[SOLVED] Best practice for very dynamic network?
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Hi, I'd like to use gephi to show evolution of a neural network simulation, in which the weights of the edges change constantly, and pop in and out of existence. Can anyone suggest a good way of doing this? I suppose I am really trying to stream the graph, but I realize that that is still being developed.
Is there a more generic way of describing time, instead of dates? seconds really make more sense in my data, so if I could just give a float, that would be pretty helpful?
Would something like
<edge id="10" source="0" target="3">
<attvalue for="weight" value="1" start="0"/>
<attvalue for="weight" value="1.1" start="1"/>
<attvalue for="weight" value="1.2" start="2"/>
<attvalue for="weight" value="1.1" start="3"/>
<attvalue for="weight" value="1" start="4"/>
<spells>
<spell> start="1" end="2" </spell>
<spell> start="3" end="5" </spell>
</spells>
</edge>
work? Can I change the edge-weight like that?
I think I saw something in the primer about values overwriting each other quite easily, so that's why I'm only giving start-times.
Of course I'm going to write a matlab script that creates the gexf-file, but it is still a quality that the file doesn't become too large, so unnecessary text should be avoided. It's also a quality that gephi can handle the file easily. Under those constraints, does anyone have suggestions to best practice?
Thanks
Is there a more generic way of describing time, instead of dates? seconds really make more sense in my data, so if I could just give a float, that would be pretty helpful?
Would something like
<edge id="10" source="0" target="3">
<attvalue for="weight" value="1" start="0"/>
<attvalue for="weight" value="1.1" start="1"/>
<attvalue for="weight" value="1.2" start="2"/>
<attvalue for="weight" value="1.1" start="3"/>
<attvalue for="weight" value="1" start="4"/>
<spells>
<spell> start="1" end="2" </spell>
<spell> start="3" end="5" </spell>
</spells>
</edge>
work? Can I change the edge-weight like that?
I think I saw something in the primer about values overwriting each other quite easily, so that's why I'm only giving start-times.
Of course I'm going to write a matlab script that creates the gexf-file, but it is still a quality that the file doesn't become too large, so unnecessary text should be avoided. It's also a quality that gephi can handle the file easily. Under those constraints, does anyone have suggestions to best practice?
Thanks
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Re: Best practice for very dynamic network?
Hi, this should work.
You can compress your GEXF file because Gephi handles ZIP and GZIP files.
You can compress your GEXF file because Gephi handles ZIP and GZIP files.
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Re: Best practice for very dynamic network?
hmm, for some reason it's not working.
This is my header (as you can see, mostly copy-pasted from the primer):
and this is an example of an edge:
however, when I load the file into gephi, I get
gephi reports the loaded file as not dynamic.
This is my header (as you can see, mostly copy-pasted from the primer):
Code: Select all
<?xml version="1.0" encoding="UTF8"?>
<gexf xmlns="http://www.gexf.net/1.2draft"
xmlns:xsi="http://www.w3.org/2001/XMLSchemainstance"
xsi:schemaLocation="http://www.gexf.net/1.2draft
http://www.gexf.net/1.2draft/gexf.xsd"
version="1.2">
<meta lastmodifieddate="20090320">
<creator>Gephi.org</creator>
<description>A hello world! file</description>
<keywords>undefined</keywords>
</meta>
<graph mode="dynamic" timeformat="double" defaultedgetype="directed">
Code: Select all
<edge id="1" source="29" target="1">
<attvalue for="weight" value="1.9216" start="9.9626"/>
<spells>
<spell> start="9.9626" end="900010" </spell>
</spells>
</edge>
when I try to copy-paste that message, I get "org.gephi.io.importer.api.Issue@20547840 SEVERE ", which I suppose is the identifier?The time interval for edge 'edge id=1' attribute could not be parsed. Use xsd:date, xsd:dateTime or Double formatting.
gephi reports the loaded file as not dynamic.
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Re: Best practice for very dynamic network?
thanks. however, that didn't change anything...
- eduramiba
- Gephi Code Manager
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Re: Best practice for very dynamic network?
Perhaps there is another syntax problem.
Check this page http://gexf.net/format/dynamics.html to see if everything is correct.
Eduardo
Check this page http://gexf.net/format/dynamics.html to see if everything is correct.
Eduardo
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Re: Best practice for very dynamic network?
Please send the smallest GEXF which is not working, so we can find the issue.
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Re: Best practice for very dynamic network?
I hope this is small enough:
gephi is now recognising that the network is dynamic - this may have been fixed by changing the spell-syntax, but I still get the same error-message for both edges.
Code: Select all
<?xml version="1.0" encoding="UTF8"?>
<gexf xmlns="http://www.gexf.net/1.2draft"
xmlns:xsi="http://www.w3.org/2001/XMLSchemainstance"
xsi:schemaLocation="http://www.gexf.net/1.2draft
http://www.gexf.net/1.2draft/gexf.xsd"
version="1.2">
<meta lastmodifieddate="20090320">
<creator>Gephi.org</creator>
<description>A hello world! file</description>
<keywords>undefined</keywords>
</meta>
<graph mode="dynamic" timeformat="double" defaultedgetype="directed">
<nodes>
<node id="1" />
<node id="2" />
<node id="29" />
</nodes>
<edges>
<edge id="1" source="29" target="1">
<attvalue for="weight" value="1.9216" start="9.9626"/>
<spells>
<spell start="9.9626" end="900010" />
</spells>
</edge>
<edge id="2" source="29" target="2">
<attvalue for="weight" value="1.9216" start="9.9626"/>
<spells>
<spell start="9.9626" end="900010" />
</spells>
</edge>
</edges>
</graph>
</gexf>
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- Gephi Community Manager
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Re: Best practice for very dynamic network?
<attvalue> should be inside <attvalues>:
Code: Select all
<attvalues><attvalue ... /></attvalues>
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- Posts:23
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Re: Best practice for very dynamic network?
I'm afraid that didn't change anything. the new file is:
Code: Select all
<?xml version="1.0" encoding="UTF8"?>
<gexf xmlns="http://www.gexf.net/1.2draft"
xmlns:xsi="http://www.w3.org/2001/XMLSchemainstance"
xsi:schemaLocation="http://www.gexf.net/1.2draft
http://www.gexf.net/1.2draft/gexf.xsd"
version="1.2">
<meta lastmodifieddate="20090320">
<creator>Gephi.org</creator>
<description>A hello world! file</description>
<keywords>undefined</keywords>
</meta>
<graph mode="dynamic" timeformat="double" defaultedgetype="directed">
<nodes>
<node id="1" />
<node id="2" />
<node id="29" />
</nodes>
<edges>
<edge id="1" source="29" target="1">
<attvalues>
<attvalue for="weight" value="1.9216" start="9.9626"/>
</attvalues>
<spells>
<spell start="9.9626" end="900010" />
</spells>
</edge>
<edge id="2" source="29" target="2">
<attvalues>
<attvalue for="weight" value="1.9216" start="9.9626"/>
</attvalues>
<spells>
<spell start="9.9626" end="900010" />
</spells>
</edge>
</edges>
</graph>
</gexf>