127 research outputs found
Variable binding, symmetric monoidal closed theories, and bigraphs
This paper investigates the use of symmetric monoidal closed (SMC) structure
for representing syntax with variable binding, in particular for languages with
linear aspects. In our setting, one first specifies an SMC theory T, which may
express binding operations, in a way reminiscent from higher-order abstract
syntax. This theory generates an SMC category S(T) whose morphisms are, in a
sense, terms in the desired syntax. We apply our approach to Jensen and
Milner's (abstract binding) bigraphs, which are linear w.r.t. processes. This
leads to an alternative category of bigraphs, which we compare to the original.Comment: An introduction to two more technical previous preprints. Accepted at
Concur '0
Spatial Logics for Bigraphs
Bigraphs are emerging as an interesting model for concurrent calculi, like CCS, pi-calculus, and Petri nets. Bigraphs are built orthogonally on two structures: a hierarchical place graph for locations and a link (hyper-)graph for connections. With the aim of describing bigraphical structures, we introduce a general framework for logics whose terms represent arrows in monoidal categories. We then instantiate the framework to bigraphical structures and obtain a logic that is a natural composition of a place graph logic and a link graph logic. We explore the concepts of separation and sharing in these logics and we prove that they generalise some known spatial logics for trees, graphs and tree contexts
Bigraphical models for protein and membrane interactions
We present a bigraphical framework suited for modeling biological systems
both at protein level and at membrane level. We characterize formally bigraphs
corresponding to biologically meaningful systems, and bigraphic rewriting rules
representing biologically admissible interactions. At the protein level, these
bigraphic reactive systems correspond exactly to systems of kappa-calculus.
Membrane-level interactions are represented by just two general rules, whose
application can be triggered by protein-level interactions in a well-de\"ined
and precise way. This framework can be used to compare and merge models at
different abstraction levels; in particular, higher-level (e.g. mobility)
activities can be given a formal biological justification in terms of low-level
(i.e., protein) interactions. As examples, we formalize in our framework the
vesiculation and the phagocytosis processes
Modelling IEEE 802.11 CSMA/CA RTS/CTS with stochastic bigraphs with sharing
Stochastic bigraphical reactive systems (SBRS) is a recent formalism for modelling systems that evolve
in time and space. However, the underlying spatial model is based on sets of trees and thus cannot represent
spatial locations that are shared among several entities in a simple or intuitive way. We adopt an extension of
the formalism, SBRS with sharing, in which the topology is modelled by a directed acyclic graph structure. We
give an overview of SBRS with sharing, we extend it with rule priorities, and then use it to develop a model
of the 802.11 CSMA/CA RTS/CTS protocol with exponential backoff, for an arbitrary network topology with
possibly overlapping signals. The model uses sharing to model overlapping connectedness areas, instantaneous
prioritised rules for deterministic computations, and stochastic rules with exponential reaction rates to model
constant and uniformly distributed timeouts and constant transmission times. Equivalence classes of model states
modulo instantaneous reactions yield states in a CTMC that can be analysed using the model checker PRISM.
We illustrate the model on a simple example wireless network with three overlapping signals and we present some
example quantitative properties
Bigraphs with sharing
Bigraphical Reactive Systems (BRS) were designed by Milner as a universal formalism for modelling systems that evolve in time, locality, co-locality and connectivity. But the underlying model of location (the place graph) is a forest, which means there is no straightforward representation of locations that can overlap or intersect. This occurs in many domains, for example in wireless signalling, social interactions and audio communications. Here, we define bigraphs with sharing, which solves this problem by an extension of the basic formalism: we define the place graph as a directed acyclic graph, thus allowing a natural representation of overlapping or intersecting locations. We give a complete presentation of the theory of bigraphs with sharing, including a categorical semantics, algebraic properties, and several essential procedures for computation: bigraph with sharing matching, a SAT encoding of matching, and checking a fragment of the logic BiLog. We show that matching is an instance of the NP-complete sub-graph isomorphism problem and our approach based on a SAT encoding is also efficient for standard bigraphs. We give an overview of BigraphER (Bigraph Evaluator & Rewriting), an efficient implementation of bigraphs with sharing that provides manipulation, simulation and visualisation. The matching engine is based on the SAT encoding of the matching algorithm. Examples from the 802.11 CSMA/CA RTS/CTS protocol and a network management support system illustrate the applicability of the new theory
Fuzzy Bigraphs: An Exercise in Fuzzy Communicating Agents
Bigraphs and their algebra is a model of concurrency. Fuzzy bigraphs are a
generalization of birgraphs intended to be a model of concurrency that
incorporates vagueness. More specifically, this model assumes that agents are
similar, communication is not perfect, and, in general, everything is or
happens to some degree.Comment: 11 pages, 3 figure
A framework for protein and membrane interactions
We introduce the BioBeta Framework, a meta-model for both protein-level and
membrane-level interactions of living cells. This formalism aims to provide a
formal setting where to encode, compare and merge models at different
abstraction levels; in particular, higher-level (e.g. membrane) activities can
be given a formal biological justification in terms of low-level (i.e.,
protein) interactions. A BioBeta specification provides a protein signature
together a set of protein reactions, in the spirit of the kappa-calculus.
Moreover, the specification describes when a protein configuration triggers one
of the only two membrane interaction allowed, that is "pinch" and "fuse". In
this paper we define the syntax and semantics of BioBeta, analyse its
properties, give it an interpretation as biobigraphical reactive systems, and
discuss its expressivity by comparing with kappa-calculus and modelling
significant examples. Notably, BioBeta has been designed after a bigraphical
metamodel for the same purposes. Hence, each instance of the calculus
corresponds to a bigraphical reactive system, and vice versa (almost).
Therefore, we can inherith the rich theory of bigraphs, such as the automatic
construction of labelled transition systems and behavioural congruences
On the Construction of Sorted Reactive Systems
We develop a theory of sorted bigraphical reactive systems. Every application of bigraphs in the literature has required an extension, a sorting, of pure bigraphs. In turn, every such application has required a redevelopment of the theory of pure bigraphical reactive systems for the sorting at hand. Here we present a general construction of sortings. The constructed sortings always sustain the behavioural theory of pure bigraphs (in a precise sense), thus obviating the need to redevelop that theory for each new application. As an example, we recover Milner’s local bigraphs as a sorting on pure bigraphs. Technically, we give our construction for ordinary reactive systems, then lift it to bigraphical reactive systems. As such, we give also a construction of sortings for ordinary reactive systems. This construction is an improvement over previous attempts in that it produces smaller and much more natural sortings, as witnessed by our recovery of local bigraphs as a sorting
Binding bigraphs as symmetric monoidal closed theories
Milner's bigraphs are a general framework for reasoning about distributed and
concurrent programming languages. Notably, it has been designed to encompass
both the pi-calculus and the Ambient calculus. This paper is only concerned
with bigraphical syntax: given what we here call a bigraphical signature K,
Milner constructs a (pre-) category of bigraphs BBig(K), whose main features
are (1) the presence of relative pushouts (RPOs), which makes them well-behaved
w.r.t. bisimulations, and that (2) the so-called structural equations become
equalities. Examples of the latter include, e.g., in pi and Ambient, renaming
of bound variables, associativity and commutativity of parallel composition, or
scope extrusion for restricted names. Also, bigraphs follow a scoping
discipline ensuring that, roughly, bound variables never escape their scope.
Here, we reconstruct bigraphs using a standard categorical tool: symmetric
monoidal closed (SMC) theories. Our theory enforces the same scoping discipline
as bigraphs, as a direct property of SMC structure. Furthermore, it elucidates
the slightly mysterious status of so-called links in bigraphs. Finally, our
category is also considerably larger than the category of bigraphs, notably
encompassing in the same framework terms and a flexible form of higher-order
contexts.Comment: 17 pages, uses Paul Taylor's diagram
Reactive Systems over Cospans
The theory of reactive systems, introduced by Leifer and Milner and previously extended by the authors, allows the derivation of well-behaved labelled transition systems (LTS) for semantic models with an underlying reduction semantics. The derivation procedure requires the presence of certain colimits (or, more usually and generally, bicolimits) which need to be constructed separately within each model. In this paper, we offer a general construction of such bicolimits in a class of bicategories of cospans. The construction sheds light on as well as extends Ehrig and Konig’s rewriting via borrowed contexts and opens the way to a unified treatment of several applications
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