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

arXiv: https://arxiv.org/abs/2603.00793 · HTML: https://mlsanity.com/paper/2603.00793/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 40 references that are in the map.
- First posted on arXiv 28 Feb 2026.

## Builds on (most cited first, 13 of 13)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [HuBERT: Self-Supervised Speech Representation Learning by Masked Prediction of Hidden Units](https://mlsanity.com/paper/2106.07447/) (2021)
- [data2vec: A General Framework for Self-supervised Learning in Speech, Vision and Language](https://mlsanity.com/paper/2202.03555/) (2022)
- [The Platonic Representation Hypothesis](https://mlsanity.com/paper/2405.07987/) (2024)
- [Scaling laws for language encoding models in fMRI](https://mlsanity.com/paper/2305.11863/) (2023)
- [Universality and individuality in neural dynamics across large populations of recurrent networks](https://mlsanity.com/paper/1907.08549/) (2019)
- [Attractor and integrator networks in the brain](https://mlsanity.com/paper/2112.03978/) (2021)
- [The Algonauts Project 2021 Challenge: How the Human Brain Makes Sense of a World in Motion](https://mlsanity.com/paper/2104.13714/) (2021)

## Abstract (arXiv)

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