Constructing VAE Latent Spaces with Prescribed Topology
Jilles S. van Hulst, Jakub M. Tomczak, W. P. M. H. Heemels, Duarte J. Antunes
Abstract
Variational autoencoders (VAEs) learn low-dimensional latent representations of high-dimensional data. When the data lies on a manifold with non-Euclidean topology, the standard Gaussian prior introduces a topological mismatch that degrades reconstruction quality and prevents faithful representation. We present a constructive mathematical framework that resolves this mismatch for all manifolds that admit a product covering space. These are manifolds expressible as products of elementary factors (circles, intervals, or lines) or as quotients of such products by a finite symmetry group. The class includes cylinders, tori, Möbius strips, Klein bottles, and real projective spaces. Factorized distributions over the elementary factors yield product topologies with closed-form, decoupled KL divergences, so that each latent factor can be shaped independently while keeping training tractable. We catalogue reparametrizable encoder-prior pairs for periodic, bounded, and unbounded supports, and provide coordinate transformations that allow standard neural networks to output non-Euclidean parameters with smooth gradients. For quotient manifolds, the decoder receives group-invariant features of the covering-space coordinates, so that identified points produce identical outputs. Anchor constraints fix the coordinate system relative to the data or create soft topological holes. Experiments on synthetic manifolds and real-image datasets (rotated and cyclically shifted MNIST) confirm that a topology-matched prior aligns KL regularization with the data manifold. The resulting topology-aware models outperform the Gaussian baseline at all practically relevant regularization strengths. The code is available at https://github.com/JvHulst/VAE-Topology.
Topics
Classified with taxonomy v2 on Sat, 5 Sept 2026.