Neurons can display highly variable dynamics.

The traditional approach to data-driven modeling of a neural population typically involves two separate stages. First, neural population activity is recorded while an animal performs a task of interest.

Modern neural interfaces allow access to the activity of up to a million neurons withinbraincircuits.

Facedwithanunfamiliar experimental system, itisoftenimpossible toknowaprioriwhichquantities to measure in order to gain insight into the system's dynamics. Instead, one typically must rely onwhichevermeasurements arereadily observable ortechnically feasible, resulting inpartial measurements that fail to fully describe a system's important properties.

Spectral gradient methods, such as the Muon optimizer, modify gradient updates by preserving directional information while discarding scale, and have shown strong empirical performance in deep learning. We investigate the mechanisms underlying these gains through a dynamical analysis of a nonlinear phase retrieval model with anisotropic Gaussian inputs, equivalent to training a two-layer neural network with the quadratic activation and fixed second-layer weights. Focusing on a spiked covariance setting where the dominant variance direction is orthogonal to the signal, we show that gradient descent (GD) suffers from a variance-induced misalignment: during the early escaping stage, the high-variance but uninformative spike direction is multiplicatively amplified, degrading alignment with the true signal under strong anisotropy. In contrast, spectral gradient descent (SpecGD) removes this spike amplification effect, leading to stable alignment and accelerated noise contraction. Numerical experiments confirm the theory and show that these phenomena persist under broader anisotropic covariances.

Neurons can display highly variable dynamics. While such variability presumably supports the wide range of behaviors generated by the organism, their gene expressions are relatively stable in the adult brain. This suggests that neuronal activity is a combination of its time-invariant identity and the inputs the neuron receives from the rest of the circuit. Here, we propose a self-supervised learning based method to assign time-invariant representations to individual neurons based on permutation-, and population size-invariant summary of population recordings. We fit dynamical models to neuronal activity to learn a representation by considering the activity of both the individual and the neighboring population. Our self-supervised approach and use of implicit representations enable robust inference against imperfections such as partial overlap of neurons across sessions, trial-to-trial variability, and limited availability of molecular (transcriptomic) labels for downstream supervised tasks. We demonstrate our method on a public multimodal dataset of mouse cortical neuronal activity and transcriptomic labels. We report >35\% improvement in predicting the transcriptomic subclass identity and >20\% improvement in predicting class identity with respect to the state-of-the-art.

The aim of this work is to learn models of population dynamics of physical systems that feature stochastic and mean-field effects and that depend on physics parameters. The learned models can act as surrogates of classical numerical models to efficiently predict the system behavior over the physics parameters. Building on the Benamou-Brenier formula from optimal transport and action matching, we use a variational problem to infer parameter-and time-dependent gradient fields that represent approximations of the population dynamics. The inferred gradient fields can then be used to rapidly generate sample trajectories that mimic the dynamics of the physical system on a population level over varying physics parameters. We show that combining Monte Carlo sampling with higher-order quadrature rules is critical for accurately estimating the training objective from sample data and for stabilizing the training process. We demonstrate on Vlasov-Poisson instabilities as well as on high-dimensional particle and chaotic systems that our approach accurately predicts population dynamics over a wide range of parameters and outperforms state-of-the-art diffusion-based and flow-based modeling that simply condition on time and physics parameters.

Modern neural interfaces allow access to the activity of up to a million neurons within brain circuits. However, bandwidth limits often create a trade-off between greater spatial sampling (more channels or pixels) and the temporal frequency of sampling. Here we demonstrate that it is possible to obtain spatio-temporal super-resolution in neuronal time series by exploiting relationships among neurons, embedded in latent low-dimensional population dynamics. Our novel neural network training strategy, selective backpropagation through time (SBTT), enables learning of deep generative models of latent dynamics from data in which the set of observed variables changes at each time step. The resulting models are able to infer activity for missing samples by combining observations with learned latent dynamics. We test SBTT applied to sequential autoencoders and demonstrate more efficient and higher-fidelity characterization of neural population dynamics in electrophysiological and calcium imaging data. In electrophysiology, SBTT enables accurate inference of neuronal population dynamics with lower interface bandwidths, providing an avenue to significant power savings for implanted neuroelectronic interfaces.