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Class balanced sampling #524

Merged
merged 40 commits into from
Aug 10, 2024
Merged

Class balanced sampling #524

merged 40 commits into from
Aug 10, 2024

Commits on Jan 29, 2024

  1. feat: add data/check_pandas.py

    @MicPie
    MicPie committed Jan 29, 2024
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  2. add data/check_smiles_split.py

    @MicPie
    MicPie committed Jan 29, 2024
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  3. update kg meta.yaml files

    @MicPie
    MicPie committed Jan 29, 2024
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  4. add data/natural

    @MicPie
    MicPie committed Jan 29, 2024
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  5. add dataset scripts

    @MicPie
    MicPie committed Jan 29, 2024
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  6. update data/text_sampling/

    @MicPie
    MicPie committed Jan 29, 2024
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  7. update meta and transform

    @MicPie
    MicPie committed Jan 29, 2024
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  8. additional fixes

    @MicPie
    MicPie committed Jan 29, 2024
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  9. apply pre-commit hook

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    MicPie committed Jan 29, 2024
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  10. sort exclude_from_standard_tabular_text_templates

    @MicPie
    MicPie committed Jan 29, 2024
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Commits on Jan 31, 2024

  1. more fixes (#517) 

    * fix: use SMILES__description instead of SMILES__names__noun for mol. repr. sampling

* fix: mol_repr_transl/transform.py w/o SMILES with H and with split col only

* fix: exclude uniprot binding ..

* fix: missing ! and wrong variable name in template

* fix: missing ! in templates

* fix: and rheadb and sort exclude_from_standard_tabular_text_templates

* fix: RedDB templates and fully export to meta.yaml

* fix: aminoacids templates var name

* fix: polymer_data templates var name

* fix: var dtypes

* fix: name and id

* fix: add rdkit_features to /exclude_from_standard_tabular_text_templates

* fix: # missing in template var

* fix: # missing in template var 2

* fix: fix dialogue template in compound_protein_compound_*

* fix: QC templates 1

* update reddb

* update zhu

* add description of representation

* orexin1_receptor_butkiewicz

* smiles__description

* molecule with SMILES

* fix: QC templates 2

* fix: QC templates 3

* fix: QC templates 3

* fix: QC templates

* fix: QC templates

* fix: QC templates

* fix: QC templates

* add organism

* make explicit

* add representation name

* add representation name

* update standard templates

* add representation name

* add representation names

* representation name use

* smiles usage

* must to

* add representation name

* Update data/kg/compound_protein_protein/meta.yaml

Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>

* Update data/tabular/freesolv/meta.yaml

Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>

* Update data/tabular/freesolv/transform.py

Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>

* Update data/tabular/freesolv/transform.py

Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>

* Update data/tabular/sr_p53_tox21/meta.yaml

Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>

* Update data/kg/compound_protein_protein/meta.yaml

* Update data/kg/compound_protein_protein/meta.yaml

* Update data/kg/compound_protein_protein/meta.yaml

* Update data/tabular/freesolv/meta.yaml

* Update data/tabular/sr_p53_tox21/meta.yaml

* Update data/kg/compound_protein_compound_1/meta.yaml

* Update data/kg/compound_protein_compound_1/meta.yaml

* Update data/kg/compound_protein_compound_1/meta.yaml

* Update data/kg/compound_protein_compound_1/meta.yaml

* Update data/kg/compound_protein_compound_1/meta.yaml

* Update data/kg/compound_protein_compound_3/meta.yaml

* Update data/kg/compound_protein_compound_3/meta.yaml

* Update data/kg/compound_protein_compound_3/meta.yaml

* Update data/kg/compound_protein_compound_3/meta.yaml

* Update data/kg/compound_protein_compound_3/meta.yaml

* Update data/kg/compound_protein_go_term_1/meta.yaml

* Update data/kg/compound_protein_go_term_1/meta.yaml

* Update data/kg/compound_protein_go_term_2/meta.yaml

* Update data/kg/compound_protein_go_term_2/meta.yaml

* Update data/kg/compound_protein_go_term_3/meta.yaml

* Update data/kg/compound_protein_go_term_3/meta.yaml

* Update data/kg/compound_protein_go_term_4/meta.yaml

* Update data/kg/compound_protein_go_term_4/meta.yaml

* Update data/kg/compound_protein_pathway_disease_2/meta.yaml

* Update data/kg/drug_protein_hpo_disease/meta.yaml

* Update data/tabular/chemcaption_rdkit/meta.yaml

* Update data/tabular/mona/meta.yaml

* Update data/tabular/mona/transform.py

---------

Co-authored-by: Michael Pieler <Michael.Pieler@Gmail.com>
Co-authored-by: Kevin Maik Jablonka <kevin.jablonka@epfl.ch>
Co-authored-by: Michael Pieler <36303596+MicPie@users.noreply.github.com>
    @kjappelbaum @MicPie
    4 people authored Jan 31, 2024
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  2. additional fixes

    @MicPie
    MicPie committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. Update data/check_pandas.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  2. Update data/check_pandas.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  3. Update data/check_smiles_split.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  4. Update data/natural/preprocess_europepmc.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  5. Update data/natural/preprocess_msds.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  6. Update data/natural/preprocess_nougat.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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  7. Update data/postprocess_split.py 

    Co-authored-by: Kevin M Jablonka <32935233+kjappelbaum@users.noreply.github.com>
    @MicPie @kjappelbaum
    MicPie and kjappelbaum authored Feb 1, 2024
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Commits on Feb 5, 2024

  1. additional fixes 2

    @MicPie
    MicPie committed Feb 5, 2024
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  2. additional fixes 3

    @MicPie
    MicPie committed Feb 5, 2024
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  3. additional fixes 4

    @MicPie
    MicPie committed Feb 5, 2024
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  4. additional fixes 5

    @MicPie
    MicPie committed Feb 5, 2024
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  5. additional fixes 6

    @MicPie
    MicPie committed Feb 5, 2024
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  6. additional fixes 7

    @MicPie
    MicPie committed Feb 5, 2024
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  7. additional fixes 8

    @MicPie
    MicPie committed Feb 5, 2024
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  8. remove linebreak

    @kjappelbaum
    kjappelbaum authored Feb 5, 2024
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  9. remove linebreak

    @kjappelbaum
    kjappelbaum authored Feb 5, 2024
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  10. Delete data/tabular/bicerano_dataset/meta.yaml 

    those changes are incorrect, the CTE and density are not there for all polymers
    @kjappelbaum
    kjappelbaum authored Feb 5, 2024
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Commits on Feb 6, 2024

  1. feat: update yamls

    @MicPie
    MicPie committed Feb 6, 2024
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Commits on Feb 8, 2024

  1. feat: draft class balanced sampling

    @MicPie
    MicPie committed Feb 8, 2024
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  2. feat: resolve merge conflicts with main

    @MicPie
    MicPie committed Feb 8, 2024
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  3. feat: update to latest sampling setup

    @MicPie
    MicPie committed Feb 8, 2024
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  4. feat: pre-commit fixes

    @MicPie
    MicPie committed Feb 8, 2024
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  5. feat: pre-commit fixes 2

    @MicPie
    MicPie committed Feb 8, 2024
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  6. Merge branch 'main' into class_balanced_sampling

    @MicPie
    MicPie committed Feb 8, 2024
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Commits on Feb 9, 2024

  1. feat: update benchmarking text sampling

    @MicPie
    MicPie committed Feb 9, 2024
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Commits on Aug 10, 2024

  1. feat: update

    @MicPie
    MicPie committed Aug 10, 2024
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  2. Update data/text_sampling/text_sampling.py

    @kjappelbaum
    kjappelbaum authored Aug 10, 2024
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  3. Update data/text_sampling/text_sampling.py

    @kjappelbaum
    kjappelbaum authored Aug 10, 2024
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