2021 6th International Conference for Convergence in Technology (I2CT)
Pune, India. Apr 02-04, 2021
Smote-DL: A Deep Learning Based Plant Disease
Detection Method
Subham Divakar
Persistent Systems
India
shubham.divakar@gmail.com
Abstract: In the due course of time, computer vision,
machine learning and deep learning has been widely used to
detect disease in the plant leaf. Most works done in this area
focuses upon coming up with accurate models but does not
focus on the false predictions which could be a serious cause.
Misdiagnosis of the plant leaf could cause large scale crop
destruction. We used a publicly available dataset which
contained four categories of images belonging to Apple Plant-
2021 6th International Conference for Convergence in Technology (I2CT) | 978-1-7281-8876-8/21/$31.00 ©2021 IEEE | DOI: 10.1109/I2CT51068.2021.9417920
Healthy, Scab, Rust and Multiple disease.However this dataset
upon visualization was found to be imbalanced.Our main
objective isto reduce the false predictions. The main
contribution lies in the use of SMOTE method to balance the
dataset and the novel Ensemble algorithm which uses both F1
score and accuracy to compare and come up with the best
classifier from among the classifiers. Upon experimentation we
came up with Efficient NetB7 as the best classifier from our list
of classifier which had both good accuracy and good F1 Score.
It also predicts whether a leaf image has multiple disease or
not which helps to reduce false predictions further.
Keywords- Ensemble learning, Deep Learning,
Skewness, Classification
I. INTRODUCTION
India is country of farmers where more than 40% of the
population thrives on agriculture as its source of income.
With so much of people working daily on farms, the
experience and knowledge of farming is passed on from
generations to generations. Traditionally people who are
engaged in farming develop expertise in detecting disease in
plants just by looking at the leaf. However with the rapid
increase in DNA modification and the coming of the hybrid
variety of plants not everyone is able to detect the disease
because just like humans plants also get infected with new
disease [1]. We are living in the 20th Century which is
seeing a tremendous rise in innovation of new technology in
each and every domain. In the agricultural domain it has
been seen a tremendous rise in use of modern techniques and
machinery for farming. When it comes to plant disease
detection, modern techniques like Deep Learning, Lab
Testing, Computer Vision and lots of other techniques have
come into picture but plant disease detection in still a major
concern in this fast growing world because there exists a
very large number of disease that are related to plants and yet
are not properly discovered or treated timely. There are
various types of disease that are related to crops such as
viral, bacterial or fungus. Not all disease are visible to naked
eyes so detection in time is very difficult.
Detection of disease using computer science means
working on the digital images of the diseased plants. These
algorithms process these images to find out the desired
results. Traditional ways of finding out disease was by using
a microscope and performing scientific laboratory
medications on the plants [2]. Our proposed work aims at the
978-1-7281-8876-8/21/$31.00 ©2021 IEEE
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Abhishek Bhattacharjee Rojalina Priyadarshini
Cogizant Solutions C.V.Raman Global University
India Bhubaneswar, Odisha
abhishekb496@gmail.com priyadarshini.rojalina@gmail.com
most fundamental aspect in plant disease detection which is
reducing the number of false predictions that might lead to
misdiagnosis. The result of which could be large scale crop
destruction.Our main contributions in this paper are:
1. We have done vast data-pre-processing and
visualization to understand the data and then used
SMOTE to handle our imbalanced dataset.
2. The unique Ensemble algorithm which identifies
both single and multiple diseased leaf with a good
accuracy and low false predictions.
3. The use of two parameters at a time to come up with
a good classifier using both F1 score and Accuracy
to compare the models.
The entire paper is divided into seven section. The first
section introduces the paper and its contributions followed
by the related work section. In the third section we have
given detailed explanation of the problem statement. The
Data fourth section talks about the pro-posed work followed by
the fifth section which discusses the results. The sixth
section concludes the paper with future scope mentioned in it
and the last section gives the references.
II. RELATED WORK
The literature survey is done in the domain of plant
disease detection to understand the use of computer vision
techniques used in the process. K.P Ferentinos in his study
developed specialized deep learning models based on
convolutional neural networks architecture for identification
of plant diseases through simple leaf images of healthy or
diseased plant[5]. He used an open database of 87848 images
for the training of the model. He got a success rate of
99.53% on 17548 previously unseen images in a VGG
convolutional neural network model. S.P Mohanty et.al in
there paper used a public dataset of 54306 images of
diseased and healthy plant leaves and trained the dataset in a
deep convolutional neural network to identify 14 crop
species and 26 diseases. They used the Alexnet and
GoogleNet deep learning architecture and used transfer
learning and training from scratch for training the dataset.
They received an accuracy of 99.35% on the test set [6].
Sachin D. Khirade et al. in their work found out the plant
disease using image processing [7]. They used number of
steps to determine the disease such as image acquisition in
which they captured the RBG for the leaf. A.K Mahlein
showed in her work how plant disease can be found out
using Imaging Sensors. She has shown in her work the
optical techniques such as RGB imaging, multi and
hyperspectral sensors, thermography or chlorophyll
fluorescence which all can be used for identification and
quantification of plant disease at early points[8]. Yi Fang
et.al in their work discussed two types of disease
1
identification methods used in agriculture which is direct and
indirect [9]. P Moghadam et.al in their paper used
hyperspectral imaging (VNIR and SWIR) and machine
learning techniques for the detection of Tomato Spotted Wilt
Virus (TSWV) in capsicum plants. They received an
accuracy of 90% in their trained model[10].Vijai Singh et.al
in their work found out unhealthy part plant leaf using image
processing and genetic algorithm. They used leaf samples
that are in RGB format and applied image acquisition and
pre processing on the image sample then they segmented the
components using genetic algorithm and obtained useful
segments to classify the leaf disease. They performed the
experiment in MATLAB[11].S. AashaNandhini et.al
provided a web enabled disease detection system (WEDDS)
based on compressed sensing (CS) to detect and classify the
disease in leaves. They upload the CS measurements of the
segmented leaf to the cloud and retrieved it in the monitoring
site and extracted the features from it. They did the analysis
and classification using support vector machine (SVM).
They achieved an overall accuracy of 98.5% and
classification accuracy of 98.4%[12].
III. PROBLEM STATEMENT
From the above section it is evident that the use of
computer vision to solve the problem of manual disease
detection is increasing which decreases human efforts. We
also saw few works done in the recent years which claim
high accuracy obtained by their machine learning or deep
learning models yet none of them claim to perform multiple
disease detection in a single leaf with high accuracy along
with proper identification.There are variations in symptoms
of the disease due to age difference of plants, severity of
disease itself, genetic variation due to hybrid genetic
modifications and light intensity of the images which cause
the accuracy to fall very low when it comes to testing on
actual images in a crop field. Due to the drop in the
accuracy misdiagnosis is prone to occur which could lead to
crop damage on a large scale. Thus to prevent this the
proposed deep learning or machine learning model should be
able to predict single diseased plant leaf with high accuracy
and it should clearly distinguishin case of single leaf with
multiple diseasewhich will increase the overall accuracy and
reduce the false predictions. One of the main reasons in the
lack of research into this is the lack of images having a
single leaf with multiple diseases. Thus we could have a
dataset of leaf images with multiple disease along with a
good deep learning model that has low false predictions and
high accuracy.
IV. PROPOSED WORK
A. Data Collection
The image dataset [9] was gathered from Kaggle
competition “Plant Pathology 2020-FGVC7” [8], organized
in the month of April-May 2020.The dataset contains images
belonging toapple leaf diseases. It contains images belonging
to 4 category of images“healthy”,
“multiple_diseases”,“scab” and “rust”. “scab” and “rust”
refers to the apple scab and apple rust disease and
“multiple_diseases” refer to the images having multiple
diseases. Few samples of the three categories of images
could be seen in Fig 1,2,3, 4. As explained in the problem
statement section that lack of dataset of leaf images with
multiple images is a major block thus now with the new
dataset that we have gathered, we can easily perform
multiple disease detection in a single leaf using neural
networks which will now identify such leaves as a separate
category and not detect them as any other disease.
Fig. 1. Samples of healthy leaf Fig. 2. Samples of multiple
images diseased leaf images
Fig. 3. Samples of Apple Scab Fig. 4. Samples of Apple Rust
disease leaf images diseased leaf images
B. Data Pre-Processing and vizualization
Data Preprocessing and Visualization is a very important
step before building Machine Learning and Deep Learning
models. It gives us an insight into the data and evenshows
the distribution of data. We also thought of looking into the
data before going for model selection and training part. The
dataset contains 3642 images of Apple Leaves divided into
Train and Test which belongs to 4 categories.“scab”- this
refers to the Apple Scab leaf disease, “rust”- this refers to the
Apple Rust leaf disease, ”multiple_disease”- this refers to the
Apple Leaves images having multiple disease and “healthy”-
this refers to the healthy Apple Leaf images.
Since, we are dealing with the leaf disease detection
dataset therefore it will be quite interesting to observe the
spread of the Red,Blue and Green channel values in the
images to identify which channel in dominant with the
healthy leaf and which is dominant with the diseased leaf.
We first analyzed some random images from training set to
see the channel distribution and understand about the
intensity of channel values in diseased and healthy leaf
images. Fig 5 shows the RGB values in a healthy leaf
image,Fig 6shows the RGB values of diseased part of the
leaf having only one disease and Fig 7 shows the RGB
values of amultiple diseased leaf and these values are of the
diseased part as shown in image. From Table 1, we can see
that the blue values are quite low in case of healthy leaf and
high for diseased leafimages. Thus it is now clear that the
blue channel is the key point of our observation and that it is
themain key to detect the leaf disease.Yet we need to study
the channel distribution in more detail to be sure of our
observation.

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Fig. 5. RGB value in a healthy leaf
Fig. 7. RBG value in a leaf with
multiple disease
The three RGB values obtained are presented in Table-1.
TABLE I. COMPARISON OF RGB VALUES OF LEAVES
Leaf Category
Healthy
Single Disease in a Leaf
Multiple Disease in a Leaf
Thus we plotted thechannel distribution of RGB values.
Fig 8, 9 and 10 shows the channel distribution of Red,
Blue and Green values. Upon observing Fig 8 which is the
red channel distribution plot, we found that the plot is rightly
skewed (slightly) with a positive skew and the red channel
valuesare roughly normally distributed.This indicates that
the red channel values are more concentratedat 100 which
can also be observed from the plot. Also we can observe that
there is large variation in averagered channel values across
the dataset. Fig 9 is the plot for green channel distribution
Fig. 6. RGB value in a leaf with
single disease
and as compared to the red channel plot Fig 8, the green
channel values have a more uniform distribution but smaller
peak than the red channel plot. Also we can clearly observe
that this plot has left skew and larger mode of 140,
aroundwhich the green channel values are concentrated. This
clearly indicates the presence of more green color in the
dataset with a good distribution as compared to red channel.
This is quite obvious because the images are of leaf which
are green in color. Fig 10 is the plot for the blue channel
distribution which is most uniformly distributed as compared
to the red and green channel plots. Also this channel shows
more variation than other two channels in the entire dataset.
The plot has a slightly leftward or minimal skew.Fig 11
shows the overall distribution of RGBchannels from which
we canobserve that the channel values are concentrated
Red Green Blue around 105 with a roughly normal distribution. Fig 12 shows
60 137 33 the combined plot of RGB channel values which shows us
115 111 57 the variation of the channels throughout the images. Also we
141 128 115 observed green to be the most pronounced color followed by
red and blue.Fig 13 shows the mean value vs. the color
channel plot which is in alignment with the values which we
figured out from the channel plots. For red we figured out
the values to be concentrated at 100 which are same as
observed in Fig 13 for the red channel. Similar is the case for
green and blue channels.Due to this variation of blue channel
in the image it is becoming clearer that it is the key point for
leaf disease detection.

Fig. 8. Red channel distribution in dataset

Fig. 11. Overall distribution of channel values in dataset

Fig. 9. Blue channel distribution in dataset

Fig. 12. RGB channel distribution in dataset

Fig. 10. Green channel distribution in dataset

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 Fig. 15. Parallel categories plot showing relationship of categories

Fig. 13. Mean Value vs RGB Channel

Then we visualized the categories and observed the

distribution of data in them along with their relationship with
each other. Fig 14 shows a pie-chart of data distribution in
various categories and we can observe that 71.7% leaves in
the dataset are unhealthy, rust and scab occupy one-third of
the pie-chart and multiple disease leaves are only 5%.This Fig. 16. Healthy leaf images distribution
gives us an indication of imbalanced dataset which will
cause the accuracy to fall. Fig 15 is a parallel category plot
which helps us to understand the relationship among the
various category and as expected, it is impossible for a
healthy leaf to have scab, rust, or multiple diseases. Even
every unhealthy leaf has one of either scab, rust, or multiple
diseases. Fig 16 is a bar graph to understand the distribution
of healthy category as compared to the entire dataset which
tells that there are more unhealthy leaves than healthyones.
There are 1305 (72%) unhealthy plants and 516 (28%) Fig. 17. Apple Scab leaf images distribution
healthy plants.Fig 17 is a bar graph to understand the
distribution of scab category as compared to the entire
dataset which conveys that there are 592 (33%) unhealthy
leaves with scab disease and 1229 (67%) leaves without
scab. Fig 18 is a bar graph to understand the distribution of
rust category as compared to the entire dataset which tells
that rust infected leaves are 622 (34%) and 1199
(66%)without rust. The percentage of leaves without rust
(67%) and without scab (66%) are almost same. Fig 19 is a
bar graph to understand the distribution of multiple diseases Fig. 18. Apple Rust leaf images distribution
category as compared to the entire dataset which tells that
there are only 91 (5%) leaves with multiple disease and rest
95% without multiple disease. From this vast visualization
we can come to the points that:
1. Blue channel is the key to plant disease detection in
our dataset
2. Our dataset is imbalanced as it only contains 5 % of
dataset belonging to multiple disease dataset.
Now to get rid of this imbalanced dataset problem which
will cause a problem if not solved now, we will be
performing re-sampling of our dataset using Synthetic Fig. 19. Multiple diseased leaf images distribution
Minority Oversampling technique (SMOTE)[10] method.
C. Resampling using SMOT and dataset splitting
As seen in the above section that ourdataset is highly
imbalanced as it contains only 91 images in the “multiple
disease” category which is only 5% of the entire
dataset.Although there are other methods but we choose
SMOTE because it is a type of image augmentation
technique and it creates new samples from the existing
samples only. It works by selecting examples that are close
in the feature space, drawing a line between the examples in
Fig. 14. Pie chart showing distribution of dataset the feature space and drawing a new sample at a point along

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that line.Thus we applied SMOTE re-sampling and the 1.For i=1 to k, do
“multiple disease” category is the minority class in our case 2. From P2 set, pick ‫ܥ‬௜ and ‫ͳܨ‬௜ . Let this be ‫ܥ‬ଵ and ‫ͳܨ‬ଵଵ
which will be oversampled. Then we split the dataset into 3. Check if ‫ܥ‬ଵ and ‫ͳܨ‬ଵଵ are present simultaneously in
training and validation which will help us evaluate the model any tuple of P1. If yes, then ‫ܥ‬ଵ is the model we are looking
better. We took 80% dataset for training and the rest 20% for for and ‫ܥ‬௕௘௦௧ ൌ ‫ܥ‬ଵ , break the loop
validation 4. Else continue from step 2
5.If no such ‫ܥ‬ଵ found that lies between ‫ͳܨ‬ଵଵ and ‫ͳܨ‬ଵሺ௞Ȁଶሻ then
D. Transfer Learning ‫ܥ‬ଵ (first model from P2 set) is the best model.
We used the Transfer Learning to train the pre-trained
models on the dataset. The main reason to choose Transfer
Learning is that there can be many classes which could V. RESULTS AND DISCUSSIONS
resemble close to the leaf dataset thus the features extracted S:NO Pre-Trained Accuracy F1 Precision
by the pre-trained models in Table 1, could be used for Model Score
training on our dataset which increases the overall accuracy. 1 MobileNetsV2 0.8677 0.8509 0.8827
This process also reduces the training time of the models. 2 InceptionV3 0.8236 0.8036 0.7848
3 VGG19 0.669 0.6518 0.6376
E. Ensemble Algorithm 4 DenseNet 0.9228 0.9124 0.9193
Ensemble Methods like bagging and boosting have 5 VGG16 0.6335 0.6219 0.6146
proven to be a good way to build classifiers which increases 6 Xception 0.8787 0.8658 0.8615
the accuracy.Generally ensemble methods have been found 7 EfficientNetB7 0.9146 0.91903 0.9261
to take only one performance metric – accuracy which is not 8 NASNET Large 0.9090 0.9078 0.9077
always the only metrics for evaluation of models. Often in
real life classification problem like ours we have to deal with TABLE II. ACCURACY, F1 SCORE AND PRECISION OF CLASSIFIERS
imbalanced dataset and penalties of every wrong prediction
could be both deadly and economically disastrous. In our
scenario where we are dealing with Plant Disease
Classification, every wrong prediction can lead to wrong
chemical use which ultimately can destroy the crops causing
huge economic loss. So the model cannot be judged on only
one parameter accuracy, which simply tells the total correct
predictions in the dataset.F1 score is another parameter
which is used along-with accuracy to test a model’s
performance. It is the harmonic mean of recall and precision.
Recall and Precision are the two most important parameters
upon which the F1 Score depends, so instead of getting high
range of these two values we only need to focus on getting
good F1 Score. Good F1 score would mean good recall and
precision values.Thusin this paper we have proposed a novel
ensemble method which unlike other ensemble method takes
both accuracy and f1 score into account for choosing the best
classifier.The proposed algorithm- Algorithm 1 and 2, shows Fig. 20. Accuracy vs F1 Score comparison of classifiers
the detailed steps of the approach.
Algorithm 1 – Ensemble Algorithm Table 2, presents a summary of the Accuracy, F1 Score
Input - C- {ଵ ,….., ୩ } - Set of classifiers, k: No:of classifiers and Precision of the various classifiers which were trained
D – Training dataset using Transfer Learning process and using Ensemble
Output – Set P1-{(୧ ǡ ୧ ǡ ͳ୧ ), ……} – Sorted in decreasing order Method. Since, our proposed work consists of unique
of ୧ ensemble method to come up with the best classifier which
P2-{(୧ ǡ ୧ ǡ ͳ୧ ),(…), ……} – Sorted in decreasing order of ͳ୧ uses Algorithm 1 and 2, thus one cannot simply say that the
1. Set ‫ܥ‬௜ - Set of Classifiers model with the best accuracy is the best performing model.
2. For i=1 to k, do According to our Algorithm 1 and 2 the best model should
3. Train ‫ܥ‬௜ on D. have high F1 Score and its Accuracy should lie in the top
4. Evaluate the model. k/2, accuracies.k(total number of classifiers)=8.Thus after
5. Calculate and Save the accuracy in ‫ܣ‬௜ andF1 Score in applying the algorithm, our Ensemble Method came up with
‫ͳܨ‬௜ EfficientNetB7 as the best classifier as it had the best F1
6. Store ‫ܥ‬௜ ,‫ܣ‬௜ and ‫ͳܨ‬௜ as a set in Set P1 and P2 Score and its accuracy also lies in the top 4 accuracies. The
7. Sort P1 in decreasing order of ‫ܣ‬௜ and keep top k/2 plot in Fig 20 resembles the comparison of accuracy and F1
elements. Score of all the models. It can also be clearly observed that
8. Sort P2 in decreasing order of ‫ͳܨ‬௜ . EfficientNetB7has highest F1 Scorebut its accuracy is just
slightly less than the top accuracy which satisfies our
Algorithm 2 Algorithm 1, 2.Thus the proposed algorithm comes with a
classifier which is having a good F1 Score which indicates
Input Set P1-{(‫ܥ‬௜ ǡ ‫ܣ‬௜ ǡ ‫ͳܨ‬௜ ), ……} – Sorted in decreasing order of good recall and precision and which shows lesser wrong
‫ܣ‬௜ predictions. Also it predicts whether a leaf imageis having
P2-{(‫ܥ‬௜ ǡ ‫ܣ‬௜ ǡ ‫ͳܨ‬௜ ),(…), ……} – Sorted in decreasing order of ‫ͳܨ‬௜ multiple disease or single leaf which reduces false
Output –‫ܥ‬௕௘௦௧ (Best classifier) predictions in real-life scenario.

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 VI. CONCLUSION
In this paper we have presented a unique Ensemble
algorithm –Algorithm1 and 2 which uses both accuracy and
F1 Score to choose the best classifier from among the list of
classifiers [Table 1]. We have performed data pre-processing
and found that the blue channel was more abundant in the
diseased part as compared to the healthy part. We then
analyzed the data and found it to be imbalanced as the
multiple diseased leaf category only had 91 images which is
only 5% of the dataset. We performed SMOTEresampling
method to handle imbalanced dataset.From our
experimentation, our proposed algorithmcame up with
EfficientNetB7 as the best classifier which has best F1 score
and its accuracy was also among the top k/2 classifiers.Using
our proposed algorithm and new dataset(having multiple
disease leaf as a separate category) our proposed work
successfully reduces false predictions by first predicting
whether a leaf image has single or multiple disease and
secondly the classifier has low false predictions and good
accuracy as our algorithm chooses classifier with good F1
score and accuracy.
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