We consider the inverse problem of reconstructing the posterior measure over the trajec- tories of a diffusion process from discrete time observations and continuous time constraints. We cast the problem in a Bayesian framework and derive approximations to the posterior distributions of single time marginals using variational approximate inference. We then show how the approximation can be extended to a wide class of discrete-state Markov jump pro- cesses by making use of the chemical Langevin equation. Our empirical results show that the proposed method is computationally efficient and provides good approximations for these classes of inverse problems.
In @cite_5 we propose an expectation propagation method for diffusion process models where the prior process is Gaussian--Markov. In this paper, we extend this method to models with non-nonlinear prior processes. Here we use expectation propagation only to approximate the likelihood terms. We avoid approximating the prior process by using moment-closure approximations on the process resulting from the prior and the likelihood approximations. When we choose a Gaussian--Markov prior process, the method proposed in this paper is identical to the one proposed in @cite_5 .
@cite_5
2117804315 1934021597 2126334242 2030656756
We propose an approximate inference algorithm for continuous time Gaussian Markov process models with both discrete and continuous time likelihoods. We show that the continuous time limit of the expectation propagation algorithm exists and results in a hybrid fixed point iteration consisting of (1) expectation propagation updates for discrete time terms and (2) variational updates for the continuous time term. We introduce post-inference corrections methods that improve on the marginals of the approximation. This approach extends the classical Kalman-Bucy smoothing procedure to non-Gaussian observations, enabling continuous-time inference in a variety of models, including spiking neuronal models (state-space models with point process observations) and box likelihood models. Experimental results on real and simulated data demonstrate high distributional accuracy and significant computational savings compared to discrete-time approaches in a neural application. This paper presents a new deterministic approximation technique in Bayesian networks. This method, "Expectation Propagation," unifies two previous techniques: assumed-density filtering, an extension of the Kalman filter, and loopy belief propagation, an extension of belief propagation in Bayesian networks. Loopy belief propagation, because it propagates exact belief states, is useful for a limited class of belief networks, such as those which are purely discrete. Expectation Propagation approximates the belief states by only retaining expectations, such as mean and varitmce, and iterates until these expectations are consistent throughout the network. This makes it applicable to hybrid networks with discrete and continuous nodes. Experiments with Gaussian mixture models show Expectation Propagation to be donvincingly better than methods with similar computational cost: Laplace's method, variational Bayes, and Monte Carlo. Expectation Propagation also provides an efficient algorithm for training Bayes point machine classifiers. Stimulus reconstruction or decoding methods provide an important tool for understanding how sensory and motor information is represented in neural activity. We discuss Bayesian decoding methods based on an encoding generalized linear model (GLM) that accurately describes how stimuli are transformed into the spike trains of a group of neurons. The form of the GLM likelihood ensures that the posterior distribution over the stimuli that caused an observed set of spike trains is log concave so long as the prior is. This allows the maximum a posteriori (MAP) stimulus estimate to be obtained using efficient optimization algorithms. Unfortunately, the MAP estimate can have a relatively large average error when the posterior is highly nongaussian. Here we compare several Markov chain Monte Carlo (MCMC) algorithms that allow for the calculation of general Bayesian estimators involving posterior expectations (conditional on model parameters). An efficient version of the hybrid Monte Carlo (HMC) algorithm was significantly superior to other MCMC methods for gaussian priors. When the prior distribution has sharp edges and corners, on the other hand, the “hit-and-run” algorithm performed better than other MCMC methods. Using these algorithms, we show that for this latter class of priors, the posterior mean estimate can have a considerably lower average error than MAP, whereas for gaussian priors, the two estimators have roughly equal efficiency. We also address the application of MCMC methods for extracting nonmarginal properties of the posterior distribution. For example, by using MCMC to calculate the mutual information between the stimulus and response, we verify the validity of a computationally efficient Laplace approximation to this quantity for gaussian priors in a wide range of model parameters; this makes direct model-based computation of the mutual information tractable even in the case of large observed neural populations, where methods based on binning the spike train fail. Finally, we consider the effect of uncertainty in the GLM parameters on the posterior estimators. In this paper, we propose a Gaussian process (GP) model for analysis of nonlinear time series. Formulation of our model is based on the consideration that the observed data are functions of latent variables, with the associated mapping between observations and latent representations modeled through GP priors. In addition, to capture the temporal dynamics in the modeled data, we assume that subsequent latent representations depend on each other on the basis of a hidden Markov prior imposed over them. Derivation of our model is performed by marginalizing out the model parameters in closed form using GP priors for observation mappings, and appropriate stick-breaking priors for the latent variable (Markovian) dynamics. This way, we eventually obtain a nonparametric Bayesian model for dynamical systems that accounts for uncertainty in the modeled data. We provide efficient inference algorithms for our model on the basis of a truncated variational Bayesian approximation. We demonstrate the efficacy of our approach considering a number of applications dealing with real-world data, and compare it with the related state-of-the-art approaches.