Getting started with

Weka
The HIV Data Management and
Data Mining Workshop.

December, 13-16th 2004

Durban, South Africa
Contents

1. What is Weka and why use it?

2. First view on the Weka explorer
3. Importing a data set in Weka
4. Preprocess-tab
5. Visualize-tab
What is Weka?

• “Waikato Environment for

Knowledge Analysis”
• Weka is a collection of
machine learning
algorithms for data mining
• Open Source Machine
Learning Software in Java

http://www.cs.waikato.ac.nz/ml/weka/
Why use Weka?

• It contains tools for a whole range of data

mining tasks:
– Data pre-processing
– Classification
– Regression
– Clustering
– Association
– Visualization
• You can download it for free!
Launching Weka

• We will only make

use of the
‘Explorer’ user
interface
 First view on the Weka Explorer
Tabs for
different tasks:
•preprocessing
•classification
•clustering
•association
•attribute
selection
•visualization
Importing a data set (1)
Importing a data set (2)

• Format of your data:

– ARFF-format: special Weka format
– CSV format (can be exported from Excell)
Importing a data set (3)

• ARFF-format:
@RELATION stanford_data
@ATTRIBUTE Subtype { "D", "K", "F1", "C", "A1", "B", "A2", "G", ""}
@ATTRIBUTE Bootstrap numeric
@ATTRIBUTE eNFV { "n", "y"}
@ATTRIBUTE SeqId { "NDK_198301", "SE554_199808", "SE474_199808", …,
"KDR_pat152_200101", "IL210_200104"}
@ATTRIBUTE PR2 { "Q", "K", "R", "H", "*", "E"}
…
@ATTRIBUTE PR99 { "F", "N", "Y", "L"}
@DATA
"D", "38.0", "n", "NDK_198301", "Q", "I", "T", "L", "W", "Q", "R", "P", "L", "V", "T", …, "F"
"F1", "50.0", "n", "CDC7944_199501", "Q", "I", "T", "L", "W", "Q", "R", "P", "L", "V", …, "F"
 Importing a data set (4)

• CSV format:
can be
exported
from Excel

eNFV,subtype,bootstrap,seqid,PR2,PR3,PR4, …,PR97,PR98,PR99

n,D,44,NDK_198301,Q,I,T,…,L,N,F
n,C,95,BRP2139_200208,Q,I,P,…,L,N,F
y,C,97,TCDD13_200103, ,I,T,…,L,N,F
Preprocess-tab
Preprocess-tab
gives
information
about the
loaded data
and allows you
to preprocess it
further
Preprocess-tab

Filters can be applied

to preprocess the data
Preprocess-tab

describes the current

relation:
• nb of instances
• nb of attributes
Preprocess-tab
list of all attributes

allows you to
remove selected
attributes
Preprocess-tab
gives info about
attribute selected
from list

for nominal attributes:

possible values and
number of times each
value occurs
Preprocess-tab

for numeric attributes:

minimum, maximum,
mean, standard
deviation
Preprocess-tab
visualizes the
selected attribute
with colours
according to
selected class
attribute

D N V
Preprocess-tab
visualizes the
selected attribute
with colours
according to
selected class
attribute

instances without instances with

therapy experience therapy experience
Visualize-tab

• Preprocess-tab allows you to look at

interactions between two different
attributes (eg. PR30 and eNFV)
• Visualize-tab allows you to look at
interactions between three different
attributes (eg. PR90, PR30 and eNFV)
 Visualize-tab
plot matrix of all
attributes plotted
increase the against each other
PlotSize, PointSize
and Jitter

click update!

select the target

attribute eNFV for
the colouring
Visualize-tab
click a plot to
see it in more
detail
Visualize-tab
Practice

• Import the data set and play with the

visualization tools
1. Do these visualizations agree with all
the IAS mutations for Nelfinavir? (30N,
36I, 46I, 63P, 71V, 77I, 84V, 88D, 90M)
2. Do you see any other protease
positions that seem to correlate with
therapy experience?