Related papers: Towards modular verification of pathways: fairness…

The spread of autonomous systems into safety-critical areas has increased the demand for their formal verification, not only due to stronger certification requirements but also to public uncertainty over these new technologies. However, the…

Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…

This work utilizes the plethora of work on verification of sequential programs for the purpose of verifying concurrent programs. We reduce the verification of a concurrent program to a series of verification tasks of sequential programs.…

A lot of progress has been made in recent times for simulating accurately the ground state energy of small molecules and their potential energy surface, using quantum-classical hybrid computing architecture. While these single point energy…

Reactions forming a pathway can be rewritten by making explicit the different molecular components involved in them. A molecular component represents a biological entity (e.g. a protein) in all its states (free, bound, degraded, etc.). In…

We are interested in verifying dynamic properties of finite state reactive systems under fairness assumptions by model checking. The systems we want to verify are specified through a top-down refinement process. In order to deal with the…

The case study analyzed in the paper illustrates the example of model checking in the COSMA environment. The system itself is a three-stage pipeline consisting of mutually concurrent modules which also compete for a shared resource. System…

The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…

Although they differ in the functionality they offer, low-level systems exhibit certain patterns of design and utilization of computing resources. In this paper, we argue the position that modalities, in the sense of modal logic, should be…

We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…

Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…

The correctness of many algorithms and data structures depends on reachability properties, that is, on the existence of chains of references between objects in the heap. Reasoning about reachability is difficult for two main reasons. First,…

A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…

This paper addresses the decomposition of biochemical networks into functional modules that preserve their dynamic properties upon interconnection with other modules, which permits the inference of network behavior from the properties of…

This paper deals with the problem of enforcing modular diagnosability for discrete-event systems that don't satisfy this property by their natural modularity. We introduce an approach to achieve this property combining existing modules into…

Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…

In this thesis a comprehensive verification framework is proposed to contend with some important issues in composability verification and a verification process is suggested to verify composability of different kinds of systems models, such…

Modern autonomous systems with machine learning components often use uncertainty quantification to help produce assurances about system operation. However, there is a lack of consensus in the community on what uncertainty is and how to…

Context: The complexity of modern safety-critical systems in industries keep on increasing due to the rising number of features and functionalities. This calls for formal methods in order to entrust confidence in such systems. Nevertheless,…

Process equivalences are formal methods that relate programs and system which, informally, behave in the same way. Since there is no unique notion of what it means for two dynamic systems to display the same behaviour there are a multitude…