9,248 research outputs found
Ten virtues of structured graphs
This paper extends the invited talk by the first author about the virtues
of structured graphs. The motivation behind the talk and this paper relies on our
experience on the development of ADR, a formal approach for the design of styleconformant,
reconfigurable software systems. ADR is based on hierarchical graphs
with interfaces and it has been conceived in the attempt of reconciling software architectures
and process calculi by means of graphical methods. We have tried to
write an ADR agnostic paper where we raise some drawbacks of flat, unstructured
graphs for the design and analysis of software systems and we argue that hierarchical,
structured graphs can alleviate such drawbacks
Modeling and Reasoning over Distributed Systems using Aspect-Oriented Graph Grammars
Aspect-orientation is a relatively new paradigm that introduces abstractions
to modularize the implementation of system-wide policies. It is based on a
composition operation, called aspect weaving, that implicitly modifies a base
system by performing related changes within the system modules. Aspect-oriented
graph grammars (AOGG) extend the classic graph grammar formalism by defining
aspects as sets of rule-based modifications over a base graph grammar. Despite
the advantages of aspect-oriented concepts regarding modularity, the implicit
nature of the aspect weaving operation may also introduce issues when reasoning
about the system behavior. Since in AOGGs aspect weaving is characterized by
means of rule-based rewriting, we can overcome these problems by using known
analysis techniques from the graph transformation literature to study aspect
composition. In this paper, we present a case study of a distributed
client-server system with global policies, modeled as an aspect-oriented graph
grammar, and discuss how to use the AGG tool to identify potential conflicts in
aspect weaving
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
Modeling molecules as undirected graphs and chemical reactions as graph
rewriting operations is a natural and convenient approach tom odeling
chemistry. Graph grammar rules are most naturally employed to model elementary
reactions like merging, splitting, and isomerisation of molecules. It is often
convenient, in particular in the analysis of larger systems, to summarize
several subsequent reactions into a single composite chemical reaction. We use
a generic approach for composing graph grammar rules to define a chemically
useful rule compositions. We iteratively apply these rule compositions to
elementary transformations in order to automatically infer complex
transformation patterns. This is useful for instance to understand the net
effect of complex catalytic cycles such as the Formose reaction. The
automatically inferred graph grammar rule is a generic representative that also
covers the overall reaction pattern of the Formose cycle, namely two carbonyl
groups that can react with a bound glycolaldehyde to a second glycolaldehyde.
Rule composition also can be used to study polymerization reactions as well as
more complicated iterative reaction schemes. Terpenes and the polyketides, for
instance, form two naturally occurring classes of compounds of utmost
pharmaceutical interest that can be understood as "generalized polymers"
consisting of five-carbon (isoprene) and two-carbon units, respectively
Generic Strategies for Chemical Space Exploration
Computational approaches to exploring "chemical universes", i.e., very large
sets, potentially infinite sets of compounds that can be constructed by a
prescribed collection of reaction mechanisms, in practice suffer from a
combinatorial explosion. It quickly becomes impossible to test, for all pairs
of compounds in a rapidly growing network, whether they can react with each
other. More sophisticated and efficient strategies are therefore required to
construct very large chemical reaction networks.
Undirected labeled graphs and graph rewriting are natural models of chemical
compounds and chemical reactions. Borrowing the idea of partial evaluation from
functional programming, we introduce partial applications of rewrite rules.
Binding substrate to rules increases the number of rules but drastically prunes
the substrate sets to which it might match, resulting in dramatically reduced
resource requirements. At the same time, exploration strategies can be guided,
e.g. based on restrictions on the product molecules to avoid the explicit
enumeration of very unlikely compounds. To this end we introduce here a generic
framework for the specification of exploration strategies in graph-rewriting
systems. Using key examples of complex chemical networks from sugar chemistry
and the realm of metabolic networks we demonstrate the feasibility of a
high-level strategy framework.
The ideas presented here can not only be used for a strategy-based chemical
space exploration that has close correspondence of experimental results, but
are much more general. In particular, the framework can be used to emulate
higher-level transformation models such as illustrated in a small puzzle game
Graphical Encoding of a Spatial Logic for the pi-Calculus
This paper extends our graph-based approach to the verification of spatial properties of Ļ-calculus specifications. The mechanism is based on an encoding for mobile calculi where each process is mapped into a graph (with interfaces) such that the denotation is fully abstract with respect to the usual structural congruence, i.e., two processes are equivalent exactly when the corresponding encodings yield isomorphic graphs. Behavioral and structural properties of Ļ-calculus processes expressed in a spatial logic can then be verified on the graphical encoding of a process rather than on its textual representation. In this paper we introduce a modal logic for graphs and define a translation of spatial formulae such that a process verifies a spatial formula exactly when its graphical representation verifies the translated modal graph formula
Multiple Context-Free Tree Grammars: Lexicalization and Characterization
Multiple (simple) context-free tree grammars are investigated, where "simple"
means "linear and nondeleting". Every multiple context-free tree grammar that
is finitely ambiguous can be lexicalized; i.e., it can be transformed into an
equivalent one (generating the same tree language) in which each rule of the
grammar contains a lexical symbol. Due to this transformation, the rank of the
nonterminals increases at most by 1, and the multiplicity (or fan-out) of the
grammar increases at most by the maximal rank of the lexical symbols; in
particular, the multiplicity does not increase when all lexical symbols have
rank 0. Multiple context-free tree grammars have the same tree generating power
as multi-component tree adjoining grammars (provided the latter can use a
root-marker). Moreover, every multi-component tree adjoining grammar that is
finitely ambiguous can be lexicalized. Multiple context-free tree grammars have
the same string generating power as multiple context-free (string) grammars and
polynomial time parsing algorithms. A tree language can be generated by a
multiple context-free tree grammar if and only if it is the image of a regular
tree language under a deterministic finite-copying macro tree transducer.
Multiple context-free tree grammars can be used as a synchronous translation
device.Comment: 78 pages, 13 figure
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