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Picai detection#306

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itaijj wants to merge 96 commits intomasterBiomedSciAI/fuse-med-ml:masterfrom picai_detectionBiomedSciAI/fuse-med-ml:picai_detectionCopy head branch name to clipboard

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Commits on Aug 23, 2022

• - aug updates

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  avihu111

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Commits on Aug 24, 2022

• add pool layer, and fix color normalization

  avihu111

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  863021a

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• remove stack

  avihu111

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• Merge remote-tracking branch 'origin/master' into ukbb_changes

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  avihu111

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• minor

  avihu111

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Commits on Aug 25, 2022

• select series on dynamic

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  avihu111

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• add descriptor to cacher/sampler tqdm

  avihu111

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  d3cbe0d

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• Revert "add descriptor to cacher/sampler tqdm"

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  avihu111

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• add descriptor to cacher/sampler tqdm

  avihu111

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• fix for descriptor in caching

  avihu111

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Commits on Aug 30, 2022

• support return None in no cache mode

  

  itaiguez

  committed
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• Merge branch 'ukbb_changes' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  

  itaiguez

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• Merge branch 'master' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

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Commits on Sep 1, 2022

• support missing image key in augmentations.

  avihu111

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Commits on Sep 5, 2022

• revert support of missing key

  avihu111

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• Merge branch 'ukbb_changes' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

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  0b80edb

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• added cindex metrics

  

  Iti Guez

  committed
  c3f64e9

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• created cindex test

  

  Iti Guez

  committed
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• updated req

  

  Iti Guez

  committed
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• updated documentation on cindex

  

  Iti Guez

  committed
  c0ab8c8

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• small fix

  

  itaiguez

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Commits on Sep 6, 2022

• collate only relevant keys

  avihu111

  committed
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• Merge branch 'ukbb_changes' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

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Commits on Sep 10, 2022

• work on c-ndex metric

  michalozeryflato

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Commits on Sep 11, 2022

• change cindex after review with Alex

  michalozeryflato

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Commits on Sep 14, 2022

• fix c-index score (invert order when higher score => more likely to have an event)

  avihu111

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Commits on Sep 30, 2022

• remove 2 warnings

  michalozeryflato

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• support time_unit in c-index

  michalozeryflato

  committed
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Commits on Oct 2, 2022

• support: (1) no hidden layers, (2) no bias in MLP

  michalozeryflato

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Commits on Oct 8, 2022

• fix cindex to predict for hazard

  michalozeryflato

  committed
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Commits on Oct 11, 2022

• Merge branch 'ukbb_changes' of https://github.com/IBM/fuse-med-ml into ukbb_changes

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• Merge branch 'ukbb_changes' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

  committed
  c6ba955

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• minor refractoring

  avihu111

  committed
  159319a

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Commits on Nov 2, 2022

• Merge branch 'master' of https://github.com/IBM/fuse-med-ml into ukbb_changes

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  avihu111

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Commits on Nov 6, 2022

• Merge branch 'master' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

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  3f2fb75

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• PR review changes.

  avihu111

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  fe68f40

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• black for PR.

  avihu111

  committed
  82a86d1

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• flake8 fix

  avihu111

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Commits on Nov 7, 2022

• fix for PR

  avihu111

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  851047a

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• fix for PR

  avihu111

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  d4f00b7

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• Merge branch 'master' of https://github.com/IBM/fuse-med-ml into ukbb_changes

  avihu111

  committed
  7907b56

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• fix for PR

  avihu111

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  32b0cd4

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• missing init file

  avihu111

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Commits on Nov 9, 2022

• start challenge

  

  Itai Guez [email protected]

  committed
  7a011a9

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• updated yaml

  

  Itai Guez [email protected]

  committed
  3cbdee8

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Commits on Nov 10, 2022

• modified to work with seg - in progress

  

  Itai Guez [email protected]

  committed
  28f7139

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• fixed pipe

  

  Itai Guez [email protected]

  committed
  2db52d4

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• fixed pipe

  

  Itai Guez [email protected]

  committed
  bb36ff1

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• fixed pipe

  

  Itai Guez [email protected]

  committed
  a534207

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• fixed normalize op and no seg

  

  Itai Guez [email protected]

  committed
  9b598dd

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• fix dynamic

  

  Itai Guez [email protected]

  committed
  5a21946

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• fix dynamic

  

  Itai Guez [email protected]

  committed
  dbc8ca6

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• fixed type

  

  Itai Guez [email protected]

  committed
  7ed2d78

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• changed tto conf template|

  

  Itai Guez [email protected]

  committed
  36f2a27

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• sequence config from yaml

  

  Itai Guez [email protected]

  committed
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Commits on Nov 12, 2022

• running version with 2d unet - TODO - use the challenge code for validation

  

  Amir Egozi

  authored and

  Amir Egozi

  committed
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Commits on Nov 13, 2022

• fixed augmentation and fuse bug

  

  Itai Guez [email protected]

  committed
  cca1c1d

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• added picai metric

  

  Itai Guez [email protected]

  committed
  d204f1e

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• Working version (no metrics)

  

  Amir Egozi

  committed
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• metric update

  

  Itai Guez [email protected]

  committed
  fea6ee4

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• fix eval bug

  

  Amir Egozi

  committed
  8b4a070

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Commits on Nov 14, 2022

• return several picai metrics now

  

  Itai Guez [email protected]

  committed
  ce6d1d9

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• added num workers to eval

  

  Itai Guez [email protected]

  committed
  99c1327

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• changed reshape size and model

  

  Itai Guez [email protected]

  committed
  13f4342

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• fixed pipe

  

  Itai Guez [email protected]

  committed
  fbdd570

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• fix eval

  

  Itai Guez [email protected]

  committed
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Commits on Nov 15, 2022

• working version + add opt for 3d

  

  Amir Egozi

  committed
  4d70004

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• support both unet modes

  

  Itai Guez [email protected]

  committed
  7348491

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• change create model API

  

  itaiguez

  committed
  1bdce22

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• fix back loss - Amir dice loss should be generic

  

  Itai Guez [email protected]

  committed
  1f2e1f2

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• used MONAI loss for 3d unet

  

  Itai Guez [email protected]

  committed
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• metric and loss running with 3d unet

  

  Itai Guez [email protected]

  committed
  10d3c9f

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• remove softmax warninig

  

  Itai Guez [email protected]

  committed
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• softmax back as before

  

  Itai Guez [email protected]

  committed
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Commits on Nov 16, 2022

• detection algo inserted to metric calc

  

  itaiguez

  committed
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• Changes that every one will be happy

  

  Amir Egozi

  committed
  6d749d5

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• change to general GPU

  

  itaiguez

  committed
  a1a3f47

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• changed loss to focal

  

  Itai Guez [email protected]

  committed
  6650f33

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• fix loss by amir suggestion

  

  Itai Guez [email protected]

  committed
  e0a25b3

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• typo fix

  

  Itai Guez [email protected]

  committed
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Commits on Nov 17, 2022

• competition test dataset

  

  Itai Guez [email protected]

  committed
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• added axis to softmax

  

  Itai Guez [email protected]

  committed
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• added run test

  

  Itai Guez [email protected]

  committed
  75dd5b1

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• cleanup

  

  Itai Guez [email protected]

  committed
  7eafd9d

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• merged with itai

  

  Amir Egozi

  committed
  740fb52

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• small fix

  

  Itai Guez [email protected]

  committed
  c62001e

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• push back

  

  Itai Guez [email protected]

  committed
  e7523bf

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• small fix

  

  Itai Guez [email protected]

  committed
  59374ab

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• moved picai dataset

  

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• done

  

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  committed
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Commits on Feb 7, 2023

• cclean PICAI to unet 3d

  

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  committed
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Commits on May 2, 2023

• cleaning to PR

  

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  committed
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Commits on May 3, 2023

• cleanup

  

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  committed
  0898b82

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• cleanup

  

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  dc6d511

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• update config

  

  Itai Guez [email protected]

  committed
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Commits on May 7, 2023

• merge

  

  Itai Guez [email protected]

  committed
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