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

Neural networks exhibit a remarkable degree of representational convergence across diverse architectures, training objectives, and even data modalities. This convergence is predictive of alignment with brain representation. A recent hypothesis suggests this arises from learning the underlying structure in the environment in similar ways. However, it is unclear how individual stimuli elicit convergent representations across networks. An image can be perceived in multiple ways and expressed differently using words. Here, we introduce a methodology based on the Generalized Procrustes Algorithm to measure intra-modal representational convergence at the single-stimulus level. We applied this to vision models with distinct training objectives, selecting stimuli based on their degree of alignment (intra-modal dispersion). Crucially, we found that this intra-modal dispersion strongly modulates alignment between vision and language models (cross-modal convergence). Specifically, stimuli with low intra-modal dispersion (high agreement among vision models) elicited significantly higher cross-modal alignment than those with high dispersion, by up to a factor of two (e.g., in pairings of DINOv2 with language models). This effect was robust to stimulus selection criteria and generalized across different pairings of vision and language models. Measuring convergence at the single-stimulus level provides a path toward understanding the sources of convergence and divergence across modalities, and between neural networks and human neural representations.

A foundational principle of connectionism is that perception, action, and cognition emerge from parallel computations among simple, interconnected units that generate and rely on neural representations. Accordingly, researchers employ multivariate pattern analysis to decode and compare the neural codes of artificial and biological networks, aiming to uncover their functions. However, there is limited analytical understanding of how a network's representation and function relate, despite this being essential to any quantitative notion of underlying function or functional similarity. We address this question using analysable two-layer linear networks and numerical simulations in non-linear networks. We find that function and representation are dissociated, allowing representational similarity without functional similarity and vice versa. Further, we show that neither robustness to input noise nor the level of generalization error constrain representations to the task. In contrast, networks robust to parameter noise have limited representational flexibility and must employ task-specific representations. Our findings suggest that representational alignment reflects computational advantages beyond functional alignment alone, with significant implications for interpreting and comparing the representations of connectionist systems.

Comparing internal representations is a central goal in neuroscience and machine learning, but standard linear alignment metrics (Representational Similarity Analysis, Centered Kernel Alignment, and linear regression) are frequently applied to neural activity coordinates rather than on the underlying features. We show this matters when neural systems operate in superposition, encoding more features than they have neurons via linear compression. Closed-form derivations prove that these metrics depend on the Gram matrices of each system's projection, not on the latent features themselves: alignment thus combines what a system represents with how it is encoded. For those interested in what features two systems share, this is a problem: Two networks can have identical feature content yet appear more dissimilar than networks exhibiting partial feature overlap. This apparent misalignment need not reflect lost information as compressed sensing guarantees sparse features remain recoverable from the compressed activity. We confirm this by training supervised TopK sparse autoencoders that realize solvable compressed sensing by construction, finding alignment on recovered latents restored even when raw-activation alignment remains deflated. We extend the result to unsupervised SAEs trained without ground-truth latents, and to pretrained vision and language model SAEs, where SAE-latent alignment exceeds raw-activation alignment, consistent with superposition in real systems.