How can an analyst decide whether a nonlinear dimensionality reduction embedding can be trusted? Existing diagnostics provide only partial answers: projection glyphs characterize local sensitivity, map-continuity scores measure local conditioning, and transport-based analyses reveal path-dependent inconsistencies. However, these methods appear unrelated and provide no common framework for understanding when they agree or not. We show that they are all derived from a single geometric object induced by every differentiable embedding, whether defined implicitly through optimization or explicitly by a learned mapping. This framework provides two complementary geometric views of an embedding. The differential view explains local behavior: its first-order term recovers projection glyphs, while its second-order curvature quantifies how far their linear approximation remains reliable. The integral view follows the same geometry along high dimensional paths and determines whether an embedding depends only on the current state or also on the path taken to reach it. We further show that map-continuity is a prerequisite for the other analyses. The framework is theoretically complete for diagnostics derived from the embedding geometry, and we prove the integral view irreducible: no amount of local measurement at any number of points, to any order of derivative, reproduces what it detects. Classical rank-based metrics form a complementary class based on finite-scale neighborhood relationships. Experiments on synthetic and real datasets validate theoretical predictions, demonstrate accurate curvature-based trust estimates on single-cell embeddings, and show that the integral analysis distinguishes single-valued embeddings from path-dependent optimization-based embeddings in ways that existing pointwise diagnostics cannot.
Dimensionality reduction methods such as UMAP and t-SNE are central tools for visualising high-dimensional data, but their local-neighborhood objectives can preserve sampling noise while distorting global topology. We show that standard local metrics reward this noise memorisation: top-performing embeddings invent cycles and disconnected islands absent from the data. We introduce a topology-faithfulness benchmark based on noisy manifolds with known homology, tune DiRe against it, and find Pareto-optimal configurations that match or beat GPU-accelerated UMAP on classification while recovering exact first Betti numbers on stress tests. On 723K arXiv paper embeddings, DiRe preserves 3-4 times more topological structure than UMAP at comparable wall-clock.
Low-dimensional embeddings are widely used as visual summaries of high-dimensional data and to enable downstream scientific discoveries. Yet, popular nonlinear dimension reduction methods, such as t-SNE and UMAP, are often selected based on visual appeal alone and without rigorous quantitative validation. A major reason is that manifold embeddings typically do not provide an out-of-sample map nor an inverse back to the original feature space; this makes held-out validation, the gold standard in supervised learning, all but impossible. To address these challenges, we develop a novel framework, MEDAL (Manifold Embedding Distillation via Autoencoder Learning), which distills a fitted manifold embedding into a reusable encoder--decoder model. MEDAL trains a constrained autoencoder whose bottleneck exactly matches any teacher embedding while the decoder reconstructs the original input; this yields an explicit map for new samples, an approximate inverse, and a pointwise reconstruction-based measure of distortion in the manifold space. This converts static manifold embeddings into models that can be evaluated on held-out data, enabling quantitative validation including comparing different dimension reduction methods as well as hyperparameter tuning. Across multiple benchmark and scientific case studies, we show that MEDAL enables held-out validation to determine optimal manifold embeddings and hyperparameters, reveals biologically coherent regions that are difficult to preserve in two dimensional embeddings, and detects distribution shift when new samples are mapped into a fixed reference manifold. MEDAL provides a general validation wrapper to any existing dimension reduction technique that will improve the rigor and reliability of dimension reduction in scientific workflows.
We introduce EntroPath, a manifold learning method that recovers geodesic geometry from data graphs through ensembles of diffusion paths. Many existing graph-based embeddings rely either on locally normalised random walks or on shortest-path distances. The former can concentrate diffusion in densely sampled regions, while the latter are sensitive to spurious shortcut edges in the graph. EntroPath instead builds its dissimilarities from the maximum entropy random walk (MERW), which aggregates the full ensemble of k-step paths between points rather than relying on any single trajectory. We show that the resulting free-energy dissimilarity converges to squared geodesic distance in the short-time limit, via Varadhan's heat-kernel formula. The diffusion depth k interpolates smoothly between local neighbourhood structure and global manifold geometry, and the symmetrised kernel admits an exact Gram factorisation connecting EntroPath to kernel methods. We further provide scalable extensions via landmark projection and diffusion-potential pseudotime. Across synthetic manifolds and single-cell benchmarks, EntroPath consistently matches or outperforms diffusion- and shortest-path-based methods, while remaining competitive with neighbourhood-preserving embeddings (UMAP, t-SNE) on local-structure metrics. Its gains are most pronounced on manifolds with non-uniform sampling density and well-separated branching trajectories, where path-ensemble diffusion more faithfully preserves the underlying geodesic geometry.