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v2.1 #118

Merged
merged 142 commits into from
Jul 9, 2024
Merged

v2.1 #118

merged 142 commits into from
Jul 9, 2024

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egillax
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@egillax egillax commented Jul 8, 2024

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egillax and others added 30 commits November 14, 2022 14:29
@egillax
speed up data conversion about 3-5x
64fce91
@egillax
updated news
30e67fd
@egillax
make sure tensorList matches dataset length
131c434
@egillax
user integers for tensorList
38504b3
@egillax
test a different way of getting torch binaries
5d89faa
@egillax
test a different way of getting torch binaries
2f8d6d6
@egillax
fix tidyselect warnings
e79a43f
@egillax
Merge branch 'main' into 43-hotfix-lantern-binaries
6c69427
@egillax
Update description and news
887fac9
@egillax
remove torch install env variable from actions
72f813e
@egillax
merge hotfix to develop
d66c47e
@egillax
fixed dataset
ad0ad19
@egillax
fix numericalIndex and address pull warning
03ff99b
@lhjohn
Allow dimToken and numHeads to take the form of vectors
517f675
@lhjohn
Merge pull request #47 from OHDSI/transformer-bug
b87b769 
Allow dimToken and numHeads to take the form of vectors
@egillax
Modeltype fix (#48)
dfca29a 
* added modelType to modelSettings
@egillax
update default ResNet and Transformer to have custom LR and WD
65302bd
@lhjohn
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
@egillax
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
@lhjohn
Derive dimension of feedforward block from embedding dimension (#53)
e580c2a 
* Add dimHiddenRatio parameter to Transformer

* Update Transformer documentation
@lhjohn
Divisible check for Transformer not comprehensive (#55)
fba85ec 
* Resolve an issue with divisible check

* Update Transformer tests
@egillax
Update NEWS.md
e50d2e4
@egillax
Merge branch 'main' into develop
b66de7f
@egillax
update website and docs
051ea88
@egillax
remove docs folder from code branches
793338a
@egillax
render dev website
d0cb45b
@egillax
fix action
609df5b
@egillax
fix action
3330c28
@egillax
fix badge in readme
dcb9423
@egillax
prepare version for release
ce5e235
egillax and others added 29 commits December 22, 2023 16:38
@egillax
merge with main
07dd58a
@egillax
fix merging mistake
a52d831
@egillax
fitEstimator can be called from PLP
6d3e65f
@egillax
predictDeepEstimator can also be called from PLP
1ea7d5f
@egillax
chore: styling
d2469f6
@lhjohn @egillax
Transfer Learning (#109)
dcfc7fa 
* Transfer learning first prototype working

* linting

* add unit tests for transfer learning
---------

Co-authored-by: egillax <[email protected]>
@egillax
Trigger GA
a438ca7
@egillax
accumulation in estimator and LRFinder (#113)
f343e72 
* gradient accumulation
@egillax
Cuda memory catch (#115)
b95d31a 
Added a try catch  so that in case of OOM errors on GPU it tries to clear gpu memory and continue when doing hyperparameter tuning.
@egillax
accumulation_steps can be a function
cff3363
@egillax
fixes for module
7f668e7
@egillax
fix accumulation when leftover batch is maller than batch/2
549703e
@egillax
fix lrFinder, forgot to change to snakecase
4177eee
@egillax
only change to snakecase if not null
e1db512
@egillax
add codecov token
c103bab
@egillax
fix edge cases with few lr rate iterations and if minimum is at zero
caeb8a3
@egillax
handle case if modelType isn't in modelParams (#116)
ad79a06
@egillax
use device from modelDesign when validating
14bb13c
@egillax
Fix docs and use torch as an exported object
153b611
@egillax
prepare release
5fd3195
@egillax
try numpy<2 for windows and torch
4d6813c
@egillax
fix operator
882bb50
@egillax
pathlib resolve on the finetune model path for windows and macOS
15fe0de
@egillax
cast pathlib object back to string
713af0d
@egillax
revert and normalize tempdir call in tests
215df23
@egillax
normalizePath... and simplify virtualenv setup
fbf0fd4
@egillax
normalizePath... v2
d47e890
@egillax
improve cache of r dependenceis
effcc7f
@egillax @lhjohn
110 docker (#119)
b53c7f3 
* Add docker file

* Add docker release workflow

---------

Co-authored-by: Henrik John <[email protected]>
@egillax egillax merged commit bb7c453 into main Jul 9, 2024
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2 participants
@egillax @lhjohn