Grigori Guitchounts

Jesseba Fernando, Grigori Guitchounts

Large language models are remarkably capable, yet how computation propagates through their layers remains poorly understood. A growing line of work treats depth as discrete time and the residual stream as a dynamical system, where each layer's nonlinear update has a local linear description. However, previous analyses have relied on scalar summaries or approximate linearizations, leaving the full spectral geometry of trained LLMs unknown. We perform full Jacobian eigendecomposition across three production--scale LLMs and show that training installs a monotonic spectral gradient through depth -- from non-normal, rotation-dominated early layers to near--symmetric late layers -- together with a cumulative low-rank bottleneck that funnels perturbations into a small fraction of the residual stream's effective dimensions. Our experiments reveal that this gradient and the dimensional collapse are learned rather than architectural, and is largely dissolved when structured non-normality is removed. We further show that the topological positioning of graph communities predicts whether the Jacobian amplifies or suppresses them, with the sign of the coupling determined by the local operator type, a relationship absent at initialization. These results map a learned spectral geometry in LLMs that links perturbation propagation and compression to the network's functional topology.

Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts et al.

Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules. Yet understanding which internal features drive their outputs remains challenging. Standard sparse autoencoders (SAEs), effective on transformer-style sequence embeddings, do not transfer cleanly to pairformer-like architectures: naively operating on pairwise representations yields a quadratic blow-up of features and obscures concepts distributed jointly across sequence and pair representations. We introduce PairSAE, which summarizes pairwise tensors via an N-mode SVD into token-wise interaction roles, then uses a sparse autoencoder to learn a shared set of token-level features that decode into both sequence and pair representations. Evaluated on Boltz-2 activations for PLINDER protein-ligand complexes, PairSAE yields interpretable features that align with UniProt annotations and predict Boltz-2 affinity values. These results indicate that PairSAE links the latent space of foundation models for structural biology to interpretable structural concepts, clarifying what the model "knows" while avoiding pairformer-induced pitfalls that limit conventional SAEs.

Jesseba Fernando, Grigori Guitchounts

As artificial intelligence models have exploded in scale and capability, understanding of their internal mechanisms remains a critical challenge. Inspired by the success of dynamical systems approaches in neuroscience, here we propose a novel framework for studying computations in deep learning systems. We focus on the residual stream (RS) in transformer models, conceptualizing it as a dynamical system evolving across layers. We find that activations of individual RS units exhibit strong continuity across layers, despite the RS being a non-privileged basis. Activations in the RS accelerate and grow denser over layers, while individual units trace unstable periodic orbits. In reduced-dimensional spaces, the RS follows a curved trajectory with attractor-like dynamics in the lower layers. These insights bridge dynamical systems theory and mechanistic interpretability, establishing a foundation for a "neuroscience of AI" that combines theoretical rigor with large-scale data analysis to advance our understanding of modern neural networks.