Compressed Active Subspaces for Scalable Bayesian Inference

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.

Gaussian processes (GPs) provide a principled Bayesian framework for uncertainty estimation, but their computational complexity severely limits scalability to large datasets. We propose SIKA-GP, which accelerates GP inference using sparse inducing kernel approximations based on a dyadic ordered template basis, incurring only ${O}(\log M)$ complexity dependence on the number of inducing points. Our approach constructs compact and expressive kernel representations from sparsely activated bases, enabling efficient tensorized GPU computation and seamless integration with modern large-scale models. SIKA-GP can be naturally embedded into Bayesian neural networks (BNNs) with sparse activations, yielding significant speedups in both training and inference without sacrificing predictive performance. The method naturally extends to deep feature learning, addressing the scalability challenges introduced by deep architectures and high-dimensional feature representations. Empirical results on vision and transformer-based language benchmarks demonstrate that our approach consistently delivers fast and accurate GP models, providing a principled path toward scalable kernel learning.

Since the turn of the century, approximate Bayesian inference has steadily evolved as new computational techniques have been incorporated to handle increasingly complex, large-scale predictive problems. The recent success of deep neural networks and foundation models has now given rise to a new paradigm in statistical modeling, in which Bayesian inference can be amortized through large-scale learned predictors. In amortized inference, substantial computation is required at the beginning to train a neural network, but it can subsequently produce approximate posteriors or predictions at much lower computational cost across a wide range of tasks. While the typical Bayesian inference procedures are computationally expensive due to repeated likelihood calculations and Monte Carlo steps for each new dataset, amortized inference provides a much lower computational cost at deployment. Despite the growing popularity of amortized inference, its statistical interpretation and position within Bayesian inference remain poorly explored. In this paper, we present a statistical perspective on several major neural architectures, including feedforward networks, Deep Sets, and Transformers, and examine how they naturally support amortized Bayesian inference. We explore how these models perform structured approximation and also probabilistic reasoning in ways that yield controlled generalization error throughout a wide range of deployment scenarios, and how these properties can be harnessed for Bayesian computation. Via simulation studies, we evaluate the accuracy, robustness, and uncertainty quantification of amortized inference across varying sample sizes, varying noise distributional families, varying sparsity levels, and multimodality, highlighting its strengths and limitations.