Markov jump processes are continuous-time stochastic processes which describe dynamical systems evolving in discrete state spaces. These processes find wide application in the natural sciences and machine learning, but their inference is known to be far from trivial. In this work we introduce a methodology for of Markov jump processes (MJPs), on bounded state spaces, from noisy and sparse observations, which consists of two components. First, a broad probability distribution over families of MJPs, as well as over possible observation times and noise mechanisms, with which we simulate a synthetic dataset of hidden MJPs and their noisy observations. Second, a neural recognition model that processes subsets of the simulated observations, and that is trained to output the initial condition and rate matrix of the target MJP in a supervised way. We empirically demonstrate that (pretrained) recognition model can infer,, hidden MJPs evolving in state spaces of different dimensionalities. Specifically, we infer MJPs which describe (i) discrete flashing ratchet systems, which are a type of Brownian motors, and the conformational dynamics in (ii) molecular simulations, (iii) experimental ion channel data and (iv) simple protein folding models. What is more, we show that our model performs on par with state-of-the-art models which are trained on the target datasets.Our pretrained model is available online.

Markov jump processes are continuous-time stochastic processes widely used in statistical applications in the natural sciences, and more recently in machine learning. Inference for these models typically proceeds via Markov chain Monte Carlo, and can suffer from various computational challenges. In this work, we propose a novel collapsed variational inference algorithm to address this issue. Our work leverages ideas from discrete-time Markov chains, and exploits a connection between these two through an idea called uniformization.

Neural Information Processing Systems http://nips.cc/

Switching dynamical systems provide a powerful, interpretable modeling framework for inference in time-series data in, e.g., the natural sciences or engineering applications. Since many areas, such as biology or discrete-event systems, are naturally described in continuous time, we present a model based on a Markov jump process modulating a subordinated diffusion process. We provide the exact evolution equations for the prior and posterior marginal densities, the direct solutions of which are however computationally intractable. Therefore, we develop a new continuous-time variational inference algorithm, combining a Gaussian process approximation on the diffusion level with posterior inference for Markov jump processes. By minimizing the path-wise Kullback-Leibler divergence we obtain (i) Bayesian latent state estimates for arbitrary points on the real axis and (ii) point estimates of unknown system parameters, utilizing variational expectation maximization. We extensively evaluate our algorithm under the model assumption and for real-world examples.

Markov jump processes are continuous-time stochastic processes widely used in statistical applications in the natural sciences, and more recently in machine learning. Inference for these models typically proceeds via Markov chain Monte Carlo, and can suffer from various computational challenges. In this work, we propose a novel collapsed variational inference algorithm to address this issue. Our work leverages ideas from discrete-time Markov chains, and exploits a connection between these two through an idea called uniformization.

Neural Information Processing Systems http://nips.cc/

However, traditional neural network blocks aim to learn the feature representations in a local sense. For example, both convolutional and recurrent operations process a local neighborhood (several nearest neighboring neurons) in either space or time.