2019 International Seminar on Research of Information Technology and Intelligent Systems (ISRITI)

Bottleneck RGB Features for Tea Clones

Identification
R. Sandra Yuwana∗ , Endang Suryawati∗ , Ana Heryana∗ , Vicky Zilvan∗ , Dadan Rohdiana† and Heri Syahrian K†
∗ Research
Center for Informatics
Indonesian Institute of Sciences - LIPI, Bandung, Indonesia
Email:{rade014,enda029,anah002,vick001}@lipi.go.id
† Research Institute for Tea and Cinchona

Indonesian Agency for Agricultural Research and Development, Gambung, Indonesia

Email:{rohdiana,heri.syahrian}@ritc.id

Abstract—As each tea clone may produce different quality of
tea, it is important to have them identified in the field. Tea Clones
identification is one application of ICT technologies in agricul-
ture. Tea clones may have very similar characteristics between
them, required to have a good amount of data to train a machine
learning-based classifiers to have good performances. However,
we may have to deal with a small amount of data in many cases.
To overcome this, we propose to use an encoder-based feature
reduction to produce RGB-based bottleneck features. The output
features are then fed into an SVM classifier. We evaluate our
features on the classification of two tea clones of the Gambung
Assamica (GMB) series. Our experimental results show that
our proposed features achieve better performance than using
full dimensions RGB.
Index Terms—Dimensionality reduction, bottleneck features,
Support Vector Machine (SVM), Tea clones.
I. I NTRODUCTION
Indonesia is one of the tea producing countries in the
world. There are currently many varieties of tea. In Indonesia,
Research Institute for Tea and Cinchona (RITC)in Gambung,
West Java, is one of the centers of excellence for tea and
quinine studies. RITC succeeded in producing a series of su-
perior tea clones, and they are 11 Gambung Assamica (GMB)
clones, and 5 Gambung Sinensis (GMBS) clones. Each clone
has almost the same characteristics. Different clones produce
different quality and quantity of tea. High physical similarities
between clones make it difficult for ordinary people like farm-
ers to distinguish them. Expertise is needed to differentiate
between these clone varieties. Currently, there are not many
experts who can identify these clones, and they still identify
them manually. Automatic identification will be beneficial
to resolve this problem. Research on identifying plant types
using neural networks has shown many successes [1]–[5].
They use the Multi-Layer Perceptron (MLP) approach and
deep learning in solving problems.
The use of MLP and in-depth learning in agriculture have
been carried out. For MLP, Kusumo et al. [6] proposed the
detection of disease in maize using SVM, Decision Tree
(DT), Random Forest (RF), and Naive Bayes (NB) using
various image processing features. The results show RGB has
the best accuracy value when compared to other extraction
features This result is a reference in our experiment, using
RGB data as a comparison for this experiment. Spesifically
for tea plants, the study was carried out by Zhang et al. [7]
conducting real-time monitoring of tea leaf harvest time,
research on tea leaf quality was carried out by Gejima et
al. [8] used the RGB model of a tea leaf image. In many of
these studies, vast and varied data sets are needed to achieve
good results.
The research of deep learning technology in plants was
conducted by Sun et al. [9], who used CNN to identify tea
leaf disease. The accuracy obtained is 93.75 %. Pardede et
al. [10] use a convolutional auto encoder for the detection of
plant diseases. The results show that the use of conventional
autoencoders with more hidden layers gives better results. The
use of convolutional networks indicates better performance.
One reliable machine learning method for classification
is Support Vector Machine (SVM). SVM is a method for
classification and regression, which is a machine learning
algorithm for labeled data [11]. The advantages of using
SVM include that SVM works effectively on large dimension
sizes, its effectiveness is maintained when the number of
dimensions is more significant when compared to the number
of samples, efficient memory usage because it uses a decision
function called support vectors [11]. Research on plants using
SVM, among others, was conducted by Saranka et al. [12],
who examined the monitoring of fermentation of black tea
processing by using SVM as a classifier.
In recent years, data have become very valuable because
they can provide useful information. For tea leaves, there
is currently no specific digital dataset for GMB and GMBS
tea leaf clones. We collected the Gambung Assamica (GMB)
series tea leaf dataset in this study manually by taking photos
of tea leaves directly. However, collecting data from the
beginning is an activity that requires effort and high costs.
Original image data has high dimensions. This condition is a
challenge because it affects the size of the dataset. If the data
has many dimensions, then machine learning techniques may
not be optimal when trained. Dimension reduction is a way
to overcome this problem.

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 Dimensionality reduction (DR) is the reduction of dimen-
sions from high to low dimensions by transforming data into
meaningful representations [13]. There are 2 ways to make
dimensionality reduction, namely, feature selection (FS) and
feature extraction (FE). FS aims to find the most relevant
features in the dataset, as well as to maintain a new dataset
schema that has variables that remain relevant to the original
dataset [14], while FE maps high-dimensional data into low-
dimensional data [15]. Both have the same goal, which is
to streamline data processing and improve data quality by
dealing with the dimensions of the data set. Research on DR
has been carried out in various fields with good performance
results, such as text [16]–[21]. Fig. 1. The Schema of Proposed Method
One type of DR is an autoencoder. Autoencoder is a deep
neural network with 2 main processes, namely encoder, and
encoder stage, the image is compressed from high to low
decoder. Research on autoencoder related to DR was carried
dimensions. The encoder scheme design has 2 convolution
out by Wang et al. [22], who tried to use autoencoder on
layers, 2 pooling layers, which are CNN layers, and flatten
MNIST data, and Olivetti faces datasets by focusing on the
and dense, which are MLP layers. Input for the convolutional
process of reducing the dimensions of the dataset. The result
layer in the form of a 64x64 tea leaf image, then by the
is the use of autoencoders based on DR will produce better
pooling layer, is reduced to 32x32. In the second pooling
visualization.
layer, the image is reduced again so that the resolution is
In this paper, we propose a feature reduction (FR) scheme
11x11. The pooling layer causes the input data to decrease in
in the image using an encoder to produce an RGB-based bot-
dimensions. The SVM classification is used to classify images
tleneck feature, and SVM as a classifier, so the identification
into members of the GMB 3 or GMB 9 classes, as shown in
of images becomes more effective.
Fig. 2.
The rest of this paper is organized as follow. Section II
explains the dimension reduction method that we propose
for GMB 3 and GMB 9 tea clones identification. Section III
describe our experimental setup. In Section IV we present our
results and discussions, and finally this work is concluded in
Section V.
II. T HE P ROPOSED M ETHOD
Besides text and speech, current image data show very
promising potential as a basis for information to support
various implementations in many fields. The digital image
data set are now widely available, both open access and not,
labeled, and unlabeled data. Today, processing digital image
data is much easier due to the increasing ability of multimedia
computing. However, some tasks using image data may be
limited to data availability. To make maximum use of it, we
need a way to reduce the dimensions of the data set to smaller
sizes, but useful information is still stored.
The original image data (RGB), which will be classified
as data classes, has a large enough dimension. This has an
effect on data processing time and large storage size. Fig.1 is
a schema diagram of the proposed method. Before classifying
an image class, the image must first be processed using an
encoder scheme. It aims to reduce the image dimensions by
reducing the features using an encoder. The result is an RGB-
based bottleneck feature. Then the image is classified using
SVM. Fig. 2. The process of identifying GMB 3 and GMB 9 tea leaves
The input for the encoder process is an RGB image of
the 64x64x3 GMB 3 and GMB 9 tea leaves. The input As a comparison for our proposed method, we use red-
shape is 12,288, we vary the input data by 20% (2457), 50% green-blue (RGB) image input, directly classify the image
(6144), and 80% (9830) of the original dimensions. In the class using SVM classifier, without experiencing a reduction

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in dimensions. We use a linear kernels for SVM. The penalty
parameters (C) set to 1; this parameter is used to control
outliers, so misclassification in each training data can be
avoided.

III. E XPERIMENTAL S ETUP

In this experiment, we used tea leaf data from The Research
Institute for Tea and Cinchona (RITC) in Gambung, West Java
- Indonesia. Based on Prawira Atmaja et al. [23], RITC has
two superior varieties of tea leaves, namely Camellia sinensis
var. Assamica from Assam in India and Camellia sinensis
var sinensis from China. At present, for varieties Camellia
sinensis var. sinensis RITC has five classes of tea leaf clones,
namely GMBS 1, GMBS 2, GMBS 3, GMBS 4, and GMBS
5 [24]. As for Camellia Sinensis var. Assamica, there are
11 classes of Gambung clones (GMB), namely GMB clones
Fig. 4. Sample Images of GMB 9
1 to GMB 11. Between these classes of clones have quite
similar characteristics. In this experiment, we only focus on
TABLE II
two categories, namely GMB 3 and GMB 9 clones, because THE DETAILS DISTRIBUTION OF DATA IN THE EXPERIMENTS
it has a high level of production productivity. The difference
between these classes can be seen in Table I. Clones Training Validation Testing Total
GMB 3 483 59 56 598
TABLE I
THE DESCRIPTION OF GMB 3 AND GMB 9 GMB 9 548 86 65 699
Total 1031 145 121 1297
Descriptions GMB 3 GMB 9
Color dark green yellowish-green
Thick leaf 0.19 mm 0.23 mm In this experiment, we used 1297 images of tea leaves,
consisting of 598 tea leaves for GMB 3 and 699 for GMB 9,
Resistant resistant to smallpox leaves less resistant to smallpox
as shown in Table II. Randomly, the dataset was divided into
Production 4.25 tons/year 4.7 tons/year
80% training data, 10% as data validation, and 10% as data
Area medium-high low-high testing. We set various times to 50, 100, 150, and 200. Relu
activation is used in the encoder process. This experiment
Data sets of GMB clone tea leaf images in this experiment uses in-depth learning of Tensorflow, Hard and Python 3.7
were collected in mid-December 2018, using several types of
smartphones and DSLR cameras. Some examples of GMB 3 IV. R ESULTS AND D ISCUSSIONS
and GMB 9, as shown in Figs. 3 and 4. The optimum value is obtained when the epoch reaches
150 and 200, where performance around 91% is achieved.
Whereas at epoch 50 and 100, the optimum value only reaches
88% accuracy, see Table III. Overall, reduction of dimensions
using epoch 50, 100, 150, and 200 results in a minimum
accuracy value of 83.4%. Where this value is actually quite
good for accuracy.
When compared with RGB data, on epoch 200, the reduc-
tion in image features by 20%, 50%, and 80%, 3 points more
superior when compared to RGB, as shown in Table IV. Even
using only 20% data shows to be slightly better than using
full RGB features. RGB only achieves accuracy of 80.1%.
V. C ONCLUSIONS AND F UTURE W ORKS
In this paper, We applied encoder to produce a bottleneck
features for identifying and classifying 2 classes of Tea leaves
of GMB 3 and GMB 9 series clone. Using an encoder for
the dimension reduction process, we extract and reduced full
Fig. 3. Sample Images of GMB 3 RGB features and then the output features are used as inputs
to an SVM classifiers. The results show that by taking a

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