Applied Visual Anthropology

We study a new partial order semantics of Petri nets with read arcs, where read arcs model reading without consuming, which is often more adequate than the destructive-read-and-rewrite modelled in ordinary nets. As basic observations we take ST-traces, which are sequences of transition starts and ends. We define processes of our nets and derive two partial orders modelling causality and start precedence. These partial orders are related to observations and system states just as in the ordinary approach the single partial order of a process is related to firing sequences and reachable markings. Our approach also supports a new view of concurrency as captured by steps. 1 Introduction Describing the runs of a concurrent system by sequences of actions ignores the possible concurrency of these actions, which can be important e.g. for judging the temporal efficiency of the system. Alternatively to this so-called interleaving approach, one can take step sequences, where a step consists of si..

Two Algebraic Process Semantics for Contextual Nets

We show that the so-called 'Petri nets are monoids' approach initiated by Meseguer and Montanari can be extended from ordinary place/transition Petri nets to contextual nets by considering suitable non-free monoids of places. The algebraic characterizations of net concurrent computations we provide cover both the collective and the individual token philosophy, uniformly along the two interpretations, and coincide with the classical proposals for place/transition Petri nets in the absence of read-arcs

Algebraic Models for Contextual Nets

We extend the algebraic approach of Meseguer and Montanari from ordinary place/transition Petri nets to contextual nets, covering both the collective and the individual token philosophy uniformly along the two interpretations of net behaviors

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Encoding Higher Level Extensions of Petri Nets in Answer Set Programming

Answering realistic questions about biological systems and pathways similar to the ones used by text books to test understanding of students about biological systems is one of our long term research goals. Often these questions require simulation based reasoning. To answer such questions, we need formalisms to build pathway models, add extensions, simulate, and reason with them. We chose Petri Nets and Answer Set Programming (ASP) as suitable formalisms, since Petri Net models are similar to biological pathway diagrams; and ASP provides easy extension and strong reasoning abilities. We found that certain aspects of biological pathways, such as locations and substance types, cannot be represented succinctly using regular Petri Nets. As a result, we need higher level constructs like colored tokens. In this paper, we show how Petri Nets with colored tokens can be encoded in ASP in an intuitive manner, how additional Petri Net extensions can be added by making small code changes, and how this work furthers our long term research goals. Our approach can be adapted to other domains with similar modeling needs

Read Operators and their Expressiveness in Process Algebras

We study two different ways to enhance PAFAS, a process algebra for modelling asynchronous timed concurrent systems, with non-blocking reading actions. We first add reading in the form of a read-action prefix operator. This operator is very flexible, but its somewhat complex semantics requires two types of transition relations. We also present a read-set prefix operator with a simpler semantics, but with syntactic restrictions. We discuss the expressiveness of read prefixes; in particular, we compare them to read-arcs in Petri nets and justify the simple semantics of the second variant by showing that its processes can be translated into processes of the first with timed-bisimilar behaviour. It is still an open problem whether the first algebra is more expressive than the second; we give a number of laws that are interesting in their own right, and can help to find a backward translation.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407

Size-Change Termination as a Contract

Termination is an important but undecidable program property, which has led to a large body of work on static methods for conservatively predicting or enforcing termination. One such method is the size-change termination approach of Lee, Jones, and Ben-Amram, which operates in two phases: (1) abstract programs into "size-change graphs," and (2) check these graphs for the size-change property: the existence of paths that lead to infinite decreasing sequences. We transpose these two phases with an operational semantics that accounts for the run-time enforcement of the size-change property, postponing (or entirely avoiding) program abstraction. This choice has two key consequences: (1) size-change termination can be checked at run-time and (2) termination can be rephrased as a safety property analyzed using existing methods for systematic abstraction. We formulate run-time size-change checks as contracts in the style of Findler and Felleisen. The result compliments existing contracts that enforce partial correctness specifications to obtain contracts for total correctness. Our approach combines the robustness of the size-change principle for termination with the precise information available at run-time. It has tunable overhead and can check for nontermination without the conservativeness necessary in static checking. To obtain a sound and computable termination analysis, we apply existing abstract interpretation techniques directly to the operational semantics, avoiding the need for custom abstractions for termination. The resulting analyzer is competitive with with existing, purpose-built analyzers

A Formal Framework for Linguistic Annotation

`Linguistic annotation' covers any descriptive or analytic notations applied to raw language data. The basic data may be in the form of time functions -- audio, video and/or physiological recordings -- or it may be textual. The added notations may include transcriptions of all sorts (from phonetic features to discourse structures), part-of-speech and sense tagging, syntactic analysis, `named entity' identification, co-reference annotation, and so on. While there are several ongoing efforts to provide formats and tools for such annotations and to publish annotated linguistic databases, the lack of widely accepted standards is becoming a critical problem. Proposed standards, to the extent they exist, have focussed on file formats. This paper focuses instead on the logical structure of linguistic annotations. We survey a wide variety of existing annotation formats and demonstrate a common conceptual core, the annotation graph. This provides a formal framework for constructing, maintaining and searching linguistic annotations, while remaining consistent with many alternative data structures and file formats.Comment: 49 page