Rebase ESM PR and update all file formats (#19055)

* 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>
2022-09-30 14:16:25 +01:00
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--- a/README_ko.md
+++ b/README_ko.md
@@ -250,6 +250,7 @@ Flax, PyTorch, TensorFlow 설치 페이지에서 이들을 conda로 설치하는
 1. **[ELECTRA](https://huggingface.co/docs/transformers/model_doc/electra)** (from Google Research/Stanford University) released with the paper [ELECTRA: Pre-training text encoders as discriminators rather than generators](https://arxiv.org/abs/2003.10555) by Kevin Clark, Minh-Thang Luong, Quoc V. Le, Christopher D. Manning.
 1. **[EncoderDecoder](https://huggingface.co/docs/transformers/model_doc/encoder-decoder)** (from Google Research) released with the paper [Leveraging Pre-trained Checkpoints for Sequence Generation Tasks](https://arxiv.org/abs/1907.12461) by Sascha Rothe, Shashi Narayan, Aliaksei Severyn.
 1. **[ERNIE](https://huggingface.co/docs/transformers/model_doc/ernie)** (from Baidu) released with the paper [ERNIE: Enhanced Representation through Knowledge Integration](https://arxiv.org/abs/1904.09223) by Yu Sun, Shuohuan Wang, Yukun Li, Shikun Feng, Xuyi Chen, Han Zhang, Xin Tian, Danxiang Zhu, Hao Tian, Hua Wu.
+1. **[ESM](https://huggingface.co/docs/transformers/main/model_doc/esm)** (from Meta AI) are transformer protein language models.  **ESM-1b** was released with the paper [Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences](https://www.pnas.org/content/118/15/e2016239118) by Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus. **ESM-1v** was released with the paper [Language models enable zero-shot prediction of the effects of mutations on protein function](https://doi.org/10.1101/2021.07.09.450648) by Joshua Meier, Roshan Rao, Robert Verkuil, Jason Liu, Tom Sercu and Alexander Rives. **ESM-2** was released with the paper [Language models of protein sequences at the scale of evolution enable accurate structure prediction](https://doi.org/10.1101/2022.07.20.500902) by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives.
 1. **[FlauBERT](https://huggingface.co/docs/transformers/model_doc/flaubert)** (from CNRS) released with the paper [FlauBERT: Unsupervised Language Model Pre-training for French](https://arxiv.org/abs/1912.05372) by Hang Le, Loïc Vial, Jibril Frej, Vincent Segonne, Maximin Coavoux, Benjamin Lecouteux, Alexandre Allauzen, Benoît Crabbé, Laurent Besacier, Didier Schwab.
 1. **[FLAVA](https://huggingface.co/docs/transformers/model_doc/flava)** (from Facebook AI) released with the paper [FLAVA: A Foundational Language And Vision Alignment Model](https://arxiv.org/abs/2112.04482) by Amanpreet Singh, Ronghang Hu, Vedanuj Goswami, Guillaume Couairon, Wojciech Galuba, Marcus Rohrbach, and Douwe Kiela.
 1. **[FNet](https://huggingface.co/docs/transformers/model_doc/fnet)** (from Google Research) released with the paper [FNet: Mixing Tokens with Fourier Transforms](https://arxiv.org/abs/2105.03824) by James Lee-Thorp, Joshua Ainslie, Ilya Eckstein, Santiago Ontanon.