Plant Disease Detection Using AI Based VGG 16 Model
Plant Disease Detection Using AI Based VGG 16 Model
Plant Disease Detection Using AI Based VGG 16 Model
Abstract—Agriculture and modern farming is one of the fields occur in plants affecting their overall growth and might lead to
where IoT and automation can have a great impact. Maintaining plant death in extreme cases. Plant diseases can occur
healthy plants and monitoring their environment in order to throughout the different stages of plant development including
identify or detect diseases is essential in order to maintain a seed development, seedling, and seedling growth [3]. When
maximum crop yield. The implementation of current high diseased, plants go through different mechanical,
rocketing technologies including artificial intelligence (AI), morphological, and biochemical changes [4, 5]. Truthfully,
machine learning, and deep learning has proved to be extremely there are two main types of plant stress classified as biotic
important in modern agriculture as a method of advanced image stress represented by living creatures that interact with plants in
analysis domain. Artificial intelligence adds time efficiency and
a way that negatively affects their growth [6] such as bacteria,
the possibility of identifying plant diseases, in addition to
monitoring and controlling the environmental conditions in
viruses, or fungi [7], or abiotic stress represented by the
farms. Several studies showed that machine learning and deep collection of non-living factors or the environmental factors.
learning technologies can detect plant diseases upon analyzing Fig. 1 illustrates the collection of factors that contribute to
plant leaves with great accuracy and sensitivity. In this study, plant diseases.
considering the worth of machine learning for disease detection, Typically, the commonly used approach for farmers,
we present a convolutional neural network VGG-16 model to scientists, and even breeders, to detect and identify plant
detect plant diseases, to allow farmers to make timely actions disease was the manual inspection of plants. Of course, this
with respect to treatment without further delay. To carry this
process requires expertise and knowledge for the proper
out, 19 different classes of plants diseases were chosen, where
15,915 plant leaf images (both diseased and healthy leaves) were
detection. With time, manual inspection became tiresome and
acquired from the Plant Village dataset for training and testing. time consuming and not as quite efficient especially when large
Based on the experimental results, the proposed model is able to amounts of plants needed to be inspected. Another factor that
achieve an accuracy of about 95.2% with the testing loss being proves the inefficiency of manual inspection is the similar
only 0.4418. The proposed model provides a clear direction conditions that might be caused by different pathogens that
toward a deep learning-based plant disease detection to apply on might look alike in their effect on the plant [6].
a large scale in future.
Fungi
Keywords—Machine learning; VGG-16; disease detection;
convolutional networks; Plant Village; modern farming Bacteria
I. INTRODUCTION
Biotic Viruses
Agriculture has always been a basic human need ever since
humans’ existence as plants were a primary source of food.
Even nowadays, agriculture is still considered an essential food Phytoplasmy
resource and is the center of several aspects in humans’ lives
[1]. As a matter of fact, agriculture serves as the pillar of
Nematodes
economy in many countries regardless of their developmental Plant Disease
stages. The various domains that show the importance of Causes
agriculture include the fact that agriculture is a main source of Nutrition
livelihood where approximately 70% of the population depends
on plants and their cultivation for livelihood. This great
Moisture
percentage reflects on agriculture being the most important
resource that can actually stand a chance in the face of the Abiotic
rapidly increasing population [2]. Temperature
One of the most critical challenges that face agriculture and
affects it trade is plant diseases and how to timely detect them Toxic Chemicals
and deal with them to improve the health of crops. By
definition, plant disease in a type of natural problems that Fig. 1. Plant Disease Causes Detailed as Biotic and Abiotic Factors.
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2) Implementing the proposed VGG-16 model which is an of several hidden nodes with weights that connect and the
effective convolutional neural network architecture, and it complete neural network has no iterations. Image pre-
achieves a great accuracy. Our proposed model is capable of processing is done on the images in the dataset including image
scanning through thousands of leave images in order to resizing, segmentation, color space conversion, and HSV. A
scatter plot of HSV is done on the resized image of tomato late
identify if a plant has a certain type of disease based on its leaf
blight, where a mask can be performed on the segmented
image. The proposed model achieves a great accuracy of image. 7,000 images of tomato leaves were selected for
detection among 19 different disease classes in a short period training (70%) whereas 3,000 were selected for testing (30%).
of time, and it doesn’t require a long time in training either. The features HSV histogram, Haralick textures, and Colour
The arrangement of the current paper is as follows: section Moments were selected and the labels were transformed into
two is a description of some of the published similar studies numerical values via the One Hot Encoding method. In the
about ML and DL in plant disease detection. Section three ELM model, using 1024 neurons and Sigmoid activation
describes the proposed methodology including the dataset and function yielded the best disease detection accuracy of 84.94%.
the proposed model. Results are provided and compared When compared to Decision Tree model, ELM achieves better
theoretically with some of existing techniques in section four, overall accuracies, 77.8% vs. 84.94%, respectively, in all of the
while section five concludes the article by sharing the future 10 classes. On the other hand, SVM is slightly better in terms
research intentions. of accuracy (91.43%) when compared with this ELM model.
In their paper discussing plant disease detection, Bedi et al.
II. RELATED WORK [22] proposed a detection model based on convolutional auto
A large number of studies have been performed and encoder “CAE” and CNN as two parts of a hybrid system. The
published about the detection of diseases in plants, especially system was implemented on leaf images of peach plants
since disease detection and classification can help in treating specifically, but it can also be used to spot diseases in other
the diseased plant. The more technology emerges, the more it plants. The dataset consists of two different classes healthy
will be implemented in the agricultural field, one of the reasons peach leaves (2160) and diseased leaves with bacterial spots
being the continuous enhancement of already existing machine (2297) which sums up 4457 images in total. 70% of the images
learning and deep learning methods that identify and classify in the dataset were used for training the system whereas the
plant diseases. This section describes five studies conducted in remaining 30% were kept for testing the detection
this regard. performance. After gathering the data into the dataset, the usual
pre-processing procedures are performed on the images. The
The study by Ashwin et al. [20] discussed the development
next step is the training of the CAE model and getting
of a machine learning approach for the detection of diseases in
compressed domain representations of leaf images from which,
Soybean plant in Mazandaran province in Iran. The study
a CNN model will be trained afterwards. Upon testing, new
aimed to illustrate the importance of incorporating
leaf images will be used as input and their respective
physiological features as well as the morphological features in
compressed representations will be compared for the CNN to
realizing the diseases presence in a plant. The dataset used by
determine if the leaf is healthy or not based on whether a defect
the authors contains two randomly chosen subsets one for the
is found. The CAE network was made up of 14 layers while the
healthy soybean plants (negative) and one for the diseased
hybrid system was made up of 17 total layers through
soybean plants (positive), which makes up to 2,500 images
concatenating layers of the CAE with the CNN layers. Adam
total. These images were collected from 10 different regions in
optimizer and binary cross entropy were used on the proposed
the Mazandaran province. Several features were selected based
system, where parameters such as NRMSE loss and accuracy
on one-way ANOVA F1-score which include stem length, root
measures were used for evaluation. As a result, the testing
length, number of pods per plant, empty pods per plants and
NRMSE loss was 0.0607, the testing accuracy reached 98.38%,
seed oil content. Six different machine learning techniques
and the F1-score was 98.36%.
with ten-fold cross validation and internal cross validation,
which are the binary Logistic Regression, Multilayer Jeyalakshmi et al. [23] developed an approach based on
Perceptron with Adam optimization, Random Forest, Gradient machine learning for classification of diseases of potato and
Tree Boosting (GBT), and Support Vector Machine. These ML grape crops depending on their leaf images. The dataset was
techniques are evaluated based on confusion matrix, precision, acquired from Pant Village dataset, consisting of 1000 healthy
F1-score, AUC, etc. Out of the six techniques, GBT achieved leaf images, as well as 2000 images of diseased potato leaves,
the best results of 96.79% accuracy, 96.68% F1-score, and and 3270 of diseased grape leaves. In the potato subset, there
97% sensitivity and specificity depending on 21 features. The exist three different classes, while there are four classes in the
same technique achieved similar results (96.13%) depending grape leaves subset. From each RGB leaf images, the
on 12 morphological features. background was removed through using “enhanced GrabCut
algorithm”. Several features were selected from the images
Xian et al. [21] relied on a supervised machine learning
such as the intensities of red, green and blue, weighted mean
termed Extreme Learning Machine “ELM” to determine the
and weighted standard deviation (belonging to histogram
presence or absence of tomato diseases. The developed system
features), and texture features including contrast, entropy, etc.
was based on analyzing tomato leaves; the whole dataset was
After that, the features were normalized and fed into several
acquired from Kaggle, specifically the Plant Village dataset.
classifiers, namely KNN, Naïve Bayes, and SVM. It was
The dataset comprises 10 classes, which makes a total of 1,000
observed that the number of features (ranging between 7 and
images. The model is a feed forward neural network made up
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13) affects the accuracy of detection such that the higher the authors concluded that in binary classification, DL with
number of features, the better the accuracy. For instance, the Softsign is the best, whereas Softmax is better suited for multi-
highest accuracies were achieved by KNN at 94% considering class classifications. Table I compares between theses similar
13 features, and 96.8% by SVM similarly in potato crops. On systems.
the other hand, in grape crops, SVM was superior achieving
96.02% accuracy with respect to 13 features. From the analysis of these previous studies, a group of
limitations can be seen, as most of the studies focus on
Lamba et al. [24] published a paper discussing the detecting the diseases in one type of crops. On the other hand,
implementation of several machine learning algorithms as well logically, most farms are interested in growing more than one
as deep learning techniques to properly detect diseases in crop, especially if the farmer is using these crops for the local
crops. The images comprising the dataset are from Kaggle and market, whereas in some cases a field might be planted with
rice dataset. In fact, four different datasets are created which one specific type of crop which is grown for a huge demand
are: the rice dataset containing 120 images, the pepper dataset and can be used for exportation and national trade. However,
containing 1,994 images, potato dataset containing 2,152 the aim is to create a model that can be used by the various
images, and tomato dataset containing 16,072 images. As farmers, whether they have a small farm growing multiple
usual, the images are pre-processed accordingly, and then auto- crops, or they had large farms with more than one type of crop.
color correlogram filter is applied as an additional pre- For this reason, we chose to take into consideration a group of
processing step. After that, classification took place through plants to be analyzed and to train our model to detect their
machine learning techniques, or through deep learning methods diseases respectively. Furthermore, the second aim is to create
with various activation functions to assess the overall a reliable model which achieves very accurate results with
performances. With respect to machine learning, fifteen minimal loss and minimal false detection (both false positive
different algorithms were tested including bayes net, random and false negative), for this reason the majority of the studies
forest, and iterative optimized classifier to name a few. On the focus on CNN models for the disease detection class.
other hand, in the deep learning method, different activation Similarly, our chosen CNN architecture in VGG-16 still stands
functions were used including SoftMax, Softsign, ReLu, etc. as one of the best computer vision models. VGG provides
The evaluation of performance was done relying on confusion better results while having smaller convolutional layers since it
matrix, specificity, F1-score, and accuracy. As a matter of fact, doesn’t rely on a large number of hyper-parameters, yet it has
each of the models (ML and DL) was implemented on each several 3x3 filters with stride 1, and max layers and padding
one of the four datasets. In Pepper dataset, random forest and with stride 2 that are distributed throughout the architecture. In
DL-Softsign achieved the best results as ML and DL addition, the VGG16 model not only perform image
techniques respectively. In rice dataset, random forest and DL- recognition and detection, but it is also capable of localization,
Softmax achieved the best results. SVM and DL-Softsign were meaning that in our case and objectives, the model can be
responsible for the better results in the tomato dataset, and improved to detect the exact location of the classified disease
SVM and DL-Hard-tanh outperformed the rest in the potato on the plant leaf.
dataset. In conclusion, from the large set of experiments, the
Year of
Study Crop Type Dataset Technique Performance Results
Publication
A Machine Learning Approach to Real samples from LR-L1, LR-L2, MLP, Accuracy: 96.7%
2021 Soybean
Prediction of Soybean Disease” [20] Mazandaran province RF, GBT and SVM F1-score: 96.5%
Plant Diseases Classification using Extreme Learning Accuracy: 84.94%
2021 Tomato Plant Village
Machine Learning [21] Machine (ELM) F1-score: -
Plant diseases detection using hybrid
model based on convolutional Accuracy: 98.38%
2021 Peach Plant Village CAE and CNN
autoencoder and convolutional neural F1-score: 98.36%
network [22]
Naïve bayes, K nearest
An effective approach to feature
neighbor and support Accuracy: 96%
extraction for classification of plant 2020 Potato and grape Plant Village
vector machine F1-score: 95%
diseases using machine learning [23]
classifier
“Classification of plant diseases using Rice, pepper, Auto-color correlogram Accuracy: 99.4%
2021 Plant Village
machine and deep learning [24] potato and tomato and deep learning F1-score: 95%
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III. IMPLEMENTATION OF THE MODEL are collected in a csv file, where each image is labeled with a
In order to maintain constant care of plants in any farm, path that indicates the health conditions of the crop within the
especially a vertical farm, you need to constantly keep a close image.
eye on the crops and their leaves as well as their stems and all
the surrounding conditions. Of course, detecting plant diseases
from looking into plant leaves manually takes a lot of time and
effort from the farmer, which is why automation could be a
game changer in the field of plant disease detection.
Computational techniques can be applied such that the images
of the plants are being taken and analyzed or screened for
diseases in a time efficient manner, without facing human
effort or human error challenges.
In this project, we implement several deep learning
technologies in order to classify the diseases in crops. Among
machine learning techniques, deep learning is an interesting
area since it can easily recognize patterns and perform
Fig. 4. Crop Disease Classes in Plant Village Dataset-1.
complicated procedures, which makes it suitable for the disease
classification task. In deep learning, deep neural networks are
created, among which is the CNN, short for Convolutional
Neural Networks, that can easily analyze images upon training.
In our project, VGG-16 was selected to be the CNN classifier
of different plant diseases.
A. Dataset
The chosen dataset for our study is the Plant Village dataset
which contains numerous images of plant diseases totaling for
15,915 images. From these images, the dataset is divided into
nineteen different classes, each class resembles a disease, and
these classes do not overlap, meaning that a single image only
belongs to one class and cannot simultaneously belong to two
or more classes.
The nineteen classes include tomato, grape, apple, tomato,
and corn diseases as well as healthy classes. The Fig. 4 and
Fig. 6 demonstrate in detail the different classes and to which
crop they belong.
The number of images per class varies between the classes, Fig. 5. Distribution of Images in Plant Village Dataset into Nineteen
as shown in the Fig. 5. After the data had been selected, they different Classes.
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and the convolution stride are fixed to 1 pixel for 3 × 3 loss function. Therefore, one of the most important loss
convolutional layers, in which the spatial resolution’s functions is the Cross Entropy Loss Function where it is used
preservation becomes easy to occur. Also, spatial pooling is for Classification model’s optimization and the complete
easier in case of a five max-pooling layers’ addition after some understanding of this loss function depends on the Softmax
of the convolutional layers and the Max-pooling layer takes activation function understanding. Moreover, in our project,
place over a 2×2-pixel window, with stride 2. the Sparse Categorical Cross Entropy is used for training our
model where it has the same loss function as that of the cross
In addition to that, a total of three varying FC (Fully entropy as in (3):
Connected) layers in depths are fixed behind a group of
convolutional layers, where the first two FC layers is made up ∑ ̂ (3)
of 4096 channels per FC layer, and the third performs 1000-
way ILSVRC classification and is made up of 1000 channels However, the truth labelling procedure is what differs
for each class. Finally, the final layer is the soft-max layer, it’s between the two loss functions, where in the case of a one hot
important to say the Fully Connected Layer’s configuration encoded true labels ([1,0,0], [0,1,0] and [0,0,1] in 3
does not vary among different networks. classification problem) the categorical cross entropy is used,
while the cross entropy is used in the case of an integer truth
The architecture of the VGG-16 model is portrayed in labels coding ([1],[2],[3]).
details in the Fig. 9.
F. Accuracy Calculation
The accuracy of the model is calculated as in (4):
(4)
IV. RESULTS
The performance of our proposed model was assessed in
terms of Loss Function and Accuracy, which was measured
during the training/validation step as well as during the testing
step. The Fig. 10 shows the performance during the training
phase.
Fig. 9. VGG-16 Detailed Architecture showing the Various Layer and their
Positioning.
⃗ (2)
∑
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