SMLG (Statistical Machine Learning Group) Discussion Forum

Dr. Yoo,

Please find attached the CSV file for the Cell Cycle. I tried running the code by removing the commented line; nevertheless, it still gave the following error:

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-----------------------------------------------------------------------------
                                 ERROR DETAILS
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- Banjo                        Bayesian Network Inference with Java Objects -
- Release 2.2.0                                                 15 Apr 2008 -
- Licensed from Duke University                                             -
- Copyright (c) 2005-08 by Alexander J. Hartemink                           -
- All rights reserved                                                       -
-----------------------------------------------------------------------------
- Project:                                               banjo static example
- User:                                                                  demo
- Dataset:                                           33-vars-320-observations
- Notes:                                    static bayesian network inference
-----------------------------------------------------------------------------

[ERROR: Banjo 2.2.0, 2/5/15 10:52:51 PM]
The following info is provided to assist in trouble-shooting:
The text line ' 0' in 'static.mandatory.str' does not contain enough information to specify a variable and its parent info.

(Warning (dev)) The number of supplied variable names (132) needs to match the number of variables (123); Banjo defaults to the variable index numbers instead.

Stack trace info:

edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.loadStructureFile(EdgesAsArrayWithCachedStatistics.java:2862)
edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.<init>(EdgesAsArrayWithCachedStatistics.java:633)
edu.duke.cs.banjo.bayesnet.BayesNetManager.<init>(BayesNetManager.java:273)
edu.duke.cs.banjo.learner.SearcherSimAnneal.setupSearch(SearcherSimAnneal.java:1092)
edu.duke.cs.banjo.learner.SearcherSimAnneal.<init>(SearcherSimAnneal.java:723)
edu.duke.cs.banjo.application.BanjoThreadHandler.<init>(BanjoThreadHandler.java:115)
edu.duke.cs.banjo.application.Banjo.runMultipleInstances(Banjo.java:200)
edu.duke.cs.banjo.application.Banjo.execute(Banjo.java:150)
edu.duke.cs.banjo.application.Banjo.main(Banjo.java:447)

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                           End of error notification
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(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
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(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).

I'll go over the settings with you tomorrow.

Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all

(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).

meninonas wrote:Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all

(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).

Please install banjo in path4 machine.

Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all

-----------------------------------------------------------------------------
(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
-----------------------------------------------------------------------------
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).

Dr. Yoo,

I just wanted to reiterate. I am going to create another dataset where there are going to be three columns per gene with the following names:

GENENAME_EXP with three states (UP, DOWN, and everything else)

GENENAME_AMP with two states (AMP;UP/DOWN; and everything else)

GENENAME_MUT with two states (MUT/HOMDEL;UP/DOWN; and everything else)

If so, when I come back tomorrow, I'll set it up as such and run it.

meninonas wrote:Dr. Yoo,

I just wanted to reiterate. I am going to create another dataset where there are going to be three columns per gene with the following names:

GENENAME_EXP with three states (UP, DOWN, and everything else)

GENENAME_AMP with two states (AMP;UP/DOWN; and everything else)

GENENAME_MUT with two states (MUT/HOMDEL;UP/DOWN; and everything else)

If so, when I come back tomorrow, I'll set it up as such and run it.

It should be:

GENENAME_EXP with three states (anywhere there is UP, anywhere there is DOWN, and everything else)

GENENAME_AMP with two states (anywhere there is AMP and everything else)

GENENAME_MUT with two states (anywhere there is MUT/HOMDEL and everything else)

Empty

meninonas wrote:Dr. Yoo,

I have worked on the dataset below. Tomorrow, I'll continue working on the dataset tomorrow.

Always use reference coding, i.e., in GENE_EXP you have 0, 1, 2 for "anywhere there is DOWN", "all others", "anywhere there is UP" respectively; in GENE_MUT, you have 0, 1 for "all others", "anywhere there is MUT" respectively; GENE_AMP, you have 0, 1 for "all others", "anywhere there is AMP" respectively.

Create three tabs for GENE_EXP, GENE_MUT, and GENE_AMP respectively.

meninonas wrote:Dr. Yoo,

I installed Banjo on the Virtual Machine and on the computer and the following error was given to me:

Code: Select all

-----------------------------------------------------------------------------
(Final Checkpoint, after post-processing) A final check revealed the following issues that were encountered during Banjo's execution:
-----------------------------------------------------------------------------
(Post-processing) Postprocessing cannot proceed because we can't process the high score network(s).

I ran it on path4 and the following is the error that proceeds the above line:

Code: Select all

[ERROR: Banjo 2.2.0, 1/29/15 6:21:16 AM]
The following info is provided to assist in trouble-shooting:
The input line ' 89 0' in 'static.mandatory.str' is a repeat entry for variable '89'.



Stack trace info:

edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.loadStructureFile(EdgesAsArrayWithCachedStatistics.java:2862)
edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.<init>(EdgesAsArrayWithCachedStatistics.java:633)
edu.duke.cs.banjo.bayesnet.BayesNetManager.<init>(BayesNetManager.java:273)
edu.duke.cs.banjo.learner.SearcherSimAnneal.setupSearch(SearcherSimAnneal.java:1092)
edu.duke.cs.banjo.learner.SearcherSimAnneal.<init>(SearcherSimAnneal.java:723)
edu.duke.cs.banjo.application.BanjoThreadHandler.<init>(BanjoThreadHandler.java:115)
edu.duke.cs.banjo.application.Banjo.runMultipleInstances(Banjo.java:200)
edu.duke.cs.banjo.application.Banjo.execute(Banjo.java:150)
edu.duke.cs.banjo.application.Banjo.main(Banjo.java:447)

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                           End of error notification
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Error message while trying to record the error:
java.lang.NullPointerException


This is due to the setting that you have indicated that you are going to use:

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 mustBePresentEdgesFile =        static.mandatory.str

I have commented it out and it runs successfully in path4.

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## mustBePresentEdgesFile =        static.mandatory.str

However, we need to use above setting and the following setting in GENE_EXP, GENE_MUT, and GENE_AMP combined data:

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mustNotBePresentEdgesFile =

Please look into those options and learn how to specify the edges in the files.

Dr. Yoo,

Please find 10 of the 11 datasets below. They are already coded and set up.