Ehrshot branch #153

Miking98 · 2023-07-07T00:05:54Z

Branch with updates needed for EHRSHOT compatibility. Basically just a cleaner version of the old few_shot_ehr_benchmark branch.

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EthanSteinberg

Mostly good, nice work!

Just a couple of comments and concerns.

tutorials/input/clmbr_model/best_info

tutorials/input/extract/ontology/main

tests/labelers/test_LabValueLabelers.py

src/femr/models/scripts.py

src/femr/models/dataloader.py

src/femr/labelers/omop.py

src/femr/labelers/benchmarks.py

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Miking98 and others added 17 commits July 6, 2023 19:37

Labelers

36e6438

cleanup

ecfcd01

[pre-commit.ci] auto fixes from pre-commit.com hooks

1e49324

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Pandas

c319c72

Merge remote-tracking branch 'origin/main' into ehrshot_branch

3bbfce0

Merge branch 'ehrshot_branch' of https://github.com/som-shahlab/femr …

8b54027

…into ehrshot_branch

[pre-commit.ci] auto fixes from pre-commit.com hooks

53ea374

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code cleanup

cf3fce5

Merge branch 'ehrshot_branch' of https://github.com/som-shahlab/femr …

ba3a931

…into ehrshot_branch

fix

2061f1e

[pre-commit.ci] auto fixes from pre-commit.com hooks

6ae8003

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updates

9a8a8f4

Merge branch 'ehrshot_branch' of https://github.com/som-shahlab/femr …

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…into ehrshot_branch

Test case passing

7f752b8

[pre-commit.ci] auto fixes from pre-commit.com hooks

2306a22

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formatting

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Merge branch 'ehrshot_branch' of https://github.com/som-shahlab/femr …

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…into ehrshot_branch

EthanSteinberg requested changes Jul 12, 2023

View reviewed changes

Miking98 and others added 12 commits July 16, 2023 02:44

revert tutorials to main

fb435a8

switched firstdiagnosis -> timehorizoneventlabeler

e1d097d

add back minute assert

20978c8

remove extraneous patient_label

65b5083

boolean assert added back

3c8c25a

minute level resolution on end of day

90b2062

iso time

9ad242c

inpatient fix

bb83a96

move ICU out of OMOP

463b2f4

rename censored label ignore

fbf6fa6

Merge branch 'main' into ehrshot_branch

a184234

chexpert cleanup

575191f

pre-commit-ci bot and others added 16 commits August 3, 2023 00:27

[pre-commit.ci] auto fixes from pre-commit.com hooks

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tests

e77c8ce

Merge branch 'ehrshot_branch' of https://github.com/som-shahlab/femr …

f772e08

…into ehrshot_branch

style

8a2f043

Sure

414bc2d

added chexpert binary labeler

ea26755

Fix numeric

ac8acd9

Merge ethan's changes

cf4ad95

[pre-commit.ci] auto fixes from pre-commit.com hooks

e3aa974

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Remove print() statements

37fbcb0

new diagnosis <= to < error

1a154b1

Update benchmarks.py

a8dafe8

Censoring to True

fdc959f

Labeling function updates from Ethan

223ea2b

Merge branch 'ethan_ehrshot_branch' into ehrshot_branch

eb8d571

[pre-commit.ci] auto fixes from pre-commit.com hooks

0bf95d6

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Miking98 closed this Dec 4, 2023

Miking98 deleted the ehrshot_branch branch December 4, 2023 02:33

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Ehrshot branch #153

Ehrshot branch #153

Miking98 commented Jul 7, 2023

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Ehrshot branch #153

Ehrshot branch #153

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