Gauge Freedom and Metric Dependence in Neural Representation Spaces

Similarity measures are widely used to interpret the representational geometries used by neural networks to solve tasks. Yet, because existing methods compare the extrinsic geometry of representations in state space, rather than their intrinsic geometry, they may fail to capture subtle yet crucial distinctions between fundamentally different neural network solutions. Here, we introduce metric similarity analysis (MSA), a novel method which leverages tools from Riemannian geometry to compare the intrinsic geometry of neural representations under the manifold hypothesis. We show that MSA can be used to i) disentangle features of neural computations in deep networks with different learning regimes, ii) compare nonlinear dynamics, and iii) investigate diffusion models. Hence, we introduce a mathematically grounded and broadly applicable framework to understand the mechanisms behind neural computations by comparing their intrinsic geometries.

Representational similarity methods compare the geometries of neural representations, but they do not measure how consistently the geometry of a single representation is recovered from subsets of its feature coordinates. We call this property geometric stability and introduce Shesha, which estimates it by correlating representational dissimilarity matrices from complementary random feature subsets. Shesha is not invariant to orthogonal rotations: representations with identical Gram matrices, and therefore identical linear CKA, can have different geometric stability. Controlled transformations further separate the quantities. Across $2{,}463$ encoder configurations spanning seven domains, similarity and stability are positively associated across non-PCA transformations ($ρ=+0.75$) but negatively associated under PCA-coordinate compression ($ρ=-0.47$). We further evaluate 170 pretrained vision models across six datasets. DINOv2 combines strong transfer performance with bottom-quartile stability on five of six datasets, showing that transferability and feature-split stability need not coincide. Across random feature subsets, the marginal relationship between Shesha and linear-probe variability is dataset-dependent; after controlling for task alignment with LogME, higher Shesha is associated with lower variability on five of six datasets. These results identify geometric stability as a basis-dependent property that complements representational similarity and task alignment.

Neural networks build representations through affine maps and nonlinear activations. Injective affine maps preserve linear separability, raising the problem of how they prepare data for nonlinear improvement and how much gain can be guaranteed before complete separation. We introduce the directional linear separability measure (D-LSM), which quantifies unavoidable competing-sample intrusion over affine halfspaces retaining every target sample, characterize its supporting geometry, and prove invariance under injective affine embeddings. For gated activations including ReLU, GELU, and SiLU, pre-activation projection bounds yield sufficient conditions for preserving all previous exclusions and recovering additional samples, with a gain bound determined by the certified recovery count. Under an aggregate-tube condition, an explicit affine construction realizes recovery with sufficient width, scaling conditions, and simultaneous multiclass guarantees through a shared layer. Exact controlled experiments compare certified and realized gains, assess certificate coverage, and exhibit bound attainment before complete separation and in affine-tube constructions. In learned Vision Transformer (ViT) representations, a feasible lower-bound estimator yields earlier post-GELU saturation certificates of exact separability, while boundary transport numerically supports affine invariance.