May 2020 - graph-tool - archives.skewed.de

module 'graph_tool' has no attribute 'minimize_blockmodel_dl'
by sam 22 May '20

22 May '20

Hi, I have been using graph-tool in the docker shell in the jupyter notebook, following the instructions here <https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#j…> . However, after moving to larger networks (not that large; 200,000 vertices) it seems that the jupyter notework environment doesn't work. I'm not sure why. I have instead moved to running it from the terminal. However, things seem to be a bit different there. In particular, if I run the following: import graph_tool as gt g = gt.load_graph("/Users/samuelgyetvay/Dropbox/jmp/data/clean/j2j", fmt="graphml") state = gt.minimize_blockmodel_dl(g, state_args=dict(recs=[g.ep.weight], rec_types=["discrete-poisson"])) I get the error message "module 'graph_tool' has no attribute 'minimize_blockmodel_dl'". I'm not sure what to do. Thanks -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Hierarchical Tree layout with transmission date
by sumau 20 May '20

20 May '20

It is possible to draw networks in hierarchical tree layout positioned by transmission date? Something similar to this: <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Remove all neighbors of a vertex
by Max 20 May '20

20 May '20

I have a Graph with 20 vertices, i.e. the index is 0, 1, 2,...19. Vertex with index 12 is connected with all other vertices except 3 and 15. I want to remove vertex 12 and all its neighbors, that is I want to keep 3 and 5 in the graph. What should I do? I tried the remove_vertex() API, it seems there is something wrong. I ask for help from You. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Weighted Clustering
by Hansen, Glenn J. 17 May '20

17 May '20

I have an edge property for weight. The weight for each edge is one integer between 1 and 4. The unweighted global clustering coefficient is about 0.45. The weighted global clustering coefficient is -0.61. Are negative values in the range? Additionally, if I filter on edge weight and calculate the weighted clustering I get values > 1.0. If all weights are 3, for example, would we not expect the same coefficient for weighted and unweighted. The unweighted coefficient for the above example is reasonable. The graph has 22K vertices and 3.7M nodes. I suspect this is something that I have overlook as I am new to graph-tool. Thank you.

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betweenness in 10,000 increments
by jamie.tratalos＠ucd.ie 16 May '20

16 May '20

Hi, I've calculated betweenness for each node in a network of approximately 100,000 nodes and one million edges. For almost all nodes, betweenness values range from 0 to 9,149.8877, in gradual increments. However, the highest nine values are as follows:: 3 nodes have the value of 10,000, 5 nodes have a betweenness of 20,000, and one node has a value of 40,000. These nodes do have relatively high out- and in- degree but there is nothing else unusual about them. I calculated these values in graph-tool about a year ago. Is this normal for the calculation of betweenness (i.e. values >= 10,0000 go up in increments of 10,0000), or has something gone wrong?

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setting vp.pos to emphasize block structure in state.draw?
by sam 15 May '20

15 May '20

hi there, are there any tips to set the position vertex property so that group structure is visible, as in this picture? https://graph-tool.skewed.de/static/doc/_images/football-sbm-fit.svg cheers, -sam -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Re: [graph-tool] graph_tool.draw.interactive_window
by Rolf Sander 13 May '20

13 May '20

Hello Tiago, > you cannot replace the underlying graph from under the hood like this. > What you can do, however, is to work with the same filtered graph the > whole time, and then change the values of the filter property map > dynamically. Thanks for the hint, this is exactly what I need! In case anyone else is interested in this great feature, I've written a small minimal working example, see below. Best regards Rolf ############################################################################## import graph_tool.all as gt def mykeypressed(self, g, keyval, picked, pos, vprops, eprops): if (chr(keyval)=='1'): g.vp.myfilter.a = True self.fit_to_window() self.regenerate_surface(reset=True) self.queue_draw() if (chr(keyval)=='2'): g.vp.myfilter.a = True g.vp.myfilter.a = [n%2==0 for n in g.vertex_index] self.fit_to_window() self.regenerate_surface(reset=True) self.queue_draw() if (chr(keyval)=='3'): g.vp.myfilter.a = True g.vp.myfilter.a = [n%3==0 for n in g.vertex_index] self.fit_to_window() self.regenerate_surface(reset=True) self.queue_draw() g1 = gt.random_graph(10, lambda: (3, 3)) g1.vp.myfilter = g1.new_vertex_property('bool') g1.vp.myfilter.a = True g1.set_vertex_filter(g1.vp.myfilter) gt.interactive_window(g1, key_press_callback=mykeypressed, vertex_text=g1.vertex_index) ############################################################################## -- ----------------------------------------------------------------------- Rolf Sander phone: [+49] 6131/305-4610 Max-Planck Institute of Chemistry email: rolf.sander(a)mpic.de PO Box 3060, 55020 Mainz, Germany homepage: www.rolf-sander.net ----------------------------------------------------------------------- https://www.encyclopedia-of-geosciences.net https://www.geoscientific-model-development.net -----------------------------------------------------------------------

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collection module not accessible from the top module
by stalaga 13 May '20

13 May '20

Hi, I am not quite sure if it is a bug or a design decision (although it seems quite inconvenient, so I guess it may be a bug), but `collection` module is not accessible from the top module object. More specifically, this code does not run: import graph_tool as gt gt.collection.data['karate'] ---- AttributeError: module 'graph_tool' has no attribute 'collection' ---- And according to the documentation it should (https://graph-tool.skewed.de/static/doc/collection.html) As a matter of fact the same problem affects also other submodules, for instance `spectral` also cannot be accesses via an attribute of the top module `gt` after importing. Graph-tool version I am using is: '2.31 (commit b1411e3e, Sun Mar 29 21:53:41 2020 +0200)' I installed it a few days ago from conda-forge, so I guess it is up-to-date. Thanks in advance for any help with this problem (maybe I am doing something wrong?). And thanks for this great package! Best, Szymon. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Block number limits in community detection with metadata
by Yan Xia 13 May '20

13 May '20

Hi, I am using the minimize_blockmodel_dl() function and the LayeredBlockState class to conduct community detection with metadata. I would like to know if it is possible to specify the block number limits separately for the user clusters and the metadata clusters (instead of the total block number limit) during the SBM inference? Since we want to have different granularity for user clusters and metadata clusters. (P.S. I tried using nested SBM and merging separately the user clusters and the metadata clusters. It worked to some extent, but it seems impossible to accurately control the final number of clusters, which we might need to.) Thanks! Yan -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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using internal properties with string type to filter graph
by mvdnheuv 12 May '20

12 May '20

Hi, I am working on a very large graph of companies and wanted to make some functions to easily filter out certain subgraphs I would need for some calculations. So I made a graph G and populated it with nodes and edges and some internal property maps because I don't want to always remake this graph. The point is to just write the complete graph out to a file once I get through all the data cleaning and have a final graph in a file. So this gives me: G, a <Graph object, directed, with 11944189 vertices and 7828750 edges at 0x7f49254e90f0> with G.list_properties() ID (vertex) (type: string) company_country (edge) (type: string) shareholder_country (edge) (type: string) shareholderdirect (edge) (type: double) Now I just want to do a filtering based on these properties as suggested earlier in this forum: g_AT = GraphView(G, efilt=G.ep.company_country.a == 'AT') But as mentioned in the docs for internal properties: "Internal graph property maps behave slightly differently. Instead of returning the property map object, the value itself is returned from the dictionaries" Which I guess is why running G.ep.company_country.a gives me None, and running G.ep['company_country'][G.edges().next()] gives me 'AT'. So for filtering I now do: ep_filter = G.new_ep('bool') for e in G.edges(): ep_filter[e] = G.ep['company_country'][e] == 'AT' But I was wondering if there is some way to not have to go through this edge by edge but rather just get the whole PropertyArray returned which would be more elegant and avoid having to constantly make new boolean properties. PS: for the double type, G.ep.shareholderdirect.a does give me a nice PropertyArray which I can directly use in the form of G.ep.shareholderdirect.a > .5, which gives me an easy to use filtering array to input into GraphViews. Thanks in advance, Milan -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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