Re: [graph-tool] Performance search vs shortest_path

dijkstra_shortest_paths_no_color_map_no_init from boost library with the class djk_max_visitor. Do you think I can just extend the class adding the examine_edge method? Sure, why not... Best, Tiago -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https

Re: [graph-tool] Performance search vs shortest_path

if you only want to compute shortest paths or distances, then you should use the specialized functions. Best, Tiago -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] confused with minimize_nested_blockmodel_dl

[e32] = 5 edge_weights[e03] = 1 state = minimize_nested_blockmodel_dl(g, overlap=False, state_args=dict(recs=[edge_weights], rec_types=['discrete-geometric']) ) print('Should be 2, but is ',state.levels[0].B) Why to you think there should be 2 groups instead of 1? -- Tiago de Paula

Re: [graph-tool] Adding edge list from file too large to fit into memory

he 'eprops' parameter), which requires a numpy array with three values, (source, target, weight). However, if you do not have enough RAM to hold the entire graph + weights into memory, this is also not going to work. Best, Tiago -- Tiago de Paula Peixoto ___

Re: [graph-tool] Segmentation fault in MeasuredBlockState copy method

approved your user now; you should be able to log in. I had to turn on manual approvals due to the huge number of spam accounts being created. I'm working on an alternative solution to this. Best, Tiago -- Tiago de Paula Peixoto ___ graph-tool mailing list

Re: [graph-tool] Drawing local clustering vertices with graph_draw ?

Am 29.01.21 um 09:04 schrieb Binon: I am working to draw the vertices included in the local clustering algorithm. But, in the documentation only coefficient values are shown. Please help! Please be more specific, otherwise it's impossible to say anything. -- Tiago de Paula Peixoto

Re: [graph-tool] Compiling graph-tool for pypy?

a shared library component. Otherwise, at the moment it would be a significant effort for me to try this myself... Best, Tiago -- Tiago de Paula Peixoto OpenPGP_signature Description: OpenPGP digital signature ___ graph-tool mailing list

Re: [graph-tool] Segmentation fault in MeasuredBlockState copy method

strange. I can reproduce a segfault with the instantiation of MeasuredBlockState (not copying), but only on buster, not on unbuntu or any other distro. Could you please open an issue for this in gitlab, so I can keep track, and investigate in more detail? Best, Tiago -- Tiago de Paula Peixoto

Re: [graph-tool] Compiling graph-tool for pypy?

speed improvement by using pypy, this would not be achieved for graph-tool, since it is implemented in C++. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_signature Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool

Re: [graph-tool] Reingold Tilford

#graph_tool.draw.radial_tree_layout If you want support for Reingold-Tilford in particular, please open an issue in the website, and I will implement it when time permits. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_signature Description: OpenPGP digital signature

Re: [graph-tool] Issue with signature for bionic repository

he key is indeed expired or if it is an issue on my side? Just try downloading the key again from the keyserver, and you should get an updated one. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_signature Description: OpenPGP digital signature ___

Re: [graph-tool] Find best paths sorted by length with graph tools

://en.wikipedia.org/wiki/K_shortest_path_routing If you open an issue in the website with a feature request, I will implement it when I find the time. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_signature Description: OpenPGP digital signature

Re: [graph-tool] Graphs into layers

gt 2.29 from conda-ostrokach. Please upgrade! There has been up-to-date graph-tool packages in conda-forge for a while now. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F25.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature

Re: [graph-tool] Dimension of graph_tool.stats.vertex_hist

Am 05.12.20 um 13:07 schrieb Ben Hong: I found that the returns of counts and bins have different dimensions , it seems strange. Did you bother to read the documentation? It returns the bin counts and the bin *edges*. If we have N bins, there are N+1 bin edges. -- Tiago de Paula Peixoto

Re: [graph-tool] Model Selection across Distributions

, in the case of discrete distributions, the derivative term is not applicable. Best, Tiago -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F25.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital signature ___ graph-tool

Re: [graph-tool] get_hierarchy_control_points return values

ecause of a boundary condition: The last point does not need to be specified, just as the first one. If it's given, it's ignored. The function get_hierarchy_control_points generates the final point because it's slightly easier in the code. -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F

Re: [graph-tool] get_hierarchy_control_points return values

for the vector, sometimes 50 or so. The documentation clearly states that it's 6 values *per spline segment*, of which there can be an arbitrary amount. -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F25.asc Description: application/pgp-keys OpenPGP_signature Description: OpenPGP digital

Re: [graph-tool] Model Selection across Distributions

is actually misleading in this context, since the value refers to a log-density rather than a log-probability.) Best, Tiago -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F25.asc Description: application/pgp-keys OpenPGP_signature Description: Op

Re: [graph-tool] get_hierarchy_control_points return values

ed to draw the edge. Each spline segment requires 6 values corresponding to the (x,y) coordinates of the two intermediary control points and the final point. Bézier splines are defined as such: https://en.wikipedia.org/wiki/B%C3%A9zier_curve Best, Tiago -- Tiago de Paula Peixoto OpenPGP_0x612DEF

Re: [graph-tool] mixed-membership SBM in graph-tool?

verlapping model. also, slightly unrelated, is there any way to fit a hierarchical model with 2 levels where the top level is overlapping and the bottom level is not? No, this is not currently implemented. -- Tiago de Paula Peixoto OpenPGP_0x612DEFB798507F25.asc Description: applicatio

Re: [graph-tool] How to perform edge contraction?

an achieve this by using the condensation_graph() function: https://graph-tool.skewed.de/static/doc/generation.html#graph_tool.generation.condensation_graph You need only to mark the vertices that need to be merged with the same property map value. Best, Tiago -- Tiago de Pau

Re: [graph-tool] problems with installing

nd it will work. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] problem with graphviz_draw()

-graph-tool installed on my computer which runs on Linux > Mint 19.2 Tina (based on Ubuntu 18.04 LTS, bionic). My graphviz version > is 2.40.1. > > Can anyone reproduce this? > > Best regards > Rolf > -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Error with pen_width

upstream, but you seem to have denied >> my access request so I can't create a merge request. If you think this >> is fine, could you make the change? In general, how do I fix bugs >> if/when I find them if access on git.skewed is not available? >> >> Thanks and regards, >> Snehal Shekatkar >> >> >> >> > > > ___ > graph-tool mailing list > graph-tool@skewed.de > https://lists.skewed.de/mailman/listinfo/graph-tool > -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Error with pen_width

he actual route is simply to clone the repository, make the changes to your cloned version, and then do a merge request. -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Feature Request: Output dominator tree as GraphView

_tool.topology.dominator_tree(graph, start, as_graph=True) That seems too ad hoc for me. I would prefer a more general function that creates a tree graph from an adjacency vector. Please open an issue for this, and I will take care when I find the time. Best, Tiago -- Tiago de Paula Peixoto

Re: [graph-tool] Questions about the .gt format

ger. See why it's important to share the actual code? Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Questions about the .gt format

on-starter. A side observation: If you are implementing a gt reader in Javascript, it is not very likely that you will get much speed improvement over graphml/gml. Significant improvements will only be seen if implementing in C/C++. Best, Tiago -- Tiago de Paula Peixoto signature.asc Desc

Re: [graph-tool] local dynamical probabilities without graph knowledge

s particular code. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Using 'groups' in call to graph_tool.draw.sfdp_layout()

ontrols the strength of the attractive force between nodes of the same group. -- Tiago de Paula Peixoto ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] n_iter with parallel edges allowed

e *never* composed of i.i.d. degrees, since they must fulfill the Erdős–Gallai inequality. For (uniformly) sparse graphs, most sequences of i.i.d. degrees will fulfill it with high probability, so we can say the degrees are approximately independent. But as long as some degrees become large, this is

Re: [graph-tool] n_iter with parallel edges allowed

ou're attempting to generate an impossible graph, so I don't understand what you were expecting would happen. Best, Tiago Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] n_iter with parallel edges allowed

sample the degrees for all vertices first, and check if the final sequence is graphical. If it's not, then a random node is selected, and its degree is re-sampled, and the test is done again. This is repeated, until the sequence obtained is graphical. Best, Tiago -- Tiago de Paula Peixoto

Re: [graph-tool] label_largest_component contains disconnected components

ause I work on a university > server that is a pain to update regularly in case this was a known bug. This is a very old release, and you should definitely upgrade. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature

Re: [graph-tool] Layered overlapping model not working on GraphView

tps://nabble.skewed.de/ > ___________ > graph-tool mailing list > graph-tool@skewed.de > https://lists.skewed.de/mailman/listinfo/graph-tool > -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] distribution for highly skewed discrete edge weights

ption to reduce the variance may be to rank the values encountered, and take the rank index as the transformed covariate. YMMV. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@

Re: [graph-tool] Multilayer graph with select aggregation over layers

ean automatic binning; unfortunately this is not yet implemented in the library. It's in my TODO list, but you know how that goes. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph

Re: [graph-tool] Extreme cpu usage by Eclipse PyDev project using graph-tool

Am 23.08.20 um 13:10 schrieb Kerr Avon: > When a pydev project includes an import of graph_tool, Eclipse consumes very > high cpu cycles by percentage. This has nothing to do with graph-tool. Please report this problem to the pydev project. -- Tiago de Paula Peixoto signatu

Re: [graph-tool] graphviz_draw() cannot plot loops anymore

aspect" is very slow and does not improve the > plots much. Examples are available here: Indeed, we still need some form of non-overlapping heuristics in graph_draw(). I'll leave graphviz_draw() for the time being. Best, Tiago -- Tiago de Paula Peixoto signature.asc D

Re: [graph-tool] graphviz_draw() cannot plot loops anymore

lds, not function > pointers) and the test case works again. Thanks for the fix, and the patch in gitlab, which has been merged. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list

Re: [graph-tool] graphviz_draw() cannot plot loops anymore

> https://lists.skewed.de/mailman/listinfo/graph-tool > > > ___ > graph-tool mailing list > graph-tool@skewed.de > https://lists.skewed.de/mailman/listinfo/graph-tool > -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Exact diameter

(If you want to help me not forget it, please open an issue for it in the website.) Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/m

Re: [graph-tool] optimize a function based on iterate_sync

uch of an improvement anyway, since the reason why it runs faster is mostly because it does not do any extra computation, such as collecting history. The version you have is basically as fast as you can get. The only thing I would suggest is to move the line s = state.get_state() outside of th

Re: [graph-tool] Wrong formula in price networks?

most appropriate version is the one with the constant outside the power, as written in the documentation. I'll fix the code shortly. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mai

Re: [graph-tool] n_iter with parallel edges allowed

nough, but I would encourage you to experiment and draw your own conclusions. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] n_iter with parallel edges allowed

Markov chains. Could you kindly point me > to the actual algorithm? This is the usual edge-swapping algorithm that has been discovered and re-discovered many times since the 50s. You can find a good description in the recent paper: https://arxiv.org/abs/1608.00607 Best, Tiago -- Tiago de Paula Pe

Re: [graph-tool] How can I know a specific edge from a Graph?

negative_weights=True)[1]: print(e, g70.edge_index[e], g70.ep.weight[e]) which will print: (0, 2) 2 -2.0 Note that it's always obvious which of the parallel edges get selected: it's always the one with the smallest weight, otherwise it would not be part of the sh

Re: [graph-tool] n_iter with parallel edges allowed

Am 20.07.20 um 13:08 schrieb Snehal Shekatkar: > If I set "model = 'configuration'" and "parallel_edges = True, > self_loops = True", will "n_inter = 1" suffice? Yes. -- Tiago de Paula Peixoto ___ graph-tool mai

Re: [graph-tool] Effect of hubs in WSBM

I would need to check. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Effect of hubs in WSBM

to cancel certain parts of the likelihood, without paying proper attention to issues of normalization, etc, and expect things to behave consistently. In other words, I do not fully agree with the alpha parameter of Aicher et al. > Is it possible to use LatentMultigraphBlockState() with a weigh

Re: [graph-tool] Effect of hubs in WSBM

sense under the model, because a random multigraph model with the same degree sequence would yield a larger number of connections between the hubs, and between the nodes with smaller degree. See an explanation for this in this paper: https://arxiv.org/abs/2002.07803 Best, Tiago -- Tiago de Paul

Re: [graph-tool] What formula is used for std in vertex_average and edge_average?

want to express the uncertainty of the mean, not of the distribution. > It is just a curiosity because I never saw that measurement :) https://en.wikipedia.org/wiki/Standard_deviation#Standard_deviation_of_the_mean -- Tiago de Paula Peixoto ___ graph-tool maili

Re: [graph-tool] Specifying number of blocks in a bipartite SBM

: model.vp['node_type'], 'pclabel': model.vp['node_type']}) > > then I will end up with a partition with G blocks. But what I want is a > partition in which the type 1 nodes are divided into G1 blocks and the type > 2 nodes into G2 blocks, where I specify G1 and G2. This is currently not yet

Re: [graph-tool] Building (and working with) bipartite graphs

o draw: > > gt.draw_hierarchy(state, layout='bipartite') > > but I get this error In order for us to investigate further you need to provide us with a minimal working example, not only the error message. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP

Re: [graph-tool] ranking vertices by value of vertex property

pr.a.argsort() Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Missing Example in Flow Algorithms?

the specific website permission, so I hope that another > person who has access can post the issue in order for it to get fixed! It's a public website, but you need to login. You can use your account on google, github, etc, or you can create a new one. -- Tiago de Paula Peixoto signature.

Re: [graph-tool] Missing Example in Flow Algorithms?

indeed missing. Thanks for spotting it! Please open an issue in the website, and I'll fix it for the next release. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Memory requirement estimate for a large graph

Is there a reason why I get that figure? Hard to say without a minimal working example. Try saving the network to disk, and loading it again from a newly started interpreter. I tried on my machine, and I got 4.5 GB. As I explained, std::vector<> may over-commit the allocations. --

Re: [graph-tool] Memory requirement estimate for a large graph

0 bytes = 3.01 GB In practice you will need a little more, since std::vector<> tends to over-commit. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Questions about PPBlockState

communities, and outside. So those two models do not fit together. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Questions about PPBlockState

e description length is useful to select the best fitting model, but not to tell if they give similar answers. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Freeze using SIRState

if it's using fork(). You should disable OpenMP in the beginning of your code with: import graph_tool as gt gt.openmp_set_num_threads(1) Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-t

Re: [graph-tool] Freeze using SIRState

l be performed. A serial run > works normally (without multiprocessing). > > Would anyone have a tip? > > Best regards, > > Ronaldo Alves > ___ > graph-tool mailing list > graph-tool@skewed.de > https://lists.

Re: [graph-tool] Unable to install on ubuntu 16.04 LTS

Am 30.06.20 um 12:32 schrieb Tiago de Paula Peixoto: > There are no packages for xenial, since it's outdated and has reached > end of life. You should upgrade to a supported ubuntu version (the > current LTS is 20.04, but 18.04 will work too). I'm sorry, this is incorrect, xenial has no

Re: [graph-tool] Unable to install on ubuntu 16.04 LTS

outdated and has reached end of life. You should upgrade to a supported ubuntu version (the current LTS is 20.04, but 18.04 will work too). -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Doubt about SIR model

ion of the node? I checked the references, but I > still couldn't understand. > Can you help me? It's right there in the documentation: r : ``float`` (optional, default: ``0.``) Spontaneous infection probability. Best, Tiago -- Tiago de Paula Peixoto signature.asc Desc

Re: [graph-tool] Could not link against boost iostream

ostreams > > > How can I solve this? > Thanks! > > > > > > -- > Sent from: https://nabble.skewed.de/ > ___ > graph-tool mailing list > graph-tool@skewed.de > https://lists.skewed.de/mailman/listinfo/gra

Re: [graph-tool] Multiple edge weights and model comparison in the SBM

mis graph object to the union graph The documentation of "copy_property" says: "The optional parameter ``g`` specifies the source graph to copy properties from (defaults to self)." Since this not owned by the same graph you need to do: ug.copy_property(src=g.vp.label, g=g) (I wil

Re: [graph-tool] Multiple edge weights and model comparison in the SBM

need to use `Graph.copy_property()`. Please show me an example of where you do something that is _supposed_ to work, so I can say what the problem is. Please send complete and minimal examples. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___

Re: [graph-tool] Multiple edge weights and model comparison in the SBM

cated). This will create parallel edges for those that appear in both graphs, which you can remove with remove_parallel_edges(). You can then copy any edge property map from either g1 or g2 by calling Graph.copy_property() on the union graph. -- Tiago de Paula Peixoto signature.asc Descr

Re: [graph-tool] Multiple edge weights and model comparison in the SBM

has been measured. Before we talk about how to do anything efficiently, can you first explain what "get around" this issue means? How do you expect two graphs with a different set of edges to share the same edge property map? -- Tiago de Paula Peixoto signature.asc Description: OpenPG

Re: [graph-tool] efficent way to assign values to vector property map

he property map? Not without looping and assiging them one by one. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] Change point detection: Inferring the mesoscale structure of layered, edge-valued, and time-varying networks

ted. You will have to do the binning yourself. But it's not that difficult... -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] ImportError: libboost_python3-py36.so.1.65.1

st graph-tool 2.32 was not built for 19.04 because it has been discontinued (reached end of life). Maybe the error above is because you installed a package for another ubuntu version? Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature

Re: [graph-tool] Error while logging in/registering git.skewed.de

Am 05.06.20 um 12:17 schrieb Enrique Castaneda: > Still the same errors (No confirmation email and account blocked while > trying with bitbucket) The email confirmation should be working now. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital sig

Re: [graph-tool] Error while logging in/registering git.skewed.de

3.nabble.com/file/t496242/2020-06-05_06_04_32-Window.png> > > > Am I doing something wrong or is there another process to register the site. Could you please try again? I have been doing maintenance on the server, which has just been moved to a new location. -- Tiago de Paula P

Re: [graph-tool] Distribution while fitting weighted SBM

spy? Or do you see a more direct way? It would be valid as a reasonable approximation, since the models become equivalent as the number of edges becomes sufficiently large. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature __

Re: [graph-tool] Distance map returned from shortest_distance function misses entries of certain vertices

ot;infinite weight" edges using an edge filter. Best, Tiago Ps. I note you are using Python 2, but current versions of graph-tool only support Python 3. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-t

Re: [graph-tool] Distribution while fitting weighted SBM

I was figuring that this should also be possible when fitting the model. Yes, this exactly what is described in the above paper, and what is implemented in graph-tool. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___

Re: [graph-tool] Multiple edge weights and model comparison in the SBM

on is ill posed. It would be like comparing a discrete geometric distribution with a Gaussian; they will always be different, as they do not even have the same support. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature _

Re: [graph-tool] Change point detection: Inferring the mesoscale structure of layered, edge-valued, and time-varying networks

ented in the > graph-tool library? I can't seem to find this implementation in the > documentation. Unfortunately, this is not currently automatized in graph_tool. It has been in my todo list for a long time, but I never manage to get to it. Sorry! -- Tiago de Paula Peixoto signature.a

Re: [graph-tool] Programatically determining blocks on visualization with hSBM

the word groups (topics) produced by the hSBM model? Yes, take a look at the "get_hierarchy_tree()" function that returns you the tree used in the layout. It returns a 'label' property map that maps the vertex of that tree to the corresponding group label. Best, Tiago -- Tiago de Paula Pe

Re: [graph-tool] Reduce function on parallel edges, and more general groupby-reduce in graph-tool

possible with condensation_graph(). Please open an issue in the website with a feature request, and I will implement it when time permits. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@

Re: [graph-tool] a lot of warning for g++ 8.3.0

graph-tool, I do not see any warnings. As I already told you two times before, these warnings come from outside of graph-tool. Fix your environment if you do not want to see them, or disable them. Just don't shoot the messenger. Best, Tiago -- Tiago de Paula Peixoto signature.asc Des

Re: [graph-tool] fail to build for GCC 8.3.0

our version of) boost. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] fail to build for GCC 8.3.0

should work. You should also think about using conda, which does not require compilation, and is specially well suited for these kinds of restrictive environments. (Also note you are trying to compile an older version, the newest one is 2.32) Best, Tiago -- Tiago de Paula Peixoto signature.

Re: [graph-tool] a lot of warning for g++ 8.3.0

trace-limit=0 ${CXXFLAGS}"] Why? You can override this with -Wno-all -Wno-extra etc. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists.skewed.de/mailman/listinfo/graph-tool

Re: [graph-tool] ./configure fail to find boost in a custom location

ocations. (But I believe "LIBS" is unnecessary.) It's all explained in the installation instructions: https://git.skewed.de/count0/graph-tool/-/wikis/installation-instructions#installing-in-a-specific-location-eg-in-a-home-directory Best, Tiago -- Tiago de Paula Peixoto signatur

Re: [graph-tool] a lot of warning for g++ 8.3.0

; rng_t&) [with Graph = boost::filt_graph int>, > graph_tool::detail::MaskFilter char, boost::adj_edge_index_property_maplong unsigned int> > >, > graph_tool::detail::MaskFilter char, boost::typed_identity_property_maplong unsigned int> > > >; State > = graph_tool::m

Re: [graph-tool] fail to build for GCC 8.3.0

/users/lisergey/ClearMap2/graph-tool/src' > make: *** [Makefile:599: install-recursive] Error 1 This is a bug in GCC that has been fixed in newer versions. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___

Re: [graph-tool] edge weights vs multi-graphs in minimize_blockmodel_dl

eing connected, but where every edge has an integer covariate that is very high, say on the order of 100, which would not be possible to generate with model 1 without the whole graph becoming dense. Best, Tiago -- Tiago de Paula Peixoto signature.as

Re: [graph-tool] module 'graph_tool' has no attribute 'minimize_blockmodel_dl'

Am 22.05.20 um 09:38 schrieb sam: > import graph_tool as gt This should be: import graph_tool.all as gt -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de ht

Re: [graph-tool] edge weights vs multi-graphs in minimize_blockmodel_dl

es in the graph, they are taken into account, since the underlying SBM accepts multigraphs. This is done automatically, and there is nothing special that needs to be done. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ gra

Re: [graph-tool] installing certain commit of graph-tool

pile the library (following the installation instructions for native compilation available in the website). -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://lists

Re: [graph-tool] Hierarchical Tree layout with transmission date

t; > It's possible to provide your own tree layout for the drawing, but there is currently no implementation for the layout that you are specifying. -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing l

Re: [graph-tool] Remove all neighbors of a vertex

ould I do? I tried the remove_vertex() API, it seems there > is something wrong. I ask for help from You. Please explain what is wrong with minimal and self-contained example that shows the problem. -- Tiago de Paula Peixoto ___ graph-tool mailing

Re: [graph-tool] betweenness in 10,000 increments

possible to say anything without knowing your network, and what your expectations were. Why would an increment of around 1 be wrong for your network? You can easily test for yourself that the betweenness values for many networks do not increment by that amount. Best, Tiago -- Tiago de Paula P

Re: [graph-tool] Weighted Clustering

ect the same coefficient for weighted and unweighted. The > unweighted coefficient for the above example is reasonable. As is explained in the documentation, the clustering values are normalized only if the weights are all below 1. Best, Tiago -- Tiago de Paula Peixoto signature.asc D

Re: [graph-tool] setting vp.pos to emphasize block structure in state.draw?

nd 'gamma' parameters of sfdp_layout(), but this does not always give very good results. YMMV. Best, Tiago -- Tiago de Paula Peixoto signature.asc Description: OpenPGP digital signature ___ graph-tool mailing list graph-tool@skewed.de https://li

Re: [graph-tool] collection module not accessible from the top module

ection graph_tool.collection.data['karate'] As is explained in the documentation, there is a convenience module called 'all' which imports all submodules, so you do not need to do this individually for each one: import graph_tool.all as gt gt.collection.data['karate'] Best, Tiago -- Tiag

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