Efficient Bipartite Projection
Dear all, I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that). I started of from (1) Gephi plugin ( https://marketplace.gephi.org/plugin/multimode-networks-transformations-2/), which after running for a couple hours almost froze my computer and output no graph (I had to force quit it). My second attempt was (and is) on igraph ( http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection ) I came across this post: http://stackoverflow.com/questions/606516/python-graph-library And read about graph-tool and how efficient it is compared to the igraph and networkx (which I was about to try but given up when I saw the time table). Thank you for your attention,
Hi, Could you specify a particular projection? `graph_tool.sfp_layout` does a pretty good job for a variety of layouts. It is also easy to setup custom projection through x, y and z propertymaps and matplotlib. Hope this helps, Guillaume Le 01/12/2014 10:47, Carlos Andrade a écrit :
Dear all,
I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that).
I started of from (1) Gephi plugin (https://marketplace.gephi.org/plugin/multimode-networks-transformations-2/), which after running for a couple hours almost froze my computer and output no graph (I had to force quit it). My second attempt was (and is) on igraph ( http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection)
I came across this post: http://stackoverflow.com/questions/606516/python-graph-library
And read about graph-tool and how efficient it is compared to the igraph and networkx (which I was about to try but given up when I saw the time table).
Thank you for your attention,
_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 01.12.2014 10:47, Carlos Andrade wrote:
Dear all,
I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that).
Bipartite projection is currently not implemented, but this is a very easy one. Just open a ticket for it on the website and I'll include an implementation when I have some time. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Dears, Thank you for the layout information Guillaume, this will come to use in due time, although it wasn't really what I was after :-) Tiago Peixoto, I opened an issue here: https://git.skewed.de/count0/graph-tool/issues/196 linked to this discussion. Thank you both for the quick reply, and the interest on implementing this feature. Best Regards, Em Mon Dec 01 2014 at 7:52:42 AM, Tiago de Paula Peixoto <tiago@skewed.de> escreveu:
On 01.12.2014 10:47, Carlos Andrade wrote:
Dear all,
I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that).
Bipartite projection is currently not implemented, but this is a very easy one. Just open a ticket for it on the website and I'll include an implementation when I have some time.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
Dears, Thank you for the layout information Guillaume, this will come to use in due time, although it wasn't really what I was after :-) Tiago Peixoto, I opened an issue here: https://git.skewed.de/count0/graph-tool/issues/196 linked to this discussion. Thank you both for the quick reply, and the interest on implementing this feature. Best Regards, Carlos A. http://carlosandrade.co Em Mon Dec 01 2014 at 7:52:42 AM, Tiago de Paula Peixoto <tiago@skewed.de> escreveu:
On 01.12.2014 10:47, Carlos Andrade wrote:
Dear all,
I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that).
Bipartite projection is currently not implemented, but this is a very easy one. Just open a ticket for it on the website and I'll include an implementation when I have some time.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
I thought about bringing this discussion here from my message on igraph mailing list since it relates to this feature: It seems to me (I may be badly mistaken) that current bipartite projection by weighted graphs do not account for the original graph weights. To contextualize, here a bad hand draw example: https://www.dropbox.com/s/fl69kekipqksd4i/Screenshot%202014-12-01%2012.51.22... I am interested on both values (red circle and orange square), however igraph documentation only accounts (or at least suggest to on the documentation) for the orange one: http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection I checked networkX as well but I couldn't find anything about weighted bipartite graph projections: http://networkx.lanl.gov/archive/networkx-1.6/_modules/ <http://networkx.lanl.gov/archive/networkx-1.6/_modules/networkx/algorithms/bipartite/projection.html> networkx/algorithms/bipartite/projection.html <http://networkx.lanl.gov/archive/networkx-1.6/_modules/networkx/algorithms/bipartite/projection.html> Is it possible for this to be taken into account when the posted 'issue' is tackled? Thank you, Carlos A. Em Mon Dec 01 2014 at 10:58:52 AM, Carlos Andrade <carlosviansi@gmail.com> escreveu:
Dears,
Thank you for the layout information Guillaume, this will come to use in due time, although it wasn't really what I was after :-)
Tiago Peixoto, I opened an issue here: https://git.skewed.de/co unt0/graph-tool/issues/196 linked to this discussion.
Thank you both for the quick reply, and the interest on implementing this feature.
Best Regards,
Carlos A. http://carlosandrade.co
Em Mon Dec 01 2014 at 7:52:42 AM, Tiago de Paula Peixoto <tiago@skewed.de> escreveu:
On 01.12.2014 10:47, Carlos Andrade wrote:
Dear all,
I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that).
Bipartite projection is currently not implemented, but this is a very easy one. Just open a ticket for it on the website and I'll include an implementation when I have some time.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de>
_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
Admin, Is the feature to get the bipartite projection implemented now in graph tools? If yes, Can you please provide the link as I am unable to find it? Would be of great help. Thanks in advance, Aditya -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 17.09.2015 12:33, adi7021 wrote:
Admin,
Is the feature to get the bipartite projection implemented now in graph tools? If yes, Can you please provide the link as I am unable to find it? Would be of great help.
Not yet. If you want to be informed when it is, follow this issue: https://git.skewed.de/count0/graph-tool/issues/196 -- Tiago de Paula Peixoto <tiago@skewed.de>
Hi, Le 01/12/2014 21:58, Carlos Andrade a écrit :
Dears,
Thank you for the layout information Guillaume, this will come to use in due time, although it wasn't really what I was after :-) Yes I guess I missed the "Bipartite" part of the message :p
G.
Tiago Peixoto, I opened an issue here: https://git.skewed.de/count0/graph-tool/issues/196 linked to this discussion.
Thank you both for the quick reply, and the interest on implementing this feature.
Best Regards,
Carlos A. http://carlosandrade.co
Em Mon Dec 01 2014 at 7:52:42 AM, Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de>> escreveu:
On 01.12.2014 10:47, Carlos Andrade wrote: > Dear all, > > I have a bipartite graph, directed and with weightened edges. It is > very large, I believe 36k nodes and 52k edges. I am trying to make a > projection of it, but I could not find any function or way to do so > with graph-tool. Is there any way I am not aware of? If there is no > current way, where would you recommend try with such a big graph? I am > currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 > ghz or something like that).
Bipartite projection is currently not implemented, but this is a very easy one. Just open a ticket for it on the website and I'll include an implementation when I have some time.
Best, Tiago
-- Tiago de Paula Peixoto <tiago@skewed.de <mailto:tiago@skewed.de>>
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participants (5)
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adi7021 -
Carlos Andrade -
Carlos Andrade -
Guillaume Gay -
Tiago de Paula Peixoto