Haisu: Hierarchically supervised nonlinear dimensionality reduction

• DOI: 10.1371/journal.pcbi.1010351
• Publication Date: 2022-07-21T18:01:59Z
• Authors: Kevin Christopher...; Murat Can Çobanoğlu
• Keywords: 0301 basic medicine; 0303 health sciences; 03 medical and health sciences; QH301-705.5; Humans; Biology (General); Algorithms; Research Article

We propose a novel strategy for incorporating hierarchical supervised label information into nonlinear dimensionality reduction techniques. Specifically, we extend t-SNE, UMAP, and PHATE to include known or predicted class labels and demonstrate the efficacy of our approach on multiple single-cell RNA sequencing datasets. Our approach, “Haisu,” is applicable across domains and methods of nonlinear dimensionality reduction. In general, the mathematical effect of Haisu can be summarized as a variable perturbation of the high dimensional space in which the original data is observed. We thereby preserve the core characteristics of the visualization method and only change the manifold to respect known or assumed class labels when provided. Our strategy is designed to aid in the discovery and understanding of underlying patterns in a dataset that is heavily influenced by parent-child relationships. We show that using our approach can also help in semi-supervised settings where labels are known for only some datapoints (for instance when only a fraction of the cells are labeled). In summary, Haisu extends existing popular visualization methods to enable a user to incorporate labels known a priori into a visualization, including their hierarchical relationships as defined by a user input graph.