Membrane Systems and Petri Net Synthesis

Automated synthesis from behavioural specifications is an attractive and powerful way of constructing concurrent systems. Here we focus on the problem of synthesising a membrane system from a behavioural specification given in the form of a transition system which specifies the desired state space of the system to be constructed. We demonstrate how a Petri net solution to this problem, based on the notion of region of a transition system, yields a method of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347

Asynchronous Multiparty Session Type Implementability is Decidable - Lessons Learned from Message Sequence Charts

Multiparty session types (MSTs) provide efficient means to specify and verify asynchronous message-passing systems. For a global type, which specifies all interactions between roles in a system, the implementability problem asks whether there are local specifications for all roles such that their composition is deadlock-free and generates precisely the specified executions. Decidability of the implementability problem is an open question. We answer it positively for global types with sender-driven choice, which allow a sender to send to different receivers upon branching and a receiver to receive from different senders. To achieve this, we generalise results from the domain of high-level message sequence charts (HMSCs). This connection also allows us to comprehensively investigate how HMSC techniques can be adapted to the MST setting. This comprises techniques to make the problem algorithmically more tractable as well as a variant of implementability that may open new design space for MSTs. Inspired by potential performance benefits, we introduce a generalisation of the implementability problem that we, unfortunately, prove to be undecidable

Application of Petri net based analysis techniques to signal transduction pathways

BACKGROUND: Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. METHODS: We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. RESULTS: We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. CONCLUSION: The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules

Synthesising process controllers from formal models of transformable assembly systems

When producing complex and highly customisable products in low volumes (or in ‘batch sizes of one’), automation of production systems is critical for competitiveness and profitability in high labour-cost economies. To facilitate batch-size-of-one production, ‘topology generation’, ‘realisability’, and ‘control’ algorithms have been developed as part of the Evolvable Assembly Systems (EAS) project. The topology generation algorithm computes all the possible sequences of parallel activities that assembly resources can perform on parts and is run offline whenever the layout of the production facility changes, whereas realisability checking and controller generation are performed at run-time to check whether a production facility with a given set of assembly resources can assemble a desired product, and how the product should be assembled, e.g., which resources to use, and when. Generated controllers are output in Business to Manufacturing Markup Language (B2MML). Taken together, the algorithms thus represent a step toward a complete path from the formal specification of an assembly system and the products to be assembled, to the automated synthesis of executable process plans. This paper presents each algorithm in sufficient detail to allow their reimplementation by other researchers. Topology generation is the most expensive step in the approach. A preliminary experimental evaluation of the scalability of topology generation is presented, which suggests that, for small to medium sized production facilities, the time required for recomputing the topology is sufficiently small not to preclude frequent factory transformations, e.g., the addition of new resources.Funded by the Engineering and Physical Sciences Research Council via grants EP/K018205/1 and EP/K014161/1

Synchronous Counting and Computational Algorithm Design

Consider a complete communication network on $n$ nodes, each of which is a state machine. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are "odd" and which are "even". We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates $f$ Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states. This work consists of two parts. In the first part, we use computational techniques (often known as synthesis) to construct very compact deterministic algorithms for the first non-trivial case of $f = 1$. While no algorithm exists for $n < 4$, we show that as few as 3 states per node are sufficient for all values $n \ge 4$. Moreover, the problem cannot be solved with only 2 states per node for $n = 4$, but there is a 2-state solution for all values $n \ge 6$. In the second part, we develop and compare two different approaches for synthesising synchronous counting algorithms. Both approaches are based on casting the synthesis problem as a propositional satisfiability (SAT) problem and employing modern SAT-solvers. The difference lies in how to solve the SAT problem: either in a direct fashion, or incrementally within a counter-example guided abstraction refinement loop. Empirical results suggest that the former technique is more efficient if we want to synthesise time-optimal algorithms, while the latter technique discovers non-optimal algorithms more quickly.Comment: 35 pages, extended and revised versio

Contributions to the deadlock problem in multithreaded software applications observed as Resource Allocation Systems

Desde el punto de vista de la competencia por recursos compartidos sucesivamente reutilizables, se dice que un sistema concurrente compuesto por procesos secuenciales está en situación de bloqueo si existe en él un conjunto de procesos que están indefinidamente esperando la liberación de ciertos recursos retenidos por miembros del mismo conjunto de procesos. En sistemas razonablemente complejos o distribuidos, establecer una política de asignación de recursos que sea libre de bloqueos puede ser un problema muy difícil de resolver de forma eficiente. En este sentido, los modelos formales, y particularmente las redes de Petri, se han ido afianzando como herramientas fructíferas que permiten abstraer el problema de asignación de recursos en este tipo de sistemas, con el fin de abordarlo analíticamente y proveer métodos eficientes para la correcta construcción o corrección de estos sistemas. En particular, la teoría estructural de redes de Petri se postula como un potente aliado para lidiar con el problema de la explosión de estados inherente a aquéllos. En este fértil contexto han florecido una serie de trabajos que defienden una propuesta metodológica de diseño orientada al estudio estructural y la correspondiente corrección física del problema de asignación de recursos en familias de sistemas muy significativas en determinados contextos de aplicación, como el de los Sistemas de Fabricación Flexible. Las clases de modelos de redes de Petri resultantes asumen ciertas restricciones, con significado físico en el contexto de aplicación para el que están destinadas, que alivian en buena medida la complejidad del problema. En la presente tesis, se intenta acercar ese tipo de aproximación metodológica al diseño de aplicaciones software multihilo libres de bloqueos. A tal efecto, se pone de manifiesto cómo aquellas restricciones procedentes del mundo de los Sistemas de Fabricación Flexible se muestran demasiado severas para aprehender la versatilidad inherente a los sistemas software en lo que respecta a la interacción de los procesos con los recursos compartidos. En particular, se han de resaltar dos necesidades de modelado fundamentales que obstaculizan la mera adopción de antiguas aproximaciones surgidas bajo el prisma de otros dominios: (1) la necesidad de soportar el anidamiento de bucles no desplegables en el interior de los procesos, y (2) la posible compartición de recursos no disponibles en el arranque del sistema pero que son creados o declarados por un proceso en ejecución. A resultas, se identifica una serie de requerimientos básicos para la definición de un tipo de modelos orientado al estudio de sistemas software multihilo y se presenta una clase de redes de Petri, llamada PC2R, que cumple dicha lista de requerimientos, manteniéndose a su vez respetuosa con la filosofía de diseño de anteriores subclases enfocadas a otros contextos de aplicación. Junto con la revisión e integración de anteriores resultados en el nuevo marco conceptual, se aborda el estudio de propiedades inherentes a los sistemas resultantes y su relación profunda con otros tipos de modelos, la confección de resultados y algoritmos eficientes para el análisis estructural de vivacidad en la nueva clase, así como la revisión y propuesta de métodos de resolución de los problemas de bloqueo adaptadas a las particularidades físicas del dominio de aplicación. Asimismo, se estudia la complejidad computacional de ciertas vertientes relacionadas con el problema de asignación de recursos en el nuevo contexto, así como la traslación de los resultados anteriormente mencionados sobre el dominio de la ingeniería de software multihilo, donde la nueva clase de redes permite afrontar problemas inabordables considerando el marco teórico y las herramientas suministradas para subclases anteriormente explotadas

Appearing Out of Nowhere: The Emergence of Spacetime in Quantum Gravity

Quantum gravity is understood as a theory that, in some sense, unifies general relativity (GR) and quantum theory, and is supposed to replace GR at extremely small distances (high-energies). It may be that quantum gravity represents the breakdown of spacetime geometry described by GR. The relationship between quantum gravity and spacetime has been deemed "emergence", and the aim of this thesis is to investigate and explicate this relation. After finding traditional philosophical accounts of emergence to be inappropriate, I develop a new conception of emergence by considering physical case studies including condensed matter physics, hydrodynamics, critical phenomena and quantum field theory understood as effective field theory. This new conception of emergence is independent of reduction and derivation. Instead, a low-energy theory is understood as emergent from a high-energy theory if it is novel and autonomous compared to the high-energy theory, and the low-energy physics is dependent (in a particular, minimal sense) on the high-energy physics (this dependence is revealed by the techniques of effective field theory and the renormalisation group). These ideas are important in exploring the relationship between quantum gravity and GR, where GR is understood as an effective, low-energy theory of quantum gravity. Without experimental data or a theory of quantum gravity, we rely on principles and techniques from other areas of physics to guide the way. As well as considering the idea of emergence appropriate to treating GR as an effective field theory, I investigate the emergence of spacetime (and other aspects of GR) in several concrete approaches to quantum gravity, including examples of the condensed matter approaches, the "discrete approaches" (causal set theory, causal dynamical triangulations, quantum causal histories and quantum graphity) and loop quantum gravity.Comment: PhD thesis submitted to the University of Sydne

Symmetric and efficient synthesis

Since the formulation of the synthesis problem for reactive systems by Church in the 60s, research on synthesis has lead to both theoretical insights and practical approaches for automatically constructing systems from their specifications. While the first solution of the problem was given by Büchi as early as 1969, only very recently, focus has shifted towards identifying ways to exploit the structure in reactive system specifications in order to lift the scalability of synthesis to industrial-sized designs. The recent progress in synthesis not only lead to a renewed interest in the subject, but also shed light onto the downsides of current synthesis approaches. In the original formulation of the problem, the structure of the produced solutions was not a concern. Experiments with current synthesis approaches has however shown that the computed implementations are usually very hard to understand and have little of the structure that manually constructed implementations have. Furthermore, the scalability of current synthesis approaches is still deemed to be insufficient for many industrial application scenarios, which prevents the introduction of reactive synthesis technology into industrial design flows. In this thesis, we tackle both of these problems for reactive synthesis. To counter the insufficient structure in the solutions, we analyse the problem of symmetric synthesis. In this alternative synthesis problem, the aim is to compute a solution that consists of multiple copies of the same process such that the overall system satisfies the specification. Such systems have no centralised control units, and are considered to be more robust and easier to maintain. We characterise undecidable and decidable cases of the problem, and provide a synthesis algorithm for rotation-symmetric architectures, which capture many cases of practical relevance. To improve the scalability in synthesis, we start with a simple but scalable approach to reactive synthesis that has shown its principal applicability in the field, and extend its main idea both in terms of scope and usability. We enhance its expressivity in a way that allows to synthesise robust systems, and remove its limitation to specifications of a very special form. Both improvements yield theoretical insights into the synthesis problem: we characterise which specification classes can be supported in synthesis approaches that use parity games with a fixed number of colours as the underlying computation model, and examine the properties of universal very-weak automata, on which we base a synthesis workflow that combines ease of specification with a low complexity of the underlying game solving step. As a side-result, we also obtain the first procedure to translate a formula in linear-time temporal logic (LTL) to a computation tree logic (CTL) formula with only universal path quantifiers, whenever possible. The new results on symmetric and efficient reactive synthesis are complemented by an easily accessible introductory chapter to the field of reactive synthesis that can also be read in isolation.paddle apparatus with membrane holder were identified.Trotz der Vorzüge der Synthese reaktiver Systeme gegenüber der manuellen Konstruktion solcher Systeme ist Synthese noch nicht als Teil industrieller Vorgehensmodelle etabliert. Als Hauptgrund für diese Diskrepanz gilt allgemein, dass sowohl die Qualität der synthetisierten Systeme bei Anwendung bisheriger Methoden unzureichend ist, als auch die Skalierbarkeit aktueller Syntheseverfahren der Verbesserung bedarf. Diese Dissertation behandelt beide diese Probleme der Synthese reaktiver Systeme auf breiter Front. Zur Verbesserung der Qualität synthetisierter Systeme wird die Synthese von strukturierten Systemen betrachtet. Experimente mit aktuellen Syntheseverfahren haben gezeigt, dass die erzeugten Implementierungen oft schwer zu verstehen sind und anders als handgeschriebene Implementierungen kaum Struktur haben. Abhilfe verschafft die Beschränkung auf die Erzeugung symmetrischer Systeme, die aus mehreren Kopien des selben Prozesses bestehen, so dass das Gesamtsystem die Spezifikation erfüllt. Solche Systeme haben keine zentrale Koordinationskomponente und werden allgemein als robuster und einfacher zu warten eingestuft. In dieser Dissertation werden entscheidbare und unentscheidbare Fälle des symmetrischen Syntheseproblems identifiziert und ein Synthesealgorithmus für rotationssymmetrische Systeme beschrieben. Diese Systemklasse deckt viele praktisch relevante Architekturen ab. Um das Problem der mangelnden Skalierbarkeit anzugehen, wird die Hauptidee des Generalised Reactivity(1) Syntheseansatzes, welcher seine praktische Anwendbarkeit bereits unter Beweis gestellt hat, aufgegriffen und sowohl bezüglich der Expressivität als auch der Benutzbarkeit vervollständigt. Die Erweiterung der Expressivität ermöglicht es, den resultierenden Ansatz für die Synthese robuster Systeme zu nutzen, während die Benutzbarkeit für industrielle Anwendungen durch die Aufhebung der Beschränkung, dass die Spezifikation eine sehr spezielle Form haben muss, erreicht wird. Beide Erweiterungen geben Einsicht in die Theorie der Synthese: Zum einen wird die Klasse der Spezifikationen, die in Syntheseansätzen verwendet werden können, die auf dem Lösen von Paritätsspielen mit einer vordefinierten Anzahl von Farben basieren, charakterisiert. Zum anderen wird Einsicht in die Eigenschaften universeller sehr schwacher Automaten gegeben. Ein Nebenprodukt der neuen Syntheseverfahren ist die erste Prozedur, um einen Ausdruck in linear-time temporal logic (LTL) in computation tree logic mit universellen Pfadquantoren (ACTL) zu übersetzen, wann immer dies möglich ist. Die Resultate zur symmetrischen und effizienten reaktiven Synthese werden von einer didaktisch aufbereiteten Einführung in das Gebiet der reaktiven Synthese begleitet, welche auch unabhängig von den übrigen Teilen der Dissertation gelesen werden kann

Synthesis of Event-Based Controllers for Software Engineering

Behavioural modelling has been widely used to aid in the design of concurrent systems. Behaviour models have shown to be useful to uncover design errors in early stages of the development process. However, building correct behaviour models is costly and requires significant experience. Controller synthesis offers a way to build models that are correct by construction. Existing software engineering techniques for synthesising controllers have various limitations. Such limitations can be seen as restrictions in the expressiveness of the controller goals and environment model, or in the relation between the controllable and monitored actions. The main aim of this thesis is the development of novel techniques overcoming known limitations of previous approaches and methodological guidelines for synthesising useful controllers. This thesis establishes the framework for controller synthesis techniques that support event-based models, expressive goal specifications, distinguish controllable from monitored actions and guarantee achievement of the desired goals. Together with these techniques, methodological guidelines are proposed to help in building more accurate descriptions of the environment and more effective controllers. In addition, this thesis presents a tool that implements the proposed techniques. Evaluation of the techniques has been conducted using the tool to model known case studies from the literature, showing that by allowing more expressive controller goals and environment models, and explicitly distinguishing controllable and monitored actions such case studies can be more accurately modelled and solutions guaranteeing satisfaction of the goals can be achieved

Foundations of Software Science and Computation Structures

This open access book constitutes the proceedings of the 23rd International Conference on Foundations of Software Science and Computational Structures, FOSSACS 2020, which took place in Dublin, Ireland, in April 2020, and was held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020. The 31 regular papers presented in this volume were carefully reviewed and selected from 98 submissions. The papers cover topics such as categorical models and logics; language theory, automata, and games; modal, spatial, and temporal logics; type theory and proof theory; concurrency theory and process calculi; rewriting theory; semantics of programming languages; program analysis, correctness, transformation, and verification; logics of programming; software specification and refinement; models of concurrent, reactive, stochastic, distributed, hybrid, and mobile systems; emerging models of computation; logical aspects of computational complexity; models of software security; and logical foundations of data bases.