.
(Emailing to the old mailing list has been disabled; all messages posted
to graph-tool@skewed.de will henceforth come to discourse automatically.
The mailing list archives are still available, but have been mirrored
there in full.)
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
history is available.
I'm in the process of configuring post via email, in which case the
forum will behave just like a mailing list. If this works well, I can
deprecate this list. However, in the mean-time it will remain active.
Best,
Tiago
Am 06.11.22 um 21:49 schrieb Tiago de Paula Pe
should be much
slower than graph-tool.
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP digital signature
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
the mailing list and forum is now available in the
project's webpage.
Feel free to use what you prefer.
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP digital signature
___
graph-tool mailing list -- graph
uld
be most welcome
___________
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP digital signature
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Any advice/help would be greatly appreciated. Thank you
If you pass a bipartite pclabel, then this bi-partition gets reflected
in the upper levels of the hierarchy as well. This is normal.
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP di
low, since this
predicate would need to be computed in the inner loop of the algorithm.
The hash approach outlined above is far faster, and easy to implement in
general.
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP di
is happening you would need to send us a
minimal but complete working example that shows the problem.
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP digital signature
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
be more
specific? Thank you so much for your help!
This warning is not applicable if minimize_nested_blockmodel_dl() is
being used, only if you are attempting to sample from the posterior
distribution (and not finding its maximum).
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPG
l/-/issues/725> and I encountered
the same error. I took a look of the source code of graph-tool and I did
not find where is the problem. Could you please help me about it? Thanks!
I cannot reproduce this. What version of graph-tool are you using?
cation,
unfortunately! Hopefully in the future...
Best,
Tiago
--
Tiago de Paula Peixoto
OpenPGP_signature
Description: OpenPGP digital signature
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
one graph but not the other? Would it suffice to identify partitions
in both graphs and then check for the differences?
I'm not sure I completely understand. What do you mean by one block
being in one graph, and not in the other? Could you give an example?
--
Tiago de Paula Pe
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
assigned degrees? Is it being done for
correctly sampling from a given degree distribution? Or am I missing
something?
This can be implemented in a trivial way simply by rejecting these large
numbers already in the `deg_sampler` function that you supply to
random_graph().
--
Ti
, the “eweight” parameter refers to edge multiplicities, not the
covariates.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
s indeed a bug, unfortunately.
Can you please open an issue in the website with the minimal example
above so I can keep track of this and fix it?
Thanks!
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 09.03.22 um 12:50 schrieb Snehal Shekatkar:
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?
Just call: g.edge(u, v, all_edges=True)
--
Tiago de
3/PhysRevX.11.021003
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
= shortest_distance(g, source=u, pred_map=True)
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
.
There is a documentation that explains how to use it, and I cannot read
your mind to determine what you did or did not understand from it.
We can only help with specific questions.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool
quot;_graphml_vertex_id"]
and
g.ep["_graphml_edge_id"]
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ience function for this, which is:
state.levels[0].sample_graph()
For non-nested model this is only:
state.sample_graph()
These are just convenience wrappers for generate_sbm().
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing
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#debian-ubuntu
[2]: https://downloads.skewed.de/apt/dists/impish/
Thanks in advance
--
Tiago de Paula Peixoto
.
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
o unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
that would be appreciated.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
still change slightly in future releases, but
you'll always be able to download any version from PyPI.
This is very interesting! Thanks for sharing.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubs
y in replying, but I don't see an obvious way to
implement what you want with the current code.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
this what you're looking for?
https://graph-tool.skewed.de/static/doc/gt_format.html
Best
Haiko
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Pe
incident on the groups. But it is still not very
clear exactly what you want to find.
In any case, this is a question about a particular research problem, so
I don't believe it is appropriate for this list, which is about using
graph-tool.
Best,
Tiago
--
Tiago de Paula Pe
ll me what you mean by this.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ok them up, it's better just to
store their index, and get a descriptor at the time you need it.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ot;.
Of course it does. Just reverse the graph with:
GraphView(g, reversed=True)
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 11.11.21 um 10:47 schrieb Monecke, Stephan:
Any ideas on how I can debug this?
Yes: try to isolate the problem by constructing a minimal,
self-contained program that reproduces the crash.
--
Tiago de Paula Peixoto
___
graph-tool mailing list
ean-time, what you can do is to fit the non-overlapping
model first, and use that as a starting point to the MCMC with overlap.
You do that simply by doing:
state = state.copy(state_args=dict(overlap=True))
Best,
Tiago
--
Tiago de Paula Peixoto
ed hat CERTIFIED SYSTEM ADMINISTRATOR - RHCSA 8
Certification ID 210-168-829
<https://rhtapps.redhat.com/certifications/badge/verify/D5UDWS5NEBPLMO5ZTQQZHQIERQAEQU3CUPSQX2KSDXT6RW46LQ3T7ULZ55KZZ56SKO7EQ3ETTLYZQ4U5NQYTCNA62RUWOCM34WWBUYQ=>
<https://redhat.com/trusted>
___________
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe
n the underlying graph.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 26.10.21 um 16:23 schrieb Tiago de Paula Peixoto:
It is possible to pass a single source but multiple targets.
It is possible to pass also a single source and no target, in which case
the function computes the distances to all other vertices.
By sub-sampling the source vertices you can
V are lists of same length with sources / targets but that's not
implemented.
It is possible to pass a single source but multiple targets.
Subsampling is usually a good technique to reduce the computation time,
but it is hard to know what is applicable to you.
Best,
Tiago
--
Tiago de Pau
State objects being created,
together the memory usage required for the minimize_blockmodel_dl()
algorithm.
I don't think there is very much you can do, except use a model that
requires less internal book-keeping, e.g. PPBlockState.
Best,
Tiago
--
Tiago de Pau
tant to tell us what version of graph-tool you are running.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
parallel using
multiprocessing. my impression is that MCMC was relatively light on memory.
As usual, it is not possible to say anything concrete without a minimal
complete working example that shows the problem.
--
Tiago de Paula Peixoto
___
graph
n_property)
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
andom.seed() initializes numpy's RNG, which different from
the one used in graph-tool (which is in C++). You need to replace that
line with:
gt.seed_rng(0)
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe s
] = g.own_property(blocks[0])
But I can only guess.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
g.org key server. Please check your network
connectivity, try another key server, or try to download the key
directly via the browser.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email
roblem to the conda-forge project:
https://github.com/conda-forge/graph-tool-feedstock/issues
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
y much.
I notice that you are subclassing Graph, and probably omitting to us
specializations that you are making to Graph.vertex() and other methods.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send a
similar to the full network.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
e only way possible.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ental/lib/python3.8/site-packages/graph_tool/inference/blockmodel.py
in remove_vertex(self, v)
1144twice.
1145 """
-> 1146 self._state.remove_vertex(int(v))
1147
1148 def add_vertex(self, v, r):
AttributeError: 'graph_tool::BlockS
(n)
Please read carefully the documentation to understand the difference
between G.iter_edges() and G.edges().
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
the original
NestedBlockState object? How do I have to write that?
Just create a new NestedBlockState (or, equivalently, copy the from the
old one):
state = NestedBlockState(g, bs=y)
or
state = state.copy(bs=y)
Best,
Tiago
--
Tiago de Paula Peixoto
similarity between layers.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 20.08.21 um 22:09 schrieb Oliver Baumann:
Tiago de Paula Peixoto wrote:
Am 20.08.21 um 20:51 schrieb oliver.baumann(a)uni-bayreuth.de:
Hi all,
I'm currently offloading construction of the uni-modal projection of a bipartite
graph from Python to C++ (NB: I am not very familiar
not mean that the
graph is not being filtered... If you iterate over it, you will get what
you expect.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ted in the library.
Furthermore, I don't think that the microcanonical priors / integrated
likelihoods will be easy to write down in closed form for this kind of
constraint.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@s
s an array indexed by the edge index, which will contain values
for non-existing edges if the indexes are not contiguous. This is what
you are seeing.
If you want to see only the property values for existing edges, you
should get a filtered array with the ".fa" property.
Best,
Tiag
the ax sizes are the exactly the same.
Can you please help me how can I sort this out?
You can set the vertex size and edge with explicitly, by passing values
to the vertex_size and edge_penwidth parameters of the graph_draw()
function.
--
Tiago de Paula Peixoto
these classes?
Will it work?
Yes, pickling is supported for property maps of type boost::python,
provided the values themselves can be pickled.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to
mouse, I am
still able to select or highlight a filter vertex.
Is there an easy way to fully hide the filtered vertices?
Without a minimal working example that shows the problem you are
describig, there is not much that we can help with...
--
Tiago de Paula Peixoto
since the python interpreter needs to be
involved. So it's better to do this once, ahead of time, and preferably
store all property map values in a single python object.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@sk
es from your
C++ extension by using python::extract().
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
layer 0 in the property
map "bm". Is this what you want?
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
-edge also belongs to a specific layer.
What else do you need?
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
get_edge_blocks. I
presume there is a relatively straightforward way to do this?
Do what? Please ask a specific question.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph
twork!
There must be something wrong going on.
Try the step-wise approach, maybe it will help you to track it down.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-to
blocks(), which will give you this
information. From this, you should be able to decompose membership
across layers, etc.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
e the optimizations that have been
included and what do they affect
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Pe
rarchies of different depths.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
NameError: name 'etype' is not defined
You seem unfamiliar with the Python syntax. In Python, objects need to
be declared before they are used.
The correct way to obtain the property map would have been:
etype = G.ep["etype"]
etype[e]
--
Tiago de Paula Peixoto
_
d an email to graph-tool-le...@skewed.de
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ds_str] = wgts
GV2 = gt.GraphView(GV, efilt=wgts.fa != np.inf)
*3) I then use GV2 for calculating Dijkstra and such...*
I could of course work on an MWE of some sorts. But would be very
nice to get an estimate on mem footprint, and to see if I'm doing
use in your particular
circumstances, we have to know first what it is...
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
ying you got a segfault is not actionable information, since we
cannot easily reproduce it.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 01.06.21 um 17:25 schrieb Davide Cittaro:
It seems this feature has already been requested :)
https://git.skewed.de/count0/graph-tool/-/issues/671
<https://git.skewed.de/count0/graph-tool/-/issues/671>
Indeed! :-)
--
Tiago de Paula P
iates is not yet implemented!
This is not very difficult to do "by hand", bit it would be a nice
addition to the library.
Could you please open an issue in the website for this request, and I
will try to include it for the next release.
Best,
Tiago
--
Tiago d
c/doc/demos/inference/inference.html#edge-weights-and-covariates
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
Am 07.05.21 um 20:17 schrieb Marat Idrisov:
Yes, I use NJOBS=1
I never needed 10GB to compile it with only one job... But in any case,
I'm afraid there is not much that can be done.
--
Tiago de Paula Peixoto
___
graph-tool mailing list --
the arm64 architecture
in the near future or can you suggest steps to optimize the build?
Change the variable NJOBS=4 to 1. This will reduce the memory usage (but
it will increase the build time).
--
Tiago de Paula Peixoto
___
graph-tool mailing list --
Thanks for this wonderful module!
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-too
Am 03.05.21 um 17:20 schrieb JohannHM:
Thank for your comment, Tiago.
Would you please recommended me one of the included methods of your gt that is
useful for comparing:
a. cover, vs partition
b. covers, vs covers
Nothing in particular comes to mind.
Best,
Tiago
--
Tiago de Paula Peixoto
n, is non-overlapping.
RMI is not applicable to this case.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
r each node, indexed by the
node index.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
m one is versus the other, when
compared to a fully random graph with the same density, but no deeper
insight.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
solid
statistical grounds.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
t all the partitions into the
lowest level and get the marginals for that.
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
points
cts = gt.draw.get_hierarchy_control_points(g, tg, tpos)
```
This is given by the "tg" (a graph representing the hierarchy tree) and
"tpos" parameters above (the position of the tree nodes).
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool
quot;
way, without plotting support.
It's perfectly possible. GTK is an optional run-time dependency. It does
not have to be present during compilation, and if it's not available at
run time, the graph-tool import will still succeed, with only a warning
that graph_draw() will not work.
e" version of the model, then the nodes of
degree zero in a given layer are considered not to be long to that
layer, i.e. they have a probability of zero of receiving edges of that type.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mail
ng I intended to fix,
but it seems I forgot.)
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list -- graph-tool@skewed.de
To unsubscribe send an email to graph-tool-le...@skewed.de
meaningful. From the point of view of model
selection, the description length can only be used to compare identical
networks.
Before you conduct your analysis, you should have a clear criterion of
what you consider a "better" partition.
Best,
Tiago
--
Tiago de Pau
, selected.get_blocks()))
--
Tiago de Paula Peixoto
___
graph-tool mailing list
graph-tool@skewed.de
https://lists.skewed.de/mailman/listinfo/graph-tool
ns you can do:
a = g.vp.pos.get_2d_array([0, 1])
The reason why this is needed is because vector properties are *not*
internally stored as contiguous 2D arrays.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list
graph-tool@sk
@skewed.de
https://lists.skewed.de/mailman/listinfo/graph-tool
--
Tiago de Paula Peixoto
___
graph-tool mailing list
graph-tool@skewed.de
https://lists.skewed.de/mailman/listinfo/graph-tool
state_ln model. Is it supposed to be so?
Shouldn't we always copy the state of the models we ran in the first place
to run merge-split algorithm?
Yes, this is an error in the howto! Thanks for noticing. It will be
fixed in the next version.
Best,
Tiago
--
Tiago de Paula Pe
s() call into some
cython-type code, do you think that would speed up this for loop?
If the bottleneck is really there, this could help, but not by much. But
again, I think it's unlikely, unless your graph is quite small.
Best,
Tiago
--
Tiago de Paula Peixoto
un into similar problem? Can anyone check this out and share how
one can get around this problem ?
Thank you so much,
Edgar
--
Sent from: https://nabble.skewed.de/
___
graph-tool mailing list
graph-tool@skewed.de
https://lists.skewed.
ins all the
answers to questions such as this:
https://graph-tool.skewed.de/static/doc/inference.html#graph_tool.inference.blockmodel.BlockState.get_nonempty_B
--
Tiago de Paula Peixoto
___
graph-tool mailing list
graph-tool@skewed.de
https://lists.skewed.de/mailman/listinfo/graph-tool
passing overlap=True to
LayeredBLockState), which will cluster the "half-edges", and hence give
partitions that (potentially) vary between the layers.
Best,
Tiago
--
Tiago de Paula Peixoto
___
graph-tool mailing list
graph-tool@skewe
1 - 100 of 1665 matches
Mail list logo
