Bene Analysis

[cwyoo]

Implements the following paper:

Tomi Silander and Petri Myllymaki (2006) A Simple Approach for Finding the Globally Optimal Bayesian Network Structure, UAI (attached in the Theory section)

Download it from Git hub: https://github.com/tomisilander/bene

[vlee14]

The 20 variable dataset stil did not produce any results after almost four hours. Should I run it with a smaller dataset?

[cwyoo]

The 20 variable dataset stil did not produce any results after almost four hours. Should I run it with a smaller dataset?

Let it run until it completes the analysis or terminates. Please post the dataset and post how to run bene here.

[vlee14]

For the 20 variable set, it produced results in about an hour. Attached is the image file produced.

[cwyoo]

For the 20 variable set, it produced results in about an hour. Attached is the image file produced.

Please post the associated dataset here. Also document how to prepare the dataset and run bene here.

[vlee14]

attached is the file for the dataset

[meninonas]

Dr. Yoo,

Please find the datasets you asked for attached below.

What I did was, I downloaded the Master Dataset from the Breast Cancer genes Forum and simply copied and pasted the corresponding amount of variables into a new excel sheet.

[meninonas]

Dr. Yoo,

Please find the results of the results of the first Bene run. It took approximately 9 hours to run.

[meninonas]

Dr. Yoo,

I've been trying to run bene on the Path-two and Path-three and I keep on running into the following error:

Code: Select all

./run.sh: line 11: ./../bin/data2net.sh: Permission denied
Score :
Acs :
./run.sh: line 14: ./../bin/net2parents: Permission denied
./run.sh: line 14: ./../bin/parents2arcs: Permission denied
./run.sh: line 17: ./../bin/net2parents: Permission denied
./run.sh: line 18: ./../bin/parents2arcs: Permission denied
./run.sh: line 19: ./../bin/arcs2dot: Permission denied
See ./resdir/iris.png for a png picture of the net.

When I place the following command ls -l for the bene.file, it gives me the following:

Code: Select all

drwxrwxr-x 5 luis luis 4096 Feb 18 14:35 banjo.2.2.0
drwxrwxr-x 6 luis luis 4096 Mar  4 18:03 bene.git
-rw-r--r-- 1 luis luis 8980 Feb 16 18:32 examples.desktop

When I do it for the run.sh (the command prompt), I get the following:

Code: Select all

total 44
-rw-rw-r-- 1 luis luis 30558 Mar  4 16:52 iris.idt
-rw-rw-r-- 1 luis luis   244 Mar  4 16:52 iris.vd
drwxrwxr-x 2 luis luis  4096 Mar  4 18:10 resdir
-rwxrwxrwx 1 luis luis   492 Mar  4 16:52 run.sh

I've been trying to execute different variations of the chmod command to no avail. Would you be able to suggest ideas please?

[cwyoo]

Dr. Yoo,

I've been trying to run bene on the Path-two and Path-three and I keep on running into the following error:

Code: Select all

./run.sh: line 11: ./../bin/data2net.sh: Permission denied
Score :
Acs :
./run.sh: line 14: ./../bin/net2parents: Permission denied
./run.sh: line 14: ./../bin/parents2arcs: Permission denied
./run.sh: line 17: ./../bin/net2parents: Permission denied
./run.sh: line 18: ./../bin/parents2arcs: Permission denied
./run.sh: line 19: ./../bin/arcs2dot: Permission denied
See ./resdir/iris.png for a png picture of the net.

When I place the following command ls -l for the bene.file, it gives me the following:

Code: Select all

drwxrwxr-x 5 luis luis 4096 Feb 18 14:35 banjo.2.2.0
drwxrwxr-x 6 luis luis 4096 Mar  4 18:03 bene.git
-rw-r--r-- 1 luis luis 8980 Feb 16 18:32 examples.desktop

When I do it for the run.sh (the command prompt), I get the following:

Code: Select all

total 44
-rw-rw-r-- 1 luis luis 30558 Mar  4 16:52 iris.idt
-rw-rw-r-- 1 luis luis   244 Mar  4 16:52 iris.vd
drwxrwxr-x 2 luis luis  4096 Mar  4 18:10 resdir
-rwxrwxrwx 1 luis luis   492 Mar  4 16:52 run.sh

I've been trying to execute different variations of the chmod command to no avail. Would you be able to suggest ideas please?

Permissions of all the files under /home/luis/bene.git/bin directory should be set to "executable". You can go to that directory and run the following command:

chmod a+x *