Improved Conflict Detection for Graph Transformation with Attributes

In graph transformation, a conflict describes a situation where two alternative transformations cannot be arbitrarily serialized. When enriching graphs with attributes, existing conflict detection techniques typically report a conflict whenever at least one of two transformations manipulates a shared attribute. In this paper, we propose an improved, less conservative condition for static conflict detection of graph transformation with attributes by explicitly taking the semantics of the attribute operations into account. The proposed technique is based on symbolic graphs, which extend the traditional notion of graphs by logic formulas used for attribute handling. The approach is proven complete, i.e., any potential conflict is guaranteed to be detected.Comment: In Proceedings GaM 2015, arXiv:1504.0244

Confluence Detection for Transformations of Labelled Transition Systems

The development of complex component software systems can be made more manageable by first creating an abstract model and then incrementally adding details. Model transformation is an approach to add such details in a controlled way. In order for model transformation systems to be useful, it is crucial that they are confluent, i.e. that when applied on a given model, they will always produce a unique output model, independent of the order in which rules of the system are applied on the input. In this work, we consider Labelled Transition Systems (LTSs) to reason about the semantics of models, and LTS transformation systems to reason about model transformations. In related work, the problem of confluence detection has been investigated for general graph structures. We observe, however, that confluence can be detected more efficiently in special cases where the graphs have particular structural properties. In this paper, we present a number of observations to detect confluence of LTS transformation systems, and propose both a new confluence detection algorithm and a conflict resolution algorithm based on them.Comment: In Proceedings GaM 2015, arXiv:1504.0244

Adhesive High-Level Replacement Systems with Negative Application Conditions

The goal of this paper is the generalization of basic results for adhesive High-Level Replacement (HLR) systems to adhesive HLR systems with negative application conditions. These conditions restrict the application of a rule by expressing that a specific structure should not be present before or after applying the rule to a certain context. Such a condition influences thus each rule application or transformation and therefore changes significantly the properties of the replacement system. The effect of negative application conditions on the replacement system is described in the generalization of the following results, formulated already for adhesive HLR systems without negative application conditions: Local Church-Rosser Theorem, Parallelism Theorem, Completeness Theorem for Critical Pairs, Concurrency Theorem, Embedding and Extension Theorem and Local Confluence Theorem or Critical Pair Lemma. These important generalized results will support the development of formal analysis techniques for adhesive HLR replacement systems with negative application conditions

Confluence up to Garbage

No abstract available

The Physics of Communicability in Complex Networks

A fundamental problem in the study of complex networks is to provide quantitative measures of correlation and information flow between different parts of a system. To this end, several notions of communicability have been introduced and applied to a wide variety of real-world networks in recent years. Several such communicability functions are reviewed in this paper. It is emphasized that communication and correlation in networks can take place through many more routes than the shortest paths, a fact that may not have been sufficiently appreciated in previously proposed correlation measures. In contrast to these, the communicability measures reviewed in this paper are defined by taking into account all possible routes between two nodes, assigning smaller weights to longer ones. This point of view naturally leads to the definition of communicability in terms of matrix functions, such as the exponential, resolvent, and hyperbolic functions, in which the matrix argument is either the adjacency matrix or the graph Laplacian associated with the network. Considerable insight on communicability can be gained by modeling a network as a system of oscillators and deriving physical interpretations, both classical and quantum-mechanical, of various communicability functions. Applications of communicability measures to the analysis of complex systems are illustrated on a variety of biological, physical and social networks. The last part of the paper is devoted to a review of the notion of locality in complex networks and to computational aspects that by exploiting sparsity can greatly reduce the computational efforts for the calculation of communicability functions for large networks.Comment: Review Article. 90 pages, 14 figures. Contents: Introduction; Communicability in Networks; Physical Analogies; Comparing Communicability Functions; Communicability and the Analysis of Networks; Communicability and Localization in Complex Networks; Computability of Communicability Functions; Conclusions and Prespective

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches