On the robustness of temporal properties for stochastic models

Stochastic models such as Continuous-Time Markov Chains (CTMC) and Stochastic Hybrid Automata (SHA) are powerful formalisms to model and to reason about the dynamics of biological systems, due to their ability to capture the stochasticity inherent in biological processes. A classical question in formal modelling with clear relevance to biological modelling is the model checking problem. i.e. calculate the probability that a behaviour, expressed for instance in terms of a certain temporal logic formula, may occur in a given stochastic process. However, one may not only be interested in the notion of satisfiability, but also in the capacity of a system to mantain a particular emergent behaviour unaffected by the perturbations, caused e.g. from extrinsic noise, or by possible small changes in the model parameters. To address this issue, researchers from the verification community have recently proposed several notions of robustness for temporal logic providing suitable definitions of distance between a trajectory of a (deterministic) dynamical system and the boundaries of the set of trajectories satisfying the property of interest. The contributions of this paper are twofold. First, we extend the notion of robustness to stochastic systems, showing that this naturally leads to a distribution of robustness scores. By discussing two examples, we show how to approximate the distribution of the robustness score and its key indicators: the average robustness and the conditional average robustness. Secondly, we show how to combine these indicators with the satisfaction probability to address the system design problem, where the goal is to optimize some control parameters of a stochastic model in order to best maximize robustness of the desired specifications

Adversarial Robustness Verification and Attack Synthesis in Stochastic Systems

Probabilistic model checking is a useful technique for specifying and verifying properties of stochastic systems including randomized protocols and reinforcement learning models. Existing methods rely on the assumed structure and probabilities of certain system transitions. These assumptions may be incorrect, and may even be violated by an adversary who gains control of system components. In this paper, we develop a formal framework for adversarial robustness in systems modeled as discrete time Markov chains (DTMCs). We base our framework on existing methods for verifying probabilistic temporal logic properties and extend it to include deterministic, memoryless policies acting in Markov decision processes (MDPs). Our framework includes a flexible approach for specifying structure-preserving and non structure-preserving adversarial models. We outline a class of threat models under which adversaries can perturb system transitions, constrained by an $\varepsilon$ ball around the original transition probabilities. We define three main DTMC adversarial robustness problems: adversarial robustness verification, maximal $\delta$ synthesis, and worst case attack synthesis. We present two optimization-based solutions to these three problems, leveraging traditional and parametric probabilistic model checking techniques. We then evaluate our solutions on two stochastic protocols and a collection of Grid World case studies, which model an agent acting in an environment described as an MDP. We find that the parametric solution results in fast computation for small parameter spaces. In the case of less restrictive (stronger) adversaries, the number of parameters increases, and directly computing property satisfaction probabilities is more scalable. We demonstrate the usefulness of our definitions and solutions by comparing system outcomes over various properties, threat models, and case studies.Comment: To Appear, 35th IEEE Computer Security Foundations Symposium (2022

Phase Transitions and Spatio-Temporal Fluctuations in Stochastic Lattice Lotka-Volterra Models

We study the general properties of stochastic two-species models for predator-prey competition and coexistence with Lotka-Volterra type interactions defined on a $d$-dimensional lattice. Introducing spatial degrees of freedom and allowing for stochastic fluctuations generically invalidates the classical, deterministic mean-field picture. Already within mean-field theory, however, spatial constraints, modeling locally limited resources, lead to the emergence of a continuous active-to-absorbing state phase transition. Field-theoretic arguments, supported by Monte Carlo simulation results, indicate that this transition, which represents an extinction threshold for the predator population, is governed by the directed percolation universality class. In the active state, where predators and prey coexist, the classical center singularities with associated population cycles are replaced by either nodes or foci. In the vicinity of the stable nodes, the system is characterized by essentially stationary localized clusters of predators in a sea of prey. Near the stable foci, however, the stochastic lattice Lotka-Volterra system displays complex, correlated spatio-temporal patterns of competing activity fronts. Correspondingly, the population densities in our numerical simulations turn out to oscillate irregularly in time, with amplitudes that tend to zero in the thermodynamic limit. Yet in finite systems these oscillatory fluctuations are quite persistent, and their features are determined by the intrinsic interaction rates rather than the initial conditions. We emphasize the robustness of this scenario with respect to various model perturbations.Comment: 19 pages, 11 figures, 2-column revtex4 format. Minor modifications. Accepted in the Journal of Statistical Physics. Movies corresponding to Figures 2 and 3 are available at http://www.phys.vt.edu/~tauber/PredatorPrey/movies

Turing's model for biological pattern formation and the robustness problem

One of the fundamental questions in developmental biology is how the vast range of pattern and structure we observe in nature emerges from an almost uniformly homogeneous fertilized egg. In particular, the mechanisms by which biological systems maintain robustness, despite being subject to numerous sources of noise, are shrouded in mystery. Postulating plausible theoretical models of biological heterogeneity is not only difficult, but it is also further complicated by the problem of generating robustness, i.e. once we can generate a pattern, how do we ensure that this pattern is consistently reproducible in the face of perturbations to the domain, reaction time scale, boundary conditions and so forth. In this paper, not only do we review the basic properties of Turing's theory, we highlight the successes and pitfalls of using it as a model for biological systems, and discuss emerging developments in the area

Partial differential equations for self-organization in cellular and developmental biology

Understanding the mechanisms governing and regulating the emergence of structure and heterogeneity within cellular systems, such as the developing embryo, represents a multiscale challenge typifying current integrative biology research, namely, explaining the macroscale behaviour of a system from microscale dynamics. This review will focus upon modelling how cell-based dynamics orchestrate the emergence of higher level structure. After surveying representative biological examples and the models used to describe them, we will assess how developments at the scale of molecular biology have impacted on current theoretical frameworks, and the new modelling opportunities that are emerging as a result. We shall restrict our survey of mathematical approaches to partial differential equations and the tools required for their analysis. We will discuss the gap between the modelling abstraction and biological reality, the challenges this presents and highlight some open problems in the field