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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>The Efectiveness of PCA in KNN, Gaussian Naive Bayes Classifier and SVM for Raisin Dataset</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Agnieszka Polowczyk</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Alicja Polowczyk</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Faculty of Applied Mathematics, Silesian University of Technology</institution>
          ,
          <addr-line>Kaszubska 23, 44-100 Gliwice</addr-line>
          ,
          <country country="PL">Poland</country>
        </aff>
      </contrib-group>
      <fpage>9</fpage>
      <lpage>16</lpage>
      <abstract>
        <p>Supervised learning is one of the main types machine learning in which model is trained from data which consists of features (input data) and labels, that is target values. Using our training data, the parameters of our model will be adjusted until loss function reaches a low value or until we get high accuracy on the validation data. Before we start building model, we need make data preprocessing. PCA is often used, to reduce numbers of dimensions our data. Models in which data have been reduced using PCA often have high accuracy. In this article, we will look at how well-known classifiers work such as: K-Nearest Neighbors, Gaussian Naive Bayes and Support Vector Machines, that using PCA. We will also check the performance of the classifiers for which the data has been reduced to fewer dimensions by analyzing correlation tables and we will look at models whose data contain the original number of features. We will evaluate their efectiveness based on the Raisin database and show how decision boundaries built in models that were constructed after our analysis.</p>
      </abstract>
      <kwd-group>
        <kwd>Machine learning</kwd>
        <kwd>pca</kwd>
        <kwd>knn</kwd>
        <kwd>gaussian naive bayes</kwd>
        <kwd>svm</kwd>
        <kwd>classifiers</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <p>
        KNN and Gaussian Naive Bayes there is no learning with
weights. Using KNN model on large dataset, it can lead
Supervised learning is used in many areas, such as: clas- to high consumption of computing resources. In [17] was
sification [ 1, 2], regression [3], patterns recognition, nat- proposed strategy, which improve the eficiency of KNN
ural language processing and image encryption [
        <xref ref-type="bibr" rid="ref17 ref23">4, 5, 6</xref>
        ]. classifier on Big Data.
      </p>
      <p>
        Examples of problems that can be solved using supervised
learning are: classifying whether an email is spam or not, In this paper we will compare three classifiers: KNN,
weather forecasting, classify text, whether a review is Gaussian Naive Bayes and SVM, that were built on three
positive or negative[
        <xref ref-type="bibr" rid="ref2">7, 8</xref>
        ]. various data:
The popular algorithm used during training model for
example in the case of regression or SVM classifier, is
the gradient descent, which minimizes loss function, by
adjusting the parameters of our model in the direction
of the decreasing gradient of the loss function [
        <xref ref-type="bibr" rid="ref10 ref21 ref5 ref8">9, 10</xref>
        ]. We will check the efectiveness of the above models, in
The goal of supervised learning is to achieve high accu- the case of the KNN for diferent metrics and for the SVM
racy to make right predictions on unknown data. There model we will test the performance for various kernels.
are many interesting improvements to such models for We will summarize whether reduction of the dimensions
application systems. In [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ] was presented how to use of our data allows us to get satisfactory results, leading
machine learning for imbalanced data inputs, while in to a decrease in computational complexity.
[
        <xref ref-type="bibr" rid="ref13 ref15">12, 13</xref>
        ] was presented positioning of technical systems
for power electric models. We can find also many
applications for complex input data structure ie. [14] gave it 2. Raisin database
for the graph based input relations compositions.
• model uses PCA to reduce the dimensionality of
      </p>
      <p>the data
• model uses two features selected by us
• model uses all the features</p>
      <p>In classification problem we also distinguish models The database that we used to build various classifiers
based on deep neural networks[15]. The architecture contains samples that were described by 7 morphological
of neural networks is: weights, activation functions [16], features. These features were obtained after previously
loss function and optimizer. In the case of classifier processing the photos.Values are continuous and we can
see that each feature has value from diferent ranges.</p>
      <p>There are also high values of standard deviations for
example, for Area and ConvexArea features, indicating
that the values for these features are highly dispersed</p>
      <sec id="sec-1-1">
        <title>2.1. Standardization</title>
        <p>Normalization or standardization are used to improve the
eficiency and efectiveness of the model. In the case of
KNN model, that uses distance measures to classify data
samples, if the values weren’t normalized or
standardization, features with higher values could have greater
impact on model’s result, which could lead to low
accuracy. Therefore, an important and recommended action
is to use one of the data processing techniques before
creating KNN and SVM models. Mainly for Gaussian Naive
Bayes doesn’t use data standardization, because this
algorithm doesn’t depend on distance, so doesn’t require
scaling of features. We used standardization
exceptionally in Gaussian Naive Bayes classifiers in which the PCA
technique were used and in classifiers in which used
twodimensional data to plot decision boundaries.We used
standardization, which transforms our data in a way that
the mean is equal to 0 and the standard deviation is equal
to 1. At the beginning for everyone feature we calculated
the mean value and standard deviation and then we used
the results to calculate new values using the formula
below:
 =
 −</p>
      </sec>
      <sec id="sec-1-2">
        <title>2.2. Model based on PCA</title>
        <p>One of the popular dimensionality reduction techniques
is PCA. The task of PCA is to return n-features that we
can create a model with high accuracy. Interesting
improvements to PCA models composed for graph based
classifiers were presented in [ 18]. In our models were
used PCA, which returns to us new training and test data
reduced from seven to two dimensions.</p>
      </sec>
      <sec id="sec-1-3">
        <title>2.3. Model based on two features</title>
        <p>Another way to prepare data for the model is to reduce
dimensionality based on correlation analysis. Correlation
defines the relation between two variables. Correlation
value close to 1 or -1 mean a strong correlation, but value
close to 0 mean weak correlation. The Extent feature
was removed from our training and testing data, because
its correlation value with our target feature was only
0.28. Additionally, the following features were
eliminated: ConvexArea, Perimeter, Area, MinorAxisLength,
because these attributes had strong relation with other
features and didn’t contribute relevant information to the
classification models. Finally, our classifiers were built
on other two features: MajorAxisLength and Eccentricity.
The Fig. 1 shows correlation plots between two features.</p>
      </sec>
      <sec id="sec-1-4">
        <title>2.4. Model based on all features</title>
        <p>For each classifier, we also built a model based on all
seven features. Sometimes training a model on the basis
of all attributes can be a disadvantage, because this
approach lead to slower learning of our classifier. However,
the advantage of including all features is that in some
cases it can lead to very high eficiency of our machine
learning algorithm, because we don’t lose any relevant
information. Fig. ?? illustrates our feature and correlation
graphs.
(2)
(3)
(4)
(5)
(6)
3.</p>
      </sec>
    </sec>
    <sec id="sec-2">
      <title>Methods</title>
      <p>3.1. KNN</p>
      <sec id="sec-2-1">
        <title>3.1.1. Formulas</title>
        <p>Euclidean distance:
Manhattan distance:
Minkowski distance:
⎯⎸ 
(, ) = ⎷⎸∑︁( − )2
(, ) = ∑︁ | − |
=1

=1</p>
        <p>Canberra distance:
Chebyshev distance:
(, ) =
︃( 
∑︁ | − |
=1</p>
        <p>)︃ 1

(, ) = ∑︁ | − |
=1 || + ||</p>
        <p>(, ) = m=a1x | − |
Cosine distance:</p>
        <p>(, ) = 1 −</p>
      </sec>
      <sec id="sec-2-2">
        <title>3.1.2. Algorithm</title>
        <p>∑︀</p>
        <p>=1  · 
√︀∑︀=1 2 · √︀∑︀=1 2
(7)</p>
        <p>Updating weights and bias:
 =  −  ∇()</p>
        <p>=  −  ∇()
Minimizing the cost function using Stochastic Gradient
Descent (SGD):
KNN classifier is mathematical model, that doesn’t
require training. New, unknown points are predicted based
on the k-nearest points voting. When classifying a new () =  ||||2 + max(0, 1 −  ()) (14)
sample, model calculates distances between the sam- 1
ple and each point in the specified n-dimensional space.  =   (15)
Among all the distances the model chooses k-smallest
and voting takes place. The class that occurs most
frequently among the selected points becomes the predicted 3.3.2. Algorithm
class for the new sample. We compared performance of SVM classifier (Support Vector Machines) creates a
hyKNN classifier for diferent distance measures (metrics): perplane that maximizes the distance between the closest
Euclidean, Manhattan, Minkowski for  = 3, Canberra, points of two classes (support vectors). When creating
Chebyshev and Cosine. a hyperplane, two techniques are used: soft margin and
hard margin. Soft margin during the process of
training allows our algorithms to make mistakes, so it allows
3.2. Gaussian Naive Bayes points to be on the wrong side of the hyperplane or inside
3.2.1. Formulas the margin. Hard margin during the process of training
doesn’t tolerate any errors, so points cannot be on the
Bayes’ Theorem in our model: wrong side of the hyperplane or inside the margin. In our
 (|1, 2, ..., ) = (()|· ∏1︀,=21, ...(,|)) (8) cuasseed, twhheesroefotumradragtianitsenc’htncoiqmupeleatnedlyulsiendeavrasreiopuarsakbelern,weles
to transform our data to higher dimensionality. We also
 (|) = √︀21 2 · exp(− (2−  2 ) ) (9) wusheidchreognuelaorifzathtieonclpasasreasmiesteerquCa. lWtoe 1craenatdedthme oodtehlesr, iins
Sample variance: equal to -1. Then, using Stochastic Gradient Descent, we
 2 = 1 ∑︁( − ¯) 2 (10) wupedtaetsetdedouoruwremigohdteslsa,nidf tbhaeftperreedaicctheddavtaalsuaems pwlee.reFinneagllay-,
 − 1 =1 tive, they were assigned the label -1, if non-negative, they
are assigned the label 1. We compared the performance
of classifiers using diferent kernels such as: linear, poly,
3.2.2. Algorithm rbf, laplacian and sigmoid.</p>
        <p>Gaussian Naive Bayes is probabilistic model, that uses
Bayes’ Theorem to determine the probability of sample
belonging to a specific class. The classifier assumes, that
the features are independent. We used this type of
classifier, because our data is continuous and the data is
approximately normally distributed. During the training
process, our model calculated the mean and variance for
each attribute from every class and the "a priori"
probabilities for each class. When predicting a test data, two
probabilities are returned because we have binary
classiifcation. We chose the highest probability with its label.
3.3. SVM</p>
      </sec>
      <sec id="sec-2-3">
        <title>3.3.1. Formulas</title>
        <p>Hinge Loss:
 = max(0, 1 −  ())
(11)</p>
      </sec>
    </sec>
    <sec id="sec-3">
      <title>4. Experiments</title>
      <p>4.1. KNN
We created the KNN models for diferent metrics for which the prediction is based on 3 nearest neighbors.</p>
      <sec id="sec-3-1">
        <title>4.2. Gaussian Naive Bayes</title>
        <p>4.3. SVM
We created SVM models for diferent kernels for specific parameters. These nuclei are: linear, polynomial with
degree of 7, rbf with a gamma of 2, laplacian with a gamma of 2 and sigmoid with a gamma of 1.</p>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>5. Conclusion References</title>
      <p>After analyzing our results for three classifiers, we
conclude that using the PCA technique to reduce the
dimensionality from 7 to 2 features supported performance of
our models, also achieving high accuracies, comparable
to the results of models built on all features. After
analyzing the correlation of our data, we were able to find
two features for which the models had similar accuracy
compared to the PCA-based models, these features are:
MajorAxisLength and Eccentricity. The accuracy for the
KNN classifiers with and without PCA are very similar,
ranging from 82% to 88% depending on the metric. In
the case of Gaussian Naive Bayes classifiers the
accuracy result obtained using PCA and using 7 features gave
the same value of 85% , which only confirms the fact
that the reduction in dimensions didn’t contribute to the
loss of significant information. The last type of classifier,
that was analyzed was SVM. After analyzing for diferent
kernels, the sigmoid kernel turned out to be the best,
which in models with and without PCA indicated the
best accuracy of 88%.</p>
    </sec>
  </body>
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