graph-tool September 2019

graph-tool@skewed.de

13 participants
24 discussions

Random graph with degree sequence.
by Alvaro Sechinel 07 Nov '19

07 Nov '19

Hi, I'm using graph-tool to try to generate random graphs with a sequence of degrees. For example, in a 3-node graph, I generated a random graph with all nodes with input degrees 1 and output degrees 1. My code: >>> import graph_tool.all as gt>>> def deg_sampler():... return 1,1... >>> g = gt.random_graph(3,deg_sampler,parallel_edges=True, self_loops=False)>>> gt.graph_draw(g) Can I generate a random graph defining the input and output degrees of each node? For example, tree nodes with respectively the input degrees (1, 2, 0) and output degrees (1, 0, 2). Thanks, Alvaro

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Publications using graph-tool
by ilyco 23 Sep '19

23 Sep '19

Hi, I have a rather silly question but I hope it will not hinder anyone from answering. I have been having difficulties finding publications which use graph-tool and apply it for researching a network (not for comparison with other methods or for developing their own method). Does anyone have any link to such applications? I am interested in how people discuss/observe network properties or validate their observation of hierarchical block models. Thanks! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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How to draw a graph in shell layout (concentric circles)?
by Weitao Han 23 Sep '19

23 Sep '19

Hi, I would like to draw a graph in shell layout (concentric circle), just like the shell_layout of networkx. But I cannot find any graph layout functions that can draw a graph in concentric circle. Could someone help me? Thanks Weitao Han

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Community detection with metadata in graph-tool
by jsfog 20 Sep '19

20 Sep '19

Hi, I would like to implement the community detection with metadata method that is described in the paper "Network structure, metadata and the prediction of missing nodes and annotations" by Hric, Peixoto, and Fortunato. The paper mentions that the method is implemented in graph-tool but I haven't been able to find it anywhere in the graph-tool documentation. Could you please point me towards the relevant function(s) and any documentation that exists? Thank you, Jamie -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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problem building weighted graph
by redBlackTree 12 Sep '19

12 Sep '19

Hi all, I was trying to build a weighted graph. The input is a list of connections with their weights, something like *connections = [[edge1, edge2, weight1], [edge1, edge3, weight2], ...]* where all edges are string and all weights are float64. I called add-edge_list: *graph.add_edge_list(connections, eprops = graph.new_edge_property("float"))* but got this error: File ".conda/envs/graph-tool/lib/python3.7/site-packages/graph_tool/__init__.py", line 2460, in add_edge_list libcore.add_edge_list_iter(self.__graph, edge_list, eprops) TypeError: No registered converter was able to produce a C++ rvalue of type unsigned long from this Python object of type str What is the most efficient way to build a weighted graph in my case? Thanks! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Installation issue
by Ray M 09 Sep '19

09 Sep '19

Hi all, I wanted to install graph-tool to my AWS sagemaker notebook. I have tried all installers available on anaconda.org, but none worked... Please see one examples below: Example: conda install -n python3 -c ostrokach-forge/label/dev graph-tool Solving environment: failed PackagesNotFoundError: The following packages are not available from current channels: - graph-tool - cairomm - graph-tool - cgal=4.11 - graph-tool - sparsehash Current channels: - https://conda.anaconda.org/ostrokach-forge/label/dev/linux-64 - https://conda.anaconda.org/ostrokach-forge/label/dev/noarch - https://repo.anaconda.com/pkgs/main/linux-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/free/linux-64 - https://repo.anaconda.com/pkgs/free/noarch - https://repo.anaconda.com/pkgs/r/linux-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/pro/linux-64 - https://repo.anaconda.com/pkgs/pro/noarch Which channels do I need to add to solve this issue? Thank you!

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Determining Blocks from a nested block model in an interactive window
by timhannigan 07 Sep '19

07 Sep '19

Hi all, I'm thrilled about using Graph-tool to do topic modeling (using Martin Gerlach's code: https://github.com/martingerlach/hSBM_Topicmodel). In order for this technique to really work well, I need some help here - to be able to browse the graph (nested block model) using an interactive window and identify the blocks with a mouse click (each block in this method is a group of words, ie. a topic in this usecase). As you'll see from my uploaded image, when I select a block on the interactive graph, I'm not sure how to determine which block this is referring to. I've written a callback method (win.graph.connect("button_press_event", update_bfs), that is able to extract /widget.picked/. However, I'm not sure what this refers to. Is this an edge id? I'd like a mouseclick on a block to then programmatically trigger searching the hierarchy to print the block in the model (offscreen). <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Thanks, -Tim -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Re: [graph-tool] load_graph_from_csv() problem
by Lietz, Haiko 06 Sep '19

06 Sep '19

OK, solved it - hadn't seen the note here: https://graph-tool.skewed.de/static/doc/graph_tool.html?highlight=property%… The way to access string property maps is via g.vp.name.get_2d_array(pos=[0]) g.ep.type.get_2d_array(pos=[0]) Hope it helps someone. Best Haiko

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load_graph_from_csv() problem
by Lietz, Haiko 06 Sep '19

06 Sep '19

Hi all, I have a problem with load_graph_from_csv() using gt 2.27. from graph_tool.all import * import pandas as pd edge_list = pd.DataFrame(['a', 'b', 1, 'c']) edge_list.to_csv('edge_list.csv', index=False, header=False) g = load_graph_from_csv('edge_list.csv', string_vals=True, eprop_types=['int', 'string'], eprop_names=['weight', 'type']) After this is done, three properties are listed: g.list_properties() This happens: g.vp.name.a # supposed to be a "PropertyArray" holding the vertex names as strings, but actually a "NoneType" g.ep.type.a # supposed to be a "PropertyArray" holding the edge type as a string, but actually a "NoneType" g.ep.weight.a # supposed to be, and actually is, a "PropertyArray" holding the edge weight as an integer Is the problem with the way I call the load_graph_from_csv() function? Thanks a lot Haiko

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Hiding lower hierarchical nodes
by James Ruffle 06 Sep '19

06 Sep '19

When drawing a nested stochastic block model, the ‘hide’ option can be used to hide upper levels of the hierarchy. Is there an equivalent option to hide lower levels of the hierarchy? i.e. so I could produce a visualisation showing the original vertices and edges, overlay with the hierarchy of level 2-4 (i.e. hiding level 0 and 1) Many thanks James

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graph-tool September 2019