Contrastive Finetuning protein Language Models

This repo contains data and scripts to demonstrate how Sentence-Transformers can be used with protein Language Models, in particular ESM models, as demonstrated in the paper Optimizing protein language models with Sentence Transformers, NeurIPS (2023).

Setup

Please note that this implementation requires GPUs.

git clone https://github.com/PeptoneLtd/contrastive-finetuning-plms.git
cd contrastive-finetuning-plms
pip install -r full_env.txt

Usage

Two minimal examples showing how to train a solubility and disorder prediction are provided.

• scripts/solubility_search_seeds.py
• scripts/disorder_st_avg.py

Note that the scripts take the data from the data folder and might require adjusting of the paths depending on the environment setting. For the disorder task in case of a large scale search, one might consider caching the frozen residue level representations from ESM, as currently it automatically downloads those from huggingface on-the-fly.

Citations

If you use this work in your research, please cite the the relevant software:

@article{redloptimizing,
  title={Optimizing protein language models with Sentence Transformers},
  author={Redl, Istvan and Airoldi, Fabio and Bottaro, Sandro and Chung, Albert and Dutton, Oliver and Fisicaro, Carlo and Foerch, Patrik and Henderson, Louie and Hoffmann, Falk and Invernizzi, Michele and others}
}

Licence

This source code is licensed under the Apache 2.0 license found in the LICENSE file in the root directory of this source tree.