[gephi-dev] Generators

Cezary Bartosiak cezary.bartosiak at gmail.com
Sat Dec 18 14:58:54 CET 2010 

Oh, progress uses integer. I'll fix it.

On 18 December 2010 07:31, Mathieu Bastian <mathieu.bastian at gmail.com>wrote:

> Hi Cezary, I merged the new generators into the trunk. The code looks clean
> and the validators for the UI is great! Congrats.
>
> Small exception when running Kleinberg with 250 - 1 - 0 - 0
>
> java.lang.IllegalArgumentException: Cannot decrease processed workunit
> count (-1) to lower value than before (0)
>     at
> org.netbeans.modules.progress.spi.InternalHandle.progress(InternalHandle.java:260)
>     at
> org.netbeans.api.progress.ProgressHandle.progress(ProgressHandle.java:174)
>     at
> org.netbeans.api.progress.ProgressHandle.progress(ProgressHandle.java:156)
>     at
> org.gephi.desktop.progress.ProgressTicketImpl.progress(ProgressTicketImpl.java:74)
>     at
> org.gephi.desktop.progress.ProgressTicketImpl.progress(ProgressTicketImpl.java:61)
>     at org.gephi.utils.progress.Progress.progress(Progress.java:46)
>     at org.gephi.io.generator.plugin.Kleinberg.generate(Kleinberg.java:109)
> ...
>
> ps: The effect with Yifan Hu multilevel is not bad either :-)
>
>
>
> On Wed, Dec 15, 2010 at 6:38 PM, Cezary Bartosiak <
> cezary.bartosiak at gmail.com> wrote:
>
>> OK, it's finished and waiting for the review ;)
>>
>>
>>  On 15 December 2010 17:17, Cezary Bartosiak <cezary.bartosiak at gmail.com>wrote:
>>
>>> I have provided some changes:
>>>
>>> * changed EdgeDefault to undirected in most generators (excepting
>>> Kleinberg)
>>>
>>> * removed the old Watts-Strogatz beta model generator and added the new
>>> one
>>>
>>> I removed the old Watts-Strogatz generator, because it generated a beta
>>> model (which I create in another generator) and I discovered it "too late".
>>> Anyway, I would like to create also alpha model and write some hierarchical
>>> generator (probably balanced tree generator because it meets my needs). When
>>> I finish I'll let you know.
>>>
>>> On 15 December 2010 14:31, Cezary Bartosiak <cezary.bartosiak at gmail.com>wrote:
>>>
>>>> Yes, you can add this line:
>>>>> container.setEdgeDefault(EdgeDefault.UNDIRECTED)
>>>>>
>>>>
>>>> So, for instance, container.edgeExists(nodes[*i*], nodes[*j*]) should
>>>> return true even if I add edge this way: edge.setSource(nodes[*j*]),
>>>> edge.setTarget(nodes[*i*])?
>>>>
>>>> On 13 December 2010 07:57, Mathieu Bastian <mathieu.bastian at gmail.com>wrote:
>>>>
>>>>>
>>>>>
>>>>> On Sun, Dec 12, 2010 at 7:41 PM, Cezary Bartosiak <
>>>>> cezary.bartosiak at gmail.com> wrote:
>>>>>
>>>>>> Merging with 0.7 works perfectly :P
>>>>>>
>>>>>> By the way:
>>>>>>
>>>>>> 1. Is it enough to change a version number for Generator Plugin and
>>>>>> Generator Plugin UI modules to let people get updates? (of course I would do
>>>>>> it after I finish and my branch should be merged firstly :P)
>>>>>>
>>>>>
>>>>> Yes
>>>>>
>>>>>
>>>>>>
>>>>>> 2. Is it possible to generate undirected edges? And, even if they are
>>>>>> directed, if I set network interpretation to undirected (in metrics) all
>>>>>> edges are treated as undirected, right?
>>>>>>
>>>>>
>>>>> Yes, you can add this line:
>>>>> container.setEdgeDefault(EdgeDefault.UNDIRECTED)
>>>>>
>>>>>
>>>>>>
>>>>>> 3. To sum up generators, we need to develop the following things (in
>>>>>> the future :P):
>>>>>>
>>>>>> a) some small graph structure to make generators more optimal (and
>>>>>> easier to implement :P)
>>>>>>
>>>>>>  b) better UIs (with descriptions and so on)
>>>>>>
>>>>>
>>>>> Agree
>>>>>
>>>>>
>>>>>>
>>>>>> On 13 December 2010 04:23, Mathieu Bastian <mathieu.bastian at gmail.com
>>>>>> > wrote:
>>>>>>
>>>>>>> Awesome! That looks great...
>>>>>>>
>>>>>>> Regarding the repository format, Sebastien may have better
>>>>>>> explanation but it's probably because the trunk is now from the 0.8 branch,
>>>>>>> which has been created recently and therefore with the latest bazaar
>>>>>>> repository version. Did you tried to merge with the 0.7 branch "bzr pull
>>>>>>> lp:gephi/0.7" ?
>>>>>>>
>>>>>>>
>>>>>>> On Sun, Dec 12, 2010 at 7:08 PM, Cezary Bartosiak <
>>>>>>> cezary.bartosiak at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I have implemented all generators mentioned earlier excepting
>>>>>>>> Watts-Strogatz ones. I'll implement them as soon as possible. I pushed them
>>>>>>>> into repository. Unfortunately I can't merge with trunk because there is
>>>>>>>> another repository format (mine is KnitPack). Could you do something with it
>>>>>>>> Sébastien? You probably need to upgrade repo format.
>>>>>>>>
>>>>>>>> Some info:
>>>>>>>>
>>>>>>>> 1. These generators could be faster not only because of
>>>>>>>> optimizations, but also by reducing complexity. Unfortunately now I don't
>>>>>>>> have time to play with it :P Anyway they are good enough for my experiments.
>>>>>>>>
>>>>>>>> 2. Some of them may seem to work "strangely". For instance BA
>>>>>>>> Simplified B model generator for complete graphs will be very slow, much
>>>>>>>> slower than ER model generators because it is created for generating network
>>>>>>>> whose degree distribution follows a power law, so if you can see 99 % for a
>>>>>>>> long time in case of very dense or even complete graphs - it's normal :P
>>>>>>>>
>>>>>>>> 3. Create Kleinberg graph with such parameters (n = 25, p = 1, q =
>>>>>>>> 0, r = 0) and then fire some Yifan-Hu layout algorithm (if it stops run it
>>>>>>>> again until it creates a grid). The effect is very nice :P
>>>>>>>>
>>>>>>>> PS. As for dynamic-attr-stats branch I will work on it after I
>>>>>>>> finish similarity-plugin branch. It will take probably 3 weeks until I do
>>>>>>>> it. So lacking dynamic statistics will be created (probably) in January.
>>>>>>>>
>>>>>>>> On 11 December 2010 17:27, Sébastien Heymann <
>>>>>>>> sebastien.heymann at gephi.org> wrote:
>>>>>>>>
>>>>>>>>> Classic :P
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2010/12/11 Cezary Bartosiak <cezary.bartosiak at gmail.com>
>>>>>>>>>
>>>>>>>>>> Maybe in the future because of time constraints :P
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> On 11 December 2010 16:56, Sébastien Heymann <
>>>>>>>>>> sebastien.heymann at gephi.org> wrote:
>>>>>>>>>>
>>>>>>>>>>> That's cool!
>>>>>>>>>>>
>>>>>>>>>>> Maybe you should find a way to create a unified GUI for each
>>>>>>>>>>> generator. For instance the user select "Barabási–Albert" item on the
>>>>>>>>>>> Generator menu, then choose a version between the 4 available as 4 different
>>>>>>>>>>> tabs in the window.
>>>>>>>>>>>
>>>>>>>>>>> What do you think about it?
>>>>>>>>>>>
>>>>>>>>>>> Seb
>>>>>>>>>>>
>>>>>>>>>>> 2010/12/11 Cezary Bartosiak <cezary.bartosiak at gmail.com>
>>>>>>>>>>>
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> I need to make some generators for my work at the university, so
>>>>>>>>>>>> I'll create a branch for this purpose. Probably I'll commit them tomorrow.
>>>>>>>>>>>>
>>>>>>>>>>>> For now I need a subset of generators presented in my post
>>>>>>>>>>>> written before GSoC:
>>>>>>>>>>>>
>>>>>>>>>>>> a) Erdős-Rényi model in two versions G(n, p) and G(n, m)
>>>>>>>>>>>>
>>>>>>>>>>>> b) Alpha and Beta models of Watts and Strogatz (from what I can
>>>>>>>>>>>> see Mathieu implemented some generator of this model which takes other
>>>>>>>>>>>> parameters I plan to use ;) - so we will have got three different generators
>>>>>>>>>>>> :P)
>>>>>>>>>>>>
>>>>>>>>>>>> c) Kleinberg model
>>>>>>>>>>>>
>>>>>>>>>>>> d) Barabási–Albert model in 4 versions: basic, generalized
>>>>>>>>>>>> generator with probabilities of adding new edges and rewiring existing ones,
>>>>>>>>>>>> simplified models: A (uniform attachment) and B (no growth)
>>>>>>>>>>>>
>>>>>>>>>>>> In the close future I also plan to add HierarchicalGraph
>>>>>>>>>>>> generator.
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>> http://gephi.org/mailman/listinfo/gephi-dev
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>>
>>>>>
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