Assessing and improving reliability of neighbor embedding methods: a map-continuity perspective
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DOI: 10.1038/s41467-025-60434-9
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- Md Tauhidul Islam & Zixia Zhou & Hongyi Ren & Masoud Badiei Khuzani & Daniel Kapp & James Zou & Lu Tian & Joseph C. Liao & Lei Xing, 2023. "Revealing hidden patterns in deep neural network feature space continuum via manifold learning," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Dmitry Kobak & Philipp Berens, 2019. "The art of using t-SNE for single-cell transcriptomics," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- Karsten Bach & Sara Pensa & Marta Grzelak & James Hadfield & David J. Adams & John C. Marioni & Walid T. Khaled, 2017. "Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
- Tara Chari & Lior Pachter, 2023. "The specious art of single-cell genomics," PLOS Computational Biology, Public Library of Science, vol. 19(8), pages 1-20, August.
- Lucy Xia & Christy Lee & Jingyi Jessica Li, 2024. "Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Anna C. Belkina & Christopher O. Ciccolella & Rina Anno & Richard Halpert & Josef Spidlen & Jennifer E. Snyder-Cappione, 2019. "Automated optimized parameters for T-distributed stochastic neighbor embedding improve visualization and analysis of large datasets," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
- Tetsutaro Hayashi & Haruka Ozaki & Yohei Sasagawa & Mana Umeda & Hiroki Danno & Itoshi Nikaido, 2018. "Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
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