[gephi-dev] Generators

Thu Jan 27 08:40:19 CET 2011

OK, I've got a complete schedule for February (including my thesis and other
high priority, time consuming things). Unfortunately it follows that
generators will be published on ~13.02.2011. As I wrote earlier I must write
a documentation and I want to add some generators. I have got ideas for
extending existing ones as well.

If you think it's too late I can publish them now, but without docs (I don't
find it a good idea)... so, what do you think?

On 12 January 2011 21:48, Cezary Bartosiak <cezary.bartosiak at gmail.com>wrote:

> I'm going to release them as soon as possible. But first I need to finish
> things connected with my thesis. I mean, it's ready, but I must do some
> formalities (printing etc.).
>
> Sorry for the lateness, I would like write some docs for the generators,
> that's why I'm waiting with the release :P
>
> On 12 January 2011 17:36, Mathieu Bastian <mathieu.bastian at gmail.com>wrote:
>
>> Hello Cezary,
>>
>> some updates on packaging these new awesome set of generators?
>>
>> Mathieu
>>
>> On Sun, Dec 19, 2010 at 4:41 PM, Cezary Bartosiak
>> <cezary.bartosiak at gmail.com> wrote:
>> > 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.
>> >>>>>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>>>>> gephi-dev mailing list
>> >>>>>>>>>>>>>>>> gephi-dev at lists.gephi.org
>> >>>>>>>>>>>>>>>> http://gephi.org/mailman/listinfo/gephi-dev
>> >>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> _______________________________________________
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>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
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