ForceAtlas publication

Algorithms and parameters to put data in space
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seinecle
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Re: ForceAtlas publication

Post by seinecle » 18 Apr 2011 03:48

aurelienb wrote:Nice optimization !
BTW I cannot install it. I have " The Plugin Installer found problem timeout of loading ForceAtlas 2, Quality Layout[org.webatlas.forceatlas2/1.3] while install the following plugins: "... During the plugin install (after select plugin in Tool>Plugin >Downloaded >Install plugin
=> I had the same warning message during the installation?

admin
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Re: ForceAtlas publication

Post by admin » 18 Apr 2011 09:44

This is a general warning due to a Netbeans bug. Please restart Gephi and try again.

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martin.pernollet
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Re: ForceAtlas publication

Post by martin.pernollet » 30 May 2011 17:18

Hi Mathieu,
Thanks for the notice! I tried to look at the code to understand what changed, but it does not seem to be commited on branch 0.8 [1] neither on 0.7 [2]. Am I wrong on something?
Cheers,
Martin

[1] http://bazaar.launchpad.net/~gephi.team ... ayout.java
[2]
http://bazaar.launchpad.net/~gephi.team ... ayout.java
jacomyma wrote:Hi everybody! I'm back and I am happy.

I updated the whole ForceAtlas code to make it "modern" and the result exceeds my expectations. Just for you (since you're interested in ForceAtlas) there is my current version of the ForceAtlas2 plug-in that I will officially publish soon. It has the same formulas and options (though with different names) with some simplifications, and features two main improvements:
- A better auto-stabilization with no settings needed, except a "sort of" speed called "tolerance to swinging"
- A Barnes Hut optimization that approximates repulsion, from n² to n.log(n) complexity -> far more performance.

Feel free to try it, and I will write the paper on the basis of this code.

Here is the NBM to install in Gephi's "plug-in" center:
[Download ForceAtlas2]
NB: NEEDS Gephi 0.8alpha at least !

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jacomyma
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Re: ForceAtlas publication

Post by jacomyma » 31 May 2011 13:37

I didn't commit it in the Launchpad (mainly because I'm confused by its complexity ; I'm an impostor as a computer engineer).
I have fixed some bugs and my release is ready. I still need to build it with the last version of Gephi Dev. Once it's done, I'll release it with the source code. (this week I hope). Not on Launchpad by the way, but you'll still be able to take a look at the code.

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Re: ForceAtlas publication

Post by panisson » 04 Jun 2011 15:38

Hello Mathieu,
Thanks a lot for the relese of the new ForceAtlas version. I'm already trying it, and it seems a very promising implementation.
Please let us know when the source code will be released. I have already some requests for improvements - for example, the new version have some problems with graph streaming that the previous version doesn't have. I hope that, with the source code available, I could help with these improvements.
Cheers,
André

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jacomyma
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Re: ForceAtlas publication

Post by jacomyma » 05 Jun 2011 10:50

I've released the plugin officially. It's available as a plugin in the platform and in Gephi's catalog. The source code is available to download there:
http://webatlas.fr/tempshare/20110601_F ... 2_v1.6.zip
Unzip it, it's the folder of the Netbeans module.
I'll also push it as a branch in Launchpad (Mathieu Bastian told me how to do it).
Of course, feel free to contribute and improve it. Also, I think we might put it in Gephi's trunk. Any reports welcome !

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eduramiba
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Re: ForceAtlas publication

Post by eduramiba » 06 Jun 2011 20:22

Hi! I needed to say that Force Atlas 2 is amazing! Congratulations :)

Eduardo

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Re: ForceAtlas publication

Post by elijah » 06 Jun 2011 23:54

My autoupdate is erroring out. So either everyone is updating to ForceAtlas2 right now, or something is wrong:

Networking problem in http://gephi.org/updates/thirdparty/0.8 ... atlas2.nbm

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mbastian
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Re: ForceAtlas publication

Post by mbastian » 07 Jun 2011 02:15

Because ForceAtlas2 has been integrated in Gephi, we removed the ForceAtlas2 plugin.

Go to Installed Plugins and remove ForceAtlas2, them update your Gephi and you'll have it :-)

nullusadinfinitum
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Re: ForceAtlas publication

Post by nullusadinfinitum » 20 Sep 2011 03:24

Hello. I know there's been some talk about a ForceAtlas(2) publication, but I was wondering whether it would be possible to explain how all of the ForceAtlas2 settings factor into the algorithm? Say, perhaps, through the use of a formula? The reason why I ask is because if we cite Gephi in papers, it helps to explain what the layout algorithm does from a methodological standpoint. Any help on this would be greatly appreciated.

Currently, I just have the following descriptors from the blog post about ForceAtlas2:
  • Scaling: How much repulsion you want. More makes a more sparse graph.
    Gravity: Attracts nodes to the center. Prevents islands from drifting away.
    Dissuade Hubs: Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
    LinLog mode: Switch ForceAtlas’ model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.
    Prevent Overlap: Use only when spatialized. Should not be used with “Approximate Repulsion”
    Tolerance (speed): How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.
    Approximate Repulsion: Barnes Hut optimization: n² complexity to n.ln(n) ; allows larger graphs.
    Approximation: Theta of the Barnes Hut optimization.
    Edge Weight Influence: How much influence you give to the edges weight. 0 is “no influence” and 1 is “normal”.

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