Between Subgraph Isomorphism and Maximum Common Subgraph

When a small pattern graph does not occur inside a larger target graph, we can ask how to find "as much of the pattern as possible" inside the target graph. In general, this is known as the maximum common subgraph problem, which is much more computationally challenging in practice than subgraph isomorphism. We introduce a restricted alternative, where we ask if all but k vertices from the pattern can be found in the target graph. This allows for the development of slightly weakened forms of certain invariants from subgraph isomorphism which are based upon degree and number of paths. We show that when k is small, weakening the invariants still retains much of their effectiveness. We are then able to solve this problem on the standard problem instances used to benchmark subgraph isomorphism algorithms, despite these instances being too large for current maximum common subgraph algorithms to handle. Finally, by iteratively increasing k, we obtain an algorithm which is also competitive for the maximum common subgraph

Experimental Evaluation of Subgraph Isomorphism Solvers

International audienceSubgraph Isomorphism (SI) is an NP-complete problem which is at the heart of many structural pattern recognition tasks as it involves finding a copy of a pattern graph into a target graph. In the pattern recognition community, the most well-known SI solvers are VF2, VF3, and RI. SI is also widely studied in the constraint programming community, and many constraint-based SI solvers have been proposed since Ullman, such as LAD and Glasgow, for example. All these SI solvers can solve very quickly some large SI instances, that involve graphs with thousands of nodes. However, McCreesh et al. have recently shown how to randomly generate SI instances the hardness of which can be controlled and predicted, and they have built small instances which are computationally challenging for all solvers. They have also shown that some small instances, which are predicted to be easy and are easily solved by constraint-based solvers, appear to be challenging for VF2 and VF3. In this paper, we widen this study by considering a large test suite coming from eight benchmarks. We show that, as expected for an NP-complete problem, the solving time of an instance does not depend on its size, and that some small instances coming from real applications are not solved by any of the considered solvers. We also show that, if RI and VF3 can solve very quickly a large number of easy instances, for which Glasgow or LAD need more time, they fail at solving some other instances that are quickly solved by Glasgow or LAD, and they are clearly outperformed by Glasgow on hard instances. Finally, we show that we can easily combine solvers to take benefit of their complementarity

GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins

BACKGROUND: A large variety of biological data can be represented by graphs. These graphs can be constructed from heterogeneous data coming from genomic and post-genomic technologies, but there is still need for tools aiming at exploring and analysing such graphs. This paper describes GenoLink, a software platform for the graphical querying and exploration of graphs. RESULTS: GenoLink provides a generic framework for representing and querying data graphs. This framework provides a graph data structure, a graph query engine, allowing to retrieve sub-graphs from the entire data graph, and several graphical interfaces to express such queries and to further explore their results. A query consists in a graph pattern with constraints attached to the vertices and edges. A query result is the set of all sub-graphs of the entire data graph that are isomorphic to the pattern and satisfy the constraints. The graph data structure does not rely upon any particular data model but can dynamically accommodate for any user-supplied data model. However, for genomic and post-genomic applications, we provide a default data model and several parsers for the most popular data sources. GenoLink does not require any programming skill since all operations on graphs and the analysis of the results can be carried out graphically through several dedicated graphical interfaces. CONCLUSION: GenoLink is a generic and interactive tool allowing biologists to graphically explore various sources of information. GenoLink is distributed either as a standalone application or as a component of the Genostar/Iogma platform. Both distributions are free for academic research and teaching purposes and can be requested at [email protected]. A commercial licence form can be obtained for profit company at [email protected]. See also

Constraint-Driven Instructions Selection and Application Scheduling in the DURASE system

International audienceThis paper presents a new constraint-driven method for computational pattern selection, mapping and application scheduling using reconfigurable processor extensions. The presented method is a part of DURASE system (Generic Environment for Design and Utilization of Reconfigurable Application-Specific Processors Extensions). The selected processor extensions are implemented as specialized processor instructions. They correspond to computational patterns identified as most frequently occurring or other interesting patterns in the application graph. Our methods can handle both time-constrained and resource-constrained scheduling. Experimental results obtained for the MediaBench and MiBench benchmarks show that the presented method ensures high speed-ups in application execution

Matching of Bigraphs

We analyze the matching problem for bigraphs. In particular, we present a sound and complete inductive characterization of matching of binding bigraphs. Our results pave the way for a provably correct matching algorithm, as needed for an implementation of bigraphical reactive systems

Sélection automatique d'instructions et ordonnancement d'applications basés sur la programmation par contraintes

National audienceCe papier présente une nouvelle méthode, basée sur la programmation par contraintes, pour la sélection de motifs de calcul, le placement et l'ordonnancement d'applications sur des extensions de processeurs configurables. Cette méthode est intégrée dans l'environnement DURASE (Generic Environment for Design and Utilization of Reconfigurable Application-Specific Processors Extensions). Les extensions du proces- seur, qui mettent en œuvre les motifs de calcul et qui sont accessibles via des instructions spécialisées, sont fortement couplées au chemin de données du processeur. Ces instructions spécialisées sont géné- rées et sélectionnées à partir du graphe de l'application. Notre méthode supporte un ordonnancement sous contrainte de ressources ou sous contrainte de temps. Les résultats expérimentaux obtenus sur les benchmarks MediaBench et MiBench montrent une accélération de l'exécution des applications d'un facteur de 2,3 en moyenne