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What is WEKA ?
• Machine learning/data mining software written in Java (distributed under
the GNU Public License)
• Used for research, education, and applications
• Complements “Data Mining” by Witten & Frank
• Main features:
– Comprehensive set of data pre-processing tools, learning algorithms
and evaluation methods
– Graphical user interfaces (incl. data visualization)
– Environment for comparing learning algorithms
• Weka versions
– WEKA 3.4: “book version” compatible with description in data mining
book
– WEKA 3.5: “developer version” with lots of improvements
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Formatting Data into ARFF
@relation iris
@attribute sepallength real
@attribute sepalwidth real
@attribute petallength real
@attribute petalwidth real
@attribute class {Iris-setosa, Iris-versicolor, Iris-virginica}
@data
5.1,3.5,1.4,0.2,Iris-setosa
4.9,3.0,1.4,0.2,Iris-setosa
…
7.0,3.2,4.7,1.4,Iris-versicolor
6.4,3.2,4.5,1.5,Iris-versicolor
…
6.3,3.3,6.0,2.5,Iris-virginica
5.8,2.7,5.1,1.9,Iris-virginica
… 4
Practicing WEKA
• What is WEKA ?
• Formatting the data into ARFF
• Klasifikasi
– Tahapan membangun classifier
– Contoh kasus : Klasifikasi bunga iris
– Tahapan membangun classifier
– Merangkum hasil eksperimen k-Nearest Neighbor Classifier
– Eksperimen memakai classifier yang lain (JST, SVM)
– Classification of cancers based on gene expression
– Parkinson Disease Detection
• K-Means Clustering
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Tahapan membangun Classifier
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Contoh Kasus : Klasifikasi bunga iris
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Flower’s parts
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Tahapan membangun Classifier
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Open file “iris-training.arff”
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Klik pada Classify untuk memilih
Classifier algorithm
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Klik pada “Choose” untuk memilih
Classifier algorithm
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Naïve Bayes
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IB1 : 1-Nearest Neighbor
Classifier)
IBk : k-Nearest Neighbor
Classifier
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Multilayer Perceptron
(Jaringan Syaraf Tiruan)
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SMO singkatan dari
Sequential Minimal Optimization.
SMO adalah implementasi SVM
Mengacu pada paper John Platt
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Decision Tree J48 (C4.5)
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Misalnya kita pilih
IBk : k-Nearest Neighbor
Classifier
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Selanjutnya pilihlah skenario
Pengukuran akurasi. Dari 4
Options yang diberikan, pilihlah
“Supplied test set” dan klik
Button “Set” untuk memiilih
Testing set file “iris-testing.arff”
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Tahapan membangun Classifier
Iris-training.arff
iris setosa 25
Iris-testing.arff
iris versicolor 25
25 25
iris virginica
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Classifiers : 25
1. Naïve Bayes Akurasi
2. K-Nearest Neighbor Classifier terhadap
(lazy iBk) testing set ?
3. Artificial Neural Network
(function multilayer perceptron)
4. Support Vector Machine
(function SMO) 21
Apakah yang dimaksud “mengukur akurasi”
• Testing set “iris-testing.arff” dilengkapi dengan informasi
actual class-nya. Misalnya instance no.1 adalah suatu bunga
yang memiliki sepal length 5.0 cm, sepal width 3.0cm, petal
length 1.6 cm, petal width 0.2 cm, dan jenis bunganya (class)
“Iris setosa”
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Berbagai cara pengukuran akurasi
• “Using training set” : memakai seluruh
data sebagai training set, sekaligus testing
set. Akurasi akan sangat tinggi, tetapi
tidak memberikan estimasi akurasi yang
sebenarnya terhadap data yang lain (yang
tidak dipakai untuk training)
• Hold Out Method : Memakai sebagian
data sebagai training set, dan sisanya
sebagai testing set. Metode yang lazim
dipakai, asal jumlah sampel cukup banyak.
Ada 2 : supplied test set dan percentage
split. Pilihlah “Supplied test set” : jika file
training dan testing tersedia secara
terpisah. Pilihlah “Percentage split” jika
hanya ada 1 file yang ingin dipisahkan ke
training & testing. Persentase di kolom
adalah porsi yang dipakai sbg training set 23
Berbagai cara pengukuran akurasi
• Cross Validation Method ( fold = 5
atau 10 ) : teknik estimasi akurasi
yang dipakai, jika jumlah sampel
terbatas. Salah satu bentuk
khusus CV adalah Leave-one-out
Cross Validation (LOOCV) : dipakai
jka jumlah sampel sangat terbatas
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Ilustrasi Cross Validation (k=5)
1. Data terdiri dari 100 instances (samples), dibagi ke dalam 5 blok
dengan jumlah sampel yang sama. Nama blok : A, B, C, D dan E,
masing-masing terdiri dari 20 instances
2. Kualitas kombinasi parameter tertentu diuji dengan cara sbb.
step 1: training memakai A,B,C,D testing memakai E akurasi a
step 2: training memakai A,B,C,E testing memakai D akurasi b
step 3: training memakai A,B, D,E testing memakai C akurasi c
step 4: training memakai A, C,D,E testing memakai B akurasi d
step 5: training memakai B,C,D,E testing memakai A akurasi e
3. Rata-rata akurasi : (a+b+c+d+e)/5 mencerminkan kualitas
parameter yang dipilih
4. Ubahlah parameter model, dan ulangi dari no.2 sampai dicapai
akurasi yang diinginkan
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Kali ini memakai “Supplied test set”.
Selanjutnya klik pada bagian yang
Di dalam kotak untuk men-set nilai
Parameter. Dalam hal ini, adalah
Nilai “k” pada k-Nearest Neighbour
Classifier (Nick name : IBK)
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Set-lah nilai “k”misalnya 3 dan klik OK.
Untuk memahami parameter yang lain,
kliklah button “More” & “Capabilities”
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Klik button “Start”
Hasil eksperimen : Correct classification rate : 96%
(benar 72 dari total 75 data pada testing set)
1 1 ? ? ? ?
2 3 100% 96% 92% 96%
3 5
5
7
9
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Eksperimen memakai SVM
C: complexity parameter
(biasanya mengambil nilai
besar. 100, 1000 dst)
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Eksperimen memakai SVM
Classification of cancers based on gene expression
• Biological reference:
Classification and diagnostic prediction of cancers using gene
expression profiling and artificial neural networks,
J. Khan, et al., Nature Medicine 7, pp.673-679, 2001
(http://www.thep.lu.se/~carsten/pubs/lu_tp_01_06.pdf )
• Data is available from
http://research.nhgri.nih.gov/microarray/Supplement/
• Small Round Blue Cell Tumors (SRBCT) has two class:
– Ewing Family of Tumors (EWS)
– NB: Neuroblastoma
– BL: Burkitt lymphomas
– RMS: Rhabdomyosarcoma : RMS
• Characteristic of the data
– Training samples : 63 (EWS:23 BL:8 NB:12 RMS:20)
– Testing samples: 20 (EWS:6 BL:3 NB:6 RMS:5)
– Number of features (attributes): 2308 37
Classification of cancers based on gene expression
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Parkinson Disease Detection
Max Little (Oxford University) recorded speech signals and measured the
biomedical voice from 31 people, 23 with Parkinson Disease (PD). In the
dataset which will be distributed during final examination, each column in the
table is a particular voice measure, and each row corresponds one of 195 voice
recording from these individuals ("name" column). The main aim of the data is
to discriminate healthy people from those with PD, according to "status" column
which is set to 0 for healthy and 1 for PD. There are around six recordings per
patient, making a total of 195 instances. (Ref. 'Exploiting Nonlinear Recurrence
and Fractal Scaling Properties for Voice Disorder Detection', Little MA,
McSharry PE, Roberts SJ, Costello DAE, Moroz IM. BioMedical Engineering
OnLine 2007, 6:23, 26 June 2007).
Experiment using k-Nearest Neighbor Classifier
Conduct classification experiments using k-Nearest Neighbor Classifier and
Support Vector Machines, by using 50% of the data as training set and the rest
as testing set. Try at least 5 different values of k for k-Nearest neighbor, and
draw a graph show the relationship between k and classification rate. In case
of Support Vector Machine experiments, try several parameter combinations by
modifying the type of Kernel and its parameters (at least 5 experiments).
Compare and discuss the results obtained by both classifiers. Which of them
achieved higher accuracy ?
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Parkinson Disease Detection
Max Little (Oxford University) recorded speech signals and measured the
biomedical voice from 31 people, 23 with Parkinson Disease (PD). In the
dataset which will be distributed during final examination, each column in the
table is a particular voice measure, and each row corresponds one of 195 voice
recording from these individuals ("name" column). The main aim of the data is
to discriminate healthy people from those with PD, according to "status" column
which is set to 0 for healthy and 1 for PD. There are around six recordings per
patient, making a total of 195 instances. (Ref. 'Exploiting Nonlinear Recurrence
and Fractal Scaling Properties for Voice Disorder Detection', Little MA,
McSharry PE, Roberts SJ, Costello DAE, Moroz IM. BioMedical Engineering
OnLine 2007, 6:23, 26 June 2007).
Experiment using k-Nearest Neighbor Classifier
Conduct classification experiments using k-Nearest Neighbor Classifier and
Support Vector Machines, by using 50% of the data as training set and the rest
as testing set. Try at least 5 different values of k for k-Nearest neighbor, and
draw a graph show the relationship between k and classification rate. In case
of Support Vector Machine experiments, try several parameter combinations by
modifying the type of Kernel and its parameters (at least 5 experiments).
Compare and discuss the results obtained by both classifiers. Which of them
achieved higher accuracy ?
40
Practicing WEKA
• What is WEKA ?
• Formatting the data into ARFF
• Klasifikasi
– Tahapan membangun classifier
– Contoh kasus : Klasifikasi bunga iris
– Tahapan membangun classifier
– Merangkum hasil eksperimen k-Nearest Neighbor Classifier
– Eksperimen memakai classifier yang lain (JST, SVM)
– Classification of cancers based on gene expression
– Parkinson Disease Detection
• K-Means Clustering
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K-Means Clustering : Step by Step
• Pilihlah k buah data sebagai initial centroid
• Ulangi
– Bentuklah K buah cluster dengan meng-assign
tiap data ke centroid terdekat
– Update-lah centroid tiap cluster
• Sampai centroid tidak berubah
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K-Means Clustering : Step by Step
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Filename : kmeans_clustering.arff
1
2
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Klik untuk memilih algoritma clustering
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Klik untuk memilih nilai k
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maxIterations:
untuk menghentikan proses
clustering jika iterasi melebih
nilai tertentu
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Hasil clustering: terbentuk 3 cluster dan masing-masing
beranggotakan 50 instances
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Klik dengan button kanan mouse untuk menampilkan
visualisasi cluster
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Nilai attribute x ditampilkan pada sumbu x, dan nilai
attribute y ditampilkan pada sumbu y
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