Identifying Neural Dynamics Using Nonlinear Interventional State Space Models

Recent advances in deep-learning-based nonlinear system identification have led to encoder-based estimation of neural state-space (ANN-SS) models that achieve state-of-the-art performance in offline settings by estimating initial model states from past input-output data. These methods are typically used in multiple-shooting-based offline identification, and online learning of these models remains largely unexplored. This paper presents a batch-wise learning pipeline and a direct recursive identification algorithm for subspace encoder-based ANN-SS models. We provide convergence analysis of the recursive formulation and validate its performance through extensive simulation studies. The results demonstrate that the proposed approach enables computationally efficient online adaptation with high model accuracy.

Neural activity often exhibits multiple timescales that can vary with behavioral states and task conditions. Identifying these timescales from neural recordings is important for better understanding neural computation and function. However, traditional approaches based on autocorrelation fitting are difficult to scale to high-dimensional population recordings and can become unreliable when neural dynamics change with behavior. State-space models have been a powerful framework for modeling high-dimensional neural population activity through latent dynamical systems, but standard formulations and inference methods do not explicitly account for multiple timescales and therefore do not guarantee accurate recovery of the underlying temporal structure. Motivated by these questions, we introduce the Multi-Timescale Switching Linear Dynamical System (MTS-SLDS), a framework for identifying regime-specific latent timescales from continuous or spiking neural observations. MTS-SLDS combines a multi-lag moment initialization, which captures temporal structure across multiple observation lags, with regime-conditioned Laplace-EM inference, which reduces mixing of dynamical statistics across uncertain regimes. Characteristic timescales can then be extracted directly from the eigenvalues of the learned latent transition matrices. In synthetic and neural experiments with Gaussian and Poisson spike observations, MTS-SLDS accurately recovers timescales and switching structure over multiple datasets.

State space models (SSMs) achieve efficient sequence processing because their affine state updates are closed under composition and can therefore be evaluated with an associative parallel scan. Nonlinear recurrent models can provide richer, state-dependent dynamics, but generally lose this compositional structure: parallel evaluation then requires iterative methods that repeatedly linearize and scan the recurrence. We ask, what state-dependent nonlinear dynamics can be designed to remain exactly composable? We answer by introducing RiccatiSSM, a nonlinear SSM, in which each state dimension follows an input-conditioned Riccati differential equation. Its quadratic state dependence makes the local Jacobian explicitly state-dependent, while its exact per-step flow under piecewise-constant inputs is a Möbius transformation. Since Möbius maps are closed under composition and compose through $2\times 2$ matrix multiplication, the complete nonlinear state trajectory can be evaluated exactly with a single associative parallel scan, without iterative linearization. We further derive a constrained parameterization that ensures bounded, contractive dynamics, and avoids poles in the fractional-linear state update. Across long-sequence classification, regression, and forecasting tasks, RiccatiSSM achieves competitive predictive performance while reducing runtime by $22{-}33\%$ compared to the nonlinear LrcSSM under matched architectures. These results demonstrate that state-dependent nonlinear dynamics can retain exact composability and be evaluated efficiently within a single parallel scan.