Computation-Aware Kalman Filtering with Model Selection for Neural Dynamics
Authors: JR Huml, Jonathan Wenger, John P. Cunningham
Organizations: Department of Statistics, Columbia University; Zyphra Technologies · Department of Statistics, Columbia University; Zuckerman Institute
Abstract
Due to their explicit priors and ability to model uncertainty, Bayesian methods have played a major role in dynamical latent variable modeling of single-cell neural recordings. However, modern-sized datasets have made overparameterized deep networks the preferred methods of choice due to their predictive power and favorable computational scaling. While many posterior approximations exist, all incur approximation errors. Recent work accounts for this error in the form of computational uncertainty but comes at the cost of quadratic complexity and assumes fixed model hyperparameters. Here we extend this development to model selection, including a novel training loss and optimization scheme, which yields tractable inference in large state-spaces. We introduce a framework, the Computation-Aware State-Space Model (CASSM), specifically designed for the scale-imbalanced regime, where the number of trials is significantly lower than the number of recorded neurons. In this regime, for both synthetic and real data, we show that our method is competitive with data-hungry deep networks, with significantly improved uncertainty calibration over previous attempts to scale Bayesian methods. Our experiments provide a roadmap to neuroscience researchers in choosing from a host of potential dynamical latent variable models given key dataset properties and constraints.
Active subspace methods provide a framework for quantifying predictive uncertainty in high-dimensional models by identifying and performing inference along parameter directions that have the greatest influence on the model output. However, the construction of active subspaces requires storing many full-dimensional model gradients, which becomes prohibitive as model size increases. We address this limitation by proposing Compressed Active Subspaces (CAS), a scalable approach that first maps the model parameters to a compressed space using a structured isometric embedding and then constructs the active subspace within this reduced parameterization. Our approach substantially reduces the memory required for active subspace construction and enables Bayesian inference for large models where standard active subspace methods become impractical. We demonstrate the scalability of CAS on neural networks of increasing size while maintaining predictive performance and robust uncertainty estimates.
Recent developments in brain recording are driving a demand for machine learning tools capable of decoding the latent structure of large populations of neurons. In this paper, we provide a comprehensive survey that outlines the trajectory of Latent Variable Models (LVMs) from early state-space models to more recent deep generative models. We organize the literature into three closely related domains: (1) Single-Region Latent Dynamics, which includes models such as linear dynamical systems to more complex dynamics represented by Recurrent Neural Networks (RNNs) and Neural Ordinary Differential Equations (ODEs); (2) Multi-Region Communication, which employs probabilistic as well as subspace methods to study how information is transferred across different brain areas considering synaptic propagation delays and network connectivity; and (3) Behavior-Aligned Modeling, which seeks to disentangle neural activity related to task performance from other internal states via supervised or contrastive learning. This survey also includes large-scale neural foundation models, such as Transformers and diffusion models, that rely on large-scale pre-training for optimal performance across subjects. Finally, we conclude and discuss benchmarks, evaluation criteria, and open challenges, such as the ability to identify causal links or directionality of communication, to facilitate future research for bridging interpretable brain dynamics with reliable neural decoding.
Nonlinear state estimation requires sequentially fusing model-based predictions with noisy measurements. Under imperfect dynamics and unknown, time-varying noise statistics, this fusion can degrade in both accuracy and statistical consistency. Existing learning-aided filters largely treat accuracy and uncertainty estimation separately, limiting their ability to correct model-mismatch-induced bias while retaining an explicit, calibrated posterior covariance. This paper introduces Unscented KalmanNet (UKN), a model-based deep learning architecture that extends the Unscented Kalman Filter (UKF) with learned mechanisms for these two sources of filtering error while preserving explicit posterior covariance propagation. NoiseNet learns time-varying process and measurement covariances as bounded multiplicative corrections to baseline covariances, guaranteeing positive definiteness, while GainNet learns a bounded residual correction to the analytical UKF gain to compensate for model-mismatch-induced bias. A calibration-aware training objective couples state error with posterior covariance and innovation consistency terms through adaptive weighting, jointly optimizing accuracy and calibration. UKN is benchmarked against UKF, KalmanNet, and Bayesian KalmanNet on three synthetic systems and real-flight UZH-FPV data. It achieves the lowest state-estimation error in all four examples and reduces RMSE by 26.4-49.7% compared with UKF in the synthetic cases. Leave-one-sequence-out cross-validation over 11 flights shows 22.4% and 34.3% reductions in mean position and velocity RMSE, respectively. UKN also yields the lowest fold-to-fold variability, with dimension-normalized NEES and empirical coverage closest to nominal values among covariance-reporting filters. These results show that structured learned adaptation improves estimation accuracy while retaining calibrated uncertainty.