[gephi-dev] Generators

Wed Jan 12 21:48:02 CET 2011

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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