Version 2.0 #81

egillax · 2023-08-28T11:08:37Z

New pytorch backend

Allow dimToken and numHeads to take the form of vectors

* added modelType to modelSettings

* Add random seed to sample hyperparameter combinations * Supress warnings message due to NULL seed * Add withr dependency

* add LRfinder, add setEstimator function for all estimator parameters, add metric to earlystopper. Adjust tests for setEstimator * add tests for coverage * add custom metric for scheduler/earlyStopping

* Add dimHiddenRatio parameter to Transformer * Update Transformer documentation

* Resolve an issue with divisible check * Update Transformer tests

* Add training cache + tests --------- Co-authored-by: Egill Axfjord Fridgeirsson <[email protected]>

…ediction into develop

* Resolve an issue with hidden dimension ratio * Optimize solution * add test case --------- Co-authored-by: egillax <[email protected]>

codecov · 2023-08-28T11:43:00Z

Codecov Report

Patch coverage: 98.98% and project coverage change: +0.05% 🎉

Comparison is base (2c88d3a) 99.53% compared to head (04c4871) 99.59%.

❗ Current head 04c4871 differs from pull request most recent head 904e926. Consider uploading reports for the commit 904e926 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #81      +/-   ##
==========================================
+ Coverage   99.53%   99.59%   +0.05%     
==========================================
  Files           7        9       +2     
  Lines         641      488     -153     
==========================================
- Hits          638      486     -152     
+ Misses          3        2       -1

Files Changed	Coverage Δ
R/DeepPatientLevelPrediction.R	`0.00% <0.00%> (ø)`
R/Dataset.R	`100.00% <100.00%> (ø)`
R/Estimator.R	`100.00% <100.00%> (ø)`
R/HelperFunctions.R	`100.00% <100.00%> (ø)`
R/LRFinder.R	`100.00% <100.00%> (ø)`
R/MLP.R	`100.00% <100.00%> (ø)`
R/ResNet.R	`100.00% <100.00%> (ø)`
R/TrainingCache-class.R	`100.00% <100.00%> (ø)`
R/Transformer.R	`100.00% <100.00%> (+5.55%)`	⬆️

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* integer handling in python * add input checks * add tests for wrong inputs

egillax · 2023-09-08T08:32:40Z

Closes #79 , #82 , #75 , #25, #31

egillax and others added 30 commits November 14, 2022 14:29

speed up data conversion about 3-5x

64fce91

updated news

30e67fd

make sure tensorList matches dataset length

131c434

user integers for tensorList

38504b3

test a different way of getting torch binaries

5d89faa

test a different way of getting torch binaries

2f8d6d6

fix tidyselect warnings

e79a43f

Merge branch 'main' into 43-hotfix-lantern-binaries

6c69427

Update description and news

887fac9

remove torch install env variable from actions

72f813e

merge hotfix to develop

d66c47e

fixed dataset

ad0ad19

fix numericalIndex and address pull warning

03ff99b

Allow dimToken and numHeads to take the form of vectors

517f675

Merge pull request #47 from OHDSI/transformer-bug

b87b769

Allow dimToken and numHeads to take the form of vectors

Modeltype fix (#48)

dfca29a

* added modelType to modelSettings

update default ResNet and Transformer to have custom LR and WD

65302bd

Add seed for sampling hyperparameter combinations (#50)

353e0ba

* Add random seed to sample hyperparameter combinations * Supress warnings message due to NULL seed * Add withr dependency

Lr find (#51)

926e7d0

* add LRfinder, add setEstimator function for all estimator parameters, add metric to earlystopper. Adjust tests for setEstimator * add tests for coverage * add custom metric for scheduler/earlyStopping

Derive dimension of feedforward block from embedding dimension (#53)

e580c2a

* Add dimHiddenRatio parameter to Transformer * Update Transformer documentation

Divisible check for Transformer not comprehensive (#55)

fba85ec

* Resolve an issue with divisible check * Update Transformer tests

Update NEWS.md

e50d2e4

Merge branch 'main' into develop

b66de7f

update website and docs

051ea88

remove docs folder from code branches

793338a

render dev website

d0cb45b

fix action

609df5b

fix action

3330c28

fix badge in readme

dcb9423

prepare version for release

ce5e235

egillax and others added 22 commits April 18, 2023 15:19

add device as expression with tests (#66)

a1cb2e7

Merge branch 'main' into develop

01ce148

remove torchopt

2113a48

update news and version

575d2e5

fix docs

20d4a0d

update version number

f97b37f

LRFinder works with device fun (#68)

783f417

update version and news

0a6f9de

Merge branch 'main' into develop

58df70c

update version

2883b5e

fix bug when test subject has no features

8a01ed7

Add parameter caching for training persistence and continuity (#63)

e555710

* Add training cache + tests --------- Co-authored-by: Egill Axfjord Fridgeirsson <[email protected]>

fix incs issue

1e640ee

Merge branch 'develop' of https://github.com/OHDSI/DeepPatientLevelPr…

6326cd6

…ediction into develop

Release version and news updated

5d9dc59

Merge branch 'main' into develop

af02541

Release and NEWS

506b940

Resolve an issue with hidden dimension ratio (#74)

74608ff

* Resolve an issue with hidden dimension ratio * Optimize solution * add test case --------- Co-authored-by: egillax <[email protected]>

Cache single hyperparameter combination (#78)

ba60c28

Change backend to pytorch (#80)

bd9b357

Merge branch 'main' into develop

04c2b36

fix dataset

e501124

egillax and others added 4 commits September 7, 2023 10:16

update PLP version in DESCRIPTION

31ef832

integer handling in python and input checks (#83)

66b8c84

* integer handling in python * add input checks * add tests for wrong inputs

Ensure that param search is completed in empty cache test (#84)

85be689

use ubuntu 22.04 in CI (#85)

4c83897

Update NEWS.md

904e926

egillax merged commit b353e41 into main Sep 8, 2023
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Version 2.0 #81

Version 2.0 #81

egillax commented Aug 28, 2023

codecov bot commented Aug 28, 2023 •

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egillax commented Sep 8, 2023

Version 2.0 #81

Version 2.0 #81

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