SAM-SoS: A stochastic software architecture modeling and verification approach for complex System-of-Systems

A System-of-Systems (SoS) is a complex, dynamic system whose Constituent Systems (CSs) are not known precisely at design time, and the environment in which they operate is uncertain. SoS behavior is unpredictable due to underlying architectural characteristics such as autonomy and independence. Although the stochastic composition of CSs is vital to achieving SoS missions, their unknown behaviors and impact on system properties are unavoidable. Moreover, unknown conditions and volatility have significant effects on crucial Quality Attributes (QAs) such as performance, reliability and security. Hence, the structure and behavior of a SoS must be modeled and validated quantitatively to foresee any potential impact on the properties critical for achieving the missions. Current modeling approaches lack the essential syntax and semantics required to model and verify SoS behaviors at design time and cannot offer alternative design choices for better design decisions. Therefore, the majority of existing techniques fail to provide qualitative and quantitative verification of SoS architecture models. Consequently, we have proposed an approach to model and verify Non-Deterministic (ND) SoS in advance by extending the current algebraic notations for the formal models as a hybrid stochastic formalism to specify and reason architectural elements with the required semantics. A formal stochastic model is developed using a hybrid approach for architectural descriptions of SoS with behavioral constraints. Through a model-driven approach, stochastic models are then translated into PRISM using formal verification rules. The effectiveness of the approach has been tested with an end-to-end case study design of an emergency response SoS for dealing with a fire situation. Architectural analysis is conducted on the stochastic model, using various qualitative and quantitative measures for SoS missions. Experimental results reveal critical aspects of SoS architecture model that facilitate better achievement of missions and QAs with improved design, using the proposed approach

Model-based dependability analysis : state-of-the-art, challenges and future outlook

Abstract: Over the past two decades, the study of model-based dependability analysis has gathered significant research interest. Different approaches have been developed to automate and address various limitations of classical dependability techniques to contend with the increasing complexity and challenges of modern safety-critical system. Two leading paradigms have emerged, one which constructs predictive system failure models from component failure models compositionally using the topology of the system. The other utilizes design models - typically state automata - to explore system behaviour through fault injection. This paper reviews a number of prominent techniques under these two paradigms, and provides an insight into their working mechanism, applicability, strengths and challenges, as well as recent developments within these fields. We also discuss the emerging trends on integrated approaches and advanced analysis capabilities. Lastly, we outline the future outlook for model-based dependability analysis

Modeling Time in Computing: A Taxonomy and a Comparative Survey

The increasing relevance of areas such as real-time and embedded systems, pervasive computing, hybrid systems control, and biological and social systems modeling is bringing a growing attention to the temporal aspects of computing, not only in the computer science domain, but also in more traditional fields of engineering. This article surveys various approaches to the formal modeling and analysis of the temporal features of computer-based systems, with a level of detail that is suitable also for non-specialists. In doing so, it provides a unifying framework, rather than just a comprehensive list of formalisms. The paper first lays out some key dimensions along which the various formalisms can be evaluated and compared. Then, a significant sample of formalisms for time modeling in computing are presented and discussed according to these dimensions. The adopted perspective is, to some extent, historical, going from "traditional" models and formalisms to more modern ones.Comment: More typos fixe

Towards Cancer Hybrid Automata

This paper introduces Cancer Hybrid Automata (CHAs), a formalism to model the progression of cancers through discrete phenotypes. The classification of cancer progression using discrete states like stages and hallmarks has become common in the biology literature, but primarily as an organizing principle, and not as an executable formalism. The precise computational model developed here aims to exploit this untapped potential, namely, through automatic verification of progression models (e.g., consistency, causal connections, etc.), classification of unreachable or unstable states and computer-generated (individualized or universal) therapy plans. The paper builds on a phenomenological approach, and as such does not need to assume a model for the biochemistry of the underlying natural progression. Rather, it abstractly models transition timings between states as well as the effects of drugs and clinical tests, and thus allows formalization of temporal statements about the progression as well as notions of timed therapies. The model proposed here is ultimately based on hybrid automata, and we show how existing controller synthesis algorithms can be generalized to CHA models, so that therapies can be generated automatically. Throughout this paper we use cancer hallmarks to represent the discrete states through which cancer progresses, but other notions of discretely or continuously varying state formalisms could also be used to derive similar therapies.Comment: In Proceedings HSB 2012, arXiv:1208.315

A review of modelling and verification approaches for computational biology

This paper reviews most frequently used computational modelling approaches and formal verification techniques in computational biology. The paper also compares a number of model checking tools and software suits used in analysing biological systems and biochemical networks and verifiying a wide range of biological properties

Counterfactual Causality from First Principles?

In this position paper we discuss three main shortcomings of existing approaches to counterfactual causality from the computer science perspective, and sketch lines of work to try and overcome these issues: (1) causality definitions should be driven by a set of precisely specified requirements rather than specific examples; (2) causality frameworks should support system dynamics; (3) causality analysis should have a well-understood behavior in presence of abstraction.Comment: In Proceedings CREST 2017, arXiv:1710.0277

"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis

<p>Abstract</p> <p>Background</p> <p>In Thomas' formalism for modeling gene regulatory networks (GRNs), <it>branching time</it>, where a state can have <it>more than one possible future</it>, plays a prominent role. By representing a certain degree of unpredictability, branching time can model several important phenomena, such as (a) asynchrony, (b) incompletely specified behavior, and (c) interaction with the environment. Introducing more than one possible future for a state, however, creates a difficulty for ordinary simulators, because <it>infinitely many </it>paths may appear, limiting ordinary simulators to statistical conclusions. <it>Model checkers </it>for branching time, by contrast, are able to prove properties in the presence of infinitely many paths.</p> <p>Results</p> <p>We have developed <it>Antelope </it>("Analysis of Networks through TEmporal-LOgic sPEcifications", <url>http://turing.iimas.unam.mx:8080/AntelopeWEB/</url>), a model checker for analyzing and constructing Boolean GRNs. Currently, software systems for Boolean GRNs use branching time almost exclusively for asynchrony. <it>Antelope</it>, by contrast, also uses branching time for incompletely specified behavior and environment interaction. We show the usefulness of modeling these two phenomena in the development of a Boolean GRN of the <it>Arabidopsis thaliana </it>root stem cell niche.</p> <p>There are two obstacles to a direct approach when applying model checking to Boolean GRN analysis. First, ordinary model checkers normally only verify whether or not a <it>given </it>set of model states has a given property. In comparison, a model checker for Boolean GRNs is preferable if it <it>reports </it>the set of states having a desired property. Second, for efficiency, the expressiveness of many model checkers is limited, resulting in the inability to express some interesting properties of Boolean GRNs.</p> <p><it>Antelope </it>tries to overcome these two drawbacks: Apart from reporting the set of all states having a given property, our model checker can express, at the expense of efficiency, some properties that ordinary model checkers (e.g., NuSMV) cannot. This additional expressiveness is achieved by employing a logic extending the standard Computation-Tree Logic (CTL) with hybrid-logic operators.</p> <p>Conclusions</p> <p>We illustrate the advantages of <it>Antelope </it>when (a) modeling incomplete networks and environment interaction, (b) exhibiting the set of all states having a given property, and (c) representing Boolean GRN properties with hybrid CTL.</p

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings