Trajectory Seriation via Spectral Tangent Alignment and Global Embedding

We study linear seriation from noisy point clouds: given samples from an unknown one-dimensional curve embedded in $\mathbb{R}^d$, recover their latent order along the curve, up to reversal. Unlike much of the seriation literature, which starts from a precomputed similarity matrix, this setting retains ambient coordinates and therefore local geometric information. We propose STAGE, a geometric ordering method that estimates local tangent directions by neighborhood PCA, resolves their sign ambiguity through a graph-wide $\mathbb{Z}_2$ synchronization step, and constructs signed local displacement estimates by projecting ambient differences onto the oriented tangents. These increments are then integrated into a global scalar embedding through an inhomogeneous least-squares problem, equivalently a Laplacian linear system with a nonzero right-hand side, and the final order is obtained by sorting the embedding. We prove a finite-sample Kendall's $\tau$ recovery bound that makes explicit the roles of curvature, noise, neighborhood scale, sampling density, and graph connectivity. Empirically, STAGE gives accurate and fast order recovery on high-dimensional synthetic curves, compares favorably with spectral seriation, 1D UMAP, 1D t-SNE, Recanati's method, LTSA, and SABRE, and produces meaningful pseudotime orderings on single-cell RNA-seq datasets.