ML4H merge: tranche 1 - #1185

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will-pang wants to merge 27 commits into

sunlabuiuc:masterfrom

Multimodal-PyHealth:ml4h-merge-tranche-1

Commits on Aug 11, 2026

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2b7b2c5

Commits on Aug 17, 2026

Stop emitting fake missing-event placeholders.

Rian354
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9782aca
Keep frozen text encoders in eval when Trainer calls train().

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869ac8e
Cache frozen [CLS] embeddings keyed on real tokens, not padded rows.

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11beefc

Commits on Aug 18, 2026

Restore BaseDataset parquet scanning that MEDS still calls.

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86fe73b
Fill attention masks with dtype min and use fused SDPA.

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965a87b
Record batch padding and skip those slots in the unified sequence.

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7c4c056
Keep padding_idx=0 on nested code embeddings.

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ca9b63d
Accept resized_images and write sunlab CXR metadata to cache.

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b6fb31e
Refuse unknown amp_dtype instead of silently selecting fp16.

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7494787
Thread collate pad_mask through the unified MLP path.

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f3689cb
Fit lab z-scores on observed train rows via region_of_interest.

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ee17eb6
Write run_config.json next to the metrics of a finished run.

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224e7f4
Stop dropping later stays against the first admission's CXR window.

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8ae3c54
Keep paired runs from overwriting each other or reporting train as test.

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5def4ea
Give NotesLabs a 24h window and put concatenated stays on one timeline.

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cursoragent
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5be22e4

Commits on Aug 19, 2026

Give time embeddings a 10-year span and drop ICDLabsMIMIC4.

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9f50b76
Point the old unified_embedding import at the package copy.

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89f7bc7
Point AMP autocast at the trainer device instead of hardcoding CUDA.

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b50bf2f
Default to a full stay and stamp admission-context notes at admit.

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8d4a4c9