{"id":33121489,"url":"https://github.com/Westlake-AI/OpenBioSeq","last_synced_at":"2025-11-24T17:00:54.487Z","repository":{"id":65192259,"uuid":"495750773","full_name":"Westlake-AI/OpenBioSeq","owner":"Westlake-AI","description":"This repo focuses on supervised and self-supervised bio-sequence representation learning","archived":false,"fork":false,"pushed_at":"2023-10-11T21:04:22.000Z","size":640,"stargazers_count":22,"open_issues_count":2,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-23T03:50:37.649Z","etag":null,"topics":["bio-sequences","classification-regression","genetic-engineering","pytorch","self-supervised","transformer"],"latest_commit_sha":null,"homepage":"https://openbioseq.readthedocs.io/en/latest/","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/Westlake-AI.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","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":"2022-05-24T09:16:26.000Z","updated_at":"2025-03-14T08:03:55.000Z","dependencies_parsed_at":"2024-11-18T04:36:39.915Z","dependency_job_id":"81a9108f-7ec0-4688-ab40-cb747acab94f","html_url":"https://github.com/Westlake-AI/OpenBioSeq","commit_stats":{"total_commits":15,"total_committers":2,"mean_commits":7.5,"dds":0.1333333333333333,"last_synced_commit":"2ea2ff881ff6ded8f6c4bdd4bf16b21ffe268d17"},"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/Westlake-AI/OpenBioSeq","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Westlake-AI%2FOpenBioSeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Westlake-AI%2FOpenBioSeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Westlake-AI%2FOpenBioSeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Westlake-AI%2FOpenBioSeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Westlake-AI","download_url":"https://codeload.github.com/Westlake-AI/OpenBioSeq/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Westlake-AI%2FOpenBioSeq/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286079811,"owners_count":27282121,"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","status":"online","status_checked_at":"2025-11-24T02:00:07.096Z","response_time":68,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["bio-sequences","classification-regression","genetic-engineering","pytorch","self-supervised","transformer"],"created_at":"2025-11-15T05:00:23.871Z","updated_at":"2025-11-24T17:00:54.473Z","avatar_url":"https://github.com/Westlake-AI.png","language":"Python","readme":"# OpenBioSeq\n[![PyPI](https://img.shields.io/pypi/v/OpenBioSeq)](https://pypi.org/project/OpenBioSeq)\n[![license](https://img.shields.io/badge/license-Apache--2.0-%23B7A800)](https://github.com/Westlake-AI/OpenBioSeq/blob/main/LICENSE)\n![open issues](https://img.shields.io/github/issues-raw/Westlake-AI/OpenBioSeq?color=%23FF9600)\n[![issue resolution](https://img.shields.io/badge/issue%20resolution-1%20d-%23009763)](https://github.com/Westlake-AI/OpenBioSeq/issues)\n\n**News**\n\n* OpenBioSeq v0.1.1 is released, which supports classification and regression tasks on bio-sequence datasets. It inherited most features in [OpenMixup](https://github.com/Westlake-AI/openmixup).\n* OpenBioSeq v0.1.0 is initialized.\n\n## Introduction\n\nThe main branch works with **PyTorch 1.8** (required by some self-supervised methods) or higher (we recommend **PyTorch 1.12**). You can still use **PyTorch 1.6** for most methods.\n\n`OpenBioSeq` is an open-source supervised and self-supervised bio-sequence representation learning toolbox based on PyTorch. `OpenBioSeq` supports popular backbones, pre-training methods, and various features.\n\n### What does this repo do?\n\nLearning useful bio-sequence representation efficiently facilitates various downstream tasks in biological and chemical fields. This repo focuses on supervised and self-supervised bio-sequence representation learning and is named `OpenBioSeq`.\n\n### Major features\n\nThis repo will be continued to update in 2022! Please watch us for latest update!\n\n## Change Log\n\nPlease refer to [CHANGELOG.md](docs/CHANGELOG.md) for details and release history.\n\n[2022-06-09] `OpenBioSeq` v0.1.1 is released.\n\n[2022-05-24] `OpenBioSeq` v0.1.0 is initialized.\n\n## Installation\n\nThere are quick installation steps for develepment:\n\n```shell\nconda create -n openbioseq python=3.8 -y\nconda activate openbioseq\npip install torch==1.11.0+cu113 torchvision==0.12.0+cu113 torchaudio==0.11.0 --extra-index-url https://download.pytorch.org/whl/cu113 # as an example\npip install openmim\nmim install mmcv-full\ngit clone https://github.com/Westlake-AI/OpenBioSeq.git\ncd OpenBioSeq\npython setup.py develop\n```\n\nPlease refer to [INSTALL.md](docs/INSTALL.md) for detailed installation instructions and dataset preparation.\n\n## Get Started\n\nPlease see [Getting Started](docs/GETTING_STARTED.md) for the basic usage of OpenBioSeq (based on OpenMixup and MMSelfSup). As an example, you can start a multiple GPUs training with a certain `CONFIG_FILE` using the following script: \n```shell\nbash tools/dist_train.sh ${CONFIG_FILE} ${GPUS} [optional arguments]\n```\nThen, please see [tutorials](docs/tutorials) for more tech details (based on MMClassification).\n\n## License\n\nThis project is released under the [Apache 2.0 license](LICENSE).\n\n## Acknowledgement\n\n- `OpenBioSeq` is an open-source project for supervised and self-supervised methods on bio-sequence datasets created by researchers in CAIRI AI LAB. We encourage researchers interested in bio-sequence research and applications to contribute to `OpenBioSeq`!\n- This repo is mainly based on [OpenMixup](https://github.com/Westlake-AI/openmixup), and borrows the architecture design and part of the code from [MMSelfSup](https://github.com/open-mmlab/mmselfsup) and [MMClassification](https://github.com/open-mmlab/mmclassification).\n\n## Citation\n\nIf you find this project useful in your research, please consider cite:\n\n```BibTeX\n@misc{2022openbioseq,\n    title={{OpenBioSeq}: Open Toolbox and Benchmark for Bio-sequence Representation Learning},\n    author={Li, Siyuan and Liu, Zicheng and Wu, Di and Stan Z. Li},\n    howpublished = {\\url{https://github.com/Westlake-AI/openbioseq}},\n    year={2022}\n}\n```\n\n## Contributors\n\nFor now, the direct contributors include: Siyuan Li ([@Lupin1998](https://github.com/Lupin1998)) and Zicheng Liu ([@pone7](https://github.com/pone7)). We thanks contributors for OpenMixup, MMSelfSup, and MMClassification.\n\n## Contact\n\nThis repo is currently maintained by Siyuan Li (lisiyuan@westlake.edu.cn) and Zicheng Liu (liuzicheng@westlake.edu.cn).\n","funding_links":[],"categories":["Time Series and Neuroscience Learning"],"sub_categories":["Physics"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FWestlake-AI%2FOpenBioSeq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FWestlake-AI%2FOpenBioSeq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FWestlake-AI%2FOpenBioSeq/lists"}