Beyond Coordinate Gauge: An Audited Protocol for Detecting Donor-Specific Functional Fingerprints after Neural Collapse

Activation-alignment measures such as Representational Similarity Analysis (RSA), Canonical Correlation Analysis (CCA), and Centered Kernel Alignment (CKA) are widely used to compare biological and artificial neural representations. Recent theoretical work interprets many of these methods as assessing agreement between optimal linear readouts over broad families of global tasks. However, agreement at the level of global readouts does not determine how a system uses local stimulus evidence. Specifically, representations may align in activation space yet differ in their sensitivity to small perturbations. To address this challenge, we introduce a complementary framework based on local decodable information, which focuses on a representation's ability, under noise, to discriminate small perturbations within a specified stimulus-coordinate subspace. Building on Fisher information and local representation geometry, we summarize each representation using the expected projected pullback/Fisher metric over that subspace. This formulation induces a second-moment family of local discrimination tasks, for which the resulting operator provides a minimal, complete dataset-level summary of expected discriminability. We compare these regularized signatures using a log-spectral distance on the manifold of symmetric positive definite (SPD) matrices, yielding the Spectral Riemannian Alignment Score (S-RAS) and a uniform multiplicative certificate over the corresponding family of lifted task values. Empirically, this framework enables the recovery of corresponding layers across independently trained artificial neural networks, supports transferable class-conditional probes, reveals controlled dissociations between standard and robust training, and uncovers stimulus-coordinate family effects across mouse visual cortex using the Allen Brain Observatory static gratings dataset.

A series of results from the NeuroAI over the past fifteen years have raised core questions both about how to compare Deep Neural Network (DNN) models to the brain, and about how much convergent evolution to expect between artificial networks and real brain networks. Here, we show that for any two minimal DNN solutions to a sufficiently hard task: (i) "weak" alignment of network representations based on affine mappings guarantees "strong" alignment of privileged axes, and (ii) alignment "zippers" up the network hierarchy, causing the emergence of privileged axes from end-to-end task optimization. These results formalize the notion of contravariance from Cao and Yamins [2024], and illustrate important consequences for the theory of NeuroAI: with sufficiently strong tasks, choice of metric for inter-network comparison is not all that sensitive, and that convergent evolution is probably inevitable.

Alignment, the tendency of adjacent weight matrices in deep networks to develop compatible subspace orientations, underlies gradient flow, Neural Collapse, and representation similarity across architectures. Despite extensive empirical documentation, these phenomena have resisted unified theoretical treatment: existing explanations are post-hoc, each fitted to a specific observation with whatever mathematics is at hand. We reverse this direction by deriving the mathematical structure that layerwise alignment inherently demands. Using geometric invariant theory, we prove that alignment geometry has a canonical closed, polystable stratum given by a flag variety, and that subspace intersection dimension is its unique reparameterization-invariant observable, establishing that subspace metrics are not empirical conventions but mathematical necessities. This unified framework yields two dynamical consequences: ridge regularization drives subspace alignment at an exponential rate set by weight decay, whereas nonlinear activations induce a commutator obstruction to exact basis alignment, generically present in nonlinear networks and absent in linear ones. Together these give a geometric explanation of the Level-2/3 hierarchy in Neural Collapse from first principles rather than post-hoc analysis. The commutator magnitude and head subspace overlap further serve as weight-space windows into internal alignment structure, requiring no forward passes. Experiments on multilayer perceptrons, residual networks, and pretrained language models support the proposed diagnostics and delineate their scope.