The mutual information (MI) of Poisson-type channels has been linked to a filtering problem since the 70s, but its evaluation for specific continuous-time, discrete-state systems remains a demanding task. As an advantage, Markov renewal processes (MrP) retain their renewal property under state space filtering. This offers a way to solve the filtering problem analytically for small systems. We consider a class of communication systems X Y that can be derived from an MrP by a custom filtering procedure. For the subclasses, where (i)$Y$is a renewal process or (ii) (X, Y) belongs to a class of MrPs, we provide an evolution equation for finite transmission duration T > 0 and limit theorems for$T$that facilitate simulation-free evaluation of the MI and its associated mutual information rate (MIR). In other cases, simulation cost is reduced to the marginal system (X, Y) or Y. We show that systems with an additional X-modulating level C, which statically chooses between different processes (c), can naturally be included in our framework, thereby giving an expression for Our primary contribution is to apply the results of classical (Markov renewal) filtering theory in a novel manner to the problem of exactly computing the MI/MIR. The theoretical framework is showcased in an application to bacterial gene expression, where filtering is analytically tractable.

Hidden semi-Markov Models (HSMM's) - while broadly in use - are restricted to a discrete and uniform time grid. They are thus not well suited to explain often irregularly spaced discrete event data from continuous-time phenomena. We show that non-sampling-based latent state inference used in HSMM's can be generalized to latent Continuous-Time semi-Markov Chains (CTSMC's). We formulate integro-differential forward and backward equations adjusted to the observation likelihood and introduce an exact integral equation for the Bayesian posterior marginals and a scalable Viterbi-type algorithm for posterior path estimates. The presented equations can be efficiently solved using well-known numerical methods. As a practical tool, variable-step HSMM's are introduced. We evaluate our approaches in latent state inference scenarios in comparison to classical HSMM's.

Structured stochastic processes evolving in continuous time present a widely adopted framework to model phenomena occurring in nature and engineering. However, such models are often chosen to satisfy the Markov property to maintain tractability. One of the more popular of such memoryless models are Continuous Time Bayesian Networks (CTBNs). In this work, we lift its restriction to exponential survival times to arbitrary distributions. Current extensions achieve this via auxiliary states, which hinder tractability. To avoid that, we introduce a set of node-wise clocks to construct a collection of graph-coupled semi-Markov chains. We provide algorithms for parameter and structure inference, which make use of local dependencies and conduct experiments on synthetic data and a data-set generated through a benchmark tool for gene regulatory networks. In doing so, we point out advantages compared to current CTBN extensions.