gorithm is Bellman-Ford, which is much slower, with
O(V * E).
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ou want more meaningful help, please be
more concrete, with an example, etc.
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quot;, line
> 484, in _attrs
> nattrs[int(attr)] = _prop(d, g, _convert(attr, v, cmap))
> File "/usr/lib/python3/dist-packages/graph_tool/draw/cairo_draw.py", line
> 323, in _convert
> cmap, alpha = cmap
> ValueError: too many values to unpack (expec
owever the edges and vertices are remain the same,
> only weights change.) Is there a faster/better way to do this?
You can access the weights as a numpy array via:
weights.fa
It can be faster to just update this array, than to re-generate the whole
thing from scratch.
Best,
Tiago
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zation like this a bit hidden. To achieve
what you want, you need to do:
minimize_blockmodel_dl(g,
mcmc_args=dict(entropy_args=dict(degree_dl_kind="uniform")))
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_
. If you
still think there is a problem, please post a minimal and self-contained
example (the one you sent isn't, because it did not contain the graph you used).
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gt
and then use directly gt.eigenvector().
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s to have solved.
???
If the problems you mention are really there, then they need to be fixed. I
ask of you to please produce a minimal and complete example for them.
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ops=[eprop1] does
not work, as the number of columns is unmatched.
What version of graph-tool are you using?
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e there is little
we can do.
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lity (remember you have to copy the state with
state.copy(g=g_new), after modifying the graph). By normalizing this over
all weight values, you have the conditional posterior distribution of the
weight.
(This could be done faster by using BlockState.get_edges_prob(), but t
nd
>
>
> *g.list_properties()*
>
>
> it doesn't show anything at all. Why so ??
Please read the documentation carefully. Graph.list_properties() only lists
the internal property maps, not all property maps created. If you want your
property map to show up, you need to d
;>>> quit()
>
>
>
> Well, googling this error did not help to solve the problem. Could you
> please suggest a solution ?
Sorry for the lack of response after such a long time, but I haven't been
able to reproduce this problems in any of my systems Could you give me
mor information about your setup (OS, compiler, cairo version, etc.)?
Best,
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ry for graph-tool. You should use 'bionic' instead.
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tates for the individual layers?
The simplest option is again to use filtering:
u = GraphView(g, efilt=ec.fa == l) # filter only edges from layer l
lstate = state.copy(g=u) # block state w/ same partition
lstate.draw()
Best,
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Am 25.09.18 um 00:51 schrieb Ozgun Altunkaya:
> Hi,
>
> Thanks for the reply. I've got two more questions:
>
> edges = g.edge(1, 536)
> for e in edges:
> print(e)
>
> returns None because there's no such edge. However, when I run
>
> gt.shortest_distance(g, 1, 536)
>
> it returns 2, bu
erty(g, partition, "target")
This will propagate the partition value of the target node to the edge, as
an edge property map. You then can pass this to "edge_color" in graph_draw().
Best,
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model.
>
There is no option to toggle it. But you can filter them out:
u = GraphView(g, efilt=label_self_loops(g).fa == 0)
state = state.copy(g=u)
state.draw()
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rkX with has_path. I think
> this is doable in graph-tool with StopSearch method, but I couldn't figure
> out a way to implement it. Any help is appreciated.
This is trivial, just do:
has_path = shortest_distance(g, u, v) < g.num_vert
at shows whatever problem you might be encountering. Analyzing code
fragments like this, decoupled from their context in the larger program, is
not a good use of our time.
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ot; it
as a Dataframe. You have to use the documented API to access it (which is
more appropriate than using Pandas).
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here a more efficient way to do this, if I cannot make "find_edge_range"
> work?
Just use the newest version.
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,...] to pin down a node to group 0, for example. If you use constant
values (or leave the vector empty) it will amount to a flat prior, and the
placement will be unconstrained.
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ion. ;-)
It is stateB.project_partition(3, 0).
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Am 26.07.2018 um 11:59 schrieb Tiago de Paula Peixoto:
> All that is needed if for a 'core' dev to adopt it, so it can be included in
> the main repo. You can vote for the package in AUR (and get your friends to
> do it too), and lobby the devs for inclusion.
Some more info on
umber like 3000 gives usable results.
> But How to get the vertex property label/name in subsequent blocks similar
> to what I get from vprop ?
# this projects level 3 onto level 0 and returns the property map
b = state.project_level(3, 0)
Best,
Tiago
so it can be included in
the main repo. You can vote for the package in AUR (and get your friends to
do it too), and lobby the devs for inclusion.
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Tiago
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one layer of this multilayer network? Because the input is just a single
> graph.
Right, you have to collapse them in a single graph with multiple edges. The
time-stamp on the edges (i.e. the "layers") should be stored as a property
map that you pass as the 'ec' parameter
ld I use?
It's always the same constructor, LayeredBlockState. To allow the membership
to change across layers, you need to set overlap=True.
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can run, so we can understand what
the problem may be.
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a graph with weighted edges?
Yes, it accepts 'recs/rec_types/rec_params' just like the regular BlockState.
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canonical formulation, this is technically more difficult.
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_distance(g, weights=g.edge_properties["weight"])
> g.properties['skim'] = skim_table
> p(joblib.delayed(toy_func)(GraphView(g)) for i in range(10))
That is not a complete minimal example; the function 'p' is undefi
ng --prefix. In your case it should be:
./configure --prefix=/usr/local/anaconda3
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u haven't provided
--- it is _always_ a bad idea to give code that can't be run. Please provide
*self-contained* examples. Otherwise we have to guess what the intended
behavior is, instead of looking at it ourselves.
But looking briefly, it seems you are resetting the filter even for vertices
that do belong to the current group, thus destroying it.
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at the edge). Thanks.
I assume you are talking about visualization.
No, there is not such option yet.
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ackage... You need to contact the
maintainer responsible.
To get an idea of what might be causing it, you can take a look at he GDB
backtrace.
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Tiago
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could I update this version in the conda environment to 2.27?
>
> Thanks,
> Zahra
>
>
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aph
> into the memory and share/read it between multiple threads/processes (to
> handle many requests in parallel to the same graph). Is Graph thread safe?
> For me it seems that it's not, but I would like to confirm it.
Non-modifying operations to Graph are thread-safe.
Am 21.06.2018 um 22:19 schrieb M. Vigouroux:
> As far as I Know GPU dosn't suit to openMP. I conclue CPU multi threading is
> the best option but maybe I am wrong ?
Graph-tool has no support for GPU off-loading, so the whole point is moot.
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t how GraphView works. It requires a vertex/edge mask or a filter
function. In the former case it is O(1), in the latter O(N) or O(E).
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e.
output of ./configure, contents of config.log, etc.
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data using mcmc_equilibrate it would be potentially
> less meaningful as the process is stochastic, however, information on how
> many sweeps have been completed would still be useful to give a rough
> estimate of whether completion will take hours, days, weeks, or months.
This you can g
oach
is simply:
groups = defaultdict(list)
for v in g.vertices():
groups[l0.b[v]].append(v)
Best,
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Am 05.06.2018 um 13:20 schrieb P-M:
> Hi Tiago,
>
> There seems to have been an updated to the code on GIT. Does it address this
> issue or is it about something else?
This has been fixed now in git.
Next time you want to keep track of a bug, it is best to open an issue.
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largest
> one. I guess that's the universal recipe?
I suppose. I can't think of any other reasonable definition of "largest"...
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grap
0 0 1 0 1 0 1 0 0 0 0 0 0 0]
>
> nc
>
>> array([ 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13],
>> dtype=uint64)
>
>
>
> How do I recover the largest component?
It seems the label 16 occurs most often. Just extract the vertices with
edges l
can I use this property map to extract the **largest** bicomponent?
Just look at the label that occurs most often.
Best,
Tiago
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t;
I don't know, it works for me.
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MCMC gets trapped.
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t; persists there.)
It is difficult to blindly guess, without being given more information.
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n 3 it should work fine.
Best,
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BM ensemble. For real data this
should almost never happen.
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filter for the main graph. Read about
GraphViews here:
https://graph-tool.skewed.de/static/doc/quickstart.html#graph-views
Best,
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On 29.04.2018 13:47, Snehal Shekatkar wrote:
> I am trying to install graph-tool on Ubuntu 18.04. I am encountering
> problems related to boost. What could be done?
The package need to be rebuild. I'll do so for next release.
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times, and choose the result with the
smallest description length. You get this value via the method state.entropy().
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ance matrix of edges". The
approach in question deals with graphs with edge covariates (a.k.a.
weights). A covariance matrix usually refers to something else.
> Is there also any way to get the full posterior of each node belonging to
> each block
h-tool.skewed.de/static/doc/topology.html#graph_tool.topology.label_biconnected_components
The algorithm for 2-edge-connectivity is simple, and think can be
implemented in time O(E). If you open an issue for this in the website, I'll
implement it when I find the t
u have to do
print comp.fa
which will return an array of length 16, instead of 25.
But note that this array will also only contain zeros. But this is correct,
as the graph has only one component, which is labeled zero.
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ion:
https://graph-tool.skewed.de/static/doc/demos/inference/inference.html#edge-weights-and-covariates
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l might underfit (albeit probably
only very slightly). It can't be too large, so it's better to be safe and
give it enough room.
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On 24.04.2018 14:13, P-M wrote:
> Are you able to push the current git version to apt-get?
No, you would have to wait until the next release.
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st levels should have only one group most of the time. A value of
L=10 is good enough for most purposes.
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On 23.04.2018 23:28, P-M wrote:
> Update: as far as I can tell the Segmentation fault also arises if I am using
> the lesmis data collection which hopefully makes this more reproducible for
> others:
This seems to run fine with the current git version. Can you verify?
Best,
Tiago
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s installed.
Optionally, install the provided ubuntu packages, which should be much easier.
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On 28.03.2018 13:46, Zahra Sheikhbahaee wrote:
> Any comment why it occurred or suggestion about how could it be fixed ?
Please try with a recent git version.
The next release will have this fixed.
Best,
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he above example so I can
keep track of this and fix it?
Could you also test this with "real-exponential" instead of "real-normal"
and also with the current git version?
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xpatError: no element found: line 1, column 0
>
> Any idea of the reason why it fails?
Without a minimal and self-contained example that shows the problem is
impossible to say anything. Just an error message without context is
unhelpful. (E.g. from the error message I can infer that you are
2^32 = 4
GB). It does not matter how much total memory you have.
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er[e] = 3 # edge (5, 8) exists in layer 3
# u3 below is a graph view that isolates the vertices and edges of layer 3
u3 = GraphView(g, efilt=elayer.a == 3, vfilt=lambda v: 3 in vlayers[v])
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in
their respective websites. Any issue encountered is usually easy to solve,
and the developers tend to be helpful.
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/installation-instructions#installing-in-a-specific-location-eg-in-a-home-directory
Compiling graph-tool (or any other C++ library) without understanding how
compiling and linking works in general is not advisable. Instead you should
use macports or homebrew, if using MacOS.
Best,
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ge multipliers, there are many available resources, e.g.
https://en.wikipedia.org/wiki/Lagrange_multiplier
As for further references, the paper you cite has more than 100 of them...
What other kind of further reading do you want?
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si
ost=yes --disable-cairo --disable-sparsehash
> " is attched as out_config.txt, config.log.
Your LDFLAGS and CPPFLAGS point to the same directory, which does not make
sense. The first need to point to the shared object files, and the latter
the inc
e.
As usual, without a minimal self-contained example of what you are doing, it
is impossible to give any concrete help.
Best,
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provides newer versions of a number of
> important binaries.
This is appreciated. If you would be willing to host this somewhere (e.g. as
a snipped in github), and maintain it from time to time, I would be happy to
put a link to it in the installation instructions.
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main bottle neck. On top of this there is the version
of Boost, which I also think is too old there. In short, CentOS decides to
stay 7 years behind everything else, and is difficult to maintain this kind
of backward compatibility, given the recent speed with which C++ has b
s your sparse matrix, you can do:
g = Graph()
g.add_edge_list(array(a.nonzero()).T)
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one would like to join me
> in this small project, I can share what I've tried until now.
Take a look at the "groups" and "gamma" parameters in sfdp_layout(), as it
seems to address what you want.
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ntu 17.10 virtual machine.
>
>
Sorry for taking so long to reply. Indeed, you are not supposed to use the
epsilon parameters in this way... If it is too large, it adds loops to the
shortest path tree, creating an infinite loop in the algorithm. The only way
to achieve what you want is to
On 20.01.2018 06:53, Spencer Gardner wrote:
> Is the key server currently down? I've tried to add the apt key from
> computers on two different networks and in both cases I get a keyserver time
> out.
This has been fixed; thanks!
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e simplest thing you can do is access the property map directly
using its array interface:
idx = numpy.array([13, 43, 22]) # vertices
prop.a[idx] # corresponding property values
Best,
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si
all_preds_map))
> MemoryError
As usual, without a minimal and self-contained (i.e. complete) example that
shows the problem, it is not possible to say anything. An error message
without any context is not very useful.
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they are encountered, and a vertex property map with the vertex values
is returned. If ``string_vals == True``, the algorithm assumes that the
vertex values are strings. Otherwise, they will be assumed to be numeric
if ``edge_list`` is a :class:`~numpy.ndarray`, or arbitrary python
e
paths! It does *not* store them all in memory. You must be doing some list
conversion...
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less awkward solution than what I did to get
> graph_tool up and running. Otherwise, I'd label this issue as "resolved.
Just installing from a clean Debian install using the steps explained in the
graph-tool website should just work. The is
are things in /usr/local? Do you have a custom Python install?
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On 10.01.2018 04:05, Percy wrote:
> Are there any suggestions for this phenomenon?
It is always the same issue: The values returned must be picklable. If you
encapsulate things in a class, its members must also be picklable.
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something like
> [1,2,3,4,5].
>
> Is there any thing I misunderstand ?
As the error says, the iterator objects returned by all_shortest_paths()
cannot be pickled. The values returned by the function fed to pool.map()
must be pickable. Hence you need to convert the iterator to lists or
som
self what "periphery"
means.
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stores a
list of Vertex objects. It should be changed to store a list of ints instead.
> My OS is 16.04, python 2.7.14, graph-tool is
> from Ostrokach's Anaconda.
Please say what version of graph-tool you are using.
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ou have a GDB stack trace of the
segfault?
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he same problem when you import scipy.stats without
importing graph-tool?
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algorithms for monolayer networks, but represent the multilayer graph as an
edge-annotated monolayer network, where each node appears multiple times for
each layer it belongs, and their copies are connected by intra-layer edges.
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Tiago de Paula Peixoto
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this is related
to the following homebrew bug:
https://github.com/Homebrew/homebrew-core/issues/21212 )
Best,
Tiago
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Tiago de Paula Peixoto
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y that does the mapping:
vertices = dict((name[v], v) for v in g.vertices())
The reason why this is not built-in is because the property map values are
not in general unique.
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Setting the LONG LAT as attributes is enough to later draw the network
> with the nodes in the correct coordinate position?
If you mean to ask if graph_draw() automatically projects latitude and
longitude to cartesian coordinates, the answer is no.
Best,
Tiago
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Tiago de Paula Peixo
n problem, you have to provide context,
otherwise it is impossible to help. What is your OS, exact GCC and Boost
versions, etc.
>From what I can tell from the error message, it seems that your boost
version is too old.
Best,
Tiago
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the problem.
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