Dear Tiago,
I have a directed graph of about half a million nodes and approximately a
million edges following scale free behaviour and a power law degree
distribution. To test some of my hypothesis, I would like to generate random
smaller graphs (about 50 up to 200 nodes) representative of the big one.
When I used a sample function that samples straight away from the real
distribution of the big network, I have following problems:
- I generate unconnected nodes with both 0 in AND out degree.
- I generate small sub parts of a few nodes that are not connected to the
main graph.
- If only sampling from nodes with at least 1 degree, the generated graph is
coherent, but not representative anymore as I need a big portion of nodes
with either only one in or one out degree.
Here is the part of my script I used for that, where samples are drawn from
dictionaries of the degrees:
def sample_in():
a=np.random.randint(num)
k_in = in_degrees[a]
return k_in
def sample_out():
if sample_in()==0:
b=np.random.randint(num_out)
k_out=out_zero_zeros.values()[b]
return k_out
else:
b=np.random.randint(num)
k_out=out_degrees[b]
return k_out
N=200
g=gt.random_graph(N, lambda:(sample_in(), sample_out()),
model="constrained-configuration", directed=True)
I also tried sampling from a list of tuples as you have mentioned before in
the forum, but I didn't receive any results, as the tuples randomly drawn
from my list might not be combinable.
degs=[(7,1),(4,3),(5,6),(2,4),(6,8),(2,0),(3,5),(0,3),(2,7),(2,1)]
g = gt.random_graph(4, lambda i: degs[i], directed=True)
- Is there any option I could active that would help me in those cases I
described above?
- Is there a better way how to create representative small networks?
Any help on that issue will be much appreciated.
Best wishes,
Jana
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I am curious what is being used to calculate the standard deviation of the
average in gt.vertex_average and gt.edge_average
>>> t2=gt.Graph()
>>> t2.add_vertex(2)
>>> t2.add_edge(t2.vertex(0), t2.vertex(1))
>>> gt.vertex_average(t2, "in")
(0.5, 0.35355339059327373)
Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ?
also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710
0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some
relation to that.
A little bigger graph.
>>> t3=gt.Graph()
>>> t3.add_vertex(5)
>>> t3.add_edge(t3.vertex(0), t3.vertex(1))
>>> gt.vertex_average(t3, "in")
(0.2, 0.17888543819998318)
Now, we should have 0,1,0,0,0 series for vertex incoming degree.
So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854
come from ?
Reason, I am asking because, I have a large graph, where the average looks
quite alright but the std makes no sense, as going by the histogram, degree
values are quite a bit more distributed than the std would indicate.
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Hi,
I was wondering if there is any way to assign vertex properties while
adding edges to the graph. for example using "add_edge_list" I can assign
edge properties but later I have to iterate through all vertices again to
assign their properties.
I know this is not a problem when the vertex property is of the type "int"
or "float" because then one can use "vprop.a = values", but in case of
"string" and "object" this method doesn't work
What would be the best/fastest way to handle this situation.
I guess it would be very helpful to extend the "add_edge_list" function to
accept vertex property in some way.
cheers,
--
Mohsen

I ran mcmc_equilibrate on a nested block state model in a weighted graph. As
per instructions, I copied the initially computed state in another object
with increased hierarchy depth to 10. However, this fixed the depth to 10.
Everything computed afterwards has depth 10 even if is clear that after 3 or
4 levels the nodes converge to one.
There are many empty branches and when I try to plot it with empty_branches
= False, I get an error stating it is not a tree.
RuntimeError: Invalid hierarchical tree: No path from source to target.
Did anybody perform any similar analyses?
The hierarchy after mcmc_equilibrate:
<NestedBlockState object, with base <BlockState object with 24 blocks (24
nonempty), degree-corrected, with 1 edge covariate, for graph <Graph
object, undirected, with 230 vertices and 11230 edges, edges filtered by
(<PropertyMap object with key type 'Edge' and value type 'bool', for
Graph 0x7fc3a89f1210, at 0x7fc3a64911d0>, False), vertices filtered by
(<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph
0x7fc3a89f1210, at 0x7fc3a64912d0>, False) at 0x7fc3a89f1210>, at
0x7fc3a6491950>, and 10 levels of sizes [(230, 24), (24, 5), (5, 1), (1, 1),
(1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1)] at 0x7fc3a6491590>
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Dear all,
I am a bit confused about the use of the weighted network models for a
weight prediction task;
Suppose we have a weighted network where edges are integers. We fit a
SBM with a Poisson kernel as follows:
|data = gt.load_graph(...) # The adjacency matrix has integer entries,
and weights greater than zero are stored in data.ep.weights. state =
gt.inference.minimize_blockmodel(data, B_min=10, B_max=10, state_args=
{'recs':[data.ep.weights], 'rec_types' : ["discrete-poisson"]}) |
My question, is how can we obtain, from |state|, a point estimate of the
Poisson parameters in order to compute the distribution of the weights
between pairs of nodes.
Regards,
Adrien Dulac

Hi,
I need a graph library that is accessible for both Python and C++
together with a few other requirements.
graph-tool seems to fulfill all this requirements. However, I don't find
any information whether the library is usable from C++ code as well.
My project consists out of several modules that are all aware a one main
graph object. Each module can be written either in Python or C++. The
modules itself are managed with some Python code.
So my question is: Is it possible to get the C++ graph object out of the
Python graph object? Is it possible to fill the C++ graph object
directly with nodes and edges?
Another point is that I need to attach a pointer (or shared_ptr) to a
custom C++ type to some nodes. The pointer does not need to be
accessible or visible from Python. Is this possible in a simple way?
(Of course I can workaround with an e.g. map of type (vertex id,
pointer).)
Regards,
Gerion

I'm running anaconda on a redhat 7.4 linux box and when I try to generate a
graph with text on the vertices. I get the error below:
/opt/anaconda5.3.0-2.7/envs/GraphTool366_102318/bin/python3: symbol lookup
error:
/opt/anaconda5.3.0-2.7/envs/GraphTool366_102318/lib/python3.6/site-packages/graph_tool/draw/libgraph_tool_draw.so:
undefined symbol:
_ZN5Cairo7Context16select_font_faceERKSsNS_9FontSlantENS_10FontWeightE
The code below is what's being used
gt.graph_draw(gMol, pos = pos, edge_pen_width = weightProp,
vertex_font_family = 'serif', edge_color = weightProp, vertex_size = vSize,
vertex_fill_color = countProp, vertex_text = keywordProp, output_size =
(1000,1000), output = '~/myGraph.png')
Any ideas?
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Hi,
I have some questions. Does graph-tool only allow creating images of the graph topology?
Or is there some interaction possible? And is the graphics tools part of the graph-tool?
I managed to use graph-tool via the docker container, but I only create snapshot pictures.
- thanks
(FWIW, I wrote some tool my self that displays an interactive graph: https://github.com/mwarning/GraphViewer/)

Hi,
I've just started reading about Graph cut and Boykov-Kolmogorov algorithm in
particular, which is implemented in Graph-tool. I need it to perform an
object-based segmentation of an image that was previously thresholded to
getting rid of the noise.
I was wondering if it was possible to go from an image to a graph (and the
other way around) in graph-tool? and what would be an efficient way to do
it?
Thanks.
Hakim.
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Hello,
I recently had to repartition my hard-drive and went with the new Ubuntu
build. I have spent the last many few hours trying to build graph-tool with
all of the correct dependencies. I thought I had made it as the make file
was being prepared, however, while it was "Making all in draw" I got the
following error:
/bin/grep: /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such file or
directory
/bin/sed: can't read /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such
file or directory
libtool: error: '/home/getzinmw/anaconda3/lib/libsigc-2.0.la' is not a
valid libtool archive
I have done quite a bit of digging and it seems like, despite having
libsigc-2.0.so.0 file(s) the libtool archive that it is looking for does not
exist.
Can you help me get past this?
Thanks in advance...Sorry for an inconvenience.
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