[gephi-dev] Generators

Cezary Bartosiak cezary.bartosiak at gmail.com
Mon Dec 20 01:41:52 CET 2010 

No problem - I'm planning to work on these generators in January since I
need them for my another experimental branch (spread-simulator - it is for
the experiments at my university, it's rather not going to be published, I
wanted to use the toolkit, but I need visualization, that's why I develop it
this way :P). Anyway I'll work on the generators soon (in January), so then
I'll do all these things you want :)

On 20 December 2010 01:20, Mathieu Bastian <mathieu.bastian at gmail.com>wrote:

> Hi Cezary,
>
> Thought it is an awesome work, I think the new long list of generators in
> the UI could make new users feel a bit lost. That's why I think it would be
> better to have these 'scientific' generators as a plug-in and keep the list
> very simple, with Random Graph.
>
> There is a new branch
> https://code.launchpad.net/~gephi.team/gephi/generators
>
> Could you please create a new module for that, ComplexGenerator?
> ScienceGenerators?
>
> As for other plug-ins that have a UI module, the best would be to create a
> third 'empty' module that depends on both UI and business modules, with the
> description. I also count on you to document and upload these candies on the
> plug-in center :-) Many researchers will be happy about this new plug-in.
>
> Mathieu
>
>
> On Sat, Dec 18, 2010 at 2:43 PM, Cezary Bartosiak <
> cezary.bartosiak at gmail.com> wrote:
>
>> 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.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>> gephi-dev at lists.gephi.org
>>>>>>>>>>>>>>> http://gephi.org/mailman/listinfo/gephi-dev
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
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>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
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