References

References#

[AUzBH+25]

Lucas Arnoldt, Julius Upmeier zu Belzen, Luis Herrmann, Khue Nguyen, Fabian Theis, Benjamin Wild, and Roland Eils. Biologically guided variational inference for interpretable multimodal single-cell integration. bioRxiv, 2025.

[LNL+22]

Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V. Misharin, and Fabian J. Theis. Mapping single-cell data to reference atlases by transfer learning. Nature Biotechnology, 40(1):121–130, 2022. URL: https://doi.org/10.1038/s41587-021-01001-7, doi:10.1038/s41587-021-01001-7.

[LBC+21]

Malte Luecken, Daniel Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann Chen, Louise Deconinck, Angela Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Kim, Dominik Klein, BONY DE KUMAR, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Joaquin Melgarejo, Honey Mekonen, Maurizio Morri, Michaela Müller, Norma Neff, Sheryl Paul, Bastian Rieck, Kaylie Schneider, Scott Steelman, Michael Sterr, Daniel Treacy, Alexander Tong, Alexandra-Chloe Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela Pisco, Smita Krishnaswamy, Fabian Theis, and Jonathan M Bloom. A sandbox for prediction and integration of dna, rna, and proteins in single cells. In J. Vanschoren and S. Yeung, editors, Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks, volume 1. 2021. URL: https://datasets-benchmarks-proceedings.neurips.cc/paper_files/paper/2021/file/158f3069a435b314a80bdcb024f8e422-Paper-round2.pdf.

[MYF+18]

Jianzhu Ma, Michael Ku Yu, Samson Fong, Keiichiro Ono, Eric Sage, Barry Demchak, Roded Sharan, and Trey Ideker. Using deep learning to model the hierarchical structure and function of a cell. Nature Methods, 15(4):290–298, 2018. URL: https://doi.org/10.1038/nmeth.4627, doi:10.1038/nmeth.4627.

[VSP+17]

Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N. Gomez, Lukasz Kaiser, and Illia Polosukhin. Attention is all you need. 2017. URL: https://arxiv.org/abs/1706.03762, arXiv:1706.03762.