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.

In the first case, points arrive sequentially, and only a summary can be stored in memory.

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

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

Zhang et al. have recently shown that geodesic convex concave Riemannian problems always admit saddle-point solutions.

We consider the problem of estimating the Fréchet and conditional Fréchet mean from data taking values in separable metric spaces. Unlike Euclidean spaces, where well-established methods are available, there is no practical estimator that works universally for all metric spaces. Therefore, we introduce a computable estimator for the Fréchet mean based on random quantization techniques and establish its universal consistency across any separable metric spaces. Additionally, we propose another estimator for the conditional Fréchet mean, leveraging data-driven partitioning and quantization, and demonstrate its universal consistency when the output space is any Banach space.

Learning useful representations is a key ingredient to the success of modern machine learning. Currently, representation learning mostly relies on embedding data into Euclidean space. However, recent work has shown that data in some domains is better modeled by non-euclidean metric spaces, and inappropriate geometry can result in inferior performance. In this paper, we aim to eliminate the inductive bias imposed by the embedding space geometry. Namely, we propose to map data into more general non-vector metric spaces: a weighted graph with a shortest path distance. By design, such graphs can model arbitrary geometry with a proper configuration of edges and weights. Our main contribution is PRODIGE: a method that learns a weighted graph representation of data end-to-end by gradient descent. Greater generality and fewer model assumptions make PRODIGE more powerful than existing embedding-based approaches. We confirm the superiority of our method via extensive experiments on a wide range of tasks, including classification, compression, and collaborative filtering.