* initial commit
* First draft that gets outputs without crashing!
* Add all the ported openfold dependencies
* testing
* Restructure config files for ESMFold
* Debugging to find output discrepancies
* Mainly style
* Make model runnable without extra deps
* Remove utils and merge them to the modeling file
* Use correct gelu and remove some debug prints
* More cleanup
* Update esm docs
* Update conversion script to support ESMFold properly
* Port some top-level changes from ESMFold repo
* Expand EsmFold docstrings
* Make attention_mask optional (default to all 1s)
* Add inference test for ESMFold
* Use config and not n kwargs
* Add modeling output class
* Remove einops
* Remove chunking in ESM FFN
* Update tests for ESMFold
* Quality
* REpo consistency
* Remove tree dependency from ESMFold
* make fixup
* Add an error in case my structure map function breaks later
* Remove needless code
* Stop auto-casting the LM to float16 so CPU tests pass
* Stop auto-casting the LM to float16 so CPU tests pass
* Final test updates
* Split test file
* Copyright and quality
* Unpin PyTorch to see built doc
* Fix config file to_dict() method
* Add some docstrings to the output
* Skip TF checkpoint tests for ESM until we reupload those
* make fixup
* More docstrings
* Unpin to get even with main
* Flag example to write
Co-authored-by: Sylvain Gugger <Sylvain.gugger@gmail.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>
* Rebase ESM PR and update all file formats
* Fix test relative imports
* Add __init__.py to the test dir
* Disable gradient checkpointing
* Remove references to TFESM... FOR NOW >:|
* Remove completed TODOs from tests
* Convert docstrings to mdx, fix-copies from BERT
* fix-copies for the README and index
* Update ESM's __init__.py to the modern format
* Add to _toctree.yml
* Ensure we correctly copy the pad_token_id from the original ESM model
* Ensure we correctly copy the pad_token_id from the original ESM model
* Tiny grammar nitpicks
* Make the layer norm after embeddings an optional flag
* Make the layer norm after embeddings an optional flag
* Update the conversion script to handle other model classes
* Remove token_type_ids entirely, fix attention_masking and add checks to convert_esm.py
* Break the copied from link from BertModel.forward to remove token_type_ids
* Remove debug array saves
* Begin ESM-2 porting
* Add a hacky workaround for the precision issue in original repo
* Code cleanup
* Remove unused checkpoint conversion code
* Remove unused checkpoint conversion code
* Fix copyright notices
* Get rid of all references to the TF weights conversion
* Remove token_type_ids from the tests
* Fix test code
* Update src/transformers/__init__.py
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
* Update src/transformers/__init__.py
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
* Update README.md
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
* Add credit
* Remove _ args and __ kwargs in rotary embedding
* Assertively remove asserts
* Replace einsum with torch.outer()
* Fix docstring formatting
* Remove assertions in tokenization
* Add paper citation to ESMModel docstring
* Move vocab list to single line
* Remove ESMLayer from init
* Add Facebook copyrights
* Clean up RotaryEmbedding docstring
* Fix docstring formatting
* Fix docstring for config object
* Add explanation for new config methods
* make fix-copies
* Rename all the ESM- classes to Esm-
* Update conversion script to allow pushing to hub
* Update tests to point at my repo for now
* Set config properly for tests
* Remove the gross hack that forced loss of precision in inv_freq and instead copy the data from the model being converted
* make fixup
* Update expected values for slow tests
* make fixup
* Remove EsmForCausalLM for now
* Remove EsmForCausalLM for now
* Fix padding idx test
* Updated README and docs with ESM-1b and ESM-2 separately (#19221)
* Updated README and docs with ESM-1b and ESM-2 separately
* Update READMEs, longer entry with 3 citations
* make fix-copies
Co-authored-by: Your Name <you@example.com>
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
Co-authored-by: Tom Sercu <tsercu@fb.com>
Co-authored-by: Your Name <you@example.com>
