Dev/keep embeddings#1065

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christyanamarie wants to merge 75 commits intosunlabuiuc:masterfrom

lookman-olowo:dev/keep-embeddings

Commits on Feb 21, 2026

Commits on Feb 23, 2026

Commits on Mar 30, 2026

merge upstream/master v2.0.0, resolve rnn + concare conflicts
capccode
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Commits on Apr 5, 2026

fix(test): add valid NDC to test prescriptions so readmit test produces both labels
capccode
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Commits on Apr 7, 2026

feat(keep): scaffold KEEP embedding pipeline, OMOP graph builder, and Node2Vec Stage 1

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feat(keep): add patient co-occurrence matrix builder for KEEP Stage 2 input

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feat(keep): implement regularized GloVe training (KEEP Stage 2 core)

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feat(keep): add SNOMED vocabulary, cross-maps, and embedding export (Option A)

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feat(keep): add end-to-end example and fix GRASP pretrained embedding support

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chore(keep): update example with sweep-best hyperparameters

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feat(keep): add run_keep_pipeline() and simplify example

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fix(keep): support compressed Athena files (.csv.gz) in pipeline runner

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Commits on Apr 8, 2026

fix(keep): critical bugfixes in regularized GloVe to match reference code

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Commits on Apr 13, 2026

Commits on Apr 14, 2026

Commits on Apr 18, 2026

Commits on Apr 19, 2026

fix(keep): default run_keep_pipeline device to cuda
capccode
committed

Commits on Apr 20, 2026

feat(keep): split manifest into config+results, flatten output, remove reg_reduction knob

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Commits on Apr 21, 2026

Commits on Apr 22, 2026

Commits on Apr 23, 2026