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

Installation issue on AWS
by redBlackTree 01 Mar '20

01 Mar '20

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! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Collecting marginals during or after equilibrate
by Davide Cittaro 28 Feb '20

28 Feb '20

Dear all, We have a doubt about good practices in collecting vertex marginals during equilibration. In the howto, collection is done with an additional mcmc_equilibrate step with force_niter set to the desired "precision" but in principle this can be done during a single mcmc_equilibrate after mcmc_sweep. We observed some differences (especially when we collect the marginals for groups at each level of the NSBM), so we wonder which would be preferred. Thanks d

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Memory usage
by Deklan Webster 27 Feb '20

27 Feb '20

I was trying to do a nested degree-corrected SBM on my laptop, but I was running out of RAM, 14-15GB before stopping with "Killed". The graph is directed with 20k nodes 2.8m edges. Is that a typical amount of memory usage or did I do something wrong? If it's normal, is there any way for me to work around this such that I can run it on my computer

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getting the hierarchy tree
by Davide Cittaro 26 Feb '20

26 Feb '20

Hi again, How is it possible to return the hierarchy tree from a NestedBlockModel? I've found that the gt.get_hierarchy_tree returns the tree as graph, but I couldn't understand how to map partition names at each level n to the ones at level n+1. Actually I'm doing this iteratively running state.project_partition() and using crosstabs to do the matches, but I wonder if there's a smarter way to proceed. Cheers, d

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choose version of graphtool
by tshpak 26 Feb '20

26 Feb '20

Hello Tiago, I am wondering can I choose the version of graphtool library. I have now the version 2.29 and my colleague has an older one 2.27. Can I install version 2.27? I save a block state created with 2.29 as .pkl and he can not open it with 2.27 and got an error: "AttributeError: Can't get attribute 'VertexPropertyMap' on <module 'graph_tool' from '/usr/lib/python3/dist-packages/graph_tool/__init__.py'>" Best regards -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Re: [graph-tool] distances and similarities as edge weights
by Davide Cittaro 24 Feb '20

24 Feb '20

Excellent, thank you > On 24 Feb 2020, at 19:37, Tiago de Paula Peixoto <tiago(a)skewed.de> wrote: >

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How to use graph-tool to create and modify graphs dynamically?
by kant kodali 24 Feb '20

24 Feb '20

Hi All, I am new to graph-tool and I am trying to figure out how to create and display graphs dynamically by which I mean the following. To simplify the problem Lets say I have the following edges (1,2) (3,4) (3,7) (3, 8) (2, 3) I don't want to construct the graph with all the edges at once. instead I want to add or delete an edge one by one and render/display that immediately such that I can show the user how the graph is evolving after each edge. Think of it more like a stream of edges that can be either added or deleted. Please let me know if you need more information on the question. otherwise, I hope to hear how this can be achieved using graph-tool? Thanks, Kant

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distances and similarities as edge weights
by Davide Cittaro 24 Feb '20

24 Feb '20

Hello, when performing inference on a graph using SBM including edge weights, does it make any difference if weights are intended as distances or similarities between the vertexes? d

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the graph becomes non-existent
by admweiss 24 Feb '20

24 Feb '20

When I create a graph like this: self.graph = Graph(directed=True) self.is_on = self.graph.new_vertex_property("boolean") and want to use it in another class method: self.is_on.set_value(False) I get the error: libcore.set_vertex_property(g._Graph__graph, _prop("v", g, self), val) AttributeError: 'NoneType' object has no attribute '_Graph__graph' -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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NSBM vs optimization of modularity
by Davide Cittaro 20 Feb '20

20 Feb '20

I’m testing and implementing NABM for a specific research field (single cell biology) in which graph partitioning is the standard way to identify groups of cells, and this is done with Louvain (and more recently Leiden) approaches. We already have collected some evidences that NSBM works well and overcomes the issue of setting resolution (as a matter of fact one of the FAQ is “where should I set the threshold). Now, given a partition with those algorithms would it make sense to compare to NSBM using entropy? I could create a PropertMap from Leiden partitions and set it into a BlockState, would it work? Sent from my iPhone

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