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 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.