A System for Deduction-based Formal Verification of Workflow-oriented Software Models

The work concerns formal verification of workflow-oriented software models using deductive approach. The formal correctness of a model's behaviour is considered. Manually building logical specifications, which are considered as a set of temporal logic formulas, seems to be the significant obstacle for an inexperienced user when applying the deductive approach. A system, and its architecture, for the deduction-based verification of workflow-oriented models is proposed. The process of inference is based on the semantic tableaux method which has some advantages when compared to traditional deduction strategies. The algorithm for an automatic generation of logical specifications is proposed. The generation procedure is based on the predefined workflow patterns for BPMN, which is a standard and dominant notation for the modeling of business processes. The main idea for the approach is to consider patterns, defined in terms of temporal logic,as a kind of (logical) primitives which enable the transformation of models to temporal logic formulas constituting a logical specification. Automation of the generation process is crucial for bridging the gap between intuitiveness of the deductive reasoning and the difficulty of its practical application in the case when logical specifications are built manually. This approach has gone some way towards supporting, hopefully enhancing our understanding of, the deduction-based formal verification of workflow-oriented models.Comment: International Journal of Applied Mathematics and Computer Scienc

Adaptive Process Management in Cyber-Physical Domains

The increasing application of process-oriented approaches in new challenging cyber-physical domains beyond business computing (e.g., personalized healthcare, emergency management, factories of the future, home automation, etc.) has led to reconsider the level of flexibility and support required to manage complex processes in such domains. A cyber-physical domain is characterized by the presence of a cyber-physical system coordinating heterogeneous ICT components (PCs, smartphones, sensors, actuators) and involving real world entities (humans, machines, agents, robots, etc.) that perform complex tasks in the “physical” real world to achieve a common goal. The physical world, however, is not entirely predictable, and processes enacted in cyber-physical domains must be robust to unexpected conditions and adaptable to unanticipated exceptions. This demands a more flexible approach in process design and enactment, recognizing that in real-world environments it is not adequate to assume that all possible recovery activities can be predefined for dealing with the exceptions that can ensue. In this chapter, we tackle the above issue and we propose a general approach, a concrete framework and a process management system implementation, called SmartPM, for automatically adapting processes enacted in cyber-physical domains in case of unanticipated exceptions and exogenous events. The adaptation mechanism provided by SmartPM is based on declarative task specifications, execution monitoring for detecting failures and context changes at run-time, and automated planning techniques to self-repair the running process, without requiring to predefine any specific adaptation policy or exception handler at design-time

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Fine-Grained Workflow Interoperability in Life Sciences

In den vergangenen Jahrzehnten führten Fortschritte in den Schlüsseltechnologien der Lebenswissenschaften zu einer exponentiellen Zunahme der zur Verfügung stehenden biologischen Daten. Um Ergebnisse zeitnah generieren zu können werden sowohl spezialisierte Rechensystem als auch Programmierfähigkeiten benötigt: Desktopcomputer oder monolithische Ansätze sind weder in der Lage mit dem Wachstum der verfügbaren biologischen Daten noch mit der Komplexität der Analysetechniken Schritt zu halten. Workflows erlauben diesem Trend durch Parallelisierungsansätzen und verteilten Rechensystemen entgegenzuwirken. Ihre transparenten Abläufe, gegeben durch ihre klar definierten Strukturen, ebenso ihre Wiederholbarkeit, erfüllen die Standards der Reproduzierbarkeit, welche an wissenschaftliche Methoden gestellt werden. Eines der Ziele unserer Arbeit ist es Forschern beim Bedienen von Rechensystemen zu unterstützen, ohne dass Programmierkenntnisse notwendig sind. Dafür wurde eine Sammlung von Tools entwickelt, welche jedes Kommandozeilenprogramm in ein Workflowsystem integrieren kann. Ohne weitere Anpassungen kann unser Programm zwei weit verbreitete Workflowsysteme unterstützen. Unser modularer Entwurf erlaubt zudem Unterstützung für weitere Workflowmaschinen hinzuzufügen. Basierend auf der Bedeutung von frühen und robusten Workflowentwürfen, haben wir außerdem eine wohl etablierte Desktop–basierte Analyseplattform erweitert. Diese enthält über 2.000 Aufgaben, wobei jede als Baustein in einem Workflow fungiert. Die Plattform erlaubt einfache Entwicklung neuer Aufgaben und die Integration externer Kommandozeilenprogramme. In dieser Arbeit wurde ein Plugin zur Konvertierung entwickelt, welches nutzerfreundliche Mechanismen bereitstellt, um Workflows auf verteilten Hochleistungsrechensystemen auszuführen—eine Aufgabe, die sonst technische Kenntnisse erfordert, die gewöhnlich nicht zum Anforderungsprofil eines Lebenswissenschaftlers gehören. Unsere Konverter–Erweiterung generiert quasi identische Versionen desselben Workflows, welche im Anschluss auf leistungsfähigen Berechnungsressourcen ausgeführt werden können. Infolgedessen werden nicht nur die Möglichkeiten von verteilten hochperformanten Rechensystemen sowie die Bequemlichkeit eines für Desktopcomputer entwickelte Workflowsystems ausgenutzt, sondern zusätzlich werden Berechnungsbeschränkungen von Desktopcomputern und die steile Lernkurve, die mit dem Workflowentwurf auf verteilten Systemen verbunden ist, umgangen. Unser Konverter–Plugin hat sofortige Anwendung für Forscher. Wir zeigen dies in drei für die Lebenswissenschaften relevanten Anwendungsbeispielen: Strukturelle Bioinformatik, Immuninformatik, und Metabolomik.Recent decades have witnessed an exponential increase of available biological data due to advances in key technologies for life sciences. Specialized computing resources and scripting skills are now required to deliver results in a timely fashion: desktop computers or monolithic approaches can no longer keep pace with neither the growth of available biological data nor the complexity of analysis techniques. Workflows offer an accessible way to counter against this trend by facilitating parallelization and distribution of computations. Given their structured and repeatable nature, workflows also provide a transparent process to satisfy strict reproducibility standards required by the scientific method. One of the goals of our work is to assist researchers in accessing computing resources without the need for programming or scripting skills. To this effect, we created a toolset able to integrate any command line tool into workflow systems. Out of the box, our toolset supports two widely–used workflow systems, but our modular design allows for seamless additions in order to support further workflow engines. Recognizing the importance of early and robust workflow design, we also extended a well–established, desktop–based analytics platform that contains more than two thousand tasks (each being a building block for a workflow), allows easy development of new tasks and is able to integrate external command line tools. We developed a converter plug–in that offers a user–friendly mechanism to execute workflows on distributed high–performance computing resources—an exercise that would otherwise require technical skills typically not associated with the average life scientist's profile. Our converter extension generates virtually identical versions of the same workflows, which can then be executed on more capable computing resources. That is, not only did we leverage the capacity of distributed high–performance resources and the conveniences of a workflow engine designed for personal computers but we also circumvented computing limitations of personal computers and the steep learning curve associated with creating workflows for distributed environments. Our converter extension has immediate applications for researchers and we showcase our results by means of three use cases relevant for life scientists: structural bioinformatics, immunoinformatics and metabolomics

Symbolic Model-Checking using ITS-tools

International audienceWe present the symbolic model-checking toolset ITS-tools. The model-checking back-end engine is based on hierarchical set decision diagrams (SDD) and supports reachability, CTL and LTL model-checking, using both classical and original algorithms. As front-end input language, we promote a Guarded Action Language (GAL), a simple yet expressive language for concurrency. Transformations from popular formalisms into GAL are provided enabling fully symbolic model-checking of third party (Uppaal, Spin, Divine...) specifications. The tool design allows to easily build your own transformation, leveraging tools from the meta-modeling community. The ITS-tools additionally come with a user friendly GUI embedded in Eclipse

A Process Modelling Framework Based on Point Interval Temporal Logic with an Application to Modelling Patient Flows

This thesis considers an application of a temporal theory to describe and model the patient journey in the hospital accident and emergency (A&E) department. The aim is to introduce a generic but dynamic method applied to any setting, including healthcare. Constructing a consistent process model can be instrumental in streamlining healthcare issues. Current process modelling techniques used in healthcare such as flowcharts, unified modelling language activity diagram (UML AD), and business process modelling notation (BPMN) are intuitive and imprecise. They cannot fully capture the complexities of the types of activities and the full extent of temporal constraints to an extent where one could reason about the flows. Formal approaches such as Petri have also been reviewed to investigate their applicability to the healthcare domain to model processes. Additionally, to schedule patient flows, current modelling standards do not offer any formal mechanism, so healthcare relies on critical path method (CPM) and program evaluation review technique (PERT), that also have limitations, i.e. finish-start barrier. It is imperative to specify the temporal constraints between the start and/or end of a process, e.g., the beginning of a process A precedes the start (or end) of a process B. However, these approaches failed to provide us with a mechanism for handling these temporal situations. If provided, a formal representation can assist in effective knowledge representation and quality enhancement concerning a process. Also, it would help in uncovering complexities of a system and assist in modelling it in a consistent way which is not possible with the existing modelling techniques. The above issues are addressed in this thesis by proposing a framework that would provide a knowledge base to model patient flows for accurate representation based on point interval temporal logic (PITL) that treats point and interval as primitives. These objects would constitute the knowledge base for the formal description of a system. With the aid of the inference mechanism of the temporal theory presented here, exhaustive temporal constraints derived from the proposed axiomatic system’ components serves as a knowledge base. The proposed methodological framework would adopt a model-theoretic approach in which a theory is developed and considered as a model while the corresponding instance is considered as its application. Using this approach would assist in identifying core components of the system and their precise operation representing a real-life domain deemed suitable to the process modelling issues specified in this thesis. Thus, I have evaluated the modelling standards for their most-used terminologies and constructs to identify their key components. It will also assist in the generalisation of the critical terms (of process modelling standards) based on their ontology. A set of generalised terms proposed would serve as an enumeration of the theory and subsume the core modelling elements of the process modelling standards. The catalogue presents a knowledge base for the business and healthcare domains, and its components are formally defined (semantics). Furthermore, a resolution theorem-proof is used to show the structural features of the theory (model) to establish it is sound and complete. After establishing that the theory is sound and complete, the next step is to provide the instantiation of the theory. This is achieved by mapping the core components of the theory to their corresponding instances. Additionally, a formal graphical tool termed as point graph (PG) is used to visualise the cases of the proposed axiomatic system. PG facilitates in modelling, and scheduling patient flows and enables analysing existing models for possible inaccuracies and inconsistencies supported by a reasoning mechanism based on PITL. Following that, a transformation is developed to map the core modelling components of the standards into the extended PG (PG*) based on the semantics presented by the axiomatic system. A real-life case (from the King’s College hospital accident and emergency (A&E) department’s trauma patient pathway) is considered to validate the framework. It is divided into three patient flows to depict the journey of a patient with significant trauma, arriving at A&E, undergoing a procedure and subsequently discharged. Their staff relied upon the UML-AD and BPMN to model the patient flows. An evaluation of their representation is presented to show the shortfalls of the modelling standards to model patient flows. The last step is to model these patient flows using the developed approach, which is supported by enhanced reasoning and scheduling