Create README.md

README.md

@@ -0,0 +1,51 @@
+# ISM
+
+By [Jeffrey Ouyang-Zhang](https://jozhang97.github.io/), [Chengyue Gong](https://sites.google.com/view/chengyue-gong), [Yue Zhao](https://zhaoyue-zephyrus.github.io), [Philipp Krähenbühl](http://www.philkr.net/), [Adam Klivans](https://www.cs.utexas.edu/users/klivans/), [Daniel J. Diaz](http://danny305.github.io)
+
+This repository contains the model presented in the paper [Distilling Structural Representations into Protein Sequence Models](https://www.biorxiv.org/content/10.1101/2024.11.08.622579v1).
+The official github can be found at https://github.com/jozhang97/ism.
+
+**TL; DR.** ESM2 with enriched structural representations
+
+## Quickstart
+
+This quickstart assumes that the user is already working with ESM2 and is interested in replacing ESM with ISM. First, download ISM.
+```bash
+# recommended
+huggingface-cli download jozhang97/ism_t33_650M_uc30pdb --local-dir /path/to/save/ism
+
+# alternative
+git clone https://huggingface.co/jozhang97/ism_t33_650M_uc30pdb
+```
+
+If the user is starting from [fair-esm](https://github.com/facebookresearch/esm), add the following lines of code.
+```python
+import esm
+model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
+ckpt = torch.load('/path/to/ism_t33_650M_uc30pdb/checkpoint.pth')
+model.load_state_dict(ckpt)
+```
+
+If the user is starting from [huggingface](https://huggingface.co/facebook/esm2_t33_650M_UR50D), replace the model and tokenizer with the following line of code.
+```python
+from transformers import AutoTokenizer, AutoModel
+config_path = "/path/to/ism_t33_650M_uc30pdb/"
+model = AutoModel.from_pretrained(config_path)
+tokenizer = AutoTokenizer.from_pretrained(config_path)
+```
+
+Please change `/path/to/ism_t33_650M_uc30pdb` to the path where the model is downloaded.
+
+## Citing ISM
+If you find ISM useful in your research, please consider citing:
+
+```bibtex
+@article{ouyangzhang2024distilling,
+  title={Distilling Structural Representations into Protein Sequence Models},
+  author={Ouyang-Zhang, Jeffrey and Gong, Chengyue and Zhao, Yue and Kr{\"a}henb{\"u}hl, Philipp and Klivans, Adam and Diaz, Daniel J},
+  journal={bioRxiv},
+  doi={10.1101/2024.11.08.622579},
+  year={2024},
+  publisher={Cold Spring Harbor Laboratory}
+}
+```