https://github.com/theislab/multimil
Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
https://github.com/theislab/multimil
Last synced: 10 months ago
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Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
- Host: GitHub
- URL: https://github.com/theislab/multimil
- Owner: theislab
- License: bsd-3-clause
- Created: 2019-12-06T21:15:46.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2025-09-30T11:32:14.000Z (10 months ago)
- Last Synced: 2025-09-30T13:23:16.070Z (10 months ago)
- Language: Python
- Homepage: https://multimil.rtfd.io/
- Size: 155 MB
- Stars: 34
- Watchers: 5
- Forks: 6
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: docs/contributing.md
- License: LICENSE
Awesome Lists containing this project
README
# Multimodal weakly supervised learning to identify disease-specific changes in single-cell atlases
[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/theislab/multimil/test.yaml?branch=main
[link-tests]: https://github.com/theislab/multimil/actions/workflows/test.yml
[badge-docs]: https://img.shields.io/readthedocs/multimil
[badge-colab]: https://colab.research.google.com/assets/colab-badge.svg
## Getting started
Please refer to the [documentation][link-docs]. In particular, the
- [API documentation][link-api]
and the tutorials:
- [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)
## Installation
You need to have Python 3.10 or newer installed on your system. We recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
To create and activate a new environment:
```bash
mamba create --name multimil python=3.10
mamba activate multimil
```
Next, there are several alternative options to install multimil:
1. Install the latest release of `multimil` from [PyPI][link-pypi]:
```bash
pip install multimil
```
2. Or install the latest development version:
```bash
pip install git+https://github.com/theislab/multimil.git@main
```
## Release notes
See the [changelog][changelog].
## Contact
If you found a bug, please use the [issue tracker][issue-tracker].
## Citation
> **Multimodal Weakly Supervised Learning to Identify Disease-Specific Changes in Single-Cell Atlases**
>
> 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.
## Reproducibility
Code and notebooks to reproduce the results from the paper are available at [theislab/multimil_reproducibility](/https://github.com/theislab/multimil_reproducibility).
[issue-tracker]: https://github.com/theislab/multimil/issues
[changelog]: https://multimil.readthedocs.io/en/latest/changelog.html
[link-docs]: https://multimil.readthedocs.io
[link-api]: https://multimil.readthedocs.io/en/latest/api.html
[link-pypi]: https://pypi.org/project/multimil