Mesoscopic structure graphs for interpreting uncertainty in non-linear embeddings

Probabilistic-based non-linear dimensionality reduction (PB-NL-DR) methods, such as t-SNE and UMAP, are effective in unfolding complex high-dimensional manifolds, allowing users to explore and understand the structural patterns of data. However, due to the trade-off between global and local structure preservation and the randomness during computation, these methods may introduce false neighborhood relationships, known as distortion errors and misleading visualizations. To address this issue, we first conduct a detailed survey to illustrate the design space of prior layout enrichment visualizations for interpreting DR results, and then propose a node-link visualization technique, ManiGraph. This technique rethinks the neighborhood fidelity between the high- and low-dimensional spaces by constructing dynamic mesoscopic structure graphs and measuring region-adapted trustworthiness. ManiGraph also addresses the overplotting issue in scatterplot visualization for large-scale datasets and supports examining in unsupervised scenarios. We demonstrate the effectiveness of ManiGraph in different analytical cases, including generic machine learning using 3D toy data illustrations and fashion-MNIST, a computational biology study using a single-cell RNA sequencing dataset, and a deep learning-enabled colorectal cancer study with histopathology-MNIST. •ManiGraph, a node-link technique, enhances neighborhood fidelity and addresses overplotting in large-scale datasets.•ManiGraph interprets uncertainties resulting from distortion errors.•ManiGraph is validated on sc-RNA-seq and histology image analysis.•Our survey highlights SOTA DR visualization techniques.