[gephi-dev] Generators

Cezary Bartosiak cezary.bartosiak at gmail.com
Sat Dec 18 23:43:14 CET 2010 

OK, fixed. Unfortunately my i7 processor can't process YifanHu's algorithm
in reasonable time for 62500 nodes. But for 10k it's ok :P

On 18 December 2010 14:58, Cezary Bartosiak <cezary.bartosiak at gmail.com>wrote:

> 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.
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> gephi-dev mailing list
>>>>>>>>>>>>> gephi-dev at lists.gephi.org
>>>>>>>>>>>>> http://gephi.org/mailman/listinfo/gephi-dev
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> gephi-dev mailing list
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>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
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>>>>>>>>>
>>>>>>>>>
>>>>>>>>
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>>>>>>>>
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>>>>>>
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>>>>>
>>>>
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>
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