Early Prediction of Wheat Diseases Using SVM

Multiclass

Ahmed Reda1, Essam Fakharany2, and Maryam Hazman3

1,2
College of Computing and Information Technology,
Arab Academy for Science, Technology and Maritime Transport, Cairo, Egypt
ahmedreda101@hotmail.com,essam.elfakharany@aast.edu
3
Central Laboratory for Agricultural Expert System Giza, Egypt
m.hazman@mail.claes.sci.eg

Abstract. The early prediction of Plant diseases based on learning algorithms is

one of promising research areas. Several types of classification techniques can
be utilized on such data to early predict the different kinds of wheat diseases.
However, the high dimension of the dataset in our case study and how selecting
of the best data mining classifiers is one of the challenges. For that, Principle
Component Analysis (PCA) technique was carried out for reducing the dimen-
sion by combining a set of correlated features as preprocessing step. Then, the
Support Vector Machine (SVM) classifier with different multiclass techniques
has been applied to predict of wheat diseases. The results have been combined
with different voting methods in conjunction with PCA. The proposed system
evaluated by several measurements and the classification accuracy reached to
96%.

Keywords: Data Mining, Data Preprocessing, Principle Component Analysis,

Wheat Diseases, Support Vector Machine.

1 Introduction

Wheat crop is one of the most important crops for Egypt because it is used in making
Baladi bread which is considered a vital source to feed the Egyptian population
because for what it provides a high source of nutritive values. Wheat crop contains a
lot of important minerals such as potassium and calcium, in addition, vitamins A, E
and vitamin K. Egypt is one of the top 20 commodities production for wheat globally
in 2014 with 9.3 Million tons per year, according to the international wheat produc-
tion statistics produced by the food and agriculture organization1.Thus, it is consid-
ered one of the most strategic food crops in Egypt because it used in the Egyptian
diet, and it produces more than one-third of the daily caloric intake of the Egyptian
population and more than 45% of the total daily protein consumed by the Egyptians.
Data mining technique play an important role as Knowledge Discovery in Database
(KDD) tool by extracting the hidden patterns from exhaustive data records in Multi-
dimensional scaling.
The goal of classification is to assign unknown objects to one of the already prede-
fined groups. Its target function is applied to map the input of attribute space to one of
2

the predefined groups by adding a class label to the input [2]. Recently, the huge
number of classifiers used to solve such classification problem reached 179 classifiers
as in [3] with 17 families. The common types of classifiers can be (probabilistic, dis-
criminant, decision tree and support vector machine). The performance of each type
has pros and cons, and it shows a high variation in accuracy according to the number
of patterns, the size of training samples and numbers of input variables [4]. Many
studies show that Neural Network (NN) classifier is used in many applications and it
allows handling noisy data, moreover, it can work well with a high dimension data.
However, it has some limitations such as; NN can fall in local minima, besides NN
suffers from the difficulty to determine the number of neurons needed in the hidden
layer. Also, NN needs a long time to build a training model and it does not work well
with the small size of training samples. On the other side, the decision trees achieve
high accuracy in classification problems [5], but they suffer from the overfitting and
fragmentation problems related to the nature of data or if sub-trees are replicated in
decision tree [6]. Therefore, according to previous drawbacks of NN and decision
trees, in this paper we utilized SVM classifier which has the following advantages:
High generalization ability to overcome the overfitting problem.
Easily handle nonlinear data point.
High performance in the high-dimensional dataset.
High performance in small training data.
Since SVM has a previous advantage, initially we reduce the effects of the high
dimension of features space dataset by using PCA [7] as processing step. SVM mul-
ticlass has been utilized by different types of kernel functions for identifying and pre-
dicting the Egyptian wheat diseases. The main object of this research work is increas-
ing the national income of wheat crop by preventing wheat losing. Therefore, it will
reduce the cost and minimize the agrochemicals use aiming to reduce the losses of
wheat yield due to dwarfing of the plants and malformations of the leaves. Besides, it
will prevent contaminating other crops within the same area. In this research, the main
contribution is to compare the results and measure the performance metrics of various
data mining classifiers for early prediction of Egyptian wheat diseases. The rest of
this paper is organized as follows: Section 2 describes the literature review. Section 3
presents the proposed system. Section 4 describes the wheat dataset. Section 5 ex-
plains the metrics of evaluation. The results of experiments and discussion are illus-
trated in Section 6. Finally, the conclusion and future work are in Section 7.

2 Proposed system

The proposed system as shown in Fig1 for early prediction of wheat diseases based
on SVM multiclass is composed of the following stages: (1) Building of Egyptian
knowledge base of wheat disease: based on a powerful web-based tool developed by
the central laboratory for agricultural expert systems (CLAES) [14]. (2) Pre-
processing stage: Replacing all missing values in a dataset with null as nominal
attribute values. (3) Reduce of dataset dimensionality: Performs a principal compo-
nents analysis to reduce the high number of dataset attributes. (4) Classification
stage: is used to build an SVM multiclass model based on training data which con-
tains (name of wheat diseases and related symptoms).

Fig. 1. Proposed model of wheat diseases

Then, in the final stage, the predictive model for diseases can be tested by entry the
new symptoms. Theses stages details will be explained in the next subsection.

2.1 Building of Egyptian knowledge base of wheat disease

Knowledge Base (KB) of wheat diseases is built by using the web-based knowledge
acquisition tool developed by CLAES in 2010. This tool allows the human experts
and agriculture knowledge engineers to add data and knowledge about different kinds
of diseases related to wheat crop remotely on the internet. In addition, this tool in-
cludes variety selection tasks that allow their user to select the types and names of
diseases, and assign the values of related symptoms. Also, it has several properties for
plant diseases parts, color, appearance, and soil types. Finally, the rule-based
knowledge scheme has been created based on the rule instance as numbers of IF-
THEN condition statements in XML standard data language. The role of the inference
engine enables the expert system to build reasoning mechanism from the rules in
the KB.

2.2 Preprocessing stage

The objective of Preprocessing is to make the wheat dataset format suitable for work-
ing with different data mining classifiers. Most of our experiments are implemented in
WEKA [15]. The WEKA is a tool that has the ability to simulate and perform many
data mining tasks. First, most of the attributes in the wheat dataset are a nominal data
type, and WEKA uses ARFF (Attribute-Relation File Format). ARFF declares the
nominal datatype as case-sensitive values. For that, the values having the same sub-
types of wheat diseases has been handled manually with assuring that all distinct at-
tribute values appear with their unique statistical indicators in WEKA such as (Label,
4

Count, and Weight). Second, to get the best performance, the missing values have
been replaced by a constant value null because it can be inconsistent with other
recorded data.

2.3 Reduce of dataset dimensionality

This paper mainly aims to enhance the accuracy of the SVM classifier by reducing the
dimension of the wheat dataset. PCA has been used to reduce the size of attributes of
the wheat dataset by compressing the dataset and keeping only important information.
The main idea of PCA is to choose the dimensions which have the largest variance
based on the statistical techniques to improve the predictive performance of the ma-
chine learning classifier. Arithmetical procedures have been applied to convert a set
of numbers of correlated variables into a set of a linearly uncorrelated variable which
called Principal Components (PCs) [17]. The properties of PCs depend on the eigen-
values and eigenvectors of the covariance matrix [16], the mathematical calculation of
values and eigenvectors described in [18]. For example, the dimension problem can
be denoted as: given the random variable X= (X1, , X n) T, Y= (Y1, , YN) T where
n, N refers to the dimension of data before applying PCA and after applying PCA.
Find a lower dimensional y where N < n and T is the transpose vector. In our dataset,
the number of input attributes is highly correlated with each other which can lead to
an overfitting problem that affects the accuracy of the classification model. For that,
we apply PCA to select a subset of the attributes set that is weighted combinations of
the original attribute. At the same time, PCA keeps the same power of accuracy of full
original dimension.

2.4 Classification based on SVM

SVM is a machine learning algorithm proposed by Vapnik [19] it is considered a type
of unsupervised learning. SVM is a statistical classification method that can classify
training samples by using a hyperplane or set of hyperplanes, which can be used for
classification, regression, or other tasks [19], [20]. In a q dimensional space, suppose
that the training data samples of r denoted by xi , yi , i 1,,r , yi 1, 1 . The
aim of SVM to choose an optimal separating hyperplane in the feature space that
represented by vector that separates between two classes which represented in the
positive and negative training vectors by calculating the maximum margin. Assuming
a hyperplane is represented as w x + b 0 where w is the vector of coefficients,
T

x is a point located on the hyperplane, b is a constant. SVM constructs a separating

hyperplane for two classes which can define as:

yi (w T x i +b) 1 0 (1)

2
Equation (1) combine two class yi = 1 ,the margin between the planes is
w
and we need to find w and b that minimize the objective function as:

2
1 w
2
Subject to (2)
yi (w x i +b) 1, i
T

For nonlinearly separable classes, the equation (2) after adding a penalty term will be
w2 r
min C i
2 i =1
Subject to (3)
yi (w x i +b) 1 i
T

r
The second term C i added as a penalty value when is a slack value to han-
i =1
dling non-separable data. By using the Lagrange function, this optimization problem
solved as:

N
1
L(w, b, ) w T w i [ yi (w T x i b) 1]
2 i 1
Subject to (4)
i 0, i
Where 1,2, ,N are Lagrange multipliers, and = [1,2, ,N] T. SVM Mul-
ticlass problem can be solved by single optimization problem as in Equation (5).
When m-th is a function for SVM multiclass where w Tm(x i )+b separates the train-
ing data of class m from other classes are constructed, notation refer to the map-
ping function.
n L
1
min
2
w Tm w m C i m w Tm(x i ) b yi
m=1 i 1 m yi
w,b,

w Tm (x i )+b m +2- i m
with i m 0, i=1,, L, m {1, , n} (5)
By solving equation (6) you can expect the new data of training sample and determine
that it relates to any class.

arg max m=1,, n (w Tm(x i )+b m ) (6)

6

Fig. 2. SVM Margin and hyperplane

In case of linear classification problem, a separating hyperplane can be used to divide

the data as in Fig 2. Hence, in the nonlinear problem, kernels function has been used
to transform non-linearly of the input data to a high-dimensional space [21]. Several
types of kernel functions have been used for mapping and transform of feature space
as following:
1- Linear Kernel Function
k(x,z)=<x,z> (7)

Where x , z vectors in the input space and terms are k is a kernel to an inner product
in a feature space
2- Polynomial Kernel Function
k(x,z)=(<x,z>+c)d
(8)
Where c is a free parameter trading off the influence of higher-order versus lower-
order, d is a degree of polynomial

3- Gaussian (Radial Basis Function)

-( x-z )2
k(x,z)=e (9)
1
Where is a constant, =
2 2
Several techniques have been used to solve SVM multiclass problem by decomposing
the multiclass to a set of binary problems as following methods:
One against- one: In this approach, the pair-wise comparison has applied be-
tween all n classes. Thus, from the training set of n classes all possible two-class clas-
sifiers will be evaluated. This method requires the total of n (n-1)/2 of training classi-
fiers from every pair of classes, where n is the number of classes. Finally, the class
with most votes will be assigned with classification label [22].
One against- all: In this approach, a set of binary classifiers has trained to sepa-
rate one class from the rest of classes has been generated. The final class will be cor-
responding to SVM with the largest margin, to solve SVM multiclass problem we
need solve a single optimization problem as shown in equation 5.
 Random Error Correcting output code (ECOC): In this approach, SVM mul-
ticlass can be solved by decomposing the output space into several two-class classifi-
cation problems. Each column of the error correcting code matrix has a code of bit
values that employed to reclassify the training samples that previously constructed.
The code matrix is generated randomly. Finally, different unrelated two class sub-
classifiers are constructed and the final classification results are decided based on
specific decoding rules [23]. In this study, SVM has used as a binary classifier beside
the multiclass classifier algorithm. We applied several fixed combining methods as in
below equations to combine the multi-classifier and make a decision from the outputs.
Lets suppose {yn }n=1,,N represent a set of N label that refer to the number of ob-
servations, R is the number of base classifier for each observation which can be de-
noted as z . Where Pr (y n |z) is the probability that z belongs to the class with label
y n , given the R th classifier [23] the different combination rules have been used as
shown below:
R
Product rule Z y d if d arg max n =1,, N P (y |z)
r=1
r n (10)

Majority Vote rule Z y d if d arg max n =1,, N rn

r =1

1 if j = arg max n =1,, N Pr (y n |z)

rj = (11)
0 otherwise
Max rule
Z yd if d arg max n =1,, N max r =1,,R Pr (y n |z) (12)
Min rule
Z yd if d arg max n =1,, N min r =1,,R Pr (y n |z)
(13)

3 Wheat Dataset Description

WEKA data mining tool has been used in experiments. Prediction of wheat diseases
determined by using the dataset includes 285 instances, 63 attributes and 24 classes of
wheat diseases. Description of attributes shows in table 1.

Table 1. Description of dataset attributes

Attributes Description

Variety Sakha 8, Giza 157, Sakha 61, Giza 160, Sakha 69, Giza 162

Types of disease Bacterial, Insects, Fungal, Viral

Mineral Deficiencies, Others
8

Names of diseases Genetic-flecking, Downy mildew, Barley yellow Dwarf, aphids, Leaf rust

Appearance Pustules, Spots, Streaks, Blotches, Glume Melanesia

Colors Brown, Black, Grey, Red, Purple, White

Parts Root, Stem, Leaves, Spike, Grains, Panicles

4 Metrics of Evaluation

We use the following measurements:

True Positive (TP): is the number of positive samples correctly identified.
True Negative (TN): is the number of negative samples correctly identified.
False Negative (FN): is the number of positive samples wrongly identified.
False Positive (FP): is the number of negative samples wrongly identified.

Fig. 3. Description of dataset attributes and formula

The main performance metrics are described and calculated by using different formu-
las as in Fig3.

5 The Results of Experiments

Many experiments are applied on existing wheat dataset within the WEKA platform
for many selected classification algorithms to evaluate the performance of the pro-
posed model. Our approach is based on the comparison between the numbers of clas-
sifiers such as; J48 decision tree, Random Forest (RFs), K-Nearest Neighbor (KNN),
Nave Bayes (NBs), ANN and SVM. The variance parameter of PCA has changed
from 0.95 to be 1.0 to allow flexibility to change the suitable output number of di-
mensions. The results of accuracy due to utilizing PCA are presented in Fig4. The
SVM number of attributes, for example, is reduced from 63 to 45 and the accuracy
before and after applying PCA has been kept very close as shown in Fig 4. In table 3,
the accuracy of most classifiers is very close after applying the PCA and dimension is
reduced. The accuracy of NN and Nave Bayes classifier has increased. Thus, the rate
of time to build the model is decreased especially in ANN case from 24.92 seconds to
7.49 seconds. We noticed that the accuracy of SMO (96.1404%) is the best is a
comparison to other classifiers followed by J48 (93.33%). Science RFs and KNN give
the same accuracy (91.6 %).

96.14% 95.79% 93.33% 91.58% 91.58% 90.18% 90.53%

90.53% 90.53% 87.02%
100% 87.37% 82.46%

80%
60%
Accuracy

40%
20%
0%
SVM J48 RFs KNN ANN Nave
Classifier Bayes
Without PCA With PCA

Fig. 4. Effect of PCA in accuracy

Table 4 shows that the results of different classifiers are based on different evaluation
measures. Such as mean absolute, root means square error and kappa statistic as nu-
meric value but root relative square and relative absolute error calculated as percent-
age value for all test samples. Another performance measures have been computed
such that precision, recall and Mathews Correlation Coefficient (MCC) [24] which
applied as a linear correlation coefficient. It is used as a measure of the quality of
classifications. The output value of MCC scale range between +1 indicate a (perfect
prediction), 0 refer to (average random prediction) and -1 an inverse prediction. Fig 5
shows the comparison between the different evaluation parameters of classifiers. The
specificity metric for each RFs and KNN is the same value is (91.6) but the best recall
metric for SVM (96.1) and the lowest value of specificity metric for Nave Bayes is
(87). Several experiments were run based on the fine tuning of the parameters of
SVM, then the best parameter was chosen to achieve the best accuracy.
10

95.2
96.1
94.6 95.3
93.3 92.5 90.2 90.3
91.9 92.4 91.6 89.8 91.6 89.4 89.4
90.4 90.5 89.5
89.5 89.9
87
83.7
Accuracy (%)

82.2 83.2

SVM J48 RFS KNN ANN NAVE

Classifiers BAYES
Specificity Sensitivity F. measure MCC

Fig. 5. Comparison between evaluation parameters

Table 2. Comparison of accuracy before and after PCA

Classification K- Incorrectly Correctly Time to Accuracy Error Number

Algorithms Fold Classified Classified build of attrib-
TransformationInstance Instance utes
Model
Technique
(seconds)

Multiclass 11 274 1.04 96.1404 3.8596 % 63

SVM %
J48 19 266 1.05 93.3333% 6.6667% 63
24 261 0.28 91.5789 8.4211 % 63
RFs
%
Before
KNN 24 261 0 91.5789 8.4211 % 63
PCA
%
ANN 10 28 257 24.92 90.1754 9.8246 % 63
%
Nave Bayes 50 235 0 82.4561 17.5439 63
% %
Multiclass 12 273 0.81 95.7895 4.2105 % 45
SVM %
J48 36 249 0.02 87.3684 12.6316 45
% %
RFs 27 258 0.07 90.5263 9.4737 % 45
After
%
PCA
KNN 25 260 0 91.2281 8.7719 % 40
%
ANN 27 258 7.49 90.5263 9.4737 % 40
%
Nave Bayes 37 248 0 87.0175 12.9825 40
 % %
Table 3. Error of different classification techniques

Accuracy Mean Abs. Relative Kappa Sta. Root Mean Sq. Root Relative
Measures Error Ab. Error (KS) Error Sq. Error
(MAE) (RAE)% (RMSE) (RRSE)%

SVM 0.0454 103.70% 0.9576 0.1496 103.70 %

J48 0.0034 7.672 % 0.9266 0.054 36.889%
RFs 0.0094 21.50 % 0.9072 0.0586 39.752 %

KNN 0.0098 22.29 % 0.9074 0.0624 42.302%

ANN 0.0068 15.53 % 0.892 0.0575 38.981 %

Nave Bayes 0.0062 14.11 % 0.8551 0.0786 53.296 %

A lot of experiments were run based on fine tuning, then the best parameters were
chosen as shows for SVM parameters in table 5. The -insensitive loss function has
affected the number of support vectors, and its effects on the smoothness of the
SVMs response both the complexity and the generalization capability of SVM de-
pend on its value. Parameter C controls the trade-off between margin maximization
and errors of the SVM on training data. Gamma parameter is the free parameter effect
on kernel functions. On the other side, the accuracy of SVM multiclass was tested by
using several types of kernel functions. Fig 6 shows that the polynomial kernel func-
tion achieved the best accuracy 96.1%. The effects of different multiclass methods are
shown in Fig 7, the random correcting code achieves the best results 96.14% in con-
junction with SVM multiclass because it enhances the generalization ability of binary
classifier.

Table 4. Parameters of SVM

Kernel type Polynomial

The -insensitive loss function 1.0 e-3
Parameter C 1.0
12

Accuracy (%)
96.14%
85.26% 83.85%
100% 68.07%

50%

0%
Normalized RBF Kernel PUK Kernel Polynomial
PolyKernel Kernel
SVM Kernels

Fig. 6. Effect of SVM kernel types on accuracy

100%
96.14%
96%
Accuracy (%)

91.50%
92% 90.17%

88%

84%
SVM Multiclass Methods
1-aganist-all Random Correction Code 1-aganist-1

Fig. 7. SVM Multiclass Methods versus accuracy

Finally, we evaluate the results of SVM multiclass by different combination methods

as shown in Fig 8. The maximum probability method achieves the best results
96.14%.

98%
96.14%
96%
Accuracy (%)

94% 92.98% 92.98% 92.98%

91.92%
92%
90%
88%
Max Probability Majority Voting Min Probability Product Of Average of
Probability Probability
Combination Methods for SVM Multiclass
Max Probability Majority Voting Min Probability
Product Of Probability Average of Probability

Fig. 8. Different combination methods versus accuracy

6 Conclusion and Future Work

In this paper, the SVM-based wheat diseases prediction model is proposed by using
PCA. The dataset composed of 24 kinds of wheat diseases with different symptoms
(63 attributes). 285 instances have been used for training and testing the proposed
model. In this research work, we utilized different types of SVM kernel with 10-folds
of cross-validation and the effects on accuracy has measured. In addition, the effect of
PCA in a number of attributes and training time and final accuracy has also been ob-
tained. The experimental results showed that random ECOC technique is used to
decompose the multiclass to a set of binary spaces to solve SVM multiclass problems
in conjunction with the maximum probability method as one of the voting techniques
achieved the best accuracy 96.1% compared to J48, RFs, KNN, ANN and Nave
Bayes classifiers which respectively achieved 93.3%, 91.6%, 91.6%, 90.5% and
87.0%. In the future work, we will be utilizing the deep neural network classifier for
classification which can deal with a huge number of attributes in conjunction with
extracting features directly from plant images by using pattern recognition techniques.

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