Neural Functional Alignment Space: Brain-Referenced Representation of Artificial Neural Networks

Abstract: We propose the Neural Functional Alignment Space (NFAS), a brain-referenced representational framework for characterizing artificial neural networks on equal functional grounds. NFAS departs from conventional alignment approaches that rely on layer-wise features or task-specific activations by modeling the intrinsic dynamical evolution of stimulus representations across network depth. Specifically, we model layer-wise embeddings as a depth-wise dynamical trajectory and apply Dynamic Mode Decomposition (DMD) to extract the stable mode. This representation is then projected into a biologically anchored coordinate system defined by distributed neural responses. We also introduce the Signal-to-Noise Consistency Index (SNCI) to quantify cross-model consistency at the modality level. Across 45 pretrained models spanning vision, audio, and language, NFAS reveals structured organization within this brain-referenced space, including modality-specific clustering and cross-modal convergence in integrative cortical systems. Our findings suggest that representation dynamics provide a principled basis for