graph-tool March 2022

graph-tool@skewed.de

6 participants
5 discussions

Clabels cause segmentation fault
by RESTOCCHI Valerio 24 Mar '22

24 Mar '22

Hi all, I am having some problems working with clabels. Whenever I use mcmc algorithms with clabels the kernel dies (upon inspection, I found the error is 'segmentation fault (core dumped)'). I am not sure what I am doing wrong, so here’s a minimum working example: g = gt.collection.data["lesmis"] clabel = g.vp["clabel"] = g.new_vp("int") for v in g.vertices(): clabel[v]=np.random.randint(3) state = gt.NestedBlockState(g, state_args={'clabel':clabel,'pclabel':clabel}) for i in range(100): state.multiflip_mcmc_sweep(niter=10) If it helps, I’m getting the same problem with the following changes: - use equilibrate instead of multiflip. - use two labels instead of three. - use minimize_nested_blockmodel_dl instead of NestedBlockState - pass clabels dictionary as **args Extra information: - If I run the multifip MCMC fewer times (let’s say 10) sometimes it works, sometimes it doesn’t, so it seems that the error is somewhat stochastic. - This happens on different machines, both with Linux and Mac Is this a bug or am I doing something wrong? Best, Valerio --------------------------------------------------------------------- Lecturer in Business Applications of Informatics Room 2.18a - Informatics Forum School of Informatics - University of Edinburgh The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

2 1

Contracting all paths through components of hidden vertices
by Simon Rose 18 Mar '22

18 Mar '22

Hi, I am currently filtering a graph. Sometimes hiding the vertices splits the original graph into separate components. Is there an elegant solution to avoid this? Essentially I would like to contract all paths through a component of hidden vertices into a single edge. I have found a solution that works, but it is incredibly slow: 1. Creating a GraphView with only the hidden vertices and label the components in this GraphView 2. For each of the hidden components loop over all vertices in the component and look for vertices that have a different in-degree or out-degree in the hidden GraphView and the original unfiltered graph 3. For each vertex 'I' with a different in-degree label the out-component and check which vertex 'O' with a different out-degree is part of the out-component of 'I' 4. Create an edge between all the in-neighbors of 'I' and all out-neighbors of 'O' The result is correct, all the vertices that are connected by a path through these hidden components are now connected by a single edge in the filtered graph, but the process is painfully slow on graphs with 600k-5M vertices.

1 0

Fetch all the edges between given two vertices
by Snehal Shekatkar 09 Mar '22

09 Mar '22

Dear all, I am analyzing a multigraph and I would like to fetch all the edges between given two vertices during runtime. I haven't been able to figure out an easy way to do this. For now, there are two possible ways: 1. Iterate over all the edges and catch the ones which connect vertices u and v 2. Go through all the neighbours of u and find out all the occurrences of v Both these operations, especially the first one, is expensive. Also, `g.edge(u,v)` seems to return only one edge without any information about which one it is. How can I solve this problem? Best regards, SMS -- Snehal M. Shekatkar https://inferred.in PGP key -> https://inferred.in/snehal_pub_key.txt

2 2

Saving gt.interactive_window to html
by James Ruffle 08 Mar '22

08 Mar '22

Hi all, I was wondering if there is a simple way to save gt.interactive_window to html for interactive visualisation across web browsers? i.e. similar to implemented with plotly, and so on. I have seen that gravis looks like an excellent alternative package to generate this otherwise, but wanted to first check if I was missing something within graph-tool to simply export the interactive_window. #contained example import graph_tool.all as gt import matplotlib g = gt.collection.ns["new_guinea_tribes"] state = gt.minimize_nested_blockmodel_dl(g, state_args=dict(base_type=gt.LayeredBlockState, state_args=dict(ec=g.ep.weight, layers=True))) levels=state.get_levels() l0blocks=levels[0].get_blocks() t = gt.get_hierarchy_tree(state)[0] tpos = pos = gt.radial_tree_layout(t, t.vertex(t.num_vertices() - 1), weighted=True) cts = gt.get_hierarchy_control_points(g, t, tpos) pos = g.own_property(tpos) #want to export this to HTML gt.interactive_window(g,pos=pos,edge_control_points=cts, edge_color=g.ep.weight, edge_gradient=[], vertex_fill_color=gt.prop_to_size(l0blocks), ecmap=(matplotlib.cm.coolwarm_r, .6), edge_pen_width=5, sync=True,update_layout=False,geometry=(2000,2000), vertex_text_color=[1,1,1,1],bg_color=[0,0,0,1] ) Many thanks, James

1 0

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

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

graph-tool March 2022