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EricSchrock
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* init commit * pause for now, will come back after I add a couple more naive multimodal baselines in PyHealth * fix eicu * fix length of stay, will check others later * readmission prediction is next, will look at this later * Delete old readmission prediciton tasks * Clean up readmission prediction auto formatting * Remove obsolete tests * Fix model inputs in eICU examples and update the examples to work without requiring changes to dataset paths * Update the eICU readmission task to represent ICU readmission within the same hospital admission * Add exclude_minors param to the ReadmissionPredictionEICU task * Generalize eICU patient age error handling * Update example notebooks to match improvements from #834 * fix old outdated references that are confusing and point to the 1.16 ver. * ReadmissionPredictionEICU task docs --------- Co-authored-by: EricSchrock <eric.schrock22@gmail.com>
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Overview
This PR updates most of the MIMIC3 example scripts to work with PyHealth 2.0. It does NOT update any MIMIC3 Jupyter notebook examples. It also excludes the following examples, which rely on models or metrics that are not fully working with PyHealth 2.0 (or maybe the examples just need more extensive updates to get working again).
examples/patient_linkage_mimic3_medlink.pyexamples/drug_recommendation/drug_recommendation_mimic3_micron.pyexamples/mortality_prediction/mortality_mimic3_grasp.pyexamples/readmission/readmission_mimic3_fairness.pyIf these changes look good, I can make similar updates to the following.
Updates for PyHealth 2.0
feature_keys,label_key, andmodeinput params from model initUpdates for Ease of Use
My thought is that examples should work out of the box, handle any sharp edges, and run quickly. This enables people to quickly gain confidence that they have properly installed PyHealth.
Additionally, making the examples run quickly and without changes (e.g. to paths) allows us to quickly regression test them for releases. We could even consider adding them to the automated test pipeline (but maybe only trigger when generating release?).
dev=Trueandepochs=1for speedcache_dir=tempfile.TemporaryDirectory().nameto avoid any confusion if people run the same example twiceroot="https://storage.googleapis.com/pyhealth/Synthetic_MIMIC-III"so that the example works out of the boxImportant
Discussion: I used
root="https://storage.googleapis.com/pyhealth/Synthetic_MIMIC-III"to make the examples work out of the box. Would it be better to useroot="https://physionet.org/files/mimiciii-demo/1.4/"?Testing
All updated example scripts ran locally without error.