Introducing the Concept of Activation and Blocking of Rules in the General Framework for Regulated Rewriting in Sequential Grammars

We introduce new possibilities to control the application of rules based on the preceding application of rules which can be de ned for a general model of sequential grammars and we show some similarities to other control mechanisms as graph-controlled grammars and matrix grammars with and without applicability checking as well as gram- mars with random context conditions and ordered grammars. Using both activation and blocking of rules, in the string and in the multiset case we can show computational com- pleteness of context-free grammars equipped with the control mechanism of activation and blocking of rules even when using only two nonterminal symbols

A Reformulation of Matrix Graph Grammars with Boolean Complexes

Prior publication in the Electronic Journal of Combinatorics.Graph transformation is concerned with the manipulation of graphs by means of rules. Graph grammars have been traditionally studied using techniques from category theory. In previous works, we introduced Matrix Graph Grammars (MGG) as a purely algebraic approach for the study of graph dynamics, based on the representation of simple graphs by means of their adjacency matrices. The observation that, in addition to positive information, a rule implicitly defines negative conditions for its application (edges cannot become dangling, and cannot be added twice as we work with simple digraphs) has led to a representation of graphs as two matrices encoding positive and negative information. Using this representation, we have reformulated the main concepts in MGGs, while we have introduced other new ideas. In particular, we present (i) a new formulation of productions together with an abstraction of them (so called swaps), (ii) the notion of coherence, which checks whether a production sequence can be potentially applied, (iii) the minimal graph enabling the applicability of a sequence, and (iv) the conditions for compatibility of sequences (lack of dangling edges) and G-congruence (whether two sequences have the same minimal initial graph).This work has been partially sponsored by the Spanish Ministry of Science and Innovation, project METEORIC (TIN2008-02081/TIN)

Graph Transformations and Game Theory: A Generative Mechanism for Network Formation

Many systems can be described in terms of networks with characteristic structural properties. To better understand the formation and the dynamics of complex networks one can develop generative models. We propose here a generative model (named dynamic spatial game) that combines graph transformations and game theory. The idea is that a complex network is obtained by a sequence of node-based transformations determined by the interactions of nodes present in the network. We model the node-based transformations by using graph grammars and the interactions between the nodes by using game theory. We illustrate dynamic spatial games on a couple of examples: the role of cooperation in tissue formation and tumor development and the emergence of patterns during the formation of ecological networks

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

Grammars and cellular automata for evolving neural networks architectures

IEEE International Conference on Systems, Man, and Cybernetics. Nashville, TN, 8-11 October 2000The class of feedforward neural networks trained with back-propagation admits a large variety of specific architectures applicable to approximation pattern tasks. Unfortunately, the architecture design is still a human expert job. In recent years, the interest to develop automatic methods to determine the architecture of the feedforward neural network has increased, most of them based on the evolutionary computation paradigm. From this approach, some perspectives can be considered: at one extreme, every connection and node of architecture can be specified in the chromosome representation using binary bits. This kind of representation scheme is called the direct encoding scheme. In order to reduce the length of the genotype and the search space, and to make the problem more scalable, indirect encoding schemes have been introduced. An indirect scheme under a constructive algorithm, on the other hand, starts with a minimal architecture and new levels, neurons and connections are added, step by step, via some sets of rules. The rules and/or some initial conditions are codified into a chromosome of a genetic algorithm. In this work, two indirect constructive encoding schemes based on grammars and cellular automata, respectively, are proposed to find the optimal architecture of a feedforward neural network

Exploiting lattice structures in shape grammar implementations

The ability to work with ambiguity and compute new designs based on both defined and emergent shapes are unique advantages of shape grammars. Realizing these benefits in design practice requires the implementation of general purpose shape grammar interpreters that support: (a) the detection of arbitrary subshapes in arbitrary shapes and (b) the application of shape rules that use these subshapes to create new shapes. The complexity of currently available interpreters results from their combination of shape computation (for subshape detection and the application of rules) with computational geometry (for the geometric operations need to generate new shapes). This paper proposes a shape grammar implementation method for three-dimensional circular arcs represented as rational quadratic Bézier curves based on lattice theory that reduces this complexity by separating steps in a shape computation process from the geometrical operations associated with specific grammars and shapes. The method is demonstrated through application to two well-known shape grammars: Stiny's triangles grammar and Jowers and Earl's trefoil grammar. A prototype computer implementation of an interpreter kernel has been built and its application to both grammars is presented. The use of Bézier curves in three dimensions opens the possibility to extend shape grammar implementations to cover the wider range of applications that are needed before practical implementations for use in real life product design and development processes become feasible