Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)

In this paper, a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect the imposed level of approximation provided that with increasing parameter value the approximation converges to the original continuous system. By employing this approximation technique, we present algorithms solving the reachability problem for biochemical dynamical systems. The presented method and algorithms are evaluated on several exemplary biological models and on a real case study.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Analysis of parametric biological models with non-linear dynamics

In this paper we present recent results on parametric analysis of biological models. The underlying method is based on the algorithms for computing trajectory sets of hybrid systems with polynomial dynamics. The method is then applied to two case studies of biological systems: one is a cardiac cell model for studying the conditions for cardiac abnormalities, and the second is a model of insect nest-site choice.Comment: In Proceedings HSB 2012, arXiv:1208.315

Time-Constrained Temporal Logic Control of Multi-Affine Systems

In this paper, we consider the problem of controlling a dynamical system such that its trajectories satisfy a temporal logic property in a given amount of time. We focus on multi-affine systems and specifications given as syntactically co-safe linear temporal logic formulas over rectangular regions in the state space. The proposed algorithm is based on the estimation of time bounds for facet reachability problems and solving a time optimal reachability problem on the product between a weighted transition system and an automaton that enforces the satisfaction of the specification. A random optimization algorithm is used to iteratively improve the solution

Reach Set Approximation through Decomposition with Low-dimensional Sets and High-dimensional Matrices

Approximating the set of reachable states of a dynamical system is an algorithmic yet mathematically rigorous way to reason about its safety. Although progress has been made in the development of efficient algorithms for affine dynamical systems, available algorithms still lack scalability to ensure their wide adoption in the industrial setting. While modern linear algebra packages are efficient for matrices with tens of thousands of dimensions, set-based image computations are limited to a few hundred. We propose to decompose reach set computations such that set operations are performed in low dimensions, while matrix operations like exponentiation are carried out in the full dimension. Our method is applicable both in dense- and discrete-time settings. For a set of standard benchmarks, it shows a speed-up of up to two orders of magnitude compared to the respective state-of-the art tools, with only modest losses in accuracy. For the dense-time case, we show an experiment with more than 10.000 variables, roughly two orders of magnitude higher than possible with previous approaches

Reachability analysis of linear hybrid systems via block decomposition

Reachability analysis aims at identifying states reachable by a system within a given time horizon. This task is known to be computationally expensive for linear hybrid systems. Reachability analysis works by iteratively applying continuous and discrete post operators to compute states reachable according to continuous and discrete dynamics, respectively. In this paper, we enhance both of these operators and make sure that most of the involved computations are performed in low-dimensional state space. In particular, we improve the continuous-post operator by performing computations in high-dimensional state space only for time intervals relevant for the subsequent application of the discrete-post operator. Furthermore, the new discrete-post operator performs low-dimensional computations by leveraging the structure of the guard and assignment of a considered transition. We illustrate the potential of our approach on a number of challenging benchmarks.Comment: Accepted at EMSOFT 202

Kleene Algebras and Semimodules for Energy Problems

With the purpose of unifying a number of approaches to energy problems found in the literature, we introduce generalized energy automata. These are finite automata whose edges are labeled with energy functions that define how energy levels evolve during transitions. Uncovering a close connection between energy problems and reachability and B\"uchi acceptance for semiring-weighted automata, we show that these generalized energy problems are decidable. We also provide complexity results for important special cases

Forward Stochastic Reachability Analysis for Uncontrolled Linear Systems using Fourier Transforms

We propose a scalable method for forward stochastic reachability analysis for uncontrolled linear systems with affine disturbance. Our method uses Fourier transforms to efficiently compute the forward stochastic reach probability measure (density) and the forward stochastic reach set. This method is applicable to systems with bounded or unbounded disturbance sets. We also examine the convexity properties of the forward stochastic reach set and its probability density. Motivated by the problem of a robot attempting to capture a stochastically moving, non-adversarial target, we demonstrate our method on two simple examples. Where traditional approaches provide approximations, our method provides exact analytical expressions for the densities and probability of capture.Comment: V3: HSCC 2017 (camera-ready copy), DOI updated, minor changes | V2: Review comments included | V1: 10 pages, 12 figure

BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study