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GrGen: A fast SPObased graph rewriting tool
 GRAPH TRANSFORMATIONS  ICGT 2006. LECTURE NOTES IN COMPUTER SCIENCE, SPRINGER (2006) 383 – 397
, 2006
"... Graph rewriting is a powerful technique that requires graph pattern matching, which is an NPcomplete problem. We present GrGen, a generative programming system for graph rewriting, which applies heuristic optimizations. According to Varró’s benchmark it is at least one order of magnitude faster th ..."
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Cited by 48 (7 self)
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Graph rewriting is a powerful technique that requires graph pattern matching, which is an NPcomplete problem. We present GrGen, a generative programming system for graph rewriting, which applies heuristic optimizations. According to Varró’s benchmark it is at least one order of magnitude faster than any other tool known to us. Our graph rewriting tool implements the wellfounded singlepushout approach. We define the notion of search plans to represent different matching strategies and equip these search plans with a cost model, taking the present host graph into account. The task of selecting a good search plan is then viewed as an optimization problem. For the ease of use, GrGen features an expressive specification language and generates program code with a convenient interface.
Graphical Definition of InPlace Transformations in the Eclipse Modeling Framework
 In 9th Int. Conf. on Model Driven Engineering Languages and Systems, MoDELS’06, volume 4199 of LNCS
, 2006
"... Abstract. The Eclipse Modeling Framework (EMF) provides a modeling and code generation framework for Eclipse applications based on structured data models. Although EMF provides basic operations for modifying EMF based models, a framework for graphical definition of rulebased modification of EMF mo ..."
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Cited by 38 (14 self)
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Abstract. The Eclipse Modeling Framework (EMF) provides a modeling and code generation framework for Eclipse applications based on structured data models. Although EMF provides basic operations for modifying EMF based models, a framework for graphical definition of rulebased modification of EMF models is still missing. In this paper we present a framework for inplace EMF model transformation based on graph transformation. Transformations are visually defined by rules on object patterns typed over an EMF core model. Defined transformation systems can be compiled to Java code building up on generated EMF classes. As running example different refactoring methods for Ecore models are considered. 1
Extensions of Simple Conceptual Graphs: the Complexity of Rules and Constraints
 JOUR. OF ARTIF. INTELL. RES
, 2002
"... Simple conceptual graphs are considered as the kernel of most knowledge representation formalisms built upon $owa's model. Reasoning in this model can be expressed by a graph homomorphism called projection, whose semantics is usually given in terms of positive, conjunctive, existential FOL. ..."
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Cited by 27 (1 self)
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Simple conceptual graphs are considered as the kernel of most knowledge representation formalisms built upon $owa's model. Reasoning in this model can be expressed by a graph homomorphism called projection, whose semantics is usually given in terms of positive, conjunctive, existential FOL. We present here a family of extensions of this model, based on rules and constraints, keeping graph homomorphism as the basic operation. We focus on the formal definitions of the different models obtained, including their operational semantics and relationships with FOL, and we analyze the decidability and complexity of the associated problems (consistency and deduction). As soon as rules are involved in reasonings, these problems are not decidable, but we exhibit a condition under which they fall in the polynomial hierarchy. These results extend and complete the ones already published by the authors. Moreover we systematically study the complexity of some particular cases obtained by restricting the form of constraints and/or rules.
Constrained Path Finding in Biochemical Networks
 IN 5ÈMES JOURNÉES OUVERTES BIOLOGIE INFORMATIQUE MATHÉMATIQUES
, 2004
"... The analysis of biochemical networks is mainly done using relational or procedural languages. Combining ..."
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Cited by 9 (6 self)
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The analysis of biochemical networks is mainly done using relational or procedural languages. Combining
P.: Filtering for Subgraph Isomorphism
 In: CP 2007. LNCS 4741
, 2007
"... Abstract. A subgraph isomorphism problem consists in deciding if there exists a copy of a pattern graph in a target graph. We introduce in this paper a filtering algorithm dedicated to this problem. The main idea is to label every node with respect to its relationships with other nodes of the graph, ..."
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Cited by 7 (4 self)
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Abstract. A subgraph isomorphism problem consists in deciding if there exists a copy of a pattern graph in a target graph. We introduce in this paper a filtering algorithm dedicated to this problem. The main idea is to label every node with respect to its relationships with other nodes of the graph, and to define a partial order on these labels in order to express compatibility of labels for subgraph isomorphism. This partial order over labels is used to filter domains. Labelings can also be strengthened by adding information from the labels of the neighbors. Such a strengthening can be applied iteratively until a fixpoint is reached. Practical experiments illustrate that our new filtering approach is more effective on difficult instances of scale free graphs than stateoftheart algorithms and other CP approaches. 1
The graph grammar library  a generic framework for chemical graph rewrite systems
 Theory and Practice of Model Transformations, Proc. of ICMT 2013, volume 7909 of LNCS
, 2013
"... Abstract. Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is available at the moment. The presented Graph Gramma ..."
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Cited by 6 (3 self)
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Abstract. Graph rewrite systems are powerful tools to model and study complex problems in various fields of research. Their successful application to chemical reaction modelling on a molecular level was shown but no appropriate and simple system is available at the moment. The presented Graph Grammar Library (GGL) implements a generic Double Push Out approach for general graph rewrite systems. The framework focuses on a high level of modularity as well as high performance, using stateoftheart algorithms and data structures, and comes with extensive documentation. The large GGL chemistry module enables extensive and detailed studies of chemical systems. It well meets the requirements and abilities envisioned by Yadav et al. (2004) for such chemical rewrite systems. Here, molecules are represented as undirected labeled graphs while chemical reactions are described by according graph grammar rules. Beside the graph transformation, the GGL offers advanced cheminformatics algorithms for instance to estimate energies ofmolecules or aromaticity perception. These features are illustrated using a set of reactions from polyketide chemistry a huge class of natural compounds of medical relevance. The graph grammar based simulation of chemical reactions offered by the GGL is a powerful tool for extensive cheminformatics studies on a molecular level. The GGL already provides rewrite rules for all enzymes listed in the KEGG LIGAND database is freely available at
Augur 2  a new version of a tool for the analysis of graph transformation systems
 IN PROC. WORKSHOP ON GRAPH TRANSFORMATION AND VISUAL MODELING TECHNIQUES (GTVMT’06), ENTCS
, 2006
"... We describe the design and the present state of the verification tool Augur 2 which is currently being developed. It is based on Augur 1, a tool which can analyze graph transformation systems by approximating them by Petri nets. The main reason for the new development was to create an open, flexible ..."
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Cited by 6 (0 self)
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We describe the design and the present state of the verification tool Augur 2 which is currently being developed. It is based on Augur 1, a tool which can analyze graph transformation systems by approximating them by Petri nets. The main reason for the new development was to create an open, flexible and extensible verification environment. Also, compared to the previous version, Augur 2 will include more functionality and new analysis techniques.
Solving constraints in model transformations
 Theory and Practice of Model Transformations
, 2009
"... Abstract. Constraint programming holds many promises for model driven software development (MDSD). Up to now, constraints have only started to appear in MDSD modeling languages, but have not been properly reflected in model transformation. This paper introduces constraint programming in model tran ..."
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Cited by 5 (3 self)
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Abstract. Constraint programming holds many promises for model driven software development (MDSD). Up to now, constraints have only started to appear in MDSD modeling languages, but have not been properly reflected in model transformation. This paper introduces constraint programming in model transformation, shows how constraint programming integrates with QVT Relations as a pathway to wide spread use of our approach and describes the corresponding model transformation engine. In particular, the paper will illustrate the use of constraint programming for the specification of attribute values in target models, and provide a qualitative evaluation of the benefit drawn from constraints integrated with QVT Relations.
Querying Semistructured Data Based On Schema Matching
, 2000
"... Most of today's data is still stored in les rather than in databases. This fact has become even more evident with the growth of the World Wide Web in the 1990s. Because of that observation, the research area of semistructured data has evolved. Semistructured data is typically stored in document ..."
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Cited by 5 (0 self)
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Most of today's data is still stored in les rather than in databases. This fact has become even more evident with the growth of the World Wide Web in the 1990s. Because of that observation, the research area of semistructured data has evolved. Semistructured data is typically stored in documents and has an irregular, partial, and implicit structure. The thesis presents a new framework for querying semistructured data. Traditional database management requires design and ensures declarativity. The possibilities to design are limited in the field of semistructured data, thus, a more flexible approach is needed. We argue that semistructured data should be represented by a set of partial schemata rather than by one complete schema. Because of irregularities of the data, a complete schema would be very large and not representative. Instead, partial schemata can serve as good representations of parts of the data. While finding a complete schema turns out to be difficult, a database designer may be able to provide partial schemata for the database. Also, partial schemata can be extracted from user queries if the query language is designed appropriately. We suggest to split the notion of query into a "What" and a "How"part. Partial schemata represent the "What"part. They cover semantically richer concepts than database schemata traditionally do. Among these concepts are predicates, variable definitions, and path descriptions. Schemata can be used for query optimization, but they also give users hints on the content of the database. Finding the occurrences (matches) of such a schema forms the most important part of query execution. All queries of our approach, such as the focus query or the transformation query, are based on this matching. Query execution can be optimized using kn...
An Optimization Technique for Subgraph Matching Strategies
, 2006
"... Subgraph matching (aka graph pattern matching or the subgraph isomorphism problem) is NPcomplete. But in practice subgraph matching should be performed in reasonable time if possible. In this work a heuristically optimizing approach to subgraph matching on labeled graphs is described. It relies on ..."
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Cited by 5 (2 self)
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Subgraph matching (aka graph pattern matching or the subgraph isomorphism problem) is NPcomplete. But in practice subgraph matching should be performed in reasonable time if possible. In this work a heuristically optimizing approach to subgraph matching on labeled graphs is described. It relies on the fact that the runtime of the matching process can vary significantly for different matching strategies. The finding of a good matching strategy is stated as an optimization problem which is solved heuristically. The cost model for the possible matching strategies takes the structure of the present host graph into account. The necessary information can be obtained by an analysis of the host graph. 1