[gephi-dev] Generators

Mathieu Bastian mathieu.bastian at gmail.com
Sat Dec 18 07:31:36 CET 2010 

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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