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… 

Figures from this paper

A strand graph semantics for DNA-based computation

KaDE: A Tool to Compile Kappa Rules into (Reduced) ODE Models

The main current functionalities of KaDE are described and some benchmarks on case studies are given and the definition of Kappa models as a set of context-free rewrite rules is explained.

A Modelling and Simulation Tool for DNA Strand Displacement Systems

This thesis presents a rule-based modelling pipeline RuleDSD for generating and simulating reaction networks of DSD systems, a tool that automatically generates a complete reaction network for a described DSD system and integrates with the PySB framework for further simulations using the BioNetGen engine.

References

SHOWING 1-10 OF 18 REFERENCES

Canonical labeling of graphs

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

Practical graph isomorphism, II

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

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

Scalable Simulation of Cellular Signaling Networks

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

Partitioning a Graph in O(|A| log2 |V|)