{"id":15118782,"url":"https://github.com/genentech/walk-jump","last_synced_at":"2025-04-14T00:38:09.257Z","repository":{"id":176432194,"uuid":"645969895","full_name":"Genentech/walk-jump","owner":"Genentech","description":"Official repository for discrete Walk-Jump Sampling (dWJS)","archived":false,"fork":false,"pushed_at":"2023-12-17T18:15:08.000Z","size":188,"stargazers_count":52,"open_issues_count":2,"forks_count":8,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-03-27T14:52:27.841Z","etag":null,"topics":["antibody","machine-learning","protein-design","protein-sequences","proteins"],"latest_commit_sha":null,"homepage":"https://arxiv.org/abs/2306.12360","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-05-26T22:20:27.000Z","updated_at":"2025-03-19T08:58:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"833d5911-e22c-4b5d-be7e-768271f5182f","html_url":"https://github.com/Genentech/walk-jump","commit_stats":null,"previous_names":["genentech/walk-jump"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fwalk-jump","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fwalk-jump/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fwalk-jump/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fwalk-jump/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/walk-jump/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248803811,"owners_count":21164122,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["antibody","machine-learning","protein-design","protein-sequences","proteins"],"created_at":"2024-09-26T01:53:38.056Z","updated_at":"2025-04-14T00:38:09.228Z","avatar_url":"https://github.com/Genentech.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"# discrete Walk-Jump Sampling (dWJS)\n\nThis 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)\n\nSee our experimental results immunizing against ERBB2 [here](./assets/experimental_results.pdf)!\n\n## Setup\nAssuming you have [miniconda](https://docs.conda.io/en/latest/miniconda.html) installed, clone the repository, navigate inside, and run:\n```bash\n./scripts/install.sh\n```\n\n### Training\nThe entrypoint `train` is the main driver for training and accepts parameters using Hydra syntax.\nThe available parameters for configuration can be found by running `train` --help or by looking in the `src/walkjump/hydra_config` directory\n\n### Sampling\nThe entrypoint `sample` is the main driver for training and accepts parameters using Hydra syntax.\nThe available parameters for configuration can be found by running `sample` --help or by looking in the `src/walkjump/hydra_config` directory\n\n## Contributing\n\nWe 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.\n\n## License\nLicensed 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.\n\nUnless 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.\n\n\n## Citations\nIf you use the code and/or model, please cite:\n```\n@article{frey2023protein,\n      title={Protein Discovery with Discrete Walk-Jump Sampling}, \n      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},\n      year={2023},\n      eprint={2306.12360},\n      archivePrefix={arXiv},\n      primaryClass={q-bio.BM}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fwalk-jump","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fwalk-jump","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fwalk-jump/lists"}