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added autogluon support, more models, more preprocessing strategies #81

Merged
merged 65 commits into from
Sep 10, 2024
Merged

added autogluon support, more models, more preprocessing strategies #81

merged 65 commits into from
Sep 10, 2024

Commits on Aug 19, 2024

  1. added autogluon support

    @Oufattole
    Oufattole committed Aug 19, 2024
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  2. updates for autogluon

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

  1. [wip] filtering features

    @teyaberg
    teyaberg committed Aug 20, 2024
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  2. [wip] filtering features

    @teyaberg
    teyaberg committed Aug 20, 2024
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  3. [wip] sharing for updates only

    @teyaberg
    teyaberg committed Aug 20, 2024
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  4. [wip] sharing for updates only

    @teyaberg
    teyaberg committed Aug 20, 2024
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  5. [wip] doctests

    @teyaberg
    teyaberg committed Aug 20, 2024
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  6. autogluon

    @teyaberg
    teyaberg committed Aug 20, 2024
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  7. added logged warning for static data being empty and added support fo… 

    …r launching any model via config specificaly using the launch_model.py hydra script
    @Oufattole
    Oufattole committed Aug 20, 2024
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  8. Merge branch 'generalized_load_model' into dev

    @Oufattole
    Oufattole committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. Added support via hydra for selecting among four imputation methods (… 

    …none, mean, median, mode), and three normalization methods (none, standard_scaler, and min_max_scaler)
    @Oufattole
    Oufattole committed Aug 21, 2024
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  2. fixed xgboost model yaml to load imputer and normalization from the m… 

    …odel_params which optuna can modify
    @Oufattole
    Oufattole committed Aug 21, 2024
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  3. added autogluon test and cli support

    @Oufattole
    Oufattole committed Aug 21, 2024
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  4. added three more sklearn models and fixed bug with normalzation and i… 

    …mputers so they run on mimiciv test data
    @Oufattole
    Oufattole committed Aug 21, 2024
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  5. fixed bugs so correlation code filters work now

    @Oufattole
    Oufattole committed Aug 21, 2024
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  6. sweeper

    @teyaberg
    teyaberg committed Aug 21, 2024
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  7. logging

    @teyaberg
    teyaberg committed Aug 21, 2024
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  8. made tash caching parallelize and updated tests for configs

    @Oufattole
    Oufattole committed Aug 21, 2024
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  9. Merge branch 'dev' of github.com:mmcdermott/MEDS_Tabular_AutoML into dev

    @Oufattole
    Oufattole committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. added more thourough tests for output file paths of task caching and … 

    …tabularizing. Standardized output directory for autogluon model. Additionally fixed label bug so labels are deduplicated
    @Oufattole
    Oufattole committed Aug 22, 2024
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Commits on Aug 25, 2024

  1. Merge branch 'main' into dev

    @Oufattole
    Oufattole committed Aug 25, 2024
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  2. setup dynamic versioning

    @Oufattole
    Oufattole committed Aug 25, 2024
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Commits on Sep 5, 2024

  1. version updates

    @teyaberg
    teyaberg committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. version updates

    @teyaberg
    teyaberg committed Sep 6, 2024
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  2. fix hydra-core version for experimental callback support

    @teyaberg
    teyaberg committed Sep 6, 2024
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  3. eval callback logging

    @teyaberg
    teyaberg committed Sep 6, 2024
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Commits on Sep 7, 2024

  1. added script input args checks, reduced redundancy in model launcher … 

    …configs thorugh adding hierarchical defaults
    @Oufattole
    Oufattole committed Sep 7, 2024
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  2. eval callback

    @teyaberg
    teyaberg committed Sep 7, 2024
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  3. eval callback

    @teyaberg
    teyaberg committed Sep 7, 2024
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Commits on Sep 8, 2024

  1. Updated pre-commit config too.

    @mmcdermott
    mmcdermott committed Sep 8, 2024
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  2. Removed a function that was not yet implemented.

    @mmcdermott
    mmcdermott committed Sep 8, 2024
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  3. Removing unused function in evaluation callback.

    @mmcdermott
    mmcdermott committed Sep 8, 2024
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  4. eval callback

    @teyaberg
    teyaberg committed Sep 8, 2024
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  5. added yaml hierarchy for model_launcher

    @Oufattole
    Oufattole committed Sep 8, 2024
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Commits on Sep 9, 2024

  1. updated configs, fixed most tests

    @Oufattole
    Oufattole committed Sep 9, 2024
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  2. Merged

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  3. Removed unused pass block.

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  4. Removing unnecessary keys call

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  5. Fixed workflow files

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  6. fixed tabularize tests

    @Oufattole
    Oufattole committed Sep 9, 2024
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  7. added integration tests covering multirun for all launch_model models… 

    …, and added an integration test for autogluon
    @Oufattole
    Oufattole committed Sep 9, 2024
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  8. merged dev

    @Oufattole
    Oufattole committed Sep 9, 2024
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  9. fixed tests

    @Oufattole
    Oufattole committed Sep 9, 2024
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  10. Merge pull request #90 from mmcdermott/configs 

    Simplify model launcher configs and add script input checks
    @Oufattole
    Oufattole authored Sep 9, 2024
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  11. resolved review feedback. Added a based_model docstring. Added versio… 

    …n for polars. Added github workflow test matrix over python versions, removed redundant run_command definition from test_configs
    @Oufattole
    Oufattole committed Sep 9, 2024
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  12. fixed min_code_inclusion_frequency kwarg

    @Oufattole
    Oufattole committed Sep 9, 2024
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  13. added mimic iv tutorial

    @Oufattole
    Oufattole committed Sep 9, 2024
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  14. updated tabularization script to fix bugs

    @Oufattole
    Oufattole committed Sep 9, 2024
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  15. reduced the number of workers for resharding

    @Oufattole
    Oufattole committed Sep 9, 2024
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  16. Merged.

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  17. updated tabularize meds to take string input for tasks

    @Oufattole
    Oufattole committed Sep 9, 2024
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  18. Merge pull request #91 from mmcdermott/improve_test_coverage 

    Re-worked the tabular dataset config a bit.
    @mmcdermott
    mmcdermott authored Sep 9, 2024
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  19. Improved error handling per #81 (comment)

    @mmcdermott
    mmcdermott committed Sep 9, 2024
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  20. Update README.md 

    Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
    @mmcdermott @coderabbitai
    mmcdermott and coderabbitai[bot] authored Sep 9, 2024
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Commits on Sep 10, 2024

  1. added try except around loading 0 codes

    @Oufattole
    Oufattole committed Sep 10, 2024
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  2. fixed job name config bug where we were missing the $ so it was not r… 

    …esolved. Fixed bugs in e2e meds-tab mimic script
    @Oufattole
    Oufattole committed Sep 10, 2024
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  3. Merge branch 'dev' into MIMICIV

    @Oufattole
    Oufattole committed Sep 10, 2024
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  4. fixed precommit issues

    @Oufattole
    Oufattole committed Sep 10, 2024
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  5. Merge branch 'dev' into MIMICIV

    @Oufattole
    Oufattole committed Sep 10, 2024
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  6. fix paths for eval_callback and add check to test_integration

    @teyaberg
    teyaberg committed Sep 10, 2024
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  7. fixing tests for delete_below_top_k

    @teyaberg
    teyaberg committed Sep 10, 2024
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  8. Merge pull request #92 from mmcdermott/MIMICIV 

    Mimiciv
    @Oufattole
    Oufattole authored Sep 10, 2024
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  9. fix out of memory xgboost training and added test

    @teyaberg
    teyaberg committed Sep 10, 2024
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  10. simplified pathing for results and evaluation callback

    @Oufattole
    Oufattole committed Sep 10, 2024
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  11. fixed doctest for deleting below top k models

    @Oufattole
    Oufattole committed Sep 10, 2024
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