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https://github.com/genentech/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)
https://github.com/genentech/walk-jump
antibody machine-learning protein-design protein-sequences proteins
Last synced: about 2 months ago
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Official repository for discrete Walk-Jump Sampling (dWJS)
- Host: GitHub
- URL: https://github.com/genentech/walk-jump
- Owner: Genentech
- License: apache-2.0
- Created: 2023-05-26T22:20:27.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-12-17T18:15:08.000Z (about 1 year ago)
- Last Synced: 2024-09-26T02:01:33.335Z (4 months ago)
- Topics: antibody, machine-learning, protein-design, protein-sequences, proteins
- Language: Python
- Homepage: https://arxiv.org/abs/2306.12360
- Size: 184 KB
- Stars: 50
- Watchers: 6
- Forks: 8
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# discrete Walk-Jump Sampling (dWJS)
This is the official open source repository for [discrete Walk-Jump Sampling](https://arxiv.org/abs/2306.12360) developed by [ncfrey](https://github.com/ncfrey), [djberenberg](https://github.com/djberenberg), [kleinhenz](https://github.com/kleinhenz), and [saeedsaremi](https://github.com/saeedsaremi), from [Prescient Design, a Genentech accelerator.](https://gene.com/prescient)
See our experimental results immunizing against ERBB2 [here](./assets/experimental_results.pdf)!
## Setup
Assuming you have [miniconda](https://docs.conda.io/en/latest/miniconda.html) installed, clone the repository, navigate inside, and run:
```bash
./scripts/install.sh
```
### Training
The entrypoint `train` is the main driver for training and accepts parameters using Hydra syntax.
The available parameters for configuration can be found by running `train` --help or by looking in the `src/walkjump/hydra_config` directory
### Sampling
The entrypoint `sample` is the main driver for training and accepts parameters using Hydra syntax.
The available parameters for configuration can be found by running `sample` --help or by looking in the `src/walkjump/hydra_config` directory
## Contributing
We welcome contributions. If you would like to submit pull requests, please make sure you base your pull requests off the latest version of the `main` branch.
## License
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at https://www.apache.org/licenses/LICENSE-2.0.
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
## Citations
If you use the code and/or model, please cite:
```
@article{frey2023protein,
title={Protein Discovery with Discrete Walk-Jump Sampling},
author={Nathan C. Frey and Daniel Berenberg and Karina Zadorozhny and Joseph Kleinhenz and Julien Lafrance-Vanasse and Isidro Hotzel and Yan Wu and Stephen Ra and Richard Bonneau and Kyunghyun Cho and Andreas Loukas and Vladimir Gligorijevic and Saeed Saremi},
year={2023},
eprint={2306.12360},
archivePrefix={arXiv},
primaryClass={q-bio.BM}
}
```