tiledbsoma-ml 0.1.0

Machine learning tools for use with tiledbsoma

TileDB-SOMA-ML

A Python package containing ML tools for use with TileDB-SOMA.

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/ contains tutorials and examples that use this repo to train toy models. For a general introduction to PyTorch data loading, see this tutorial. Additional information on the DataLoader/Dataset pattern can be found here.

Defects and feature requests should be filed as a GitHub issue in this repo. Please include a reproducible test case in all bug reports.

Getting Started

Installing

Install from PyPI:

pip install tiledbsoma-ml

Developers may install editable, from source, in the usual manner -- clone the repo and execute:

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:

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 team for their initial contribution.