Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

v0.5 changes: logging, computational improvements, and more #84

Merged
merged 63 commits into from
Dec 14, 2023
Merged

v0.5 changes: logging, computational improvements, and more #84

merged 63 commits into from
Dec 14, 2023

Commits on Sep 7, 2023

  1. Added flash attention.

    @mmcdermott
    mmcdermott committed Sep 7, 2023
    Configuration menu
    Copy the full SHA
    a339171 View commit details
    Browse the repository at this point in the history

Commits on Oct 25, 2023

  1. Merge branch 'dev' into enable_flash_attention

    @mmcdermott
    mmcdermott committed Oct 25, 2023
    Configuration menu
    Copy the full SHA
    f479082 View commit details
    Browse the repository at this point in the history

  2. Added a schema output to pytorch dataset.

    @mmcdermott
    mmcdermott committed Oct 25, 2023
    Configuration menu
    Copy the full SHA
    c313c1c View commit details
    Browse the repository at this point in the history

  3. Fixed small bug with schema and added test.

    @mmcdermott
    mmcdermott committed Oct 25, 2023
    Configuration menu
    Copy the full SHA
    8437fe0 View commit details
    Browse the repository at this point in the history

Commits on Nov 9, 2023

  1. Small updates to dataset for testing compute costs.

    @mmcdermott
    mmcdermott committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    8cbacb9 View commit details
    Browse the repository at this point in the history

  2. First attempt; likely very buggy.

    @mmcdermott
    mmcdermott committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    0504580 View commit details
    Browse the repository at this point in the history

  3. More changes; not sure if it is 100% working yet or not. Tests certai… 

    …nly still failing.
    @mmcdermott
    mmcdermott committed Nov 9, 2023
    Configuration menu
    Copy the full SHA
    49c4f02 View commit details
    Browse the repository at this point in the history

Commits on Nov 10, 2023

  1. Fixed some more typos; now can run up through getitem and collate at … 

    …least.
    @mmcdermott
    mmcdermott committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    3d577ab View commit details
    Browse the repository at this point in the history

  2. Fixed some small bugs; tests still not fully passing but sample data … 

    …runs now.
    @mmcdermott
    mmcdermott committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    00a0305 View commit details
    Browse the repository at this point in the history

  3. Fixed a number of small bugs; tests closer to passing.

    @mmcdermott
    mmcdermott committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    260161a View commit details
    Browse the repository at this point in the history

  4. I think all tests are now passing.

    @mmcdermott
    mmcdermott committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    6052b8a View commit details
    Browse the repository at this point in the history

  5. Updated notebook.

    @mmcdermott
    mmcdermott committed Nov 10, 2023
    Configuration menu
    Copy the full SHA
    7098db8 View commit details
    Browse the repository at this point in the history

Commits on Nov 14, 2023

  1. Starter code for nested caching and subsampling

    @mmcdermott
    mmcdermott committed Nov 14, 2023
    Configuration menu
    Copy the full SHA
    070e711 View commit details
    Browse the repository at this point in the history

Commits on Nov 21, 2023

  1. Added doctest.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    a7ab111 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'improved_compute' into duplication_bug_in_task_caching

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    c2c4a2e View commit details
    Browse the repository at this point in the history

  3. Added test for task caching bug.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    6235bd0 View commit details
    Browse the repository at this point in the history

  4. Fixed test.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    20ef6af View commit details
    Browse the repository at this point in the history

  5. Lint fixes.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    c78cb4d View commit details
    Browse the repository at this point in the history

  6. Merge pull request #77 from mmcdermott/duplication_bug_in_task_caching 

    Duplication bug in task caching
    @mmcdermott
    mmcdermott authored Nov 21, 2023
    Configuration menu
    Copy the full SHA
    3a1821c View commit details
    Browse the repository at this point in the history

  7. Merge branch 'improved_compute' into nested_caching

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    e4f3e98 View commit details
    Browse the repository at this point in the history

  8. Added loguru

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    cf7b9e3 View commit details
    Browse the repository at this point in the history

  9. Trying logger changes.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    16e0c87 View commit details
    Browse the repository at this point in the history

  10. Added some logging and got tests passing.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    e327db2 View commit details
    Browse the repository at this point in the history

  11. Removed the old increment calls.

    @mmcdermott
    mmcdermott committed Nov 21, 2023
    Configuration menu
    Copy the full SHA
    9c0eeb5 View commit details
    Browse the repository at this point in the history

Commits on Nov 22, 2023

  1. Added loguru throughout.

    @mmcdermott
    mmcdermott committed Nov 22, 2023
    Configuration menu
    Copy the full SHA
    64df044 View commit details
    Browse the repository at this point in the history

Commits on Nov 25, 2023

  1. Merge pull request #78 from mmcdermott/remove_unnecessary_increment 

    Removed the old increment calls to assign event IDs in favor of hashes of subject IDs and timestamps which can be run lazily.
    @mmcdermott
    mmcdermott authored Nov 25, 2023
    Configuration menu
    Copy the full SHA
    63a838a View commit details
    Browse the repository at this point in the history

  2. Merge pull request #79 from mmcdermott/enable_flash_attention 

    Enable flash attention
    @mmcdermott
    mmcdermott authored Nov 25, 2023
    Configuration menu
    Copy the full SHA
    33215e7 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'v0.5' into proper_logs

    @mmcdermott
    mmcdermott committed Nov 25, 2023
    Configuration menu
    Copy the full SHA
    866e5c1 View commit details
    Browse the repository at this point in the history

  4. Added loguru initialization code to all scripts.

    @mmcdermott
    mmcdermott committed Nov 25, 2023
    Configuration menu
    Copy the full SHA
    8c4d60f View commit details
    Browse the repository at this point in the history

Commits on Nov 26, 2023

  1. Fixed tests.

    @mmcdermott
    mmcdermott committed Nov 26, 2023
    Configuration menu
    Copy the full SHA
    1b5c30b View commit details
    Browse the repository at this point in the history

Commits on Nov 27, 2023

  1. Merge pull request #80 from mmcdermott/proper_logs 

    Proper logs
    @mmcdermott
    mmcdermott authored Nov 27, 2023
    Configuration menu
    Copy the full SHA
    1534c03 View commit details
    Browse the repository at this point in the history

Commits on Nov 28, 2023

  1. Added caching fns

    @pargaw
    pargaw committed Nov 28, 2023
    Configuration menu
    Copy the full SHA
    b24becd View commit details
    Browse the repository at this point in the history

  2. Partial pseudo-code for caching subsets

    @mmcdermott
    mmcdermott authored Nov 28, 2023
    Configuration menu
    Copy the full SHA
    d9fe46b View commit details
    Browse the repository at this point in the history

Commits on Nov 30, 2023

  1. Some small changes.

    @mmcdermott
    mmcdermott committed Nov 30, 2023
    Configuration menu
    Copy the full SHA
    f8447e9 View commit details
    Browse the repository at this point in the history

Commits on Dec 2, 2023

  1. Fixed cache_suset to run fully

    @pargaw
    pargaw committed Dec 2, 2023
    Configuration menu
    Copy the full SHA
    e5feba5 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #81 from mmcdermott/remove_unnecessary_subject_man… 

    …gling

Remove unnecessary subject ID conversion to streamline dataset creation.
    @mmcdermott
    mmcdermott authored Dec 2, 2023
    Configuration menu
    Copy the full SHA
    0a8a797 View commit details
    Browse the repository at this point in the history

Commits on Dec 3, 2023

  1. Fixed all tests and upgraded to polars 0.19.19

    @mmcdermott
    mmcdermott committed Dec 3, 2023
    Configuration menu
    Copy the full SHA
    dd2035f View commit details
    Browse the repository at this point in the history

  2. Merge pull request #82 from mmcdermott/remove_with_row_count 

    Remove the `with_row_count` to create new event IDs to speed up dataset creation and permit lazy frames to be used longer.
    @mmcdermott
    mmcdermott authored Dec 3, 2023
    Configuration menu
    Copy the full SHA
    273e09a View commit details
    Browse the repository at this point in the history

  3. Added logging to other aspects of ESGPT.

    @mmcdermott
    mmcdermott committed Dec 3, 2023
    Configuration menu
    Copy the full SHA
    b34b3fe View commit details
    Browse the repository at this point in the history

  4. Merge pull request #83 from mmcdermott/more_logging 

    Added logging to other aspects of ESGPT.
    @mmcdermott
    mmcdermott authored Dec 3, 2023
    Configuration menu
    Copy the full SHA
    ccf9da9 View commit details
    Browse the repository at this point in the history

  5. Removing currently unfinished and unused evaluation code.

    @mmcdermott
    mmcdermott committed Dec 3, 2023
    Configuration menu
    Copy the full SHA
    e1a3c3e View commit details
    Browse the repository at this point in the history

  6. Removed other buggy code and an unnecessary break statement in sklear… 

    …n tests and a reference to deleted generative evaluation code.
    @mmcdermott
    mmcdermott committed Dec 3, 2023
    Configuration menu
    Copy the full SHA
    ea9ce9f View commit details
    Browse the repository at this point in the history

  7. Fixed URI function bug.

    @mmcdermott
    mmcdermott committed Dec 3, 2023
    Configuration menu
    Copy the full SHA
    7d1efef View commit details
    Browse the repository at this point in the history

Commits on Dec 4, 2023

  1. Added an ESDS conversion option.

    @mmcdermott
    mmcdermott committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    cf8fe51 View commit details
    Browse the repository at this point in the history

  2. Added ESDS support; need to test with modifiers.

    @mmcdermott
    mmcdermott committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    4bd8499 View commit details
    Browse the repository at this point in the history

  3. Added modifiers into standard sample data example and fixed slight is… 

    …sues with ESDS conversion.
    @mmcdermott
    mmcdermott committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    537ec1a View commit details
    Browse the repository at this point in the history

  4. Fixed bugs with saving new data_stats fot cached subset data

    @pargaw
    pargaw committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    38a0897 View commit details
    Browse the repository at this point in the history

  5. Fixed tests by adding medications to the sample NA config.

    @mmcdermott
    mmcdermott committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    1b59238 View commit details
    Browse the repository at this point in the history

  6. Merge pull request #85 from mmcdermott/ESDS_export 

    Adds support and a script for exporting an ESDS dataset from an ESGPT dataset (with support for modifier columns).
    @mmcdermott
    mmcdermott authored Dec 4, 2023
    Configuration menu
    Copy the full SHA
    acd2bf0 View commit details
    Browse the repository at this point in the history

  7. Changed cache_subset for train vs other splits

    @pargaw
    pargaw committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    f7aa908 View commit details
    Browse the repository at this point in the history

  8. Fixed small bugs in data pipeline inhibiting runs on real data.

    @mmcdermott
    mmcdermott committed Dec 4, 2023
    Configuration menu
    Copy the full SHA
    65d3c75 View commit details
    Browse the repository at this point in the history

Commits on Dec 7, 2023

  1. Fixed subset caching to account for extra padding on time_delta

    @pargaw
    pargaw committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    3078b9e View commit details
    Browse the repository at this point in the history

  2. Stylistic changes.

    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    44704e0 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'v0.5' into nested_caching

    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    b1af020 View commit details
    Browse the repository at this point in the history

  4. Made subset size work in case of float subset size (which is supporte… 

    …d elsewhere). tests failing due to data_stats.json errors.
    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    acf5b69 View commit details
    Browse the repository at this point in the history

  5. Made all uses of full data config a consistent property.

    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    41cbcde View commit details
    Browse the repository at this point in the history

  6. Fixed tests with nested caching

    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    a303b39 View commit details
    Browse the repository at this point in the history

  7. Merge pull request #86 from mmcdermott/nested_caching 

    Nested caching
    @mmcdermott
    mmcdermott authored Dec 7, 2023
    Configuration menu
    Copy the full SHA
    0c04c89 View commit details
    Browse the repository at this point in the history

  8. Updated some deprecated polars functions.

    @mmcdermott
    mmcdermott committed Dec 7, 2023
    Configuration menu
    Copy the full SHA
    235d8b6 View commit details
    Browse the repository at this point in the history

  9. Merge pull request #87 from mmcdermott/polars_0.19 

    Updated some deprecated polars functions.
    @mmcdermott
    mmcdermott authored Dec 7, 2023
    Configuration menu
    Copy the full SHA
    8e38596 View commit details
    Browse the repository at this point in the history

Commits on Dec 8, 2023

  1. Added two more logging lines.

    @mmcdermott
    mmcdermott committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    99b7e11 View commit details
    Browse the repository at this point in the history

  2. Merge branch 'v0.5' of github.com:mmcdermott/EventStreamML into v0.5

    @mmcdermott
    mmcdermott committed Dec 8, 2023
    Configuration menu
    Copy the full SHA
    5faa9a5 View commit details
    Browse the repository at this point in the history

Commits on Dec 14, 2023

  1. re-set to dev.

    @mmcdermott
    mmcdermott committed Dec 14, 2023
    Configuration menu
    Copy the full SHA
    c017794 View commit details
    Browse the repository at this point in the history