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Haisu: Hierarchically supervised nonlinear dimensionality reduction

Fig 5

Haisu does not compromise the embedding of cells that do not have a label in the input graph.

We depict 0% and 100% replacement of the TA-1 label with a ‘dummy’ label that is not present in the hierarchy across t-SNE, UMAP, and PHATE. Even at high strength values (str) of the hierarchical distancing factor, Haisu maintains relationships in the embedding circled in the figure. Notably, TA 1 cells remain close to Cycling TA cells across the embeddings at 100% removal despite their distance in the hierarchy graph. Thus, we do not comprise the integrity of each NLDR method, allowing for the observation of unknown classes in the context of a strongly influential, known hierarchy.

Fig 5

doi: https://doi.org/10.1371/journal.pcbi.1010351.g005