0.0.9: Merge pull request #229 from mmcdermott/dev

Release Candidate

0.0.8

What's Changed

• Tokenization Stage Misalignment Fix by @Oufattole in #198
• Hotfix 0.0.8 by @mmcdermott in #199

Full Changelog: 0.0.7...0.0.8

0.0.7: Merge pull request #193 from mmcdermott/dev

Release Candidate 0.0.7

0.0.6: Merge pull request #175 from mmcdermott/dev

Release Candidate 0.0.6

0.0.5: Merge pull request #151 from mmcdermott/dev

Release 0.0.5

0.0.4: Merge pull request #146 from mmcdermott/dev

Release candidate for 0.0.4

v0.0.3: Adding some improvements and bug-fixes to the MIMIC-IV ETL

What's Changed

• Added reorder_measurements transformation. by @mmcdermott in #48
• Allow map_over to accept compute functors or partials with standardized args rather than merely direct functions. by @mmcdermott in #107
• added unzipping functionality for mimic iv example by @Oufattole in #31
• Release 0.0.3 -- ensures MIMIC-IV ETL can be run without rootutils and that it works with unzipped files. by @mmcdermott in #115

Full Changelog: v0.0.2...0.0.3

0.0.2

What's Changed

• Maintain the order of event from event_config while merging cohorts by @prenc in #46
• Added additional terminology. by @mmcdermott in #80
• Converted codes to strings for MEDS v0.3 compliance. by @mmcdermott in #83
• Updates file paths and pipeline configuration so final data and metadata outputs are written to MEDS v0.3 compatible file paths. by @mmcdermott in #86
• Fixed schema of parent_codes and description in the extract_code_metadata.py script. by @mmcdermott in #89
• Adds a finalize metadata stage that handles dataset.json, codes.parquet, and patient_splits.parquet retyping and MEDS verification. by @mmcdermott in #91
• This makes it so that if there is a dataset with a metadata/patient_splits.parquet file specified and a stage that specifies a restriction to a stage, it will filter the patients on the basis of that file. by @mmcdermott in #93
• Add a finalize_MEDS_data.py stage to validate and convert to the MEDS schema for the data files and ensure those work. by @mmcdermott in #94
• Use MEDS_BIRTH and MEDS_DEATH codes by default, per https://github.com/Medical-Event-Data-Standard/meds/blob/5f87c2fdcce7f8bab46af6f81ef7892fdee098c1/src/meds/schema.py#L26 by @mmcdermott in #96
• Full Compatability with MEDS v0.3. by @mmcdermott in #87
• Removes the unused ability to use sequences of compute functions. by @mmcdermott in #105
• Release candidate v0.0.2: MEDS v0.3 Compatability by @mmcdermott in #97

New Contributors

• @prenc made their first contribution in #46

Full Changelog: 0.0.1...v0.0.2

v0.0.1

Release 0.0.1

The initial version of a semi-stable interface, with installable modules, CLI endpoint utilities, and useful configuration endpoints. The MIMIC-IV example works in this version; eICU does not.

What's Changed

• A subset of the changes from #3 merged into main. by @mmcdermott in #4
• Added run.py file and debugged on hf cohort. by @Oufattole in #3
• Adding details to run a MIMIC-IV example (and some other small fixes) by @mmcdermott in #6
• Still in progress, but adds eICU by @mmcdermott in #9
• Updated configs and added a resolver to get informative help messages from either the config or the script docstrings. by @mmcdermott in #7
• Multirun capabilities and other improvements by @mmcdermott in #10
• Added a code metadata extraction step for core MEDS extraction. by @mmcdermott in #18
• Tokenization and Tensorization by @mmcdermott in #22
• Get the preprocessing pipeline working E2E by @mmcdermott in #21
• IN PROGRESS general dev contributions. Currently tracking: by @mmcdermott in #17
• Update convert_to_sharded_events.py by @Oufattole in #26
• Making the interface re-usable and importable. by @mmcdermott in #29
• Adds a version number to close #36 by @mmcdermott in #39
• Added ETL information to the hydra config to help solve #37 by @mmcdermott in #40
• Very preliminary code to fix #33 by @mmcdermott in #50
• Adding tests for transforms (and minimally easing the API for transforms too with a standardized config file definition) by @mmcdermott in #59
• Renames MEDS_polars_functions to MEDS_transforms by @mmcdermott in #67
• Update the MIMIC-IV example with the updated interface and installable options. by @mmcdermott in #71
• Adding an improved documentation base and (eventually) readthedocs support. by @mmcdermott in #42
• Release 0.0.1 Candidate by @mmcdermott in #75

New Contributors

• @mmcdermott made their first contribution in #4
• @Oufattole made their first contribution in #3

Full Changelog: https://github.com/mmcdermott/MEDS_transforms/commits/0.0.1