Christopher Tape | Searcharxiv

arXiv2026

RhinoNet: Unsupervised Learning for Phenoscaping and Generation of High Dimensional Point Clouds

We present RhinoNet, a simplicial complex-based point cloud neural network, that creates a geometry-preserving embedding of high-dimensional point clouds. RhinoNet takes collections of datasets, also called {\em data cohorts}, and processes each dataset (point cloud) within the cohort as a simplicial complex. These simplicial complexes have datapoints as vertices and edges learned by Vietoris-Rips filtration. Using simplicial wavelets and MLP layers, RhinoNet computes a vector representation of each dataset in a latent space produced by an autoencoder. The latent space is optimized such that an optimal transport distance between pairs of point clouds is preserved between the latent representations. We apply RhinoNet to single-cell datasets collected on patients---a common source of such high-dimensional data. RhinoNet creates a patient level representation, known in biological contexts as a phenoscape. We establish that RhinoNet generates organized phenoscapes, whereas other methods such as static maps do not. Next we show that we can generate entire point clouds by sampling and decoding this phenoscape. We show two modes of generation via 1) latent flow matching and 2) geodesic interpolation in latent space, followed by a decoding back into the point cloud space. RhinoNet achieves state-of-the-art performance on single-cell and spatial data cohorts relative to tested baselines. Overall, RhinoNet lifts the concepts of representation learning and generative modeling to the point cloud or population level and defines a neural model for phenoscaping.

cs.CV↗

arXiv2025

HiPoNet: A Multi-View Simplicial Complex Network for High Dimensional Point-Cloud and Single-Cell Data

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. We showcase the utility of HiPoNet on point-cloud level tasks, involving classification and regression of entire point-clouds in data cohorts. Experimentally, we find that HiPoNet outperforms other point-cloud and graph-based models on single-cell data. We also apply HiPoNet to spatial transcriptomics datasets using spatial coordinates as one of the views. Overall, HiPoNet offers a robust and scalable solution for high-dimensional data analysis.

cs.LG↗