Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

A Comparison of Stealthy Sensor Attacks on Control Systems

As more attention is paid to security in the context of control systems and as attacks occur to real control systems throughout the world, it has become clear that some of the most nefarious attacks are those that evade detection. The term stealthy has come to encompass a variety of techniques that attackers can employ to avoid detection. Here we show how the states of the system (in particular, the reachable set corresponding to the attack) can be manipulated under two important types of stealthy attacks. We employ the chi-squared fault detection method and demonstrate how this imposes a constraint on the attack sequence either to generate no alarms (zero-alarm attack) or to generate alarms at a rate indistinguishable from normal operation (hidden attack)

A Polynomial Translation of pi-calculus FCPs to Safe Petri Nets

We develop a polynomial translation from finite control pi-calculus processes to safe low-level Petri nets. To our knowledge, this is the first such translation. It is natural in that there is a close correspondence between the control flows, enjoys a bisimulation result, and is suitable for practical model checking.Comment: To appear in special issue on best papers of CONCUR'12 of Logical Methods in Computer Scienc

SPIDER: Fault Resilient SDN Pipeline with Recovery Delay Guarantees

When dealing with node or link failures in Software Defined Networking (SDN), the network capability to establish an alternative path depends on controller reachability and on the round trip times (RTTs) between controller and involved switches. Moreover, current SDN data plane abstractions for failure detection (e.g. OpenFlow "Fast-failover") do not allow programmers to tweak switches' detection mechanism, thus leaving SDN operators still relying on proprietary management interfaces (when available) to achieve guaranteed detection and recovery delays. We propose SPIDER, an OpenFlow-like pipeline design that provides i) a detection mechanism based on switches' periodic link probing and ii) fast reroute of traffic flows even in case of distant failures, regardless of controller availability. SPIDER can be implemented using stateful data plane abstractions such as OpenState or Open vSwitch, and it offers guaranteed short (i.e. ms) failure detection and recovery delays, with a configurable trade off between overhead and failover responsiveness. We present here the SPIDER pipeline design, behavioral model, and analysis on flow tables' memory impact. We also implemented and experimentally validated SPIDER using OpenState (an OpenFlow 1.3 extension for stateful packet processing), showing numerical results on its performance in terms of recovery latency and packet losses.Comment: 8 page

SOTER: A Runtime Assurance Framework for Programming Safe Robotics Systems

The recent drive towards achieving greater autonomy and intelligence in robotics has led to high levels of complexity. Autonomous robots increasingly depend on third party off-the-shelf components and complex machine-learning techniques. This trend makes it challenging to provide strong design-time certification of correct operation. To address these challenges, we present SOTER, a robotics programming framework with two key components: (1) a programming language for implementing and testing high-level reactive robotics software and (2) an integrated runtime assurance (RTA) system that helps enable the use of uncertified components, while still providing safety guarantees. SOTER provides language primitives to declaratively construct a RTA module consisting of an advanced, high-performance controller (uncertified), a safe, lower-performance controller (certified), and the desired safety specification. The framework provides a formal guarantee that a well-formed RTA module always satisfies the safety specification, without completely sacrificing performance by using higher performance uncertified components whenever safe. SOTER allows the complex robotics software stack to be constructed as a composition of RTA modules, where each uncertified component is protected using a RTA module. To demonstrate the efficacy of our framework, we consider a real-world case-study of building a safe drone surveillance system. Our experiments both in simulation and on actual drones show that the SOTER-enabled RTA ensures the safety of the system, including when untrusted third-party components have bugs or deviate from the desired behavior

Limited Visibility and Uncertainty Aware Motion Planning for Automated Driving

Adverse weather conditions and occlusions in urban environments result in impaired perception. The uncertainties are handled in different modules of an automated vehicle, ranging from sensor level over situation prediction until motion planning. This paper focuses on motion planning given an uncertain environment model with occlusions. We present a method to remain collision free for the worst-case evolution of the given scene. We define criteria that measure the available margins to a collision while considering visibility and interactions, and consequently integrate conditions that apply these criteria into an optimization-based motion planner. We show the generality of our method by validating it in several distinct urban scenarios

Distributed Computing with Adaptive Heuristics

We use ideas from distributed computing to study dynamic environments in which computational nodes, or decision makers, follow adaptive heuristics (Hart 2005), i.e., simple and unsophisticated rules of behavior, e.g., repeatedly "best replying" to others' actions, and minimizing "regret", that have been extensively studied in game theory and economics. We explore when convergence of such simple dynamics to an equilibrium is guaranteed in asynchronous computational environments, where nodes can act at any time. Our research agenda, distributed computing with adaptive heuristics, lies on the borderline of computer science (including distributed computing and learning) and game theory (including game dynamics and adaptive heuristics). We exhibit a general non-termination result for a broad class of heuristics with bounded recall---that is, simple rules of behavior that depend only on recent history of interaction between nodes. We consider implications of our result across a wide variety of interesting and timely applications: game theory, circuit design, social networks, routing and congestion control. We also study the computational and communication complexity of asynchronous dynamics and present some basic observations regarding the effects of asynchrony on no-regret dynamics. We believe that our work opens a new avenue for research in both distributed computing and game theory.Comment: 36 pages, four figures. Expands both technical results and discussion of v1. Revised version will appear in the proceedings of Innovations in Computer Science 201