deepgo1: further split train set into train and val for 

    - +migration structure changes
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    aditya0by0 committed Nov 13, 2024
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  2. migration script update

    @aditya0by0
    aditya0by0 committed Nov 13, 2024
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  3. add classes to use migrated deepgo data

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    aditya0by0 committed Nov 13, 2024
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  4. deepgo: minor code change

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    aditya0by0 committed Nov 13, 2024
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  5. modify prints to display actual file name

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    aditya0by0 committed Nov 13, 2024
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Commits on Nov 17, 2024

  1. create sub dir for deego dataset and move rel files

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    aditya0by0 committed Nov 17, 2024
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  2. update imports as per new deepGO dir

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    aditya0by0 committed Nov 17, 2024
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  3. update import dir for pretrain test

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    aditya0by0 committed Nov 17, 2024
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Commits on Dec 4, 2024

  1. migration fix : truncate seq and save data with labels

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    aditya0by0 committed Dec 4, 2024
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  2. Delete protein_protein_interactions.py

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    aditya0by0 committed Dec 4, 2024
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  3. migration: replace invalid amino acid with "X" notation 

    - #64 (comment)
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    aditya0by0 committed Dec 4, 2024
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  4. update deepgo configs

    @aditya0by0
    aditya0by0 committed Dec 4, 2024
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