A Generic Framework for Engineering Graph Canonization Algorithms

The state-of-the-art tools for practical graph canonization are all based on the individualization-refinement paradigm, and their difference is primarily in the choice of heuristics they include and in the actual tool implementation. It is thus not possible to make a direct comparison of how individual algorithmic ideas affect the performance on different graph classes. We present an algorithmic software framework that facilitates implementation of heuristics as independent extensions to a common core algorithm. It therefore becomes easy to perform a detailed comparison of the performance and behaviour of different algorithmic ideas. Implementations are provided of a range of algorithms for tree traversal, target cell selection, and node invariant, including choices from the literature and new variations. The framework readily supports extraction and visualization of detailed data from separate algorithm executions for subsequent analysis and development of new heuristics. Using collections of different graph classes we investigate the effect of varying the selections of heuristics, often revealing exactly which individual algorithmic choice is responsible for particularly good or bad performance. On several benchmark collections, including a newly proposed class of difficult instances, we additionally find that our implementation performs better than the current state-of-the-art tools.

[1]  Adolfo Piperno,et al.  Search Space Contraction in Canonical Labeling of Graphs (Preliminary Version) , 2008, ArXiv.

[2]  Antonio Fernández,et al.  Fast Algorithm for Graph Isomorphism Testing , 2009, SEA.

[3]  L. Babai Automorphism groups, isomorphism, reconstruction , 1996 .

[4]  Á. Seress Permutation Group Algorithms , 2003 .

[5]  László Babai,et al.  Canonical labeling of graphs , 1983, STOC.

[6]  László Babai,et al.  Graph isomorphism in quasipolynomial time [extended abstract] , 2016, STOC.

[7]  Jeremy G. Siek,et al.  The generic graph component library , 1999, OOPSLA '99.

[8]  Daniel Neuen,et al.  Benchmark Graphs for Practical Graph Isomorphism , 2017, ESA.

[9]  Jeremy G. Siek,et al.  The Boost Graph Library - User Guide and Reference Manual , 2001, C++ in-depth series.

[10]  Brendan D. McKay,et al.  Practical graph isomorphism, II , 2013, J. Symb. Comput..

[11]  Petteri Kaski,et al.  Engineering an Efficient Canonical Labeling Tool for Large and Sparse Graphs , 2007, ALENEX.

[12]  Igor L. Markov,et al.  Faster symmetry discovery using sparsity of symmetries , 2008, 2008 45th ACM/IEEE Design Automation Conference.

[13]  Igor L. Markov,et al.  Symmetry and Satisfiability: An Update , 2010, SAT.

[14]  Stephen R. Heller,et al.  InChI, the IUPAC International Chemical Identifier , 2015, Journal of Cheminformatics.

[15]  Petteri Kaski,et al.  Conflict Propagation and Component Recursion for Canonical Labeling , 2011, TAPAS.

[16]  Alexander A. Stepanov,et al.  Generic Programming , 1988, ISSAC.

[17]  Daniel Merkle,et al.  Chemical Graph Transformation with Stereo-Information , 2017, ICGT.