In this paper, we present a rewriting framework for modeling molecular complexes, biochemical reaction rules and generation of biochemical networks based on the representation of molecular complexes as a particular type of multigraphs with ports called molecular graphs. The advantage of this approach is to obtain for free a rewriting calculus which allows defining at the same level transformati...

Update propagation in deductive databases can be implemented by combining rule rewriting and fixpoint computation, analogous to the way how query answering is performed via Magic Sets. For efficiency reasons, bottom-up propagation rules have to be subject to Magic rewriting, thus possibly loosing stratifiability. We propose to use the soft stratification approach for computing the well-founded ...

Protein molecules adopt a specific global 3D structure in order to carry out their biological function. To achieve this native state a newly formed protein molecule has to fold. The folding process and the final fold are both determined by the sequence of amino acids making up the protein chain. It is not currently possible to predict the conformation of the native state from the amino acid seq...

Jungle evaluation is an approach to deene term rewriting with sharing based on graph grammars. This approach preserves important properties of term rewriting like termination, and connuence for terminating systems (under mild restrictions). In this paper, term rewriting with sharing is further accelerated, by memo zation known from functional programming languages: The result of evaluating a fu...

Rippling is a special type of rewriting which uses annotations to guide the derivation towards a particular goal. It has many desirable properties. For example, it terminates yet allows rules like associativity to be used in both directions; it is also highly goal-directed applying only those rewrite rules needed to remove the diierences between the goal and some hypothesis. Although it has bee...

Constructor rewriting systems are said to be cons-free if, roughly, constructor terms in the righthand sides of rules are subterms of constructor terms in the left-hand side; the computational intuition is that rules cannot build new data structures. It is well-known that cons-free programming languages can be used to characterize computational complexity classes, and that cons-free first-order...

Past proposals for applying to pictures or 2D languages the generative grammar approach do not match in our opinion the elegance and descriptive adequacy that made Context Free grammars so successful for 1D languages. In a renewed attempt, a model named Tile Rewriting Grammar is introduced combining the rewriting rules with the Tiling System of Giammaresi and Restivo which define the family of ...

Programming language semantics based on pure rewrite rules suffers from the gap between the rewriting strategy implemented in rewriting engines and the intended evaluation strategy. This paper shows how programmable rewriting strategies can be used to implement interpreters for programming languages based on rewrite rules. The advantage of this approach is that reduction rules are first class e...

We propose a dynamic graph-based relational learning approach using graph-rewriting rules to analyze how biological networks change over time. The analysis of dynamic biological networks is necessary to understand life at the systemlevel, because biological networks continuously change their structures and properties while an organism performs various biological activities to promote reproducti...

This chapter presents a simple yet efficient approach to translate automatically unknown biomedical terms from one language into another. This approach relies on a machine learning process able to infer rewriting rules from examples, that is, from a list of paired terms in two studied languages. Any new term is then simply translated by applying the rewriting rules to it. When different transla...