References

References#

[AKKT+19]

Miri Adler, Yael Korem Kohanim, Avichai Tendler, Avi Mayo, and Uri Alon. Continuum of gene-expression profiles provides spatial division of labor within a differentiated cell type. Cell Systems, 8(1):43–52.e5, 2019. URL: https://linkinghub.elsevier.com/retrieve/pii/S2405471218304824 (visited on 2024-12-07), arXiv:30638811, doi:10.1016/j.cels.2018.12.008.

[AMG+23]

Miri Adler, Noa Moriel, Aleksandrina Goeva, Inbal Avraham-Davidi, Simon Mages, Taylor S. Adams, Naftali Kaminski, Evan Z. Macosko, Aviv Regev, Ruslan Medzhitov, and Mor Nitzan. Emergence of division of labor in tissues through cell interactions and spatial cues. Cell Reports, 42(5):112412, 2023. URL: https://linkinghub.elsevier.com/retrieve/pii/S2211124723004230 (visited on 2024-12-07), arXiv:37086403, doi:10.1016/j.celrep.2023.112412.

[BKHT15]

Christian Bauckhage, Kristian Kersting, F. Hoppe, and Christian Thurau. Archetypal analysis as an autoencoder. Workshop "New Challenges in Neural Computation" (NC2) 2015, 2015. URL: https://www.ml.informatik.tu-darmstadt.de/papers/autoencode2015nc2.pdf (visited on 2025-02-10).

[CB94]

Adele Cutler and Leo Breiman. Archetypal analysis. Technometrics, 36(4):338–347, 1994. doi:10.1080/00401706.1994.10485840.

[EMLK+23]

Anissa El Marrahi, Fabio Lipreri, Ziqi Kang, Louise Gsell, Alper Eroglu, David Alber, and Jean Hausser. Nipmap: niche-phenotype mapping of multiplex histology data by community ecology. Nat Commun, 14(1):7182, 2023. URL: https://www.nature.com/articles/s41467-023-42878-z (visited on 2024-12-07), arXiv:37935691, doi:10.1038/s41467-023-42878-z.

[EL11]

Manuel J. A. Eugster and Friedrich Leisch. Weighted and robust archetypal analysis. Computational Statistics & Data Analysis, 55(3):1215–1225, 2011. URL: https://www.sciencedirect.com/science/article/pii/S0167947310004056 (visited on 2025-02-06), doi:10.1016/j.csda.2010.10.017.

[HSH+15]

Yuval Hart, Hila Sheftel, Jean Hausser, Pablo Szekely, Noa Bossel Ben-Moshe, Yael Korem, Avichai Tendler, Avraham E Mayo, and Uri Alon. Inferring biological tasks using pareto analysis of high-dimensional data. Nat Methods, 12(3):233–235, 2015. URL: https://www.nature.com/articles/nmeth.3254 (visited on 2024-12-07), arXiv:25622107, doi:10.1038/nmeth.3254.

[KSD+22]

Vitalii Kleshchevnikov, Artem Shmatko, Emma Dann, Alexander Aivazidis, Hamish W. King, Tong Li, Rasa Elmentaite, Artem Lomakin, others, Lauma Ramona, Elizabeth Tuck, Anna Arutyunyan, Roser Vento-Tormo, Moritz Gerstung, Louisa James, Oliver Stegle, and Omer Ali Bayraktar. Cell2location maps fine-grained cell types in spatial transcriptomics. Nature Biotechnology, 40(5):661–671, May 2022. doi:10.1038/s41587-021-01139-4.

[KSH+15]

Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi Mayo, Michael E. Rothenberg, Tomer Kalisky, and Uri Alon. Geometry of the gene expression space of individual cells. PLOS Computational Biology, 11(7):e1004224, July 2015. doi:10.1371/journal.pcbi.1004224.

[KLRubioRodriguezKirby+24]

Petra Kukanja, Christoffer M. Langseth, Leslie A. Rubio Rodríguez-Kirby, Eneritz Agirre, Chao Zheng, Amitha Raman, Chika Yokota, Christophe Avenel, Katarina Tiklová, André O. Guerreiro-Cacais, Tomas Olsson, Markus M. Hilscher, Mats Nilsson, and Gonçalo Castelo-Branco. Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology. Cell, 187(8):1990–2009.e19, April 2024. doi:10.1016/j.cell.2024.02.030.

[LBK16]

Mario Lucic, Olivier Bachem, and Andreas Krause. Strong coresets for hard and soft bregman clustering with applications to exponential family mixtures. In Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, 1–9. PMLR, May 2016.

[MB19]

Sebastian Mair and Ulf Brefeld. Coresets for archetypal analysis. Advances in Neural Information Processing Systems, 2019. URL: https://papers.nips.cc/paper_files/paper/2019/hash/7f278ad602c7f47aa76d1bfc90f20263-Abstract.html (visited on 2025-02-09).

[MS24]

Sebastian Mair and Jens Sjölund. Archetypal analysis++: rethinking the initialization strategy. 2024. URL: http://arxiv.org/abs/2301.13748 (visited on 2024-12-07), arXiv:2301.13748, doi:10.48550/arXiv.2301.13748.

[MGenoveL+20]

Lars Muhl, Guillem Genové, Stefanos Leptidis, Jianping Liu, Liqun He, Giuseppe Mocci, Ying Sun, Sonja Gustafsson, others, Åsa Segerstolpe, Elisabeth Raschperger, Emil M. Hansson, Johan L. M. Björkegren, Xiao-Rong Peng, Michael Vanlandewijck, Urban Lendahl, and Christer Betsholtz. Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination. Nature Communications, 11(1):3953, August 2020. doi:10.1038/s41467-020-17740-1.

[MH12]

Morten Mørup and Lars Kai Hansen. Archetypal analysis for machine learning and data mining. Neurocomputing, 80:54–63, 2012. URL: https://linkinghub.elsevier.com/retrieve/pii/S0925231211006060 (visited on 2024-12-07), doi:10.1016/j.neucom.2011.06.033.

[PGS+22]

Richard K. Perez, M. Grace Gordon, Meena Subramaniam, Min Cheol Kim, George C. Hartoularos, Sasha Targ, Yang Sun, Anton Ogorodnikov, others, Lawrence Fong, Maria Dall’Era, Brunilda Balliu, Aviv Regev, Jinoos Yazdany, Lindsey A. Criswell, Noah Zaitlen, and Chun Jimmie Ye. Single-cell rna-seq reveals cell type–specific molecular and genetic associations to lupus. Science, 376(6589):eabf1970, 2022. URL: https://www.science.org/doi/10.1126/science.abf1970 (visited on 2025-02-05), doi:10.1126/science.abf1970.

[TVH+24]

Demeter Túrós, Jelica Vasiljevic, Kerstin Hahn, Sven Rottenberg, and Alberto Valdeolivas. Chrysalis: decoding tissue compartments in spatial transcriptomics with archetypal analysis. Communications Biology, 7(1):1520, 2024. URL: https://www.nature.com/articles/s42003-024-07165-7 (visited on 2024-12-07), doi:10.1038/s42003-024-07165-7.

[BenMosheVM+22]

Shani Ben-Moshe, Tamar Veg, Rita Manco, Stav Dan, Delfina Papinutti, Aviezer Lifshitz, Aleksandra A. Kolodziejczyk, Keren Bahar Halpern, Eran Elinav, and Shalev Itzkovitz. The spatiotemporal program of zonal liver regeneration following acute injury. Cell Stem Cell, 29(6):973–989.e10, June 2022. doi:10.1016/j.stem.2022.04.008.