Add unetr #1

caleb-vicente · 2022-11-06T11:55:40Z

What does this PR do?

Before submitting

This PR fixes a typo or improves the docs (you can dismiss the other checks if that's the case).
Did you read the contributor guideline,
Pull Request section?
Was this discussed/approved via a Github issue or the forum? Please add a link
to it if that's the case.
Did you make sure to update the documentation with your changes? Here are the
documentation guidelines, and
here are tips on formatting docstrings.
Did you write any new necessary tests?

Who can review?

Anyone in the community is free to review the PR once the tests have passed. Feel free to tag
members/contributors who may be interested in your PR.

* [Whisper] Fix gradient checkpointing (again!) * [Whisper] Fix checkpointing (again!)

* ResNet Config for doctest * added empty lines as suggested * ran make style

* update feature extractor params * update attention mask handling * fix doc and pipeline test * add warning when skipping test * add whisper translation and transcription test * fix build doc test * Correct whisper processor * make fix copies * remove sample docstring as it does not fit whisper model * Update src/transformers/models/whisper/modeling_whisper.py Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com> * fix, doctests are passing * Nit * last nit Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

… name (huggingface#19124) * simplify loop * fix layer map split * update * update for special variables * add rag test * fixup * revert change : for next PR

…19580) * initial commit * few suggested changes

) * adds vision_encoder_decoder to Doc tests * keep the initial order

…9582) * initial changes * update the suggested order of import

…izer files (huggingface#19626)

* Data2Vec Text Config for doctest * typo fix * made suggested changes

* trocr Config for doctest * ran make style

* Remove key word argument X from pipeline predict and transform methods As __call__ of pipeline clasees require one positional argument, passing the input as a keyword argument inside predict, transform methods, causing __call__ to fail. Hence in this commit the keyword argument is modified into positional argument. * Implement basic tests for scikitcompat pipeline interface * Seperate tests instead of running with parameterized based on framework as both frameworks will not be active at the same time

* add type hints to mctct * run auto style corrections * change torch.bool to bool# * Update src/transformers/models/mctct/modeling_mctct.py Co-authored-by: Matt <Rocketknight1@users.noreply.github.com> * Remove optional tags for attention_mask and head_mask' * fix optional tags' * Update src/transformers/models/mctct/modeling_mctct.py Co-authored-by: Matt <Rocketknight1@users.noreply.github.com>

* Partial TF port for ESM model * Add ESM-TF tests * Add the various imports for TF-ESM * TF weight conversion almost ready * Stop ignoring the decoder weights in PT * Add tests and lots of fixes * fix-copies * Fix imports, add model docs * Add get_vocab() to tokenizer * Fix vocab links for pretrained files * Allow multiple inputs with a sep * Use EOS as SEP token because ESM vocab lacks SEP * Correctly return special tokens mask from ESM tokenizer * make fixup * Stop testing unsupported embedding resizing * Handle TF bias correctly * Skip all models with slow tokenizers in the token classification test * Fixing the batch/unbatcher of pipelines to accomodate the `None` being passed around. * Fixing pipeline bug caused by slow tokenizer being different. * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update src/transformers/models/esm/modeling_tf_esm.py Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com> * Update set_input_embeddings and the copyright notices Co-authored-by: Your Name <you@example.com> Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com> Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>

* added type hints for Yolos Pytorch model * make fixup * Update src/transformers/models/yolos/convert_yolos_to_pytorch.py * Update src/transformers/models/yolos/convert_yolos_to_pytorch.py * Update src/transformers/models/yolos/convert_yolos_to_pytorch.py Co-authored-by: Matt <rocketknight1@gmail.com> Co-authored-by: Matt <Rocketknight1@users.noreply.github.com>

…9584) * Fixes * update expected values * style * fix Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

* Removed Bert interdependency from Funnel transformer * passed consistency check * Revert "passed consistency check" This reverts commit ba55a08. * Fixed docstrings Co-authored-by: mukesh663 <mukesh13034@gmail.com>

* fix warnings in deberta * fix copies * Revert "fix copies" This reverts commit 324cb3f. * fix copies * fix copies again * revert changes to whitespace that make style did since it results in an infinite chain of fix-copies * argh Co-authored-by: Sander Land <sander@chatdesk.com>

install->installation

Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

* add return_tensors parameter for feature_extraction w/ test add return_tensor parameter for feature extraction Revert "Merge branch 'feature-extraction-return-tensor' of https://github.com/ajsanjoaquin/transformers into feature-extraction-return-tensor" This reverts commit d559da7, reversing changes made to bbef892. * call parameter directly Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com> * Fixup. * Update src/transformers/pipelines/feature_extraction.py Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com> Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com> Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* [Whisper Tokenizer] Make more user-friendly * use property * make indexing rigorous * small clean-up * tests * skip seq2seq tests * remove multilingual arg * reorder args * collapse to one function Co-authored-by: ArthurZucker <arthur@huggingface.co> * option to override attributes Co-authored-by: ArthurZucker <arthur@huggingface.co> * add to docs * Apply suggestions from code review Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com> * make comment more clear Co-authored-by: sgugger <sylvain@huggingface.co> * don't add special tokens in get_decoder_prompt_ids * add test for set_prefix_tokens Co-authored-by: ArthurZucker <arthur@huggingface.co> Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com> Co-authored-by: sgugger <sylvain@huggingface.co>

…ggingface#19066) * fix led eos_mask * add Futur Warning * revert uselesss cahnges * Update src/transformers/models/led/modeling_led.py Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com> Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

…t.trace tuple input sequence, update related doc (huggingface#19891) * fix jit trace error for classification usecase, update related doc Signed-off-by: Wang, Yi A <yi.a.wang@intel.com> * add implementation in torch 1.14.0 Signed-off-by: Wang, Yi A <yi.a.wang@intel.com> * update_doc Signed-off-by: Wang, Yi A <yi.a.wang@intel.com> * update_doc Signed-off-by: Wang, Yi A <yi.a.wang@intel.com> Signed-off-by: Wang, Yi A <yi.a.wang@intel.com>

* Update ESM conversion script for ESMfold * Fix bug in ESMFold example * make fixup and move restypes to one line

* Only resize embeddings when necessary * Add comment

…e tensors to numpy (huggingface#19976) * Speed up TF postprocessing by converting to numpy before * Fix bug that was triggered when offset_mapping was None Co-authored-by: Patrick Deutschmann <patrick.deutschmann@dedalus.com>

* Fix esm lm head test * make fixup

…gingface#20062)

…0048) * Poolformer image processor defaults to previous FE * Remove unnecessary math.floor

* Fix Swin * Remove file * Update code snippet * Add copied from to maskformer * Fix docstring * Add whole name to replace Co-authored-by: Niels Rogge <nielsrogge@Nielss-MacBook-Pro.local>

* Update READMEs for ESMFold and add notebooks * Fix PyCharm formatting * make fix-copies

…dings, to be in line with Tips section for BERT and GPT2 (huggingface#20068) Co-authored-by: jordiclive <jordiclive19@imperial.ac.uk>

…gface#20044) * POC * For more CLIP-like models Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

…0069) Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

* Update defaults and logic to match old FE * Use docker run rest values

HuggingFaceDocBuilderDev · 2022-11-06T12:13:57Z

The docs for this PR live here. All of your documentation changes will be reflected on that endpoint.

daspartho and others added 30 commits October 14, 2022 17:21

[Doctest] LeViT Config for doctest (huggingface#19622)

96f243c

[Doctest] DistilBERT Config for doctest (huggingface#19621)

585f9c6

[Whisper] Fix gradient checkpointing (again!) (huggingface#19548)

4e196df

* [Whisper] Fix gradient checkpointing (again!) * [Whisper] Fix checkpointing (again!)

[Doctest] Add configuration_resnet.py (huggingface#19620)

66dd802

* ResNet Config for doctest * added empty lines as suggested * ran make style

Sharding fails in TF when absolute scope was modified if . in layer…

2bd2de6

… name (huggingface#19124) * simplify loop * fix layer map split * update * update for special variables * add rag test * fixup * revert change : for next PR

[Doctest] Add configuration_vision_text_dual_encoder.py (huggingface#…

7972f99

…19580) * initial commit * few suggested changes

[Doctest] Add configuration_vision_encoder_decoder.py (huggingface#19583

31cfe9c

) * adds vision_encoder_decoder to Doc tests * keep the initial order

[Doctest] Add configuration_time_series_transformer.py (huggingface#1…

8fcf562

…9582) * initial changes * update the suggested order of import

Tokenizer from_pretrained should not use local files named like token…

3e49002

…izer files (huggingface#19626)

[Doctest] CodeGen config for doctest (huggingface#19633)

dd464e2

[Doctest] Add configuration_data2vec_text.py (huggingface#19636)

339c5a5

* Data2Vec Text Config for doctest * typo fix * made suggested changes

[Doctest] Conditional DETR config for doctest (huggingface#19641)

57505b1

[Doctest] XLNet config for doctest (huggingface#19649)

c06a5a3

[Doctest] Add configuration_trocr.py (huggingface#19658)

9bb26f2

* trocr Config for doctest * ran make style

Add doctest info in testingmdx (huggingface#19623)

d2e5b19

Add pillow to layoutlmv3 example requirements.txt (huggingface#19663)

2af36f9

add return types for tf gptj, xlm, and xlnet (huggingface#19638)

e4d56e8

A few CI fixes for DocumentQuestionAnsweringPipeline (huggingface#1…

cbc1abc

…9584) * Fixes * update expected values * style * fix Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

word replacement line huggingface#231 (huggingface#19662)

f4e31a9

install->installation

[Doctest] Add configuration_transfo_xl.py (huggingface#19651)

0027edf

Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

Update perf_train_gpu_one.mdx (huggingface#19676)

aa629e7

object-detection instead of object_detection (huggingface#19677)

59e29be

sanchit-gandhi and others added 22 commits November 3, 2022 14:22

Update esmfold conversion script (huggingface#20028)

6f257bb

* Update ESM conversion script for ESMfold * Fix bug in ESMFold example * make fixup and move restypes to one line

Fixed torch.finfo issue with torch.fx (huggingface#20040)

9080607

Only resize embeddings when necessary (huggingface#20043)

06886d5

* Only resize embeddings when necessary * Add comment

Fix ESM LM head test (huggingface#20045)

1076d58

* Fix esm lm head test * make fixup

Update README.md (huggingface#20063)

3502c20

fix tokenizer_type to avoid error when loading checkpoint back (hug…

1906771

…gingface#20062)

[Trainer] Fix model name in push_to_hub (huggingface#20064)

94e17c4

PoolformerImageProcessor defaults to match previous FE (huggingface#2…

3936411

…0048) * Poolformer image processor defaults to previous FE * Remove unnecessary math.floor

[Swin] Add Swin SimMIM checkpoints (huggingface#20034)

787620e

* Fix Swin * Remove file * Update code snippet * Add copied from to maskformer * Fix docstring * Add whole name to replace Co-authored-by: Niels Rogge <nielsrogge@Nielss-MacBook-Pro.local>

change constant torch.tensor to torch.full (huggingface#20061)

707b12a

Update READMEs for ESMFold and add notebooks (huggingface#20067)

6e1c578

* Update READMEs for ESMFold and add notebooks * Fix PyCharm formatting * make fix-copies

Update documentation on seq2seq models with absolute positional embed…

3bd0007

…dings, to be in line with Tips section for BERT and GPT2 (huggingface#20068) Co-authored-by: jordiclive <jordiclive19@imperial.ac.uk>

Allow passing arguments to model testers for CLIP-like models (huggin…

2d02178

…gface#20044) * POC * For more CLIP-like models Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

Show installed libraries and their versions in GA jobs (huggingface#2…

c06d555

…0069) Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

Update defaults and logic to match old FE (huggingface#20065)

d68c460

* Update defaults and logic to match old FE * Use docker run rest values

Update modeling_tf_utils.py (huggingface#20076)

4b86e44

Update hub.py (huggingface#20075)

504db92

autogenerated files based on vit model

f34cb62

caleb-vicente self-assigned this Nov 6, 2022

caleb-vicente and others added 6 commits November 12, 2022 18:10

forward pass using monai libraries (fail in windows)

dcce7dc

forward pass same results original paper (monai dependencies)

c2f31cc

removed unused imports

6e8d0a5

finished model test. remove unused typing.List and numpy as np

386063b

pr run file unetrfor3dimagesegmentaiton not imported

f1cf97e

pr run file typing.List imported but not used

59fe49a

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add unetr #1

Add unetr #1

caleb-vicente commented Nov 6, 2022 •

edited

HuggingFaceDocBuilderDev commented Nov 6, 2022

Add unetr #1

Are you sure you want to change the base?

Add unetr #1

Conversation

caleb-vicente commented Nov 6, 2022 • edited

What does this PR do?

Before submitting

Who can review?

HuggingFaceDocBuilderDev commented Nov 6, 2022

caleb-vicente commented Nov 6, 2022 •

edited