A Solvable High-Dimensional Model Where Nonlinear Autoencoders Learn Structure Invisible to PCA While Test Loss Misaligns With Generalization

Many real-world datasets contain hidden structure that cannot be detected by simple linear correlations between input features. For example, latent factors may influence the data in a coordinated way, even though their effect is invisible to covariance-based methods such as PCA. In practice, nonlinear neural networks often succeed in extracting such hidden structure in unsupervised and self-supervised learning. However, constructing a minimal high-dimensional model where this advantage can be rigorously analyzed has remained an open theoretical challenge. We introduce a tractable high-dimensional spiked model with two latent factors: one visible to covariance, and one statistically dependent yet uncorrelated, appearing only in higher-order moments. PCA and linear autoencoders fail to recover the latter, while a minimal nonlinear autoencoder provably extracts both. We analyze both the population risk, and empirical risk minimization. Our model also provides a tractable example where self-supervised test loss is poorly aligned with representation quality: nonlinear autoencoders recover latent structure that linear methods miss, even though their reconstruction loss is higher.