https://github.com/single-cell-data/tiledb-soma-ml
SOMA PyTorch loaders
https://github.com/single-cell-data/tiledb-soma-ml
ml pytorch soma tiledb tiledb-soma
Last synced: 2 months ago
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SOMA PyTorch loaders
- Host: GitHub
- URL: https://github.com/single-cell-data/tiledb-soma-ml
- Owner: single-cell-data
- License: mit
- Created: 2024-09-18T14:46:15.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-09-19T19:59:47.000Z (9 months ago)
- Last Synced: 2025-09-23T11:56:02.571Z (9 months ago)
- Topics: ml, pytorch, soma, tiledb, tiledb-soma
- Language: Jupyter Notebook
- Homepage: https://single-cell-data.github.io/TileDB-SOMA-ML/
- Size: 12.2 MB
- Stars: 11
- Watchers: 5
- Forks: 3
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# TileDB-SOMA-ML
A Python package containing ML tools for use with [TileDB-SOMA].
[][pypi]
Docs: [single-cell-data.github.io/TileDB-SOMA-ML].
**NOTE:** this is a _pre-release_ package, and may be subject to breaking API changes prior to first release.
## Description
The package contains a prototype PyTorch [`IterableDataset`], [`ExperimentDataset`], for use with the [`torch.utils.data.DataLoader`] API.
[notebooks/](notebooks) contains tutorials and examples that use this repo to train toy models. For a general introduction to PyTorch data loading, [see this tutorial][torch data tutorial]. Additional information on the DataLoader/Dataset pattern [can be found here][`torch.data`].
Defects and feature requests should be filed as [a GitHub issue][/issues] in this repo. Please include a reproducible test case in all bug reports.
## Getting Started
### Installing
Install [from PyPI][pypi]:
```bash
pip install tiledbsoma-ml
```
Developers may install editable, from source, in the usual manner -- clone the repo and execute:
```bash
pip install -e .
```
### Documentation
Documentation can be found at [single-cell-data.github.io/TileDB-SOMA-ML], and in the [notebooks] directory.
## Builds
This is a pure Python package. To build a wheel, ensure you have the `build` package installed, and then:
```bash
python -m build .
```
## Version History
See the [CHANGELOG.md] file.
## License
This project is licensed under the MIT License.
## Acknowledgements
The SOMA team is grateful to the Chan Zuckerberg Initiative Foundation [CELLxGENE Census](https://cellxgene.cziscience.com) team for their initial contribution.
[TileDB-SOMA]: https://github.com/single-cell-data/TileDB-SOMA
[`IterableDataset`]: https://pytorch.org/docs/stable/data.html#torch.utils.data.IterableDataset
[`ExperimentDataset`]: src/tiledbsoma_ml/dataset.py
[`torch.utils.data.DataLoader`]: https://pytorch.org/docs/stable/data.html#torch.utils.data.DataLoader
[/issues]: https://github.com/single-cell-data/TileDB-SOMA-ML/issues/new
[pypi]: https://pypi.org/project/tiledbsoma-ml/
[torch data tutorial]: https://pytorch.org/tutorials/beginner/data_loading_tutorial.html
[`torch.data`]: https://pytorch.org/docs/stable/data.html
[single-cell-data.github.io/TileDB-SOMA-ML]: https://single-cell-data.github.io/TileDB-SOMA-ML/
[notebooks]: notebooks
[CHANGELOG.md]: CHANGELOG.md
[www]: https://single-cell-data.github.io/TileDB-SOMA-ML/
[single-cell-data.github.io/TileDB-SOMA-ML]: https://single-cell-data.github.io/TileDB-SOMA-ML/