Error in visualizing a Bayes net

[Davide Cittaro-2]

Hi all, 

I've built (within weka 3.7.0) a bayesian network and apparently I'm not able to visualize it. The windows hangs on the first node and I get this error:

Exception in thread "Thread-154" java.lang.ArrayIndexOutOfBoundsException: -128

weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

The network file can still be saved. The problem is that apparently I'm not able to open the XMLBIF file with any software available (I've tried javabayes, unbbayes and others). Can anybody suggest something I can use to visualize (and analyze) the network?

If needed I can provide the xml file (or the weka model). 

Thanks

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: [phone]

e-mail: davide.cittaro@...

*/

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[NightlordTW]

Hello,
given the index of the bounds (-128), I think the problem might be related to an index overflow (the data type of the index does not allow a value as big as it was assigned to). However, this is just a vauge guess, and you might check whether this holds by running a simplified version of the net (less attributes eg)
Best regards

Thomas Debray

2009/10/22 Davide Cittaro <davide.cittaro@...>

Hi all, 

I've built (within weka 3.7.0) a bayesian network and apparently I'm not able to visualize it. The windows hangs on the first node and I get this error:

Exception in thread "Thread-154" java.lang.ArrayIndexOutOfBoundsException: -128

weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

The network file can still be saved. The problem is that apparently I'm not able to open the XMLBIF file with any software available (I've tried javabayes, unbbayes and others). Can anybody suggest something I can use to visualize (and analyze) the network?

If needed I can provide the xml file (or the weka model). 

Thanks

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: [phone]

e-mail: davide.cittaro@...

*/

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Send posts to: Wekalist@...
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--
Thomas Debray | Theoretical Epidemiology | Julius Center | Stratenum 6.131 | University Medical Center Utrecht  | P.O.Box 85500  | 3508 GA Utrecht | The Netherlands | www.juliuscenter.nl | www.thomasdebray.be | www.netstorm.be

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[Li, Jiakai]

Some parts of this message have been removed. Learn more about Nabble's security policy.

HI！I got the same question as yours.

I downloaded Weka 3.6 and ran it on input example of 32431 instances with 225 attributes.  After I finished the learning of a Bayes Net model, I try to see the graph by right click on the model and choose "Visualize graph" but the window that is supposed to show the graph with only one node.

And I got the exceptions in the consoles:

 

Exception in thread "Thread-10" java.lang.ArrayIndexOutOfBroundsException: -128

weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy ( Unknown Source)

 

weka.gui.graphvisualizer.HierarchicalBCEngine$2.run ( Unknown Source)

 

at weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy ( Unknown Source)

 

at weka.gui.graphvisualizer.HierarchicalBCEngine$2.run ( Unknown Source)

 

I tried to take off some of my attributes, and I found that when I cut them to 128 attributes and it worked and I could see the belief network. I thought there was a limitation of the number attributes.

But I needed to include all of my 225 attributes to build the model and visualize the network and save it as a BIF file. Any ideas?

 

Many thanks in advance for your help!

 

Best regards,

 

Jack

---

From: wekalist-bounces@... [wekalist-bounces@...] on behalf of Thomas Debray [tw@...]
Sent: Thursday, October 22, 2009 10:49 AM
To: Weka machine learning workbench list.
Subject: Re: [Wekalist] Error in visualizing a Bayes net

Hello,
given the index of the bounds (-128), I think the problem might be related to an index overflow (the data type of the index does not allow a value as big as it was assigned to). However, this is just a vauge guess, and you might check whether this holds by running a simplified version of the net (less attributes eg)
Best regards

Thomas Debray

2009/10/22 Davide Cittaro <davide.cittaro@...>

Hi all, 

I've built (within weka 3.7.0) a bayesian network and apparently I'm not able to visualize it. The windows hangs on the first node and I get this error:

Exception in thread "Thread-154" java.lang.ArrayIndexOutOfBoundsException: -128

weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy(Unknown Source)

at weka.gui.graphvisualizer.HierarchicalBCEngine$2.run(Unknown Source)

The network file can still be saved. The problem is that apparently I'm not able to open the XMLBIF file with any software available (I've tried javabayes, unbbayes and others). Can anybody suggest something I can use to visualize (and analyze) the network?

If needed I can provide the xml file (or the weka model). 

Thanks

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: [phone]

e-mail: davide.cittaro@...

*/

_______________________________________________
Wekalist mailing list
Send posts to: Wekalist@...
List info and subscription status: https://list.scms.waikato.ac.nz/mailman/listinfo/wekalist
List etiquette: http://www.cs.waikato.ac.nz/~ml/weka/mailinglist_etiquette.html

--
Thomas Debray | Theoretical Epidemiology | Julius Center | Stratenum 6.131 | University Medical Center Utrecht  | P.O.Box 85500  | 3508 GA Utrecht | The Netherlands | www.juliuscenter.nl | www.thomasdebray.be | www.netstorm.be

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Send posts to: Wekalist@...
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[NightlordTW]

HI！I got the same question as yours.

I downloaded Weka 3.6 and ran it on input example of 32431 instances with 225 attributes.  After I finished the learning of a Bayes Net model, I try to see the graph by right click on the model and choose "Visualize graph" but the window that is supposed to show the graph with only one node.

And I got the exceptions in the consoles:

 

Exception in thread "Thread-10" java.lang.ArrayIndexOutOfBroundsException: -128

weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy ( Unknown Source)

 

weka.gui.graphvisualizer.HierarchicalBCEngine$2.run ( Unknown Source)

 

at weka.gui.graphvisualizer.HierarchicalBCEngine.makeProperHierarchy ( Unknown Source)

 

at weka.gui.graphvisualizer.HierarchicalBCEngine$2.run ( Unknown Source)

 

I tried to take off some of my attributes, and I found that when I cut them to 128 attributes and it worked and I could see the belief network. I thought there was a limitation of the number attributes.

This means that the used data type indeed is not fit for so many attributes
 

But I needed to include all of my 225 attributes to build the model and visualize the network and save it as a BIF file. Any ideas?

The only solution I see is that you manually change the datatype in the sourcecode and recompile. This can however have implications in many functions, so this approach can be very time consuming (a typical example: the computer-datetime problem in 2000). Moreover, you might experience memory problems using such high-dimensional data. You could either perform dimensionality reduction on your data, either try another technique.

--
Thomas Debray | Theoretical Epidemiology | Julius Center | Stratenum 6.131 | University Medical Center Utrecht  | P.O.Box 85500  | 3508 GA Utrecht | The Netherlands | www.juliuscenter.nl | www.thomasdebray.be | www.netstorm.be

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Send posts to: Wekalist@...
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[Davide Cittaro-2]

On Oct 22, 2009, at 11:06 PM, wekalist-request@... wrote:

The only solution I see is that you manually change the datatype in the
sourcecode and recompile. This can however have implications in many
functions, so this approach can be very time consuming (a typical example:
the computer-datetime problem in 2000). Moreover, you might experience
memory problems using such high-dimensional data. You could either perform
dimensionality reduction on your data, either try another technique.

Thanks for the hint. Unfortunately I cannot reduce my attribute set further (I've just reduced from 18000 to 190 attrs) and I need them all.

I will try to modify the source. Also, I've been looking for an alternative network visualizer and it seems that they all have problems with XMLBIF format (i.e. javabayes doesn't support any character than [a-zA-z0-9], unbbayes loads xmlbif 0.6 but not 0.3...). Does anybody know a good (possibly multiplatform) network visualizer for xmlbif?

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: [phone]

e-mail: davide.cittaro@...

*/

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Send posts to: Wekalist@...
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[Li, Jiakai]

Some parts of this message have been removed. Learn more about Nabble's security policy.

Hi!

I met the same problem with you. I need your help.

I am also looking for solution and checking the source code now.

Do you find the classes and/or methods to solve the problem? I cannot find the correct place. 

 

I am trying to modify the source code and fix the problem also.

 

If you are done, could you please share the code with me?

 

Thank you very much.

 

Jack

The university of Toledo US

---

From: wekalist-bounces@... [wekalist-bounces@...] on behalf of Davide Cittaro [davide.cittaro@...]
Sent: Wednesday, October 28, 2009 4:26 AM
To: wekalist@...
Subject: Re: [Wekalist] Error in visualizing a Bayes net

On Oct 22, 2009, at 11:06 PM, wekalist-request@... wrote:

The only solution I see is that you manually change the datatype in the
sourcecode and recompile. This can however have implications in many
functions, so this approach can be very time consuming (a typical example:
the computer-datetime problem in 2000). Moreover, you might experience
memory problems using such high-dimensional data. You could either perform
dimensionality reduction on your data, either try another technique.

Thanks for the hint. Unfortunately I cannot reduce my attribute set further (I've just reduced from 18000 to 190 attrs) and I need them all.

I will try to modify the source. Also, I've been looking for an alternative network visualizer and it seems that they all have problems with XMLBIF format (i.e. javabayes doesn't support any character than [a-zA-z0-9], unbbayes loads xmlbif 0.6 but not 0.3...). Does anybody know a good (possibly multiplatform) network visualizer for xmlbif?

d

/*

Davide Cittaro

Cogentech - Consortium for Genomic Technologies

via adamello, 16

20139 Milano

Italy

tel.: [phone]

e-mail: davide.cittaro@...

*/

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Wekalist mailing list
Send posts to: Wekalist@...
List info and subscription status: https://list.scms.waikato.ac.nz/mailman/listinfo/wekalist
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