Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

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.

Theorem 1. Minimizing the expected loss Suppose we have T -dimensional features. Anchor nodes serve as fixed reference points within a simplicial complex, anchoring its structure and providing stability. Furthermore, anchor nodes can also represent important entities. Figure S2: Comparison of TSNE plots of representations learned by various encoders. CCA-SSG methods can not capture higher-order information and show similar artifacts. For example, the two clusters on the bottom and one from the right (corresponding to classes 1,2,3) are students from the same year but in different divisions.

Topological data analysis (TDA) delivers invaluable and complementary information on the intrinsic properties of data inaccessible to conventional methods.

We develop a framework for comparing data manifolds, aimed, in particular, towards the evaluation of deep generative models.

It is increasingly common for data to possess intricate structure, necessitating new models and analytical tools. Graphs, a prominent type of structure, can encode the relationships between any two entities (nodes). However, graphs neither allow connections that are not dyadic nor permit relationships between sets of nodes. We thus turn to simplicial complexes for connecting more than two nodes as well as modeling relationships between simplices, such as edges and triangles. Our data then consist of signals lying on topological spaces, represented by simplicial complexes. Much recent work explores these topological signals, albeit primarily through deterministic formulations. We propose a probabilistic framework for random signals defined on simplicial complexes. Specifically, we generalize the classical notion of stationarity. By spectral dualities of Hodge and Dirac theory, we define stationary topological signals as the outputs of topological filters given white noise. This definition naturally extends desirable properties of stationarity that hold for both time-series and graph signals. Crucially, we properly define topological power spectral density (PSD) through a clear spectral characterization. We then discuss the advantages of topological stationarity due to spectral properties via the PSD. In addition, we empirically demonstrate the practicality of these benefits through multiple synthetic and real-world simulations.