graph-tool February 2022

graph-tool@skewed.de

8 participants
12 discussions

overlap/mixed-membership sbm help
by Eli Draizen 07 Mar '22

07 Mar '22

Hi everyone, I was wondering if it would be possible to provide some more examples of how to run a nested mixed membership SBM with edge weights. The new version seems to have removed the "overlap=True" option for state_args in the minimize_* functions. Is this the correct way to do it now? import graph_tool as gta > import numpy as np > g = .... # build graph > e_score = .... #Set edge weights > state_args = dict( > deg_corr=deg_corr, > base_type=gta.inference.overlap_blockmodel.OverlapBlockState, > B=2*g.num_edges(), #B_max > deg_corr=True, > recs=[e_score], > rec_types=["real-normal"]) > state = gta.inference.minimize_nested_blockmodel_dl( > g, > state_args=state_args, > multilevel_mcmc_args=dict(verbose=True)) > # improve solution with merge-split > state = state.copy(bs=state.get_bs() + [np.zeros(1)] * 4, sampling=True) for i in range(100): > if i%10==0: print(".", end="") > ret = state.multiflip_mcmc_sweep(niter=10, beta=np.inf, verbose=True) I am currently running this for a fully connected bipartite graph with 3454 nodes and 55008 edges. I understand it would take longer than the non-overlapping version, but do you have any suggestions on how to speed it up? The non-overlapping version takes about 15 minutes, while the overlapping version is still running after 1 day. Thanks for your help, Eli -- PhD Candidate, Phil Bourne's lab University of Virginia _______________________________________________ graph-tool mailing list -- graph-tool(a)skewed.de To unsubscribe send an email to graph-tool-leave(a)skewed.de

2 4

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. Thanks a lot. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 5

Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

3 3

Animations with changing topology
by Caleb Howard 26 Feb '22

26 Feb '22

I need to create an interactive animation that shows a continuously updated force-directed graph that starts empty and adds nodes and edges as specified by a process - with each new node causing the force equilibrium to adjust to a new set of positions to incorporate the new node. Is there an example that anyone has seen or could provide which would the simplest idle-loop watching a queue (or other mechanism) for new items, and adding nodes and edges in a continuous interactive force-directed graph animation? Thank you! -caleb (Caleb Howard)

1 1

Accessing all ancestors
by RAFAEL SERAPILHA DURELLI 22 Feb '22

22 Feb '22

Hello guys, I am migrating from a code devised in networkx to Graph-tool. Now, I need to get all ancestors in graph-tool. Could you guys help me out here. I found the func all_predecessors, but I could not figured out how to use it.. since it is mandatory to pass diet_map and prep_map. Can you please help me inhere :D Thanks -- O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes.

2 3

Fwd: Adding label to vertices
by RAFAEL SERAPILHA DURELLI 22 Feb '22

22 Feb '22

--------- Mensagem encaminhada --------- De: RAFAEL SERAPILHA DURELLI <rafael.durelli(a)ufla.br> Data: seg., 21 de fev. de 2022 às 11:35 Assunto: Re: [graph-tool] Adding label to vertices Para: Alexandre Hannud Abdo <abdo(a)member.fsf.org> Ok, I managed to use the data/key nodes. Thanks a lot. However, how can I access them after loading the grapheme file? See the graphml example: <graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd"> <key id="d0" for="node" attr.name="label" attr.type="string"></key> <key id="d1" for="edge" attr.name="weight" attr.type="double"/> <graph id="G" edgedefault="directed"> <node id="US10095832B2"> <data key="d0">"US10095832B2"</data> </node> <edge source="US10095832B2" target="US20180002751A1"> <data key="d1">15</data> </edge> </graph> </graphml> How can I access the 15 and the label ? Thanks a lot On 21 Feb 2022, at 11:01, Alexandre Hannud Abdo <abdo(a)member.fsf.org> wrote: Ni! Hi Rafael, In graphml, ids are not graph data. If your source uses node ids for data you should fix it and use <key>/<data> instead (see 'Additional Data' in <http://graphml.graphdrawing.org/specification.html> <http://graphml.graphdrawing.org/specification.html>). Node ids are for internal parsing use and are not guaranteed to be preserved. Once your source produces labels as specified by the graphml format, in the graph-tool loaded Graph that data will be available as internal property maps: https://graph-tool.skewed.de/static/doc/quickstart.html#internal-property-m… Hope this helps, ale .~´ Le 21/02/2022 à 10:00, RAFAEL SERAPILHA DURELLI a écrit : Hello, guys I have been learning graph-tool.. I would like to know if it is possible to create/load vertices and edges with labels. Im loading a graphml file, and in this file the node id = A, B ,C etc. However, when the loading is done, all vertex are transformed into numbers. I would like to know if is it possible to preservate the vertex name, such as A, B, C, "anyStrings", etc. Thanks in advance -- At.te Prof. Dr. Rafael S. Durelli. O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes. _______________________________________________ graph-tool mailing list -- graph-tool(a)skewed.de To unsubscribe send an email to graph-tool-leave(a)skewed.de -- At.te Prof. Dr. Rafael S. Durelli. -- O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes.

3 2

Adding label to vertices
by RAFAEL SERAPILHA DURELLI 21 Feb '22

21 Feb '22

Hello, guys I have been learning graph-tool.. I would like to know if it is possible to create/load vertices and edges with labels. Im loading a graphml file, and in this file the node id = A, B ,C etc. However, when the loading is done, all vertex are transformed into numbers. I would like to know if is it possible to preservate the vertex name, such as A, B, C, "anyStrings", etc. Thanks in advance -- At.te Prof. Dr. Rafael S. Durelli. -- O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes.

1 0

Generate graph from nested sbm
by Davide Cittaro 20 Feb '22

20 Feb '22

Hi all, given a SBM fit it should be possible to generate a random graph using the fitted model. As far as I understand this is done using gt.generate.generate_sbm() function. What about nested SBM instead? I guess generating a graph from blocks at level 0 doesn't work, is there a workaround for this? Thanks d

2 1

Ubuntu Impish support
by Tanguy Fardet 12 Feb '22

12 Feb '22

Dear Tiago, the installation wiki [1] lists impish as a supported distro but the corresponding apt folder on the server [2] is empty. Is it indeed supposed to contain a deb or is it an issue with the documentation? [1]: https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#d… [2]: https://downloads.skewed.de/apt/dists/impish/ Thanks in advance -- Tanguy Fardet Postdoctoral researcher, University of Tübingen, Max Planck Institute for Biological Cybernetics. Website: https://tfardet.srht.site

2 2

Main path algorithm
by RAFAEL SERAPILHA DURELLI 11 Feb '22

11 Feb '22

I would like to know if snap has implemented the following algorithms: (1) Search path link count (SPLC) -- which is a Traversal counts algorithm (2) Path Search Thanks in advance. -- At.te Prof. Dr. Rafael S. Durelli. -- O conteúdo deste e-mail e anexos são restritos aos seus destinatários e de responsabilidade do remetente. O uso do e-mail deve estar de acordo com os regulamentos institucionais vigentes.

2 1

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

graph-tool February 2022