Single-cell RNA-seq data analysis typically requires representations that capture heterogeneous local structure across multiple scales while remaining stable and interpretable. In this work, we propose a hierarchical sheaf spectral embedding (HSSE) framework that constructs informative cell-level features based on persistent sheaf Laplacian analysis. Starting from scale-dependent low-dimensional embeddings, we define cell-centered local neighborhoods at multiple resolutions. For each local neighborhood, we construct a data-driven cellular sheaf that encodes local relationships among cells. We then compute persistent sheaf Laplacians over sampled filtration intervals and extract spectral statistics that summarize the evolution of local relational structure across scales. These spectral descriptors are aggregated into a unified feature vector for each cell and can be directly used in downstream learning tasks without additional model training. We evaluate HSSE on twelve benchmark single-cell RNA-seq datasets covering diverse biological systems and data scales. Under a consistent classification protocol, HSSE achieves competitive or improved performance compared with existing multiscale and classical embedding-based methods across multiple evaluation metrics. The results demonstrate that sheaf spectral representations provide a robust and interpretable approach for single-cell RNA-seq data representation learning.

We address the problem of setting the kernel bandwidth, epps, used by Manifold Learning algorithms to construct the graph Laplacian. Exploiting the connection between manifold geometry, represented by the Riemannian metric, and the Laplace-Beltrami operator, we set epps by optimizing the Laplacian's ability to preserve the geometry of the data.

Forl = 2, i. e., for 3 - cycles, thisrelationship is X ikX kj= X ij. Figure 1: Averagematchingerrorunderthe LBCmodel ( left) and LACmodel ( right).

Interestingly, and in a sharp departure from previous proposals, this operation on coarsened graphs is often oriented, even when the original graph is undirected.

H . (32) We refer to ( H

Neural Information Processing Systems http://nips.cc/