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I'm trying to delete isomorphic graphs from a large list. My solution is as follows:

DeleteIsoG1[gl_List]:= Module[{},
    DeleteDuplicates[gl,IsomorphicGraphQ]];

Unfortunately, it turns out very inefficient. I'm aware that graph isomorphism problem belongs to NP. I just need a relatively fast implementation in Mma.

Any comments or suggestions are welcome.

Update: I searched the forum. It looks that the performance can be improved by using other functions like DeleteDuplicatesBy or GatherBy instead of DeleteDuplicates. But according to the observation of @Mr.Wizard link, the behaviour of GatherBy is NOT a pairwise comparison. Hence it seems that we need a new method to get around here. The following is an implementation by using Gather. But it is slower than the one using DeleteDuplicates.

DeleteIsoG2[gl_List] := Module[{},
    First /@ Gather[gl, IsomorphicGraphQ]];
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You can use the CanonicalGraph function in concert with DeleteDuplicatesBy:

DeleteIso[gs_List] := DeleteDuplicatesBy[gs, CanonicalGraph]
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  • 2
    $\begingroup$ +1 Indeed, from docs: CanonicalGraph is often used to compare and match a graph to a large collection of graphs; isomorphic graphs have the same canonical graph. $\endgroup$ – ybeltukov Nov 14 '15 at 17:26
  • $\begingroup$ @Pillsy Your solution works like a charm! $\endgroup$ – hxiao Nov 15 '15 at 3:32

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