Declarative Modeling and Bayesian Inference of Dark Matter Halos

Probabilistic programming allows specification of probabilistic models in a declarative manner. Recently, several new software systems and languages for probabilistic programming have been developed on the basis of newly developed and improved methods for approximate inference in probabilistic models. In this contribution a probabilistic model for an idealized dark matter localization problem is described. We first derive the probabilistic model for the inference of dark matter locations and masses, and then show how this model can be implemented using BUGS and Infer.NET, two software systems for probabilistic programming. Finally, the different capabilities of both systems are discussed. The presented dark matter model includes mainly non-conjugate factors, thus, it is difficult to implement this model with Infer.NET.Comment: Presented at the Workshop "Intelligent Information Processing", EUROCAST2013. To appear in selected papers of Computer Aided Systems Theory - EUROCAST 2013; Volumes Editors: Roberto Moreno-D\'iaz, Franz R. Pichler, Alexis Quesada-Arencibia; LNCS Springe

Inference and Learning in Networks of Queues

Probabilistic models of the performance of computer systems are useful both for predicting system performance in new conditions, and for diagnosing past performance problems. The most popular performance models are networks of queues. However, no current methods exist for parameter estimation or inference in networks of queues with missing data. In this paper, we present a novel viewpoint that combines queueing networks and graphical models, allowing Markov chain Monte Carlo to be applied. We demonstrate the effectiveness of our sampler on real-world data from a benchmark Web application.

Using the probabilistic evaluation tool for the analytical solution of large Markov models

Stochastic Petri net-based Markov modeling is a potentially very powerful and generic approach for evaluating the performance and dependability of many different systems, such as computer systems, communication networks, manufacturing systems, etc. As a consequence of their general applicability, SPN-based Markov models form the basic solution approach for several software packages that have been developed for the analytic solution of performance and dependability models. In these tools, stochastic Petri nets are used to conveniently specify complicated models, after which an automatic mapping can be carried out to an underlying Markov reward model. Subsequently, this Markov reward model is solved by specialized solution algorithms, appropriately selected for the measure of interest. One of the major aspects that hampers the use of SPN-based Markov models for the analytic solution of performance and dependability results is the size of the state space. Although typically models of up to a few hundred thousand states can conveniently be solved on modern-day work-stations, often even larger models are required to represent all the desired detail of the system. Our tool PET (probabilistic evaluation tool) circumvents problems of large state spaces when the desired performance and dependability measure are transient measures. It does so by an approach named probabilistic evaluatio

Verification and control of partially observable probabilistic systems

We present automated techniques for the verification and control of partially observable, probabilistic systems for both discrete and dense models of time. For the discrete-time case, we formally model these systems using partially observable Markov decision processes; for dense time, we propose an extension of probabilistic timed automata in which local states are partially visible to an observer or controller. We give probabilistic temporal logics that can express a range of quantitative properties of these models, relating to the probability of an event’s occurrence or the expected value of a reward measure. We then propose techniques to either verify that such a property holds or synthesise a controller for the model which makes it true. Our approach is based on a grid-based abstraction of the uncountable belief space induced by partial observability and, for dense-time models, an integer discretisation of real-time behaviour. The former is necessarily approximate since the underlying problem is undecidable, however we show how both lower and upper bounds on numerical results can be generated. We illustrate the effectiveness of the approach by implementing it in the PRISM model checker and applying it to several case studies from the domains of task and network scheduling, computer security and planning

ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra

Background: Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, with the goal to gain a better understanding of the system. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. Although there exist sophisticated algorithms to determine the dynamics of discrete models, their implementations usually require labor-intensive formatting of the model formulation, and they are oftentimes not accessible to users without programming skills. Efficient analysis methods are needed that are accessible to modelers and easy to use. Method: By converting discrete models into algebraic models, tools from computational algebra can be used to analyze their dynamics. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Results: A method for efficiently identifying attractors, and the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness, i.e., while the number of nodes in a biological network may be quite large, each node is affected only by a small number of other nodes, and robustness, i.e., small number of attractors

Verification and Control of Partially Observable Probabilistic Real-Time Systems

We propose automated techniques for the verification and control of probabilistic real-time systems that are only partially observable. To formally model such systems, we define an extension of probabilistic timed automata in which local states are partially visible to an observer or controller. We give a probabilistic temporal logic that can express a range of quantitative properties of these models, relating to the probability of an event's occurrence or the expected value of a reward measure. We then propose techniques to either verify that such a property holds or to synthesise a controller for the model which makes it true. Our approach is based on an integer discretisation of the model's dense-time behaviour and a grid-based abstraction of the uncountable belief space induced by partial observability. The latter is necessarily approximate since the underlying problem is undecidable, however we show how both lower and upper bounds on numerical results can be generated. We illustrate the effectiveness of the approach by implementing it in the PRISM model checker and applying it to several case studies, from the domains of computer security and task scheduling

Probabilistic Inference in Queueing Networks

Although queueing models have long been used to model the performance of computer systems, they are out of favor with practitioners, because they have a reputation for requiring unrealistic distributional assumptions. In fact, these distributional assumptions are used mainly to facilitate analytic approximations such as asymptotics and large-deviations bounds. In this paper, we analyze queueing networks from the probabilistic modeling perspective, applying inference methods from graphical models that afford significantly more modeling flexibility. In particular, we present a Gibbs sampler and stochastic EM algorithm for networks of M/M/1 FIFO queues. As an application of this technique, we localize performance problems in distributed systems from incomplete system trace data. On both synthetic networks and an actual distributed Web application, the model accurately recovers the system’s service time using 1 % of the available trace data.