When One Point Is Not Enough: Addressing Ambiguous Instances in Dimensionality Reduction by Splitting
Authors: Diede P. M. van der Hoorn, Alessio Arleo, Fernando V. Paulovich
Organizations: Eindhoven University of Technology
Abstract
Dimensionality Reduction (DR) methods are widely used to visualize high-dimensional data. One key task in DR-based analysis is discovering neighborhoods, which relies on analyzing the fine-grained local structure of a projection. However, DR is an inherently lossy process; no technique can perfectly preserve the high-dimensional relationships, and projections therefore contain visual artifacts. In this paper, we highlight a typically overlooked source of visual artifacts: ambiguous instances. These are instances that are highly similar to multiple mutually dissimilar neighborhoods in the high-dimensional space. Standard DR methods cannot faithfully project such instances, since each data instance is mapped to a single point in the visual space. As a result, such an instance is placed in only one of its neighborhoods (or in none at all), so only part of its neighborhood structure is represented. We call this distortion partial neighborhood embedding. In this paper, we introduce a graph-based approach that identifies ambiguous instances and replicates them as multiple points in the projection, placing each copy within its respective neighborhood. We use UMAP for our results, but our approach also generalizes to other local graph-based DR techniques, and we show that our approach reveals previously hidden neighborhood memberships in projections and reduces partial neighborhood embedding across multiple examples, and is further supported by quantitative analyses.
While UMAP is widely used for exploring high-dimensional data, typical workflows focus on its lower-dimensional embedding, largely overlooking the rich k-nearest-neighbor (kNN) graph that UMAP constructs internally. This graph encodes the data manifold in its original high-dimensional space, before the distortion that UMAP's 2D projection introduces. We demonstrate the untapped potential of this internal representation, showing how standard graph algorithms applied to this graph enhance data sensemaking: (1) PageRank identifies representative data points, (2) k-core decomposition reveals dense core regions versus sparse periphery, and (3) clustering coefficient detects tight-knit neighborhoods with highly-similar data points. Through quantitative and qualitative evaluation on MNIST and Fashion MNIST, we show that these graph-based analyses are not only practical but also competitive with or complementary to purpose-built methods (e.g., k-medoids for exemplar selection, HDBSCAN for density-based clustering).
Nonlinear dimensionality-reduction methods such as UMAP and PaCMAP adaptively normalize local distances during graph construction, erasing neighborhood scale from the data. This distorts more than relative cluster sizes: sparse structures like bridges between transitioning cell types and narrow spectral spikes in hyperspectral images can be suppressed or lost entirely. DensMAP adds a density penalty to correct this, but this penalty competes with UMAP's attraction-repulsion forces, scattering points far from their neighborhoods. ScaleMAP takes a different approach: each pairwise embedding displacement is divided by the geometric mean of the two endpoints' original-space local radii, re-injecting scale information as a change of variables rather than as a competing objective. Across standard benchmarks and scientific datasets from transcriptomics, hyperspectral imaging, and flow cytometry, ScaleMAP matches DensMAP on density preservation while maintaining UMAP-level neighborhood preservation. In transcriptomic data, it recovers sparse bridges between cell populations that UMAP collapses; in flow cytometry, it faithfully represents density structure across 17 orders of magnitude. The same principle applied to PaCMAP yields consistently improved density preservation, suggesting the approach generalizes beyond UMAP.
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.