Re: [graph-tool] Most efficient way to access all nodes in a block
Am 19.06.2018 um 21:01 schrieb Alexandre Hannud Abdo: > Ni! Hi Philipp, > > Yes, there are more straightforward paths to the same information: > > # get some graph and model it > import graph_tool.all as gt > g = gt.collection.data["celegansneural"] > s = gt.minimize_nested_blockmodel_dl(g) > > # get your groups of vertices in a dictionary > l0 = s.levels[0] > block2vertices = dict() > for i in range(l0.B): > block2vertices[i] = gt.find_vertex(l0.g, l0.b, i) Since find_vertex() is O(N), the above is O(B * N). A faster O(N) approach is simply: groups = defaultdict(list) for v in g.vertices(): groups[l0.b[v]].append(v) Best, Tiago -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
Re: [graph-tool] Most efficient way to access all nodes in a block
Ni! Hi Philipp, Yes, there are more straightforward paths to the same information: # get some graph and model it import graph_tool.all as gt g = gt.collection.data["celegansneural"] s = gt.minimize_nested_blockmodel_dl(g) # get your groups of vertices in a dictionary l0 = s.levels[0] block2vertices = dict() for i in range(l0.B): block2vertices[i] = gt.find_vertex(l0.g, l0.b, i) Cheers .~´ On Tue, Jun 19, 2018 at 7:01 PM, P-M wrote: > (I should probably add that I am only interested in relations between the > nodes in a given block with each other, so am happy to work with vertex > filters.) > > > > -- > Sent from: http://main-discussion-list-for-the-graph-tool-project. > 982480.n3.nabble.com/ > ___ > graph-tool mailing list > graph-tool@skewed.de > https://lists.skewed.de/mailman/listinfo/graph-tool > ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
Re: [graph-tool] Most efficient way to access all nodes in a block
(I should probably add that I am only interested in relations between the nodes in a given block with each other, so am happy to work with vertex filters.) -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/ ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
[graph-tool] Most efficient way to access all nodes in a block
Hello, I have just fitted an SBM to my graph. Having run state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True) I now would like to investigate the results a bit more closely. More specifically I am after the best way to access all vertices assigned to a given block. I can use get_levels() and then get_blocks() to obtain the block membership of each vertex and from that I can use find_vertex() for a given block number to find the list of all vertices in that block which I can then use to loop through them. I wonder, however, if there is a more efficient way of obtaining all vertices in a given block? My current pseudo code looks something like the following: state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True) #now do something for all vertices in each of the blocks levels = state.get_levels() graphs = state.get_bstacks() #Return the nested levels as individual graphs. num_blocks = graphs[1].num_vertices() #find the number of blocks at level 0 blocks = levels[0].get_blocks() #Returns property map with block labels for each vertex. for i in range(num_blocks): #cycle through all blocks vs = gt.find_vertex(g,blocks,i) for v in vs: #cylce through all vertices in a given block do something Is there some more efficient way of doing this that I am missing? I would ideally ultimately run it after each sweep of the mcmc algorithm so would like to minimise looping that I am doing in python if graph-tool has methods for what I am doing which will, presumably, be faster. Thank you for any advice in advance! With best wishes, Philipp -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/ ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool
