Bridging Graph Drawing and Dimensionality Reduction with Stochastic Stress Optimization

Graphs are commonly visualized in 2D, where humans readily interpret spatial relationships, yet such layouts often distort higher-dimensional structure. We propose to embed graphs in high-dimensional space and search for informative 2D viewpoints that optimize aesthetic and readability metrics (e.g., edge crossings and angular resolution), enabled by a novel differentiable surrogate for edge crossings. Numerical experiments show that these viewpoints consistently outperform standard 2D layouts, and can even surpass methods explicitly designed to optimize these metrics. We further introduce DataFly, an interactive system for exploring multiple candidate viewpoints through seamless navigation. A usability study demonstrates that our approach reveals structural patterns that remain hidden in conventional 2D visualizations.

Dimensionality reduction (DR) involves two longstanding trade-offs. First, preserving local neighborhoods can come at the cost of global structure. Neighbor embedding methods such as t-SNE and UMAP prioritize local similarity preservation but do not explicitly constrain global organization, whereas standard spectral methods such as Laplacian Eigenmaps capture smooth, coarse-scale graph structure but offer limited flexibility to depict finer local structure. Second, the flexibility of nonlinear DR methods often comes at the cost of analytical transparency. Many methods do not explicitly reveal how high-dimensional structure produces patterns in the embedding. We introduce SDMP (Spectral Decomposition for Multiscale Projection), a nonlinear DR framework built on an explicit spectral decomposition. In this formulation, each embedding dimension is expressed as a weighted combination of Laplacian eigenvectors derived from a neighborhood graph, with the weights learned via a UMAP-style cross-entropy objective. By progressively expanding the spectral subspace to capture increasingly fine graph structure, SDMP produces a sequence of embeddings, making the evolving balance between global organization and local detail explicit, controllable, and inspectable. The explicit decomposition also reveals which spectral scales shape the overall embedding and how individual eigenvectors influence point positions. Quantitative evaluations on synthetic, image, and single-cell data show competitive local and global structure preservation, while case studies illustrate how the decomposition supports interpretation of clusters and developmental trajectories across spectral scales.

A graph layout is normally a table of $N$ free coordinates. We optimise a function with a fixed number of parameters instead. This gives a drawing a sample complexity and an extensible domain. Force-directed algorithms remain the standard tools for graph drawing. The most accurate among them minimise stress in the Kamada-Kawai formulation by directly optimising the node coordinates, at a full objective cost of $O(N^2)$ in time and space. Here, we propose Fling (Field Layout via Implicit Neural Geometry), a small neural network mapping the distances of each node to a set of landmarks, positioning it in the plane by training on the layout energy. The full spring system then becomes tractable without its distance matrix, as rest lengths follow from a landmark bound in constant time per pair while a second network learns the majorisation sums from exact anchor rows, at $O(|\mathcal{A}|N)$ per step for $|\mathcal{A}|\ll N$ anchors. Unlike neural drawers that read the graph by message passing, we represent the drawing as a function of node features. An unseen node costs one forward pass, where sparse and low-rank majorisation remain transductive. As the unknowns are weights rather than coordinates, the energy only requires a small fraction of the nodes, and a field fitted that way outperforms PivotMDS, landmark MDS, and a kernel ridge trained on the same energy and features, when the task is fitting the energy of a graph from a sample of its nodes. In addition, the same parameterisation enables a stochastic pivot stress variant, an aesthetics-optimised variant carrying a neighbour-embedding energy with node-edge clearance and crossing terms on the same field, and conditioning on the weight between two energies gives a whole layout family from one run.