Re: [graph-tool] Finding cliques

Am 16.03.20 um 19:25 schrieb tshpak: > Hello Tiago! > > Thanks for the great library. > I use a function triadic_census to find all combinations of subgraphs based > on the clique of size 3: K3. > What can you propose, if I would like to calculate the same values for all > combinations of K4 or bi

Re: [graph-tool] how to improve similarity for Ising model and SIS model

Am 18.03.20 um 03:38 schrieb gege: > Hi, everyone! > I met a problem when I'm learning how to use graph-tool. I read the paper, > network reconstruction and community detection from dynamics, and I am > trying to achieve the same result. When I followed the same settings for > real networks with s

Re: [graph-tool] Please, advise on interpreting SBM results

Am 19.03.20 um 11:51 schrieb santirdnd: > Hi everybody, > > I'm not an expert on graph theory, so forgive me if I’m misunderstanding > something. I have a dataset (V=2.5k; E=55k) representing biological entities > and edges linking them based on a similarity measure. This dataset is very > heterog

Re: [graph-tool] performance reducing drastically as more edges are processed

Am 16.03.20 um 11:48 schrieb ioana: > Hi, > I am computing a weight for each edge, in a graph of some million nodes and > about 50 mil edges. Initially, it was doing 25000 edges per minute, so it > should have finished processing in about 30+ hours. Now I check the server > for results after more

Re: [graph-tool] get_edges_prob for every possible nonedge?

Am 19.03.20 um 18:33 schrieb Deklan Webster: > I'm attempting to use get_edges_prob to find the most likely missing > edges out of every possible non-edge. I know every possible edge is O(n^2). > > Currently I'm sampling the like this: > >     non_edges_probs = [[] for _ in range(len(non_edges))]

Re: [graph-tool] Proper way to depickle NestedState?

Am 19.03.20 um 18:38 schrieb Deklan Webster: > I'm saving NestedState with pickle and then loading it later to use > get_edges_prob. > >     nested_state = pickle.load( >         open(f"output/graphtool_output/pickle/{name}_nested_blockstate.p", >              "rb")) > > I realized that NestedSta

Re: [graph-tool] Problem extracting hierarchical blocks

Am 18.03.20 um 23:13 schrieb santirdnd: > Hi Tiago! > > Could it be that the problem highlighted by this thread is fueled by a bug > in the documentation at the end of this section > > > ? This has

Re: [graph-tool] Beta-parameter value during equilibration

Am 13.03.20 um 15:40 schrieb Leonardo Morelli: > Hi! > I'm a beginner in this field, so I do apologize if my vocabulary isn't > precise enough. > Basically, I'm trying to use graph-tool library in order to perform the > unsupervised clustering step of biological samples (10³-10⁴ _nodes > _networks)

Re: [graph-tool] how to improve similarity for Ising model and SIS model

Dear professor Peixoto, Thank you for reply! The dynamic example in the document sets 100 initial infected points and iterates for 10 times simultaneously. So the epidemic process is ongoing on a network and time T belongs to [0,9]. Then the time series is copied to a same but masked network. Am

Re: [graph-tool] bipartite graphs

Am 20.03.20 um 11:22 schrieb Davide Cittaro: > Hello, > I would like to test nSBM on bipartite graphs but before going on I need to > be sure I'm able to build a bipartite graph in graph-tool starting from a > matrix: > > A_nodes = np.arange(data.shape[0]) #nodes for rows start from 0 > B_nodes

Re: [graph-tool] bipartite graphs

Hi > On 23 Mar 2020, at 15:24, Tiago de Paula Peixoto wrote: > > You can add the weights together with the edges in Graph.add_edge_list() > via the eprops parameter, but otherwise the above is fine. > Ok > Note that if your objective is to do SBM inference, it's better to make > the graph und

Re: [graph-tool] how to improve similarity for Ising model and SIS model

Am 23.03.20 um 15:25 schrieb gege: > Dear professor Peixoto, > Thank you for reply! > > The dynamic example in the document sets 100 initial infected points and > iterates for 10 times simultaneously. So the epidemic process is ongoing on > a network and time T belongs to [0,9]. Then the time se

Re: [graph-tool] efficient random sampling of paths between two nodes

Am 21.03.20 um 17:44 schrieb Franco Peschiera: > Since I could potentially do many iterations (and samplings), I would > like to have an unbiased sampling method for the Y paths without having > to enumerate them all. > > One option is to do the sampling during the construction of the paths. I >

Re: [graph-tool] bipartite graphs

(Please answer to the mailing list, not directly Am 23.03.20 um 15:31 schrieb Davide Cittaro: >> Note that if your objective is to do SBM inference, it's better to make >> the graph undirected. >> > > Why so? Is this true in general? Well, if you have a bipartite network where it is important do

[graph-tool] efficient random sampling of paths between two nodes

Hello Tiago, First of all, thanks for your time. I see what you mean by having a biased logic that would prefer shorter paths to longer ones, I had not thought about that. Regarding the self-reference part, I think it would not be a problem because of the structure of my particular (directed) gr

Re: [graph-tool] efficient random sampling of paths between two nodes

Am 23.03.20 um 22:14 schrieb Franco Peschiera: > Hello Tiago, > > First of all, thanks for your time. > > I see what you mean by having a biased logic that would prefer shorter > paths to longer ones, I had not thought about that. > > Regarding the self-reference part, I think it would not be a