WEKA Experimenter Tutorial

for Version 3-4

David Scuse
Peter Reutemann
June 1, 2007

c
2002-2007 David Scuse and University of Waikato
Contents
1 Introduction 2

2 Standard Experiments 3
Simple . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
New experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Results destination . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Experiment type . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Iteration control . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Saving the setup . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Running an Experiment . . . . . . . . . . . . . . . . . . . . . . . 10
Advanced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Defining an Experiment . . . . . . . . . . . . . . . . . . . . . . . 12
Running an Experiment . . . . . . . . . . . . . . . . . . . . . . . 15
Changing the Experiment Parameters . . . . . . . . . . . . . . . 17
Other Result Producers . . . . . . . . . . . . . . . . . . . . . . . 24

3 Remote Experiments 29
Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Database Server Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Remote Engine Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Configuring the Experimenter . . . . . . . . . . . . . . . . . . . . . . . 31
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

4 Analysing Results 33
Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Saving the Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Changing the Baseline Scheme . . . . . . . . . . . . . . . . . . . . . . 36
Statistical Significance . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Summary Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Ranking Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

1
1 Introduction
The Weka Experiment Environment enables the user to create, run, modify,
and analyse experiments in a more convenient manner than is possible when
processing the schemes individually. For example, the user can create an exper-
iment that runs several schemes against a series of datasets and then analyse
the results to determine if one of the schemes is (statistically) better than the
other schemes.
The Experiment Environment can be run from the command line using the
Simple CLI. For example, the following commands could be typed into the CLI
to run the OneR scheme on the Iris dataset using a basic train and test process.
(Note that the commands would be typed on one line into the CLI.)

java weka.experiment.Experiment -r -T data/iris.arff

-D weka.experiment.InstancesResultListener
-P weka.experiment.RandomSplitResultProducer --
-W weka.experiment.ClassifierSplitEvaluator --
-W weka.classifiers.rules.OneR

While commands can be typed directly into the CLI, this technique is not
particularly convenient and the experiments are not easy to modify.
The Experimenter comes in two flavours, either with a simple interface that
provides most of the functionality one needs for experiments, or with an interface
with full access to the Experimenter’s capabilities. You can choose between
those two with the Experiment Configuration Mode radio buttons:

• Simple

• Advanced

Both setups allow you to setup standard experiments, that are run locally on
a single machine, or remote experiments, which are distributed between several
hosts. The distribution of experiments cuts down the time the experiments will
take until completion, but on the other hand the setup takes more time.
The next section covers the standard experiments (both, simple and ad-
vanced), followed by the remote experiments and finally the analysing of the
results.
This manual is also available online on the WekaDoc Wiki [7].

2
2 Standard Experiments
Simple
New experiment
After clicking New default parameters for an Experiment are defined.

Results destination
By default, an ARFF file is the destination for the results output. But you can
choose between

• ARFF file

• CSV file

• JDBC database

ARFF file and JDBC database are discussed in detail in the following sec-
tions. CSV is similar to ARFF, but it can be used to be loaded in an external
spreadsheet application.

ARFF file
If the file name is left empty a temporary file will be created in the TEMP
directory of the system. If one wants to specify an explicit results file, click on
Browse and choose a filename, e.g., Experiment1.arff.

3
 Click on Save and the name will appear in the edit field next to ARFF file.

The advantage of ARFF or CSV files is that they can be created without
any additional classes besides the ones from Weka. The drawback is the lack
of the ability to resume an experiment that was interrupted, e.g., due to an
error or the addition of dataset or algorithms. Especially with time-consuming
experiments, this behavior can be annoying.

JDBC database
With JDBC it is easy to store the results in a database. The necessary jar
archives have to be in the CLASSPATH to make the JDBC functionality of a
particular database available.
After changing ARFF file to JDBC database click on User... to specify
JDBC URL and user credentials for accessing the database.

4
 After supplying the necessary data and clicking on OK, the URL in the main
window will be updated.
Note: at this point, the database connection is not tested; this is done when
the experiment is started.

The advantage of a JDBC database is the possibility to resume an in-

terrupted or extended experiment. Instead of re-running all the other algo-
rithm/dataset combinations again, only the missing ones are computed.

Experiment type
The user can choose between the following three different types

• Cross-validation (default)
performs stratified cross-validation with the given number of folds

• Train/Test Percentage Split (data randomized)

splits a dataset according to the given percentage into a train and a test file
(one cannot specify explicit training and test files in the Experimenter),
after the order of the data has been randomized and stratified

5
 • Train/Test Percentage Split (order preserved)
because it is impossible to specify an explicit train/test files pair, one can
abuse this type to un-merge previously merged train and test file into the
two original files (one only needs to find out the correct percentage)

Additionally, one can choose between Classification and Regression, depend-

ing on the datasets and classifiers one uses. For decision trees like J48 (Weka’s
implementation of Quinlan’s C4.5 [3]) and the iris dataset, Classification is
necessary, for a numeric classifier like M5P, on the other hand, Regression. Clas-
sification is selected by default.
Note: if the percentage splits are used, one has to make sure that the cor-
rected paired T-Tester still produces sensible results with the given ratio [2].

6
Datasets
One can add dataset files either with an absolute path or with a relative one.
The latter makes it often easier to run experiments on different machines, hence
one should check Use relative paths, before clicking on Add new....

In this example, open the data directory and choose the iris.arff dataset.

After clicking Open the file will be displayed in the datasets list. If one
selects a directory and hits Open, then all ARFF files will be added recursively.
Files can be deleted from the list by selecting them and then clicking on Delete
selected.

7
Iteration control
• Number of repetitions
In order to get statistically meaningful results, the default number of it-
erations is 10. In case of 10-fold cross-validation this means 100 calls of
one classifier with training data and tested against test data.

• Data sets first/Algorithms first

As soon as one has more than one dataset and algorithm, it can be useful
to switch from datasets being iterated over first to algorithms. This is
the case if one stores the results in a database and wants to complete the
results for all the datasets for one algorithm as early as possible.

Algorithms
New algorithms can be added via the Add new... button. Opening this dialog
for the first time, ZeroR is presented, otherwise the one that was selected last.

With the Choose button one can open the GenericObjectEditor and choose
another classifier.

8
 Additional algorithms can be added again with the Add new... button, e.g.,
the J48 decision tree.

After setting the classifier parameters, one clicks on OK to add it to the list
of algorithms.

9
 With the Load options... and Save options... buttons one can load and save
the setup of a selected classifier from and to XML. This is especially useful
for highly configured classifiers (e.g., nested meta-classifiers), where the manual
setup takes quite some time, and which are used often.

Saving the setup

For future re-use, one can save the current setup of the experiment to a file by
clicking on Save... at the top of the window.

By default, the format of the experiment files is the binary format that Java
serialization offers. The drawback of this format is the possible incompatibility
between different versions of Weka. A more robust alternative to the binary
format is the XML format.
Previously saved experiments can be loaded again via the Open... button.

Running an Experiment
To run the current experiment, click the Run tab at the top of the Experiment
Environment window. The current experiment performs 10 runs of 10-fold strat-

10
ified cross-validation on the Iris dataset using the ZeroR and J48 scheme.

Click Start to run the experiment.

If the experiment was defined correctly, the 3 messages shown above will
be displayed in the Log panel. The results of the experiment are saved to the
dataset Experiment1.arff.

11
Advanced
Defining an Experiment
When the Experimenter is started in Advanced mode, the Setup tab is displayed.
Click New to initialize an experiment. This causes default parameters to be
defined for the experiment.

To define the dataset to be processed by a scheme, first select Use relative

paths in the Datasets panel of the Setup tab and then click on Add new... to
open a dialog window.

Double click on the data folder to view the available datasets or navigate to
an alternate location. Select iris.arff and click Open to select the Iris dataset.

12
 The dataset name is now displayed in the Datasets panel of the Setup tab.

Saving the Results of the Experiment

To identify a dataset to which the results are to be sent, click on the Instances-
ResultListener entry in the Destination panel. The output file parameter is near
the bottom of the window, beside the text outputFile. Click on this parameter
to display a file selection window.

13
 Type the name of the output file, click Select, and then click close (x). The
file name is displayed in the outputFile panel. Click on OK to close the window.

The dataset name is displayed in the Destination panel of the Setup tab.

Saving the Experiment Definition

The experiment definition can be saved at any time. Select Save... at the top
of the Setup tab. Type the dataset name with the extension exp (or select the
dataset name if the experiment definition dataset already exists) for binary files
or choose Experiment configuration files (*.xml) from the file types combobox
(the XML files are robust with respect to version changes).

14
 The experiment can be restored by selecting Open in the Setup tab and then
selecting Experiment1.exp in the dialog window.

Running an Experiment
To run the current experiment, click the Run tab at the top of the Experiment
Environment window. The current experiment performs 10 randomized train
and test runs on the Iris dataset, using 66% of the patterns for training and
34% for testing, and using the ZeroR scheme.

Click Start to run the experiment.

15
 If the experiment was defined correctly, the 3 messages shown above will
be displayed in the Log panel. The results of the experiment are saved to the
dataset Experiment1.arff. The first few lines in this dataset are shown below.
@relation InstanceResultListener

@attribute Key_Dataset {iris}

@attribute Key_Run {1,2,3,4,5,6,7,8,9,10}
@attribute Key_Scheme {weka.classifiers.rules.ZeroR}
@attribute Key_Scheme_options {’’}
@attribute Key_Scheme_version_ID {48055541465867954}
@attribute Date_time numeric
@attribute Number_of_training_instances numeric
@attribute Number_of_testing_instances numeric
@attribute Number_correct numeric
@attribute Number_incorrect numeric
@attribute Number_unclassified numeric
@attribute Percent_correct numeric
@attribute Percent_incorrect numeric
@attribute Percent_unclassified numeric
@attribute Kappa_statistic numeric
@attribute Mean_absolute_error numeric
@attribute Root_mean_squared_error numeric
@attribute Relative_absolute_error numeric
@attribute Root_relative_squared_error numeric
@attribute SF_prior_entropy numeric
@attribute SF_scheme_entropy numeric
@attribute SF_entropy_gain numeric
@attribute SF_mean_prior_entropy numeric
@attribute SF_mean_scheme_entropy numeric
@attribute SF_mean_entropy_gain numeric
@attribute KB_information numeric

16
 @attribute KB_mean_information numeric
@attribute KB_relative_information numeric
@attribute True_positive_rate numeric
@attribute Num_true_positives numeric
@attribute False_positive_rate numeric
@attribute Num_false_positives numeric
@attribute True_negative_rate numeric
@attribute Num_true_negatives numeric
@attribute False_negative_rate numeric
@attribute Num_false_negatives numeric
@attribute IR_precision numeric
@attribute IR_recall numeric
@attribute F_measure numeric
@attribute Time_training numeric
@attribute Time_testing numeric
@attribute Summary string

@data

iris,1,weka.classifiers.rules.ZeroR,’’,48055541465867954,20051221.0055,99,51,
17,34,0,33.333333,66.666667,0,0,0.444444,0.471405,100,100,80.833088,80.833088,
0,1.584963,1.584963,0,0,0,0,1,17,1,34,0,0,0,0,0.333333,1,0.5,0.01,0,?

Changing the Experiment Parameters

Changing the Classifier
The parameters of an experiment can be changed by clicking on the Result
generator panel.

The RandomSplitResultProducer performs repeated train/test runs. The

number of instances (expressed as a percentage) used for training is given in the
trainPercent box. (The number of runs is specified in the Runs panel in the
Setup tab.)
A small help file can be displayed by clicking More in the About panel.

17
 Click on the splitEvaluator entry to display the SplitEvaluator properties.

Click on the classifier entry (ZeroR) to display the scheme properties.

This scheme has no modifiable properties (besides debug mode on/off) but
most other schemes do have properties that can be modified by the user. Click
on the Choose button to select a different scheme. The window below shows
the parameters available for the J48 decision-tree scheme. If desired, modify
the parameters and then click OK to close the window.

18
 The name of the new scheme is displayed in the Result generator panel.

Adding Additional Schemes

Additional schemes can be added in the Generator properties panel. To begin,
change the drop-down list entry from Disabled to Enabled in the Generator
properties panel.

19
 Click Select property and expand splitEvaluator so that the classifier entry
is visible in the property list; click Select.

The scheme name is displayed in the Generator properties panel.

20
 To add another scheme, click on the Choose button to display the Generic-
ObjectEditor window.

To change to a decision-tree scheme, select J48 (in subgroup trees).

21
 The new scheme is added to the Generator properties panel. Click Add to
add the new scheme.

Now when the experiment is run, results are generated for both schemes.
To add additional schemes, repeat this process. To remove a scheme, select
the scheme by clicking on it and then click Delete.

Adding Additional Datasets

The scheme(s) may be run on any number of datasets at a time. Additional
datasets are added by clicking Add new... in the Datasets panel. Datasets are
deleted from the experiment by selecting the dataset and then clicking Delete
Selected.

22
Raw Output
The raw output generated by a scheme during an experiment can be saved to
a file and then examined at a later time. Open the ResultProducer window by
clicking on the Result generator panel in the Setup tab.

Click on rawOutput and select the True entry from the drop-down list. By
default, the output is sent to the zip file splitEvaluatorOut.zip. The output file
can be changed by clicking on the outputFile panel in the window. Now when
the experiment is run, the result of each processing run is archived, as shown
below.

The contents of the first run are:

ClassifierSplitEvaluator: weka.classifiers.trees.J48 -C 0.25 -M 2(version -

217733168393644444)Classifier model:
J48 pruned tree
------------------

petalwidth <= 0.6: Iris-setosa (33.0)

petalwidth > 0.6
| petalwidth <= 1.5: Iris-versicolor (31.0/1.0)
| petalwidth > 1.5: Iris-virginica (35.0/3.0)

Number of Leaves : 3

Size of the tree : 5

23
Correctly Classified Instances 47 92.1569 %
Incorrectly Classified Instances 4 7.8431 %
Kappa statistic 0.8824
Mean absolute error 0.0723
Root mean squared error 0.2191
Relative absolute error 16.2754 %
Root relative squared error 46.4676 %
Total Number of Instances 51
measureTreeSize : 5.0
measureNumLeaves : 3.0
measureNumRules : 3.0

Other Result Producers

Cross-Validation Result Producer
To change from random train and test experiments to cross-validation exper-
iments, click on the Result generator entry. At the top of the window, click
on the drop-down list and select CrossValidationResultProducer. The window
now contains parameters specific to cross-validation such as the number of par-
titions/folds. The experiment performs 10-fold cross-validation instead of train
and test in the given example.

The Result generator panel now indicates that cross-validation will be per-
formed. Click on More to generate a brief description of the CrossValidation-
ResultProducer.

24
 As with the RandomSplitResultProducer, multiple schemes can be run during
cross-validation by adding them to the Generator properties panel.

The number of runs is set to 1 in the Setup tab in this example, so that only
one run of cross-validation for each scheme and dataset is executed.
When this experiment is analysed, the following results are generated. Note
that there are 30 (1 run times 10 folds times 3 schemes) result lines processed.

Averaging Result Producer

An alternative to the CrossValidationResultProducer is the AveragingResultPro-
ducer. This result producer takes the average of a set of runs (which are typ-
ically cross-validation runs). This result producer is identified by clicking the
Result generator panel and then choosing the AveragingResultProducer from
the GenericObjectEditor.

25
 The associated help file is shown below.

Clicking the resultProducer panel brings up the following window.

As with the other ResultProducers, additional schemes can be defined. When

the AveragingResultProducer is used, the classifier property is located deeper in
the Generator properties hierarchy.

26
 In this experiment, the ZeroR, OneR, and J48 schemes are run 10 times with
10-fold cross-validation. Each set of 10 cross-validation folds is then averaged,
producing one result line for each run (instead of one result line for each fold as
in the previous example using the CrossValidationResultProducer ) for a total of
30 result lines. If the raw output is saved, all 300 results are sent to the archive.

27
28
3 Remote Experiments
Remote experiments enable you to distribute the computing load across multiple
computers. In the following we will discuss the setup and operation for HSQLDB
[5] and MySQL [6].

Preparation
To run a remote experiment you will need:

• A database server.

• A number of computers to run remote engines on.

• To edit the remote engine policy file included in the Weka distribution to
allow Java class and dataset loading from your home directory.

• An invocation of the Experimenter on a machine somewhere (any will do).

For the following examples, we assume a user called johndoe with this setup:

• Access to a set of computers running a flavour of Unix (pathnames need

to be changed for Windows).

• The home directory is located at /home/johndoe.

• Weka is found in /home/johndoe/weka.

• Additional jar archives, i.e., JDBC drivers, are stored in /home/johndoe/jars.

• The directory for the datasets is /home/johndoe/datasets.

Note: The example policy file remote.policy.example is using this setup

(available in weka/experiment1 ).

Database Server Setup

• HSQLDB

– Download the JDBC driver for HSQLDB, extract the hsqldb.jar

and place it in the directory /home/johndoe/jars.
– To set up the database server, choose or create a directory to run the
database server from, and start the server with:

java -classpath /home/johndoe/jars/hsqldb.jar \

org.hsqldb.Server \
-database.0 experiment -dbname.0 experiment

Note: This will start up a database with the alias “experiment”

(-dbname.0 <alias>) and create a properties and a log file at the
current location prefixed with “experiment” (-database.0 <file>).
1 Weka’s source code can be found in the weka-src.jar archive or obtained from CVS [4].

29
 • MySQL
We won’t go into the details of setting up a MySQL server, but this is
rather straightforward and includes the following steps:
– Download a suitable version of MySQL for your server machine.
– Install and start the MySQL server.
– Create a database - for our example we will use experiment as data-
base name.
– Download the appropriate JDBC driver, extract the JDBC jar and
place it as mysql.jar in /home/johndoe/jars.

Remote Engine Setup

• First, set up a directory for scripts and policy files:
/home/johndoe/remote_engine
• Unzip the remoteExperimentServer.jar (from the Weka distribution; or
build it from the sources2 with ant remotejar) into a temporary direc-
tory.
• Next, copy remoteEngine.jar and remote.policy.example to the
/home/johndoe/remote engine directory.
• Create a script, called /home/johndoe/remote engine/startRemoteEngine,
with the following content (don’t forget to make it executable with chmod
a+x startRemoteEngine when you are on Linux/Unix):
– HSQLDB
java -Xmx256m \
-classpath /home/johndoe/jars/hsqldb.jar:remoteEngine.jar \
-Djava.security.policy=remote.policy \
weka.experiment.RemoteEngine &
– MySQL
java -Xmx256m \
-classpath /home/johndoe/jars/mysql.jar:remoteEngine.jar \
-Djava.security.policy=remote.policy \
weka.experiment.RemoteEngine &
• Now we will start the remote engines that run the experiments on the
remote computers (note that the same version of Java must be used for
the Experimenter and remote engines):
– Rename the remote.policy.example file to remote.policy.
– For each machine you want to run a remote engine on:
∗ ssh to the machine.
∗ cd to /home/johndoe/remote engine.
∗ Run /home/johndoe/startRemoteEngine (to enable the remote
engines to use more memory, modify the -Xmx option in the
startRemoteEngine script) .
2 Weka’s source code can be found in the weka-src.jar archive or obtained from CVS [4].

30
Configuring the Experimenter
Now we will run the Experimenter:

• HSQLDB
– Copy the DatabaseUtils.props.hsql file from weka/experiment in the
weka.jar archive to the /home/johndoe/remote engine directory
and rename it to DatabaseUtils.props.
– Edit this file and change the ”jdbcURL=jdbc:hsqldb:hsql://server name/database name”
entry to include the name of the machine that is running your database
server (e.g., jdbcURL=jdbc:hsqldb:hsql://dodo.company.com/experiment).
– Now start the Experimenter (inside this directory):
java \
-cp /home/johndoe/jars/hsqldb.jar:remoteEngine.jar:/home/johndoe/weka/weka.jar \
-Djava.rmi.server.codebase=file:/home/johndoe/weka/weka.jar \
weka.gui.experiment.Experimenter

• MySQL
– Copy the DatabaseUtils.props.mysql file from weka/experiment in
the weka.jar archive to the /home/johndoe/remote engine direc-
tory and rename it to DatabaseUtils.props.
– Edit this file and change the ”jdbcURL=jdbc:mysql://server name:3306/database name”
entry to include the name of the machine that is running your database
server and the name of the database the result will be stored in (e.g.,
jdbcURL=jdbc:mysql://dodo.company.com:3306/experiment).
– Now start the Experimenter (inside this directory):
java \
-cp /home/johndoe/jars/mysql.jar:remoteEngine.jar:/home/johndoe/weka/weka.jar \
-Djava.rmi.server.codebase=file:/home/johndoe/weka/weka.jar \
weka.gui.experiment.Experimenter

Note: the database name experiment can still be modified in the Exper-
imenter, this is just the default setup.

Now we will configure the experiment:

• First of all select the Advanced mode in the Setup tab

• Now choose the DatabaseResultListener in the Destination panel. Config-
ure this result producer:
– HSQLDB
Supply the value sa for the username and leave the password empty.
– MySQL
Provide the username and password that you need for connecting to
the database.
• From the Result generator panel choose either the CrossValidationResult-
Producer or the RandomSplitResultProducer (these are the most com-
monly used ones) and then configure the remaining experiment details
(e.g., datasets and classifiers).

31
 • Now enable the Distribute Experiment panel by checking the tick box.
• Click on the Hosts button and enter the names of the machines that you
started remote engines on (<Enter> adds the host to the list).

• You can choose to distribute by run or dataset.

• Save your experiment configuration.

• Now start your experiment as you would do normally.

• Check your results in the Analyse tab by clicking either the Database or
Experiment buttons.

Troubleshooting
• If you get an error at the start of an experiment that looks a bit like this:
01:13:19: RemoteExperiment (//blabla.company.com/RemoteEngine)
(sub)experiment (datataset vineyard.arff) failed :
java.sql.SQLException: Table already exists: EXPERIMENT INDEX
in statement [CREATE TABLE Experiment index ( Experiment type
LONGVARCHAR, Experiment setup LONGVARCHAR, Result table INT )]
01:13:19: dataset :vineyard.arff RemoteExperiment
(//blabla.company.com/RemoteEngine) (sub)experiment (datataset
vineyard.arff) failed : java.sql.SQLException: Table already
exists: EXPERIMENT INDEX in statement [CREATE TABLE
Experiment index ( Experiment type LONGVARCHAR, Experiment setup
LONGVARCHAR, Result table INT )]. Scheduling for execution on
another host.
then do not panic - this happens because multiple remote machines are
trying to create the same table and are temporarily locked out - this will
resolve itself so just leave your experiment running - in fact, it is a sign
that the experiment is working!

• If you serialized an experiment and then modify your DatabaseUtils.props

file due to an error (e.g., a missing type-mapping), the Experimenter will
use the DatabaseUtils.props you had at the time you serialized the ex-
periment. Keep in mind that the serialization process also serializes the
DatabaseUtils class and therefore stored your props-file! This is another
reason for storing your experiments as XML and not in the properietary
binary format the Java serialization produces.

• Using a corrupt or incomplete DatabaseUtils.props file can cause peculiar

interface errors, for example disabling the use of the ”User” button along-
side the database URL. If in doubt copy a clean DatabaseUtils.props from
CVS [4].

• If you get NullPointerException at java.util.Hashtable.get() in

the Remote Engine do not be alarmed. This will have no effect on the
results of your experiment.

32
4 Analysing Results
Setup
Weka includes an experiment analyser that can be used to analyse the results
of experiments (in this example, the results were sent to an InstancesResultLis-
tener ). The experiment shown below uses 3 schemes, ZeroR, OneR, and J48, to
classify the Iris data in an experiment using 10 train and test runs, with 66%
of the data used for training and 34% used for testing.

After the experiment setup is complete, run the experiment. Then, to

analyse the results, select the Analyse tab at the top of the Experiment En-
vironment window.
Click on Experiment to analyse the results of the current experiment.

33
 The number of result lines available (Got 30 results) is shown in the Source
panel. This experiment consisted of 10 runs, for 3 schemes, for 1 dataset, for a
total of 30 result lines. Results can also be loaded from an earlier experiment file
by clicking File and loading the appropriate .arff results file. Similarly, results
sent to a database (using the DatabaseResultListener ) can be loaded from the
database.
Select the Percent correct attribute from the Comparison field and click
Perform test to generate a comparison of the 3 schemes.

The schemes used in the experiment are shown in the columns and the
datasets used are shown in the rows.
The percentage correct for each of the 3 schemes is shown in each dataset
row: 33.33% for ZeroR, 94.31% for OneR, and 94.90% for J48. The annotation
v or * indicates that a specific result is statistically better (v) or worse (*)
than the baseline scheme (in this case, ZeroR) at the significance level specified
(currently 0.05). The results of both OneR and J48 are statistically better than
the baseline established by ZeroR. At the bottom of each column after the first
column is a count (xx/ yy/ zz) of the number of times that the scheme was
better than (xx), the same as (yy), or worse than (zz), the baseline scheme on
the datasets used in the experiment. In this example, there was only one dataset
and OneR was better than ZeroR once and never equivalent to or worse than
ZeroR (1/0/0); J48 was also better than ZeroR on the dataset.
The standard deviation of the attribute being evaluated can be generated
by selecting the Show std. deviations check box and hitting Perform test again.
The value (10) at the beginning of the iris row represents the number of esti-
mates that are used to calculate the standard deviation (the number of runs in
this case).

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 Selecting Number correct as the comparison field and clicking Perform test
generates the average number correct (out of 50 test patterns - 33% of 150
patterns in the Iris dataset).

Clicking on the button for the Output format leads to a dialog that lets you
choose the precision for the mean and the std. deviations, as well as the format
of the output.
The following formats are supported:

• Plain text (default)

• LaTeX

• CSV

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Saving the Results
The information displayed in the Test output panel is controlled by the currently-
selected entry in the Result list panel. Clicking on an entry causes the results
corresponding to that entry to be displayed.

The results shown in the Test output panel can be saved to a file by clicking
Save output. Only one set of results can be saved at a time but Weka permits
the user to save all results to the same file by saving them one at a time and
using the Append option instead of the Overwrite option for the second and
subsequent saves.

Changing the Baseline Scheme

The baseline scheme can be changed by clicking Select base... and then selecting
the desired scheme. Selecting the OneR scheme causes the other schemes to be
compared individually with the OneR scheme.

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 If the test is performed on the Percent correct field with OneR as the base
scheme, the system indicates that there is no statistical difference between the
results for OneR and J48. There is however a statistically significant difference
between OneR and ZeroR.

Statistical Significance
The term statistical significance used in the previous section refers to the re-
sult of a pair-wise comparison of schemes using either a standard T-Test or the
corrected resampled T-Test [2]. The latter test is the default, because the stan-
dard T-Test can generate too many significant differences due to dependencies
in the estimates (in particular when anything other than one run of an x-fold
cross-validation is used). For more information on the T-Test, consult the Weka
book [1] or an introductory statistics text. As the significance level is decreased,
the confidence in the conclusion increases.
In the current experiment, there is not a statistically significant difference
between the OneR and J48 schemes.

Summary Test
Selecting Summary from Test base and performing a test causes the following
information to be generated.

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 In this experiment, the first row (- 1 1) indicates that column b (OneR) is
better than row a (ZeroR) and that column c (J48) is also better than row a.
The number in brackets represents the number of significant wins for the column
with regard to the row. A 0 means that the scheme in the corresponding column
did not score a single (significant) win with regard to the scheme in the row.

Ranking Test
Selecting Ranking from Test base causes the following information to be gener-
ated.

The ranking test ranks the schemes according to the total number of sig-
nificant wins (>) and losses (<) against the other schemes. The first column
(> − <) is the difference between the number of wins and the number of losses.
This difference is used to generate the ranking.

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References
[1] Witten, I.H. and Frank, E. (2005) Data Mining: Practical machine learn-
ing tools and techniques. 2nd edition Morgan Kaufmann, San Francisco.

[2] Bengio, Y. and Nadeau, C. (1999) Inference for the Generalization Error.

[3] Ross Quinlan (1993). C4.5: Programs for Machine Learning, Morgan
Kaufmann Publishers, San Mateo, CA.

[4] CVS – http://weka.sourceforge.net/wiki/index.php/CVS

[5] HSQLDB – http://hsqldb.sourceforge.net/

[6] MySQL – http://www.mysql.com/

[7] WekaDoc – http://weka.sourceforge.net/wekadoc/

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