Flag Varieties: A Geometric Framework for Deep Network Alignment

Understanding how deep neural networks learn representations remains a central challenge in machine learning theory. In this work, we propose a feature-centric framework for analyzing neural network training by relating weight updates to feature evolution. We introduce a simple identity, the Feature Learning Equation, which identifies the weight Gram matrix as the key object capturing feature dynamics. This enables us to interpret gradient descent as implicitly inducing a hypothetical evolution of features, whose covariance structure - termed the Virtual Covariance - characterizes how representations evolve during training. Building on this perspective, we introduce Target Linearity, a measure quantifying the linear alignment between features and targets. By analyzing the training and layer-wise dynamics, we show that deep networks learn to sequentially transform representations toward target-linear structure. This linearization perspective provides a unified interpretation of several empirical phenomena, including Neural Collapse and linear interpolation in generative models.

While neural collapse (NC) predicts that a $K$-class-balanced classifier should organize terminal representations as a $(K-1)$-dimensional simplex equiangular tight frame (ETF), modular addition consistently enters a different regime: networks compress to a two-dimensional cyclic geometry in which both classifier weights and token embeddings lie on circles. We refine the explanation of this phenomenon in three directions. First, we formalize a layerwise non-uniform training mechanism: downstream classifier weights are driven by dense cross-entropy gradients into a rank-2 equiangular configuration before upstream embeddings fully reorganize, and once this classifier plane forms, backpropagated feature gradients constrain embedding motion to the same plane while weight decay suppresses orthogonal components. Second, after this subspace locking, the induced in-plane dynamics admit an entropy-regularized transport interpretation on $S^1$; combined with modular-addition labels, this reduces embedding formation to phase alignment, whose minimizers are single-frequency characters of $\mathbb{Z}/P\mathbb{Z}$ and hence equal-angle points on a circle. Third, we quantify why this solution prevails over NC: a simplex ETF gains only an $O(1)$ advantage in cross-entropy, whereas the cyclic rank-2 solution enjoys a $Θ(K)$ advantage under Schatten or weight-decay surrogates, yielding a critical threshold $λ_{\mathrm{crit}} = Θ(1/K)$. Our results explain both why classifier weights move first and why embeddings subsequently align with them, showing that grokking on modular arithmetic is governed not by maximal separation alone but by a task-structured trade-off between separation, symmetry, and complexity.

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.