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Match the MEDS label schema for MEDS dataset #72

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Tracked by #92
mmcdermott opened this issue Jul 19, 2024 · 3 comments
Closed
Tracked by #92

Match the MEDS label schema for MEDS dataset #72

mmcdermott opened this issue Jul 19, 2024 · 3 comments
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Impacts Benchmark Impacts the 2024 Summer / Fall Distributed MEDS Benchmarking Effort MEDS Compatibility Compatibility with the Medical Event Data Standard (MEDS) data schema priority:critical Things that are critical bug fixes, to be addressed immediately and pushed with minor version update Task DataFrame Format Relates to the output of a cohort extraction as well as how intermediates are stored Usability & Interface For things to make ACES more usable that don't involve fundamental configuration language changes
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MEDS Benchmarking...

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@mmcdermott
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https://github.com/Medical-Event-Data-Standard/meds/blob/main/src/meds/schema.py#L67
@mmcdermott mmcdermott added the Impacts Benchmark Impacts the 2024 Summer / Fall Distributed MEDS Benchmarking Effort label Jul 22, 2024
@justin13601
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Add some renames at the end for col names, maybe a toggle for default vs. MEDS label

justin13601 added a commit that referenced this issue Jul 26, 2024
@justin13601
Rename index_timestamp as part of #72
b52a3ae
@justin13601 justin13601 mentioned this issue Jul 26, 2024
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@mmcdermott mmcdermott added priority:critical Things that are critical bug fixes, to be addressed immediately and pushed with minor version update Usability & Interface For things to make ACES more usable that don't involve fundamental configuration language changes Task DataFrame Format Relates to the output of a cohort extraction as well as how intermediates are stored MEDS Compatibility Compatibility with the Medical Event Data Standard (MEDS) data schema labels Aug 6, 2024
This was referenced Aug 6, 2024
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@mmcdermott
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We'll want to explicitly validate against the imported MEDS schema, much as I do in MEDS transforms here: https://github.com/mmcdermott/MEDS_transforms/blob/main/src/MEDS_transforms/extract/finalize_MEDS_data.py#L15

Note this code may eventually move to the meds repo proper, per Medical-Event-Data-Standard/meds#37

justin13601 added a commit that referenced this issue Aug 12, 2024
@justin13601 @mmcdermott
Match MEDS label schema as per #72 (#80)
1bcd50b 
* Rename index_timestamp as part of #72

* Updated to overtly define in MEDS format. Not yet validated.

* Fixed expand_shards to work with arbitrary MEDS sharding strategies.

* Fixed a few other errors for MEDS v0.3 compatability. Now tested with config https://gist.github.com/mmcdermott/80a9086d8fdf36f2fd04b8e4912348ac on a tiny MIMIC cohort.

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Co-authored-by: Matthew McDermott <[email protected]>
@justin13601
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Done in #80

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Impacts Benchmark Impacts the 2024 Summer / Fall Distributed MEDS Benchmarking Effort MEDS Compatibility Compatibility with the Medical Event Data Standard (MEDS) data schema priority:critical Things that are critical bug fixes, to be addressed immediately and pushed with minor version update Task DataFrame Format Relates to the output of a cohort extraction as well as how intermediates are stored Usability & Interface For things to make ACES more usable that don't involve fundamental configuration language changes
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MEDS Benchmarking Effort v0.0.1
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@mmcdermott @justin13601