As discussed in the main text, there could be many ways to incorporate anatomical priors into our formulation. Here, we demonstrate one example--assuming that brain regions are sparsely connected, and therefore many blocks of the dynamics matrices will be zero. This can be implemented using a block-wise spike-and-slab prior on the dynamics matrices. A.1 Formulation We want a block-sparse prior for dynamics matrices. We break down this matrix into a B B set of blocks, where B is the number of neural populations.

The problem of state estimation has a long history with many successful algorithms that allow analytical derivation or approximation of posterior filtering distribution given the noisy observations. This report tries to conclude previous works to resolve the problem of latent state estimation given image-based observations and also suggests a new solution to this problem.

We study the problem of system identification for stochastic continuous-time dynamics, based on a single finite-length state trajectory. We present a method for estimating the possibly unstable open-loop matrix by employing properly randomized control inputs. Then, we establish theoretical performance guarantees showing that the estimation error decays with trajectory length, a measure of excitability, and the signal-to-noise ratio, while it grows with dimension. Numerical illustrations that showcase the rates of learning the dynamics, will be provided as well. To perform the theoretical analysis, we develop new technical tools that are of independent interest. That includes non-asymptotic stochastic bounds for highly non-stationary martingales and generalized laws of iterated logarithms, among others.

The problem of system identification for the Kalman filter, relying on the expectation-maximization (EM) procedure to learn the underlying parameters of a dynamical system, has largely been studied assuming that observations are sampled at equally-spaced time points. However, in many applications this is a restrictive and unrealistic assumption. This paper addresses system identification for the continuous-discrete filter, with the aim of generalizing learning for the Kalman filter by relying on a solution to a continuous-time It\^o stochastic differential equation (SDE) for the latent state and covariance dynamics. We introduce a novel two-filter, analytical form for the posterior with a Bayesian derivation, which yields analytical updates which do not require the forward-pass to be pre-computed. Using this analytical and efficient computation of the posterior, we provide an EM procedure which estimates the parameters of the SDE, naturally incorporating irregularly sampled measurements. Generalizing the learning of latent linear dynamical systems (LDS) to continuous-time may extend the use of the hybrid Kalman filter to data which is not regularly sampled or has intermittent missing values, and can extend the power of non-linear system identification methods such as switching LDS (SLDS), which rely on EM for the linear discrete-time Kalman filter as a sub-unit for learning locally linearized behavior of a non-linear system. We apply the method by learning the parameters of a latent, multivariate Fokker-Planck SDE representing a toggle-switch genetic circuit using biologically realistic parameters, and compare the efficacy of learning relative to the discrete-time Kalman filter as the step-size irregularity and spectral-radius of the dynamics-matrix increases.

Linear dynamical systems that obey stochastic differential equations are canonical models. While optimal control of known systems has a rich literature, the problem is technically hard under model uncertainty and there are hardly any results. We initiate study of this problem and aim to learn (and simultaneously deploy) optimal actions for minimizing a quadratic cost function. Indeed, this work is the first that comprehensively addresses the crucial challenge of balancing exploration versus exploitation in continuous-time systems. We present online policies that learn optimal actions fast by carefully randomizing the parameter estimates, and establish their performance guarantees: a regret bound that grows with square-root of time multiplied by the number of parameters. Implementation of the policy for a flight-control task demonstrates its efficacy. Further, we prove sharp stability results for inexact system dynamics and tightly specify the infinitesimal regret caused by sub-optimal actions. To obtain the results, we conduct a novel eigenvalue-sensitivity analysis for matrix perturbation, establish upper-bounds for comparative ratios of stochastic integrals, and introduce the new method of policy differentiation. Our analysis sheds light on fundamental challenges in continuous-time reinforcement learning and suggests a useful cornerstone for similar problems.