Runtime Verification of Biological Systems

International audienceComplex computational systems are ubiquitous and their study increasingly important. Given the ease with which it is possible to construct large systems with heterogeneous technology, there is strong motivation to provide automated means to verify their safety, efficiency and reliability. In another context, biological systems are supreme examples of complex systems for which there are no design specifications. In both cases it is usually difficult to reason at the level of the description of the systems and much more convenient to investigate properties of their executions. To demonstrate runtime verification of complex systems we apply statistical model checking techniques to a model of robust biological oscillations taken from the literature. The model demonstrates some of the mechanisms used by biological systems to maintain reliable performance in the face of inherent stochasticity and is therefore instructive. To perform our investigation we use two recently developed SMC platforms: that incorporated in Uppaal and Plasma. Uppaalsmc offers a generic modeling language based on stochastic hybrid automata, while Plasma aims at domain specific support with the facility to accept biological models represented in chemical syntax

Bayesian Verification under Model Uncertainty

Machine learning enables systems to build and update domain models based on runtime observations. In this paper, we study statistical model checking and runtime verification for systems with this ability. Two challenges arise: (1) Models built from limited runtime data yield uncertainty to be dealt with. (2) There is no definition of satisfaction w.r.t. uncertain hypotheses. We propose such a definition of subjective satisfaction based on recently introduced satisfaction functions. We also propose the BV algorithm as a Bayesian solution to runtime verification of subjective satisfaction under model uncertainty. BV provides user-definable stochastic bounds for type I and II errors. We discuss empirical results from an example application to illustrate our ideas.Comment: Accepted at SEsCPS @ ICSE 201

Computational Modeling, Formal Analysis, and Tools for Systems Biology.

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science

Automatic Software Repair: a Bibliography

This article presents a survey on automatic software repair. Automatic software repair consists of automatically finding a solution to software bugs without human intervention. This article considers all kinds of repairs. First, it discusses behavioral repair where test suites, contracts, models, and crashing inputs are taken as oracle. Second, it discusses state repair, also known as runtime repair or runtime recovery, with techniques such as checkpoint and restart, reconfiguration, and invariant restoration. The uniqueness of this article is that it spans the research communities that contribute to this body of knowledge: software engineering, dependability, operating systems, programming languages, and security. It provides a novel and structured overview of the diversity of bug oracles and repair operators used in the literature

Towards formal models and languages for verifiable Multi-Robot Systems

Incorrect operations of a Multi-Robot System (MRS) may not only lead to unsatisfactory results, but can also cause economic losses and threats to safety. These threats may not always be apparent, since they may arise as unforeseen consequences of the interactions between elements of the system. This call for tools and techniques that can help in providing guarantees about MRSs behaviour. We think that, whenever possible, these guarantees should be backed up by formal proofs to complement traditional approaches based on testing and simulation. We believe that tailored linguistic support to specify MRSs is a major step towards this goal. In particular, reducing the gap between typical features of an MRS and the level of abstraction of the linguistic primitives would simplify both the specification of these systems and the verification of their properties. In this work, we review different agent-oriented languages and their features; we then consider a selection of case studies of interest and implement them useing the surveyed languages. We also evaluate and compare effectiveness of the proposed solution, considering, in particular, easiness of expressing non-trivial behaviour.Comment: Changed formattin

Value Iteration for Long-run Average Reward in Markov Decision Processes

Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks