Transformers in Single-Cell Omics
This repository accompanies Transformers in Single-Cell Omics: A Review and New Perspectives. Please refer to the manuscript for the details.
We provide a curated list of single-cell transformers and their evaluation results. We skip models that work only on bulk or images of slides data and those where transformers are used only as a part of the model. Models focusing on sequential data, such as DNA or protein sequences are omitted too. New entries are added at the top of the corresponding table.
We welcome contributions to this repository. Please open a pull request or an issue if you want to add or edit an entry.
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Preprint
Peer-Reviewed Publication
Fully reproducible
Code for evaluation only
Retracted or withdrawn
Citing this work
If you find the data in this repository useful for your work, please cite:
@Article{szalata_transformers_2024,
title = {Transformers in single-cell omics: a review and new perspectives},
volume = {21},
issn = {1548-7105},
url = {https://doi.org/10.1038/s41592-024-02353-z},
doi = {10.1038/s41592-024-02353-z},
pages = {1430--1443},
number = {8},
journaltitle = {Nature Methods},
shortjournal = {Nature Methods},
author = {Szałata, Artur and Hrovatin, Karin and Becker, Sören and Tejada-Lapuerta,
Alejandro and Cui, Haotian and Wang, Bo and Theis, Fabian J.},
date = {2024-08-01}
}