Model Checking CSL for Markov Population Models

Markov population models (MPMs) are a widely used modelling formalism in the area of computational biology and related areas. The semantics of a MPM is an infinite-state continuous-time Markov chain. In this paper, we use the established continuous stochastic logic (CSL) to express properties of Markov population models. This allows us to express important measures of biological systems, such as probabilistic reachability, survivability, oscillations, switching times between attractor regions, and various others. Because of the infinite state space, available analysis techniques only apply to a very restricted subset of CSL properties. We present a full algorithm for model checking CSL for MPMs, and provide experimental evidence showing that our method is effective.Comment: In Proceedings QAPL 2014, arXiv:1406.156

Fluid Model Checking

In this paper we investigate a potential use of fluid approximation techniques in the context of stochastic model checking of CSL formulae. We focus on properties describing the behaviour of a single agent in a (large) population of agents, exploiting a limit result known also as fast simulation. In particular, we will approximate the behaviour of a single agent with a time-inhomogeneous CTMC which depends on the environment and on the other agents only through the solution of the fluid differential equation. We will prove the asymptotic correctness of our approach in terms of satisfiability of CSL formulae and of reachability probabilities. We will also present a procedure to model check time-inhomogeneous CTMC against CSL formulae

Trend-based analysis of a population model of the AKAP scaffold protein

We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system

Applying Mean-field Approximation to Continuous Time Markov Chains

The mean-field analysis technique is used to perform analysis of a systems with a large number of components to determine the emergent deterministic behaviour and how this behaviour modifies when its parameters are perturbed. The computer science performance modelling and analysis community has found the mean-field method useful for modelling large-scale computer and communication networks. Applying mean-field analysis from the computer science perspective requires the following major steps: (1) describing how the agents populations evolve by means of a system of differential equations, (2) finding the emergent deterministic behaviour of the system by solving such differential equations, and (3) analysing properties of this behaviour either by relying on simulation or by using logics. Depending on the system under analysis, performing these steps may become challenging. Often, modifications of the general idea are needed. In this tutorial we consider illustrating examples to discuss how the mean-field method is used in different application areas. Starting from the application of the classical technique, moving to cases where additional steps have to be used, such as systems with local communication. Finally we illustrate the application of the simulation and uid model checking analysis techniques

A uniformization-based algorithm for model checking the CSL until operator on labeled queueing networks

We present a model checking procedure for the CSL until operator on the CTMCs that underlie Jackson queueing networks. The key issue lies in the fact that the underlying CTMC is infinite in as many dimension as there are queues in the JQN. We need to compute the transient state probabilities for all goal states and for all possible starting states. However, for these transient probabilities no computational procedures are readily available. The contribution of this paper is the proposal of a new uniformization-based approach to compute the transient state probabilities. Furthermore, we show how the highly structured state space of JQNs allows us to compute the possible infinite satisfaction set for until formulas. A case study on an e-business site shows the feasibility of our approach

Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Efficient CSL Model Checking Using Stratification

For continuous-time Markov chains, the model-checking problem with respect to continuous-time stochastic logic (CSL) has been introduced and shown to be decidable by Aziz, Sanwal, Singhal and Brayton in 1996. Their proof can be turned into an approximation algorithm with worse than exponential complexity. In 2000, Baier, Haverkort, Hermanns and Katoen presented an efficient polynomial-time approximation algorithm for the sublogic in which only binary until is allowed. In this paper, we propose such an efficient polynomial-time approximation algorithm for full CSL. The key to our method is the notion of stratified CTMCs with respect to the CSL property to be checked. On a stratified CTMC, the probability to satisfy a CSL path formula can be approximated by a transient analysis in polynomial time (using uniformization). We present a measure-preserving, linear-time and -space transformation of any CTMC into an equivalent, stratified one. This makes the present work the centerpiece of a broadly applicable full CSL model checker. Recently, the decision algorithm by Aziz et al. was shown to work only for stratified CTMCs. As an additional contribution, our measure-preserving transformation can be used to ensure the decidability for general CTMCs.Comment: 18 pages, preprint for LMCS. An extended abstract appeared in ICALP 201

Efficient Parallel Statistical Model Checking of Biochemical Networks

We consider the problem of verifying stochastic models of biochemical networks against behavioral properties expressed in temporal logic terms. Exact probabilistic verification approaches such as, for example, CSL/PCTL model checking, are undermined by a huge computational demand which rule them out for most real case studies. Less demanding approaches, such as statistical model checking, estimate the likelihood that a property is satisfied by sampling executions out of the stochastic model. We propose a methodology for efficiently estimating the likelihood that a LTL property P holds of a stochastic model of a biochemical network. As with other statistical verification techniques, the methodology we propose uses a stochastic simulation algorithm for generating execution samples, however there are three key aspects that improve the efficiency: first, the sample generation is driven by on-the-fly verification of P which results in optimal overall simulation time. Second, the confidence interval estimation for the probability of P to hold is based on an efficient variant of the Wilson method which ensures a faster convergence. Third, the whole methodology is designed according to a parallel fashion and a prototype software tool has been implemented that performs the sampling/verification process in parallel over an HPC architecture