Promptehr pr integration#878

Draft

jalengg wants to merge 40 commits intosunlabuiuc:masterfrom

jalengg:promptehr-pr-integration

Commits on Mar 2, 2026

Add PromptEHR Colab notebook: demographic-conditioned synthetic EHR generation
jalengg
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Commits on Mar 4, 2026

Fix: idempotent Drive mount in Colab notebook
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Fix: guard scipy/mne-dependent task imports to fix Colab numpy 2.x cascade
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Feat: persist MIMIC-III files to Drive, skip re-upload on reconnect
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Fix: guard PIL/mne-dependent dataset imports to fix Colab import cascade
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Fix: force-reinstall PyHealth in setup cell; update preamble SHA
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Chore: update preamble SHA to 8c176e9c
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Chore: switch preamble timestamp to UTC (no SHA lag)
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Fix: guard optional-dep model imports to fix Colab sklearn/scipy cascade
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Chore: update notebook timestamp 2026-03-04 08:21:17 UTC
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Fix: guard EEGAbnormalTUAB/EEGEventsTUEV at source; rewrite preamble
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Fix: install scipy>=1.14 AFTER PyHealth to prevent --force-reinstall clobber
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Fix: add Pillow>=10.4.0 to post-install step to fix mixed PIL state
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Fix: guard ImageProcessor/TimeImageProcessor in processors/__init__.py (PIL/torchvision unavailable)
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Chore: update notebook timestamp to 2026-03-04 09:55:13 (UTC)
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Fix: Drive mount guard + makedirs ordering — files no longer re-uploaded each session
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Fix: force-reinstall numpy+scipy post-PyHealth to clear mixed-version state
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Chore: fix notebook timestamp to 2026-03-04 10:20:35 (UTC)
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Fix: processors/__init__ __all__ + RuntimeError guard + numpy>=2.0.0
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Chore: fix notebook timestamp to 2026-03-04 10:31:20 (UTC)
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Fix: numpy version ceiling, force-reinstall cascade, Drive stale mount
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Fix numpy mixed-version error: replace --force-reinstall with uninstall+install
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Remove step 2 dep upgrades causing Pillow mixed-version state
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Fix Pillow mixed-version state: force-reinstall Pillow after PyHealth install
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Fix Colab PIL error: hide torchvision during BART import in PromptEHR
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Fix PyHealth 2.0 API: remove code_mapping kwarg, use unique_patient_ids
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Remove icustays from MIMIC3Dataset defaults (same fix as HALO c52aa0b0)
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Fix device mismatch in synthesize_dataset: use bart_model's device
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Fix beam search crash in generate: set num_beams=1 explicitly
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Fix decode_tokens: skip BOS/EOS/PAD instead of breaking on them
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Commits on Mar 5, 2026

Commits on Mar 6, 2026

Fix: suppress wandb prompt and early_stopping warning during training
jalengg
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