[graph-tool] Performance question

Guillaume Gay guillaume at mitotic-machine.org
Fri Mar 21 10:10:37 CET 2014


Hi,

There is a propertymap that contains the out degrees of each vertex, it 
might be much faster to access it, i.e.:

`i_degree = graph.degree_property_map('out')[i]`

I guess I would also iterate over the edges rather than the indices of 
the adjacency matrix...


G.

Le 21/03/2014 09:44, Hang Mang a écrit :
> Maybe graph.vertex(i).out_degree() is slow itself? If so, should I 
> store all the degrees in a matrix then?
>
> On Friday, March 21, 2014 9:09:23 AM UTC+1, Hang Mang wrote:
>
>     I have a graph with 1034 vertices and 53498 edges. I'm manually
>     computing the preferential attachement index for the vertices, and
>     other indices. I'm aware that graph-tool has that implemented but
>     I'm doing it for personal stuff. However I noticed that my
>     computations are very slow. It took 2.7 minutes to compute that
>     for the mentioned graph. I'm not sure if it's my algorithm that is
>     slow or the something is wrong with graph-tool. I would be very
>     thankful if someone could have a little look into my code.
>
>     def pa(graph):
>
>     """
>
>             Calculates Preferential Attachment index.
>
>             Returns S the similarity matrix.
>
>         """
>
>         A = gts.adjacency(graph)
>
>         S = np.zeros(A.shape)
>
>     for i in xrange(S.shape[0]):
>
>     for j in xrange(S.shape[0]):
>
>                 i_degree = graph.vertex(i).out_degree()
>
>                 j_degree = graph.vertex(j).out_degree()
>
>                 factor = i_degree * j_degree
>
>                 S[i,j] = factor
>
>     returnS
>
>
>
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