HomID : Benchmarking Intrinsic Dimension Estimators on Homogenous Manifolds with Anisotropic Embeddings

The analysis of neural representation has become an integral part of research aiming to better understand the inner workings of neural networks. While there are many different approaches to investigate neural representations, an important line of research has focused on doing so through the lens of intrinsic dimensions (IDs). Although this perspective has provided valuable insights and stimulated substantial follow-up research, important limitations of this approach have remained largely unaddressed. In this paper, we highlight a crucial discrepancy between theory and practice of IDs in neural representations, theoretically and empirically showing that common ID estimators are, in fact, not tracking the true underlying ID of the representation. We contrast this negative result with an investigation of the underlying factors that may drive commonly reported ID-related results on neural representation in the literature. Building on these insights, we offer a new perspective on ID estimation in neural representations.

A significant gap exists between theory and practice in deep learning. Generalization and approximation error bounds are often derived for simplified models or are too loose to be informative. Many rely on the manifold hypothesis and on geometric regularity such as intrinsic dimension, curvature, and reach. Progress requires insight into data-manifold geometry and suitable benchmarks, yet existing options are polarized: analytic manifolds with known geometry but limited applicability, or real-world datasets where geometry is only coarsely estimable. We introduce a benchmarking framework for studying data geometry. We repurpose and extend dSprites and COIL-20 with additional transformation dimensions and dense, axis-aligned sampling, and pair them with finite-difference estimators that recover curvature, reach, and volume at near-ground-truth accuracy in a regime where general-purpose estimators are unreliable or difficult to deploy. The framework is intended as a controlled testbed, useful as a calibration environment for geometric estimators and a sandbox for probing theoretical assumptions. To illustrate its use, we present two application studies, namely assessing the scaling behavior of the bounds of Genovese et al. and Fefferman et al., and tracking the layer-wise geometry of a $β$-VAE, highlighting the behavior of current bounds and the value of controlled benchmarks for guiding and validating future theory. A reference implementation is available at https://github.com/koulakis/manifold-microscope.

Self-supervised learning (SSL) has emerged as a powerful paradigm for learning meaningful representations from unlabeled data. However, the standard protocol for evaluating these representations, linear probing, is computationally expensive, sensitive to hyperparameters, and provides limited insight into the geometric structure of the representation space. In this work, motivated by connections between neural network generalization and intrinsic dimension (ID) we propose IdEst, a method for estimating the ID of SSL representations via the Minimum Spanning Tree dimension estimator ($\mathrm{dim}_\mathrm{MST}$). Across diverse datasets, architectures, and SSL pretraining objectives, we show that IdEst strongly correlates with downstream linear probe performances. Furthermore, we demonstrate that IdEst enables efficient hyperparameter selection, significantly reducing the computational cost compared to supervised alternatives. Our results highlight intrinsic dimensionality as a principled geometric proxy for assessing SSL representations, complementing standard supervised probing protocols.