EmbedOR: Provable Cluster-Preserving Visualizations with Curvature-Based Stochastic Neighbor Embeddings

Stochastic Neighbor Embedding (SNE) algorithms like UMAP and tSNE often produce visualizations that do not preserve the geometry of noisy and high dimensional data. In particular, they can spuriously separate connected components of the underlying data submanifold and can fail to find clusters in well-clusterable data. To address these limitations, we propose EmbedOR, a SNE algorithm that incorporates discrete graph curvature. Our algorithm stochastically embeds the data using a curvature-enhanced distance metric that emphasizes underlying cluster structure. Critically, we prove that the EmbedOR distance metric extends consistency results for tSNE to a much broader class of datasets. We also describe extensive experiments on synthetic and real data that demonstrate the visualization and geometry-preservation capabilities of EmbedOR. We find that, unlike other SNE algorithms and UMAP, EmbedOR is much less likely to fragment continuous, high-density regions of the data. Finally, we demonstrate that the EmbedOR distance metric can be used as a tool to annotate existing visualizations to identify fragmentation and provide deeper insight into the underlying geometry of the data.

Recovering Manifold Structure Using Ollivier-Ricci Curvature

We introduce ORC-ManL, a new algorithm to prune spurious edges from nearest neighbor graphs using a criterion based on Ollivier-Ricci curvature and estimated metric distortion. Our motivation comes from manifold learning: we show that when the data generating the nearest-neighbor graph consists of noisy samples from a low-dimensional manifold, edges that shortcut through the ambient space have more negative Ollivier-Ricci curvature than edges that lie along the data manifold. We demonstrate that our method outperforms alternative pruning methods and that it significantly improves performance on many downstream geometric data analysis tasks that use nearest neighbor graphs as input. Specifically, we evaluate on manifold learning, persistent homology, dimension estimation, and others. We also show that ORC-ManL can be used to improve clustering and manifold learning of single-cell RNA sequencing data. Finally, we provide empirical convergence experiments that support our theoretical findings.

An Intrinsic Approach to Scalar-Curvature Estimation for Point Clouds

We introduce an intrinsic estimator for the scalar curvature of a data set presented as a finite metric space. Our estimator depends only on the metric structure of the data and not on an embedding in $\mathbb{R}^n$. We show that the estimator is consistent in the sense that for points sampled from a probability measure on a compact Riemannian manifold, the estimator converges to the scalar curvature as the number of points increases. To justify its use in applications, we show that the estimator is stable with respect to perturbations of the metric structure, e.g., noise in the sample or error estimating the intrinsic metric. We validate our estimator experimentally on synthetic data that is sampled from manifolds with specified curvature.