# Canonical Labelling of Site Graphs

@inproceedings{Oury2013CanonicalLO, title={Canonical Labelling of Site Graphs}, author={Nicolas Oury and Michael Pedersen and Rasmus Lerchedahl Petersen}, booktitle={CompMod}, year={2013} }

We investigate algorithms for canonical labelling of site graphs, i.e. graphs in which edges bind vertices on sites with locally unique names. We first show that the problem of canonical labelling of site graphs reduces to the problem of canonical labelling of graphs with edge colourings. We then present two canonical labelling algorithms based on edge enumeration, and a third based on an extension of Hopcroft's partition refinement algorithm. All run in quadratic worst case time individually…

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## References

SHOWING 1-10 OF 18 REFERENCES

### Canonical labeling of graphs

- MathematicsSTOC
- 1983

An algebraic approach to the problem of assigning canonical forms to graphs by computing canonical forms and the associated canonical labelings in polynomial time is announced.

### An efficient algorithm for computing bisimulation equivalence

- Computer ScienceTheor. Comput. Sci.
- 2004

### Reconstructing species-based dynamics from reduced stochastic rule-based models

- Computer Science, MathematicsProceedings Title: Proceedings of the 2012 Winter Simulation Conference (WSC)
- 2012

This paper presents a procedure for reconstructing the high-dimensional species-based dynamics from the aggregate state, and provides an algorithm for computing such de-aggregation functions explicitly, and has a quadratic time complexity in the number of molecules which constitute the site-graphs of interest.

### Re-describing an algorithm by Hopcroft

- Computer ScienceTheor. Comput. Sci.
- 2001

### Scalable Simulation of Cellular Signaling Networks

- Computer ScienceAPLAS
- 2007

A radically different method which does not attempt to count species is presented, which uses a representation of the system together with a super-approximation of its 'event horizon' (all events that may happen next), and a specific correction scheme to obtain exact timings.

### Stochastic simulation of multiple process calculi for biology

- Computer ScienceTheor. Comput. Sci.
- 2012