Skip to main content

Canonical Augmentation : How not to do it

In the interest of not publishing false information (even on a blog), this is a brief outline of why the approach outlined in the previous post does not work.

When constructing a set of graphs - from their degree sequences or otherwise - it is usual to describe the process as traversing a tree. The root of the tree is the empty set, and the leaves are the completed graphs. Internal nodes in this tree are partially completed graphs, and parent nodes are connected to children by augmentations.


An augmentation to a graph can be made in various ways: adding a single edge, adding multiple edges to a single new node, etc. However, the important thing is to avoid duplicating solutions at the leaves.

One easy way to do this is to check all newly generated leaves against all the previously generated ones. However, this requires not only storage of all the solutions so far, but also a lot of isomorphism checks. A better way is to check if a solution is canonical by some means. Even better than that is to test the partial graphs (the internal tree nodes) and only follow paths of canonical augmentations.



So this image (click for bigger) shows an example of this failing for the degree sequence [3, 3, 3, 3, 3, 3] (or 36). The first two steps (A, B) are fine : v{0} is connected to v{1,2,3} and then v{1} is connected to v{4,5}. Following the left path, we get to partial graph (C) where v{2} is now connected to v{4,5} - unfortunately the vertices are now no longer in 'degree order'. Compare to the path (B-E-F) on the right to the prism. There, each partial solution has vertices in degree order.

In short, then; canonical augmentation only works if the method to check for a canonical solution is 'aligned' with the augmentation method. When augmenting by saturating orbits, it does not seem possible to use partition refinement to check a graph as canonical, since refinement always starts by partitioning by degree.

Comments

Popular posts from this blog

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin...

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the ...

General Graph Layout : Putting the Parts Together

An essential tool for graph generation is surely the ability to draw graphs. There are, of course, many methods for doing so along with many implementations of them. This post describes one more (or perhaps an existing method - I haven't checked). Firstly, lets divide a graph up into two parts; a) the blocks, also known as ' biconnected components ', and b) trees connecting those blocks. This is illustrated in the following set of examples on 6 vertices: Trees are circled in green, and blocks in red; the vertices in the overlap between two circles are articulation points. Since all trees are planar, a graph need only have planar blocks to be planar overall. The layout then just needs to do a tree layout  on the tree bits and some other layout on the embedding of the blocks. One slight wrinkle is shown by the last example in the image above. There are three parts - two blocks and a tree - just like the one to its left, but sharing a single articulation point. I had...