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Monte Carlo estimation in plays a crucial role in stochastic reaction networks. However, reducing the statistical uncertainty of the corresponding estimators requires sampling a large number of trajectories. We propose control variates based on the statistical moments of the process to reduce the estimators' variances. We develop an algorithm that selects an efficient subset of infinitely many control variates. To this end, the algorithm uses resampling and a redundancy-aware greedy selection. We demonstrate the efficiency of our approach in several case studies., Comment: arXiv admin note: substantial text overlap with arXiv:1905.00854

Dynamical systems in which local interactions among agents give rise to complex emerging phenomena are ubiquitous in nature and society. This work explores the problem of inferring the unknown interaction structure (represented as a graph) of such a system from measurements of its constituent agents or individual components (represented as nodes). We consider a setting where the underlying dynamical model is unknown and where different measurements (i.e., snapshots) may be independent (e.g., may stem from different experiments). We propose GINA (Graph Inference Network Architecture), a graph neural network (GNN) to simultaneously learn the latent interaction graph and, conditioned on the interaction graph, the prediction of a node's observable state based on adjacent vertices. GINA is based on the hypothesis that the ground truth interaction graph -- among all other potential graphs -- allows to predict the state of a node, given the states of its neighbors, with the highest accuracy. We test this hypothesis and demonstrate GINA's effectiveness on a wide range of interaction graphs and dynamical processes.

To understand the long-run behavior of Markov population models, the computation of the stationary distribution is often a crucial part. We propose a truncation-based approximation that employs a state-space lumping scheme, aggregating states in a grid structure. The resulting approximate stationary distribution is used to iteratively refine relevant and truncate irrelevant parts of the state-space. This way, the algorithm learns a well-justified finite-state projection tailored to the stationary behavior. We demonstrate the method's applicability to a wide range of non-linear problems with complex stationary behaviors., Comment: arXiv admin note: text overlap with arXiv:2010.10096

Many probabilistic inference problems such as stochastic filtering or the computation of rare event probabilities require model analysis under initial and terminal constraints. We propose a solution to this bridging problem for the widely used class of population-structured Markov jump processes. The method is based on a state-space lumping scheme that aggregates states in a grid structure. The resulting approximate bridging distribution is used to iteratively refine relevant and truncate irrelevant parts of the state-space. This way the algorithm learns a well-justified finite-state projection yielding guaranteed lower bounds for the system behavior under endpoint constraints. We demonstrate the method's applicability to a wide range of problems such as Bayesian inference and the analysis of rare events.

We consider the problem of bounding mean first passage times for a class of continuous-time Markov chains that captures stochastic interactions between groups of identical agents. The quantitative analysis of such probabilistic population models is notoriously difficult since typically neither state-based numerical approaches nor methods based on stochastic sampling give efficient and accurate results. Here, we propose a technique that extends recently developed methods using semi-definite programming to determine bounds on mean first passage times. We further apply the technique to hybrid models and demonstrate its accuracy and efficiency for some examples from biology.

Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires the generation of a large number of simulation runs, which is computationally expensive. To reduce the number of necessary runs, we propose a variance reduction technique based on control variates. We exploit constraints on the statistical moments of the stochastic process to reduce the estimators' variances. We develop an algorithm that selects appropriate control variates in an on-line fashion and demonstrate the efficiency of our approach on several case studies.