An Introduction to the WEKA Data Mining System

Zdravko Markov
Central Connecticut State University
markovz@ccsu.edu

Ingrid Russell
University of Hartford
irussell@hartford.edu
 Agenda

• Data Mining

• Weka Project

• Basic functionality of Weka by example

• Weka for document classification and clustering

 Database management systems (DBMS), Online
Analytical Processing (OLAP) and Data Mining

Area DBMS OLAP Data Mining

Knowledge
Extraction of detailed Summaries, trends discovery of hidden
Task
and summary data and forecasts patterns and
insights
Insight and
Type of result Information Analysis
Prediction
Multidimensional Induction (Build the
Deduction (Ask the
data modeling, model, apply it to
Method question, verify with
Aggregation, new data, get the
data)
Statistics result)
What is the average Who will buy a
Example Who purchased mutual income of mutual mutual fund in the
question funds in the last 3 years? fund buyers by next 6 months and
region by year? why?
Example of DBMS, OLAP and Data Mining: Weather data
Assume we have made a record of the weather conditions during a two-week period,
along with the decisions of a tennis player whether or not to play tennis on each
particular day. Thus we have generated tuples (or examples, instances) consisting of
values of four independent variables (outlook, temperature, humidity, windy) and one
dependent variable (play).
 Data-Base Management System

• What was the temperature in the sunny days? {85, 80, 72, 69, 75}
• Which days the humidity was less than 75? {6, 7, 9, 11}
• Which days the temperature was greater than 70? {1, 2, 3, 8, 10, 11, 12, 13, 14}
• Which days the temperature was greater than 70 and the humidity was less than 75?
The intersection of the above two: {11}
 OLAP: Multidimensional Model (Data Cube)

Dimensions:
• Time: Week 1={1, 2, 3, 4, 5, 6, 7}, Week 2={8, 9, 10, 11, 12, 13, 14}
• Outlook: {sunny, rainy, overcast}
Unit: play (yes/no)

9/5 sunny rainy overcast

Week 1 0/2 2/1 2/0
Week 2 2/1 1/1 2/0

 if outlook = overcast then play = yes

 Data Mining: Association Rules

Discretize numeric attributes (data pre-processing

stage in data mining). Group the temperature values in
three intervals (hot, mild, cool) and humidity values in
two (high, normal).

1. humidity=normal windy=false 4 ==> play=yes (4, 1)

2. temperature=cool 4 ==> humidity=normal (4, 1)
3. outlook=overcast 4 ==> play=yes (4, 1)
4. temperature=cool play=yes 3 ==> humidity=normal (3, 1)
5. outlook=rainy windy=false 3 ==> play=yes (3, 1)
6. outlook=rainy play=yes 3 ==> windy=false (3, 1)
7. outlook=sunny humidity=high 3 ==> play=no (3, 1)
8. outlook=sunny play=no 3 ==> humidity=high (3, 1)
9. temperature=cool windy=false 2 ==> humidity=normal play=yes (2, 1)
10. temperature=cool humidity=normal windy=false 2 ==> play=yes (2, 1)
Data Mining: Decision Tree and Rules

If outlook = overcast then yes

If humidity = normal and windy = false then yes
If temperature = mild and humidity = normal then yes
If outlook = rainy and windy = false then yes
If outlook = sunny and humidity = high then no
If outlook = rainy and windy = true then no
 Data Mining: Prediction

P(play=yes | outlook=sunny, temperature=mild, humidity=normal, windy=false) = 0.8

P(play=no | outlook=sunny, temperature=mild, humidity=normal, windy=false) = 0.2

Weka Project
 12 Years ago …
KDnuggets : News : 2005 : n13 : item2

SIGKDD Service Award is the highest service award in the field of data mining and knowledge discovery. It is is given
to one individual or one group who has performed significant service to the data mining and knowledge discovery
field, including professional volunteer services in disseminating technical information to the field, education, and
research funding.

The 2005 ACM SIGKDD Service Award is presented to the Weka team for their development of the freely-available
Weka Data Mining Software, including the accompanying book Data Mining: Practical Machine Learning Tools and
Techniques (now in second edition) and much other documentation.

The Weka team includes Ian H. Witten and Eibe Frank, and the following major contributors (in alphabetical order of
last names): Remco R. Bouckaert, John G. Cleary, Sally Jo Cunningham, Andrew Donkin, Dale Fletcher, Steve
Garner, Mark A. Hall, Geoffrey Holmes, Matt Humphrey, Lyn Hunt, Stuart Inglis, Ashraf M. Kibriya, Richard
Kirkby, Brent Martin, Bob McQueen, Craig G. Nevill-Manning, Bernhard Pfahringer, Peter Reutemann, Gabi
Schmidberger, Lloyd A. Smith, Tony C. Smith, Kai Ming Ting, Leonard E. Trigg, Yong Wang, Malcolm Ware, and
Xin Xu.

The Weka team has put a tremendous amount of effort into continuously developing and maintaining the system since
1994. The development of Weka was funded by a grant from the New Zealand Government's Foundation for
Research, Science and Technology.

The key features responsible for Weka's success are:

– it provides many different algorithms for data mining and machine learning
– is is open source and freely available
– it is platform-independent
– it is easily usable by people who are not data mining specialists
– it provides flexible facilities for scripting experiments
– it has kept up-to-date, with new algorithms being added as they appear in the research literature.
 12 Years ago …
KDnuggets : News : 2005 : n13 : item2 (cont.)
The Weka Data Mining Software has been downloaded 200,000 times since it was put on SourceForge in April
2000, and is currently downloaded at a rate of 10,000/month. The Weka mailing list has over 1100
subscribers in 50 countries, including subscribers from many major companies.

There are 15 well-documented substantial projects that incorporate, wrap or extend Weka, and no doubt many
more that have not been reported on Sourceforge.

Ian H. Witten and Eibe Frank also wrote a very popular book "Data Mining: Practical Machine Learning
Tools and Techniques" (now in the second edition), that seamlessly integrates Weka system into teaching
of data mining and machine learning. In addition, they provided excellent teaching material on the book
website.

This book became one of the most popular textbooks for data mining and machine learning, and is very
frequently cited in scientific publications.

Weka is a landmark system in the history of the data mining and machine learning research communities,
because it is the only toolkit that has gained such widespread adoption and survived for an extended period
of time (the first version of Weka was released 11 years ago). Other data mining and machine learning
systems that have achieved this are individual systems, such as C4.5, not toolkits.

Since Weka is freely available for download and offers many powerful features (sometimes not found in
commercial data mining software), it has become one of the most widely used data mining systems. Weka
also became one of the favorite vehicles for data mining research and helped to advance it by making many
powerful features available to all.

In sum, the Weka team has made an outstanding contribution to the data mining field.
Now …
Machine Learning, Data and Web Mining
by Example
(“learning by doing” approach)

• Data preprocessing and visualization

• Attribute selection
• Classification (OneR, Decision trees)
• Prediction (Nearest neighbor)
• Model evaluation
• Clustering (K-means)
• Association rules
Data preprocessing and visualization

Initial Data Preparation

(Weka data input)

• Raw data (Japanese loan data)

• Web/Text documents (Department data)
 Data preprocessing and visualization
Japanese loan data (a sample from a loan history database of a Japanese bank)
Clients: s1,..., s20
• Approved loan: s1, s2, s4, s5, s6, s7, s8, s9, s14, s15, s17, s18, s19
• Rejected loan: s3, s10, s11, s12, s13, s16, s20

Clients data:
• unemployed clients: s3, s10, s12
• loan is to buy a personal computer: s1, s2, s3, s4, s5, s6, s7, s8, s9, s10
• loan is to buy a car: s11, s12, s13, s14, s15, s16, s17, s18, s19, s20
• male clients: s6, s7, s8, s9, s10, s16, s17, s18, s19, s20
• not married: s1, s2, s5, s6, s7, s11, s13, s14, s16, s18
• live in problematic area: s3, s5
• age: s1=18, s2=20, s3=25, s4=40, s5=50, s6=18, s7=22, s8=28, s9=40, s10=50, s11=18, s12=20,
s13=25, s14=38, s15=50, s16=19, s17=21, s18=25, s19=38, s20=50
• money in a bank (x10000 yen): s1=20, s2=10, s3=5, s4=5, s5=5, s6=10, s7=10, s8=15, s9=20, s10=5,
s11=50, s12=50, s13=50, s14=150, s15=50, s16=50, s17=150, s18=150, s19=100, s20=50
• monthly pay (x10000 yen): s1=2, s2=2, s3=4, s4=7, s5=4, s6=5, s7=3, s8=4, s9=2, s10=4, s11=8,
s12=10, s13=5, s14=10, s15=15, s16=7, s17=3, s18=10, s19=10, s20=10
• months for the loan: s1=15, s2=20, s3=12, s4=12, s5=12, s6=8, s7=8, s8=10, s9=20, s10=12, s11=20,
s12=20, s13=20, s14=20, s15=20, s16=20, s17=20, s18=20, s19=20, s20=30
• years with the last employer: s1=1, s2=2, s3=0, s4=2, s5=25, s6=1, s7=4, s8=5, s9=15, s10=0, s11=1,
s12=2, s13=5, s14=15, s15=8, s16=2, s17=3, s18=2, s19=15, s20=2
Data preprocessing and visualization
Relations, attributes, tuples (instances)

Loan data – CSV format

(LoanData.csv)
 Data preprocessing and visualization
Attribute-Relation File Format (ARFF) - http://www.cs.waikato.ac.nz/~ml/weka/arff.html
Data preprocessing and visualization
Run Weka and select the Explorer
 Data preprocessing and visualization
Load data into Weka – ARFF format or CSV format (click on “Open file…”)
Data preprocessing and visualization
Converting data formats through Weka (click on “Save…”)
Data preprocessing and visualization
Editing data in Weka (click on ”Edit…”)
 Data preprocessing and visualization
Examining data
• Attribute type and properties
• Class (last attribute) distribution
Data preprocessing and visualization
Click on “Visualize All”
 Data preprocessing and visualization
Click on “Visualize” tab, double-click on a plot to see the 2D projection of the instance space
 Data preprocessing and visualization
Using filters: click on “Choose” in the “Filter” window, select “Discretize”
 Data preprocessing and visualization
Click in the “Discretize” in the Filter window and choose parameters, then click on “Apply”

Note how the plot

of “lastemp”
changed.
Data preprocessing and visualization
Web/Text documents - Department data
 Data preprocessing and visualization
Department data document collection
http://www.cs.ccsu.edu/~markov/MDLclustering

http://www.cs.ccsu.edu/~markov/MDLclustering/data.zip
Data preprocessing and visualization
Department data: Create ARFF file

http://www.cs.ccsu.edu/~markov/MDLclustering/MDL.jar
 Data preprocessing and visualization
Department data: Create ARFF file in string format (using SimpleCLI)

1. Create file deptA with the files in folder data/departments/A with class label A:
java ARFFstring data/departments/A A deptA

2. Create file deptB with the files in folder data/departments/B with class label B:
java ARFFstring data/departments/B B deptB

3. Merge deptA and deptB into one file departments-string.arff

4. Add the following ARFF file header in the beginning of departments-string.arff:

@relation departments_string
@attribute document_name string
@attribute document_content string
@attribute document_class {A,B}
@data
Data preprocessing and visualization
Loading text data in Weka
• String format for ID and content
• One document per line
• Add class (nominal) if needed
 Data preprocessing and visualization
Converting a string attribute into nominal
Choose filters/unsupervised/attribute/StringToNominal, set attributeRange to 1, click on Apply
 Data preprocessing and visualization
Converting text data into TFIDF (Term Frequency – Inverted Document Frequency) attribute format
• Choose filters/unsupervised/attribute/StringToWordVector
• Set the parameters as needed (see “More”)
• Click on “Apply”
Data preprocessing and visualization
Make document_class last attribute
• Choose filters/unsupervised/attribute/Copy
• Set the index to 2 and click on Apply
• Remove attribute 2
Data preprocessing and visualization
• Change the attributes to nominal (use NumericToNominal filter)
• Save data on a file for further use
 Data preprocessing and visualization
ARFF department data in binary format (NonSparse and Sparse format, see SparseToNonSparse filter)
Data preprocessing and visualization
ARFF department data in TF and TFIDF format
Data preprocessing and visualization
Student Projects

• Preprocess.html
• Visualization.html
 Attribute Selection
Finding a minimal set of attributes that preserve the class distribution
Attribute relevance with respect to the class – irrelevant attribute (accounting)

IF accounting=1 THEN class=A (Error=0, Coverage = 1 instance → overfitting )

IF accounting=0 THEN class=B (Error=10/19, Coverage = 19 instances → low accuracy)
 Attribute Selection
Attribute relevance with respect to the class – relevant attribute (science)

IF science=1 THEN class=A (Error=0, Coverage = 7 instance)

IF science=0 THEN class=B (Error=4/13, Coverage = 13 instances)
Attribute Selection (with document_name)
 Attribute Selection (without document_name)

Select document_name and

click on Remove
Attribute Selection (ranking)
Attribute Selection (explanation of ranking)
 Attribute Selection (using filters)
• Choose filters/supervised/attribute/AttributeSelection
• Set parameters to InfoGainAttributeEval and Ranker
• Click on Apply and see the attribute ordering
 Attribute Selection (using filters)
Choose filters/supervised/attribute/AttributeSelection and use CfsSubsetEval and BestFirst search.
Then click on Visualize All
 Attribute Selection
Student Projects

• Attribute Selection.html
Classification – creating models (hypotheses)
Mapping (independent attributes -> class)
 Classification – creating models (hypotheses)
Inferring one-attribute rules - OneR

Weather data (weather.nominal.arff)

Attribute Rules Errors Total
error
outlook sunny -> no 2/5 4/14
overcast -> yes 0/4
rainy -> yes 2/5

temperature hot -> no 2/4 5/14

mild -> yes 2/6
cool -> yes 1/4

humidity high -> no 3/7 4/14

1/7
normal -> yes
windy false -> yes 2/8 5/14
true -> no 3/5
Classification – OneR
 Classification – decision tree
Right click on the highlighted line in Result list and choose Visualize tree
 Classification – decision tree
Top-down induction of decision trees (TDIDT, old approach know
from pattern recognition):
• Select an attribute for root node and create a branch for each
possible attribute value.
• Split the instances into subsets (one for each branch
extending from the node).
• Repeat the procedure recursively for each branch, using only
instances that reach the branch (those that satisfy the
conditions along the path from the root to the branch).
• Stop if all instances have the same class.

ID3, C4.5, J48 (Weka): Select the attribute that minimizes the class
entropy in the split.
Classification – numeric attributes
weather.arff
 Classification – predicting class
Click on Set… Click on Open file…
 Classification – predicting class
Right click on the highlighted line in Result list and choose Visualize classifier errors
Click on the square
 Classification – predicting class
Click on Save
 Classification
Student Projects

• Classification.html
 Prediction (no model, lazy learning)
test: (sunny, cool, high, TRUE, ?) • K-nearest neighbor (IBk)
Take the class of the nearest neighbor
or the majority class among K neighbors
K=1 -> no
K=3 -> no
K=5 -> yes
K=14 -> yes (Majority predictor, ZeroR)

• Weighted K-nearest neighbor

K=5 -> undecided
no=1/1+1/2=1.5
yes=1/2+1/2+1/2=1.5

X 2 8 9 11 12 … 10
Distance(test,X) 1 2 2 2 2 … 4
play no no yes yes yes … yes
• Distance is calculated as the number of different attribute values
• Euclidean distance for numeric attributes
Prediction (no model, lazy learning)
 Prediction
Student Projects

• Prediction.html
Model evaluation – holdout (percentage split)
Model evaluation – cross validation
Model evaluation – leave one out cross validation
Model evaluation – confusion (contingency) matrix

predicted

actual
yes no
yes 3 1
no 1 0

predicted
yes no

actual
yes TP FN
no FP TN

Precision = TP/(TP+FP)
Recall = TP/(TP+FN)
Model evaluation
Student Projects

• Evaluation.html
 Clustering – k-means
Click on Ignore attributes
 Clustering – classes to clusters evaluation
Right click on Result list, select Visualize cluster assignments
Click on Save
 Clustering
Student Projects

• Clustering.html
 Association Rules (A => B)
• Confidence (accuracy): P(B|A) = (# of tuples containing both A and B) / (# of tuples containing A).
• Support (coverage): P(A,B) = (# of tuples containing both A and B) / (total # of tuples)
Association Rules
Student Projects

• Association.html
Document classification and clustering
Predict the class of the Theatre document

1. Create a training set – all departments excluding Theatre

(data collection)
2. Use Binary, Term Frequency or TFIDF representation
(data preprocessing)
3. Select a relevant subset of attributes (attribute selection)
4. Use J48, IBk, and Naïve Bayes (classification)
5. Evaluate all models by cross validation (model
evaluation)
6. Choose the best model and predict the class of Theatre
(prediction)
7. Cluster the training set with K-means compare the
cluster centroids with Theatre
 Document classification and clustering
Teaching resources and student projects based on Weka

• Zdravko Markov and Daniel T. Larose, Data Mining the Web:

Uncovering Patterns in Web Content, Structure, and Usage, Wiley 2007
(free excerpts: Chapter 1, TOC, Index)
• Lecture slides: dmw1.pdf, dmw2.pdf, dmw3.pdf, dmw4.pdf, dmw5.pdf
• Data sets: http://www.cs.ccsu.edu/~markov/dmwdata.zip
• Clustering.html
http://www.cs.ccsu.edu/~markov/MDLclustering/
http://www.cs.ccsu.edu/~markov/DMWprojects