The hidden subgroup problem and quantum computation using group representations

The hidden subgroup problem is the foundation of many quantum algorithms. An efficient solution is known for the problem over abelian groups, employed by both Simon's algorithm and Shor's factoring and discrete log algorithms. The nonabelian case, however, remains open; an efficient solution would give rise to an efficient quantum algorithm for graph isomorphism. We fully analyze a natural generalization of the algorithm for the abelian case to the nonabelian case and show that the algorithm determines the normal core of a hidden subgroup: in particular, normal subgroups can be determined. We show, however, that this immediate generalization of the abelian algorithm does not efficiently solve graph isomorphism

Graph theoretic methods for the analysis of structural relationships in biological macromolecules

Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures

Using Canonical Forms for Isomorphism Reduction in Graph-based Model Checking

Graph isomorphism checking can be used in graph-based model checking to achieve symmetry reduction. Instead of one-to-one comparing the graph representations of states, canonical forms of state graphs can be computed. These canonical forms can be used to store and compare states. However, computing a canonical form for a graph is computationally expensive. Whether computing a canonical representation for states and reducing the state space is more efficient than using canonical hashcodes for states and comparing states one-to-one is not a priori clear. In this paper these approaches to isomorphism reduction are described and a preliminary comparison is presented for checking isomorphism of pairs of graphs. An existing algorithm that does not compute a canonical form performs better that tools that do for graphs that are used in graph-based model checking. Computing canonical forms seems to scale better for larger graphs