References

Bibliography

[EKU+24]

Luca Eyring, Dominik Klein, Théo Uscidda, Giovanni Palla, Niki Kilbertus, Zeynep Akata, and Fabian J Theis. Unbalancedness in neural monge maps improves unpaired domain translation. In The Twelfth International Conference on Learning Representations. 2024. URL: https://openreview.net/forum?id=2UnCj3jeao.

[FSejourneV+19]

Jean Feydy, Thibault Séjourné, François-Xavier Vialard, Shun-ichi Amari, Alain Trouve, and Gabriel Peyré. Interpolating between optimal transport and mmd using sinkhorn divergences. In Kamalika Chaudhuri and Masashi Sugiyama, editors, Proceedings of the Twenty-Second International Conference on Artificial Intelligence and Statistics, volume 89 of Proceedings of Machine Learning Research, 2681–2690. PMLR, 16–18 Apr 2019. URL: https://proceedings.mlr.press/v89/feydy19a.html.

[KUTC24]

Dominik Klein, Théo Uscidda, Fabian Theis, and Marco Cuturi. Genot: entropic (gromov) wasserstein flow matching with applications to single-cell genomics. 2024. URL: https://proceedings.neurips.cc/paper_files/paper/2024/file/bc46e29f91e676747c584ca181cb0ea1-Paper-Conference.pdf, doi:10.48550/arXiv.2310.09254.

[LJK+23]

Hsiu-Chuan Lin, Jasper Janssens, Ann-Sophie Kroell, Philipp Hornauer, Malgorzata Santel, Ryoko Okamoto, Kyriaki Karava, Marthe Priouret, Maria Pascual Garcia, Manuel Schroeter, and others. Human neuron subtype programming through combinatorial patterning with scseq readouts. bioRxiv, pages 2023–12, 2023.

[LCBH+22]

Yaron Lipman, Ricky TQ Chen, Heli Ben-Hamu, Maximilian Nickel, and Matt Le. Flow matching for generative modeling. 2022. arXiv:2210.02747, doi:10.48550/arXiv.2210.02747.

[PGS+24]

Stefan Peidli, Tessa D. Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J. Schumacher, Jake P. Taylor-King, Debora S. Marks, Augustin Luna, Nils Blüthgen, and Chris Sander. Scperturb: harmonized single-cell perturbation data. Nature Methods, 21(3):531–540, January 2024. URL: http://dx.doi.org/10.1038/s41592-023-02144-y, doi:10.1038/s41592-023-02144-y.

[PBHDE+23]

Aram-Alexandre Pooladian, Heli Ben-Hamu, Carles Domingo-Enrich, Brandon Amos, Yaron Lipman, and Ricky Chen. Multisample flow matching: straightening flows with minibatch couplings. 2023. arXiv:2304.14772, doi:10.48550/arXiv.2304.14772.

[TMH+23]

Alexander Tong, Nikolay Malkin, Guillaume Huguet, Yanlei Zhang, Jarrid Rector-Brooks, Kilian Fatras, Guy Wolf, and Yoshua Bengio. Improving and generalizing flow-based generative models with minibatch optimal transport. 2023. arXiv:2302.00482, doi:10.48550/arXiv.2302.00482.

[VSP+23]

Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N. Gomez, Lukasz Kaiser, and Illia Polosukhin. Attention is all you need. 2023. URL: https://arxiv.org/abs/1706.03762, arXiv:1706.03762.