{"id":31805724,"url":"https://github.com/theislab/multimil","last_synced_at":"2025-10-11T02:57:45.843Z","repository":{"id":247085622,"uuid":"226412247","full_name":"theislab/multimil","owner":"theislab","description":"Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases","archived":false,"fork":false,"pushed_at":"2025-09-30T11:32:14.000Z","size":162879,"stargazers_count":34,"open_issues_count":11,"forks_count":6,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-09-30T13:23:16.070Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://multimil.rtfd.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"docs/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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2019-12-06T21:15:46.000Z","updated_at":"2025-09-30T11:32:11.000Z","dependencies_parsed_at":"2024-10-18T12:06:48.574Z","dependency_job_id":"9141429d-3f5b-4442-aa84-757d8d358e44","html_url":"https://github.com/theislab/multimil","commit_stats":null,"previous_names":["theislab/multimil"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/multimil","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmultimil","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmultimil/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmultimil/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmultimil/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/multimil/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fmultimil/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005953,"owners_count":26084009,"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":"2025-10-11T02:00:06.511Z","response_time":55,"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":[],"created_at":"2025-10-11T02:57:41.603Z","updated_at":"2025-10-11T02:57:45.838Z","avatar_url":"https://github.com/theislab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases\n\n[![Tests][badge-tests]][link-tests]\n[![Documentation][badge-docs]][link-docs]\n\n[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/multimil/test.yaml?branch=main\n[link-tests]: https://github.com/theislab/multimil/actions/workflows/test.yml\n[badge-docs]: https://img.shields.io/readthedocs/multimil\n[badge-colab]: https://colab.research.google.com/assets/colab-badge.svg\n\n## Getting started\n\nPlease refer to the [documentation][link-docs]. In particular, the\n\n-   [API documentation][link-api]\n\nand the tutorials:\n\n-   [Classification with MIL](https://multimil.readthedocs.io/en/latest/notebooks/mil_classification.html) [![Open In Colab][badge-colab]](https://colab.research.google.com/github/theislab/multimil/blob/main/docs/notebooks/mil_classification.ipynb)\n\n## Installation\n\nYou need to have Python 3.10 or newer installed on your system. We recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).\n\nTo create and activate a new environment:\n\n```bash\nmamba create --name multimil python=3.10\nmamba activate multimil\n```\n\nNext, there are several alternative options to install multimil:\n\n1. Install the latest release of `multimil` from [PyPI][link-pypi]:\n\n```bash\npip install multimil\n```\n\n2. Or install the latest development version:\n\n```bash\npip install git+https://github.com/theislab/multimil.git@main\n```\n\n## Release notes\n\nSee the [changelog][changelog].\n\n## Contact\n\nIf you found a bug, please use the [issue tracker][issue-tracker].\n\n## Citation\n\n\u003e **Multimodal Weakly Supervised Learning to Identify Disease-Specific Changes in Single-Cell Atlases**\n\u003e\n\u003e Anastasia Litinetskaya, Maiia Shulman, Soroor Hediyeh-zadeh, Amir Ali Moinfar, Fabiola Curion, Artur Szalata, Alireza Omidi, Mohammad Lotfollahi, and Fabian J. Theis. 2024. bioRxiv. https://doi.org/10.1101/2024.07.29.605625.\n\n## Reproducibility\n\nCode and notebooks to reproduce the results from the paper are available at [theislab/multimil_reproducibility](/https://github.com/theislab/multimil_reproducibility).\n\n[issue-tracker]: https://github.com/theislab/multimil/issues\n[changelog]: https://multimil.readthedocs.io/en/latest/changelog.html\n[link-docs]: https://multimil.readthedocs.io\n[link-api]: https://multimil.readthedocs.io/en/latest/api.html\n[link-pypi]: https://pypi.org/project/multimil\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmultimil","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fmultimil","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fmultimil/lists"}