In this paper, we propose HiPoNet, an end-to-end differentiable neural network for regression, classification, and representation learning on high-dimensional point clouds. Our work is motivated by single-cell data which can have very high-dimensionality - exceeding the capabilities of existing methods for point clouds which are mostly tailored for 3D data. Moreover, modern single-cell and spatial experiments now yield entire cohorts of datasets (i.e., one data set for every patient), necessitating models that can process large, high-dimensional point-clouds at scale. Most current approaches build a single nearest-neighbor graph, discarding important geometric and topological information. In contrast, HiPoNet models the point-cloud as a set of higher-order simplicial complexes, with each particular complex being created using a reweighting of features. This method thus generates multiple constructs corresponding to different views of high-dimensional data, which in biology offers the possibility of disentangling distinct cellular processes. It then employs simplicial wavelet transforms to extract multiscale features, capturing both local and global topology from each view. We show that geometric and topological information is preserved in this framework both theoretically and empirically.

Graph-based recommender systems have achieved remarkable effectiveness by modeling high-order interactions between users and items. However, such approaches are significantly undermined by popularity bias, which distorts the interaction graph's structure--referred to as topology bias. This leads to overrepresentation of popular items, thereby reinforcing biases and fairness issues through the user-system feedback loop. Despite attempts to study this effect, most prior work focuses on the embedding or gradient level bias, overlooking how topology bias fundamentally distorts the message passing process itself. We bridge this gap by providing an empirical and theoretical analysis from a Dirichlet energy perspective, revealing that graph message passing inherently amplifies topology bias and consistently benefits highly connected nodes. To address these limitations, we propose Test-time Simplicial Propagation (TSP), which extends message passing to higher-order simplicial complexes. By incorporating richer structures beyond pairwise connections, TSP mitigates harmful topology bias and substantially improves the representation and recommendation of long-tail items during inference. Extensive experiments across five real-world datasets demonstrate the superiority of our approach in mitigating topology bias and enhancing recommendation quality. The implementation code is available at https://github.com/sotaagi/TSP.

We consider the problem of computing persistent homology (PH) for large-scale Euclidean point cloud data, aimed at downstream machine learning tasks, where the exponential growth of the most widely-used Vietoris-Rips complex imposes serious computational limitations. Although more scalable alternatives such as the Alpha complex or sparse Rips approximations exist, they often still result in a prohibitively large number of simplices. This poses challenges in the complex construction and in the subsequent PH computation, prohibiting their use on large-scale point clouds. To mitigate these issues, we introduce the Flood complex, inspired by the advantages of the Alpha and Witness complex constructions. Informally, at a given filtration value $r\geq 0$, the Flood complex contains all simplices from a Delaunay triangulation of a small subset of a point cloud $X$ that are fully covered by the union of balls of radius $r$ emanating from $X$, a process we call flooding. Our construction allows for efficient PH computation, possesses several desirable theoretical properties, and is amenable to GPU parallelization. Scaling experiments on 3D point cloud data show that we can compute PH of up to dimension 2 on several millions of points. Importantly, when evaluating object classification performance on real-world and synthetic data, we provide evidence that this scaling capability is needed, especially if objects are geometrically or topologically complex, yielding performance superior to other PH-based methods and neural networks for point cloud data.

A.1 Cellular WLResults In this section, we assume basic familiarity with the WL test and its higher-order variants. For an introduction to these topics, we refer the reader to the survey of Sato [62]. We begin by introducing a few useful concepts. A cellular colouring is a map c that maps a cell complex X and one of its cells to a colour from a fixed colour palette. Let X,Y be two regular cell complexes and c a cellular colouring. We say that X,Y are c-similar, denoted by cX = cY, if the number of cells in X coloured with a given colour equals the number of cells in Y with the same colour. Otherwise, we have cX 6= cY . We emphasise that in this paper we are interested only in colourings c with the property that any two isomorphic cell complexes are c-similar. A cellular colouring c refines a cellular colouring d, denoted by c v d, if for all cell complexes X and Y and all 2 PX and 2 PY, cX = cY implies dX = dY . Additionally, if d v c, we say the two colourings are equivalent and we represent it by c d. We state the following result from Bodnar et al. [8] about simplicial colourings, which we translate here directly to cell complexes. The proof is however, identical, and we refer the reader to their work for that. Let X,Y be any regular cellular complexes with A PX and B PY . Consider two cellular colourings c,d such that c v d.

In this work, we investigate the geometry of the k-th homology embedding and focus on cases reminiscent of spectral clustering. Namely, we analyze the connected sum of manifolds as a perturbation of the direct sum of their homology embeddings.

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