Harumanis Mango Flowering Stem Prediction using Machine Learning Techniques

R.S.M. Farook, H. Ali, A. Harun, Ndzi. D. L., A. Y. M. Shakaff, Mahmad Nor Jaafar, Z. Husin, A.H.A. Aziz

Harumanis Mango Flowering Stem Prediction using

Machine Learning Techniques
R.S.M. Farooka,*, H. Alib, A. Harun c, Ndzi. D. L.d, A. Y. M. Shakaff c, Mahmad Nor Jaafare , Z.
Husina , A.H.A. Aziza
a
School of Computer and Communication Engineering, University Malaysia Perlis (UNIMAP), Perlis, Malaysia ,
Block A, Kompleks Pusat Pengajian Seberang Ramai
No. 12 & 14, Jalan Satu, Taman Seberang Jaya Fasa 3
Seberang Ramai, 02000 Kuala Perlis
Perlis Darul Sunnah
Telephone Number : 604-9851654
Email: rohani@unimap.edu.my
Fax Number : 604-9851695
b
Information Technology Department, Polytechnic Tuanku Syed Sirajuddin, (PTSS), Perlis Malaysia
c
School of Mechatronic Engineering, University Malaysia Perlis (UNIMAP), Perlis, Malaysia
d
School of Engineering, University of Portsmouth, Portsmouth, UK
e
Agrotechnology Research Station, University Malaysia Perlis (UNIMAP), Perlis, Malaysia
rohassanie@yahoo.com, David.ndzi@port.ac.uk
{ zulhusin, hallis, aliyeon, mahmad }@unimap.edu.my

ABSTRACT
Harumanis Mango (Mangifera indica) is known as one of the
best table tropical fruit, due to its aroma and sweetness.
Harumanis mango cultivar is included in the national agenda as
a specialty fruit from Perlis, Malaysia for the world. Despite its
overwhelming local demand in Malaysia and also
internationally, the fruit supply never meets the demand. Mango
flowering stem prediction is important as one of the factors to
predict mango yield in order to implement effective forward
marketing. Forward marketing is a co ntract that is signed
between supplier and client based on the amount of delivery and
the price of delivery in future, based on t he predicted yield. In
this paper, machine learning techniques are used to perform
prediction of the flowering tree branches that could be used to
predict yield in mango trees. Results shows that machine
learning techniques could be used to predict the flowering
branches.
Research Notes in Information Science (RNIS)
Volume13,May 2013
doi:10.4156/rnis.vol13.10
Categories and Subject Descriptors
I.5.2 [Computing Methodologies]: Classifier Design and
Analysis, Pattern Analysis.
General Terms
Algorithms, Performance.
Keywords
Machine learning; mango flowering stem prediction; soft
computing
1. INTRODUCTION
Harumanis mango is one of the fruit that has high
economic demand and potential for Malaysia export
business especially the Perlis State in Malaysia. Perlis
exported 3.1 metric tons of Harumanis mango to Japan in
2010 and has targeted the export demand to increase to
100 metric tons by 2020. Harumanis mango tree is a
yearly fruit bearing trees and reproductive phase of the
mango trees often starts from January and ends nearly on
June. This type of mango is highly sensitive to the climate
and only grows in Perlis and part of Surabaya in
Indonesia. It requires a significant dry weather period to
initial flowering and the productive phase can be

46
 Harumanis Mango Flowering Stem Prediction using Machine Learning Techniques
R.S.M. Farook, H. Ali, A. Harun, Ndzi. D. L., A. Y. M. Shakaff, Mahmad Nor Jaafar, Z. Husin, A.H.A. Aziz
significantly affected by change in weather. Although it
does grow on Surabaya, the variety that grows in Perlis is
often highly valued for export and therefore attracts high
foreign earnings. The demand outstrips supply most of the
time and there is a need to study and understand the yield
cycle in order to accurately predict supply.
Harumanis Mango growth and reproductive phases are
illustrated in Figure 1 that depicts the growth and
reproductive phases of Harumanis Mango in Perlis
associated with the period of months. The vegetative
growth period is approximately from July to December.
December and January are considered as Pre-Flowering
phase where the flower induction process is stimulated.
January to February months is the period when the flowers
grow and bloom. Fruit bearing occurs during March to
April that leads to harvest from May to June.
Figure 1. Harumanis Mango Growth and Reproductive
Phases
The pre flowering and flowering phases are identified as
important stages in the plant reproductive physiology. The
Harumanis mango flowering induction event can be
influenced by a few factors such as pruning, defoliation
and nitrogen fertilizer application [3,4,10]. Since
Harumanis mango tree grow in Malaysia, a tropic country,
flowering induction is influenced by the climatic
factors[2,6,18], and biotic factors[10,12,15]. In tropics
climate countries, it is an important factor that the
terminal stems of the trees are allowed to rest after the
previous vegetative growth, to be able to produce
reproductive shoots [11]. This resting time is necessary to
provide the stem ample time to mature and grow sufficient
whorl, length and diameter.
The mango trees yield predictions are essential to enable
forward marketing signed between Malaysia and mango
importing countries such as Japan. The forward marketing
contract includes the specific mango quantity in tons to be
delivered at specific times. A Harumanis mango exporter
needs to know the approximate yield before agreeing to
terms of the contract. The yield can be approximated once
the farmer performs the possible flowering stems
prediction.
Machine learning techniques application in agriculture is a
relatively new approach for classification and yield
prediction in agriculture. There are a few research studies
that include machine learning techniques in agricultural
domains for yield prediction [1,5], crop classification,
crop disease detection [19], management and advisory
expert system [7,8,9,13,14,20] .
Machine learning is about learning the structures from
data. Machine learning techniques can be used to perform
classification and prediction for future observation.
Classification is a task of assigning objects to one of
several predefined classes to create a classification model,
whereas prediction is where the classification model is
used to predict the new observations. A classification
technique such as k-NN classifier, rule-based classifier
and nave Bayes classifiers employs a l earning algorithm
to find a model that best suits the relationship between the
attributes and the classification categories.
A training set consists of data whose class are known and
is used to build a classification model. The classification
model is later applied to a test data set, to test the
classification accuracy of the model. Evaluation of the
classification model is based on the counts of test records
correctly and incorrectly classified by the model. The
model performance can be displayed using performance
metrics determine the level of accuracy.
The performance of the model can be evaluated using
several methods such as Hold out Method, Random
Subsampling, Cross Validation and Bootstrap [16] . A
Cross Validation technique is used to evaluate the
performance of the classification models.
In this paper, machine learning techniques are applied to
identify the possible flowering tree branches using biotic
factors. Five different classifiers performance used to
predict the possible flowering branches are compared. The
classifiers used are k-Nearest Neighbour (k-NN), Naives
Bayes, Support Vector Machine (SVM), Classification
Trees (CAT) and Random Forest (RF).
The rest of the paper is outlined as follows; Section 2
discusses the data sets descriptions and method. Re sults
and discussion are presented in Section 3 and the paper
ends with the conclusion in Section 4.
2. METHODS
In this paper, the data from Harumanis Greenhouse at the
Institute of Agrotechnology, University Malaysia Perlis
are used. The biotic data c onsists of 254 s tems of
generative and vegetative flushes. The attributes and the
data types are given in Table 1:
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 Harumanis Mango Flowering Stem Prediction using Machine Learning Techniques
R.S.M. Farook, H. Ali, A. Harun, Ndzi. D. L., A. Y. M. Shakaff, Mahmad Nor Jaafar, Z. Husin, A.H.A. Aziz
Table 1. The Attributes and the Data Type of the
Biotic Factors of Harumanis Branches
Attributes Data Type
Lysimeter Nominal
Length of first whorl Continous
Length of second whorl Continous
Length of Third Whorl Continous
The Diameter of the Third Continous
Whorl
Stem State Categorical
There are 5 attributes that have been used in this research.
These are lysimeter, that describe the type of lysimeter
that the trees are planted in, length of the first, second and
the third stem whorl (length in mm of the 3 whorl
branches) and their diameters.
Lysimeter feature is assigned a v alue between 1 and 3
which represent the root zones of the mango trees. The
mango trees are planted in 3 different lysimeter sizes
which are micro-lysimeter (1), lysimeter (2) and
unrestricted root zones (3). The micro-lysimeter has
dimension of 50 cm in deep and a diameter of 50 c m
while the other lysimeters size with dimensions of 0.75 m
deep and 1.5 m in diameter. Mango trees with unrestricted
root zones are planted directly into the ground.
Stem State describes the state of the stem. I t is assign a
state value of flowering or vegetative. Stem State is
the class that will be used by the machine learning
techniques to learn while in the training process and build
an appropriate model. The test data set is used to validate
the models developed to predict the Stem State.
Figure 2 displays the features from the mango stem that
are measured and used to classify the flowering stems.
The stems whorls length are measured and recorded
accordingly.
Figure 2. The typical mango terminal stems
displaying the three whorls where the measurements
are taken from. The whorls are representing the
termination of each previous flush of vegetative
growth.
Machine learning techniques that were used in this work
are k-NN, Nave Bayes, SVM, CAT and RF. k-NN
algorithm is a technique used to classify the new
observations based on the closest neighbors labels. In this
technique the distance (similarity) between the test set and
the training set is used to determine the nearest-neighbor
list. The appropriate number of k (the number of
neighbor instances to be compared) is important to be
determined. A small k value might cause the classifier to
be susceptible to over fitting because of noise in the
training data. On the other hand a large k value might
cause misclassification because neighbors that are located
far from the neighborhood will also be included in the
classification decision.
The k- NN models uses Euclidean distance metrics as
shown in Equation 1 to get the nearest neighbors
d= ( x y )i i
2
(Equation 1)
Algorithm for k-NN algorithm
Data : Training Samples D= { x1:N , c1:N}, Test Point
x*.
Result : Class of new point c*
1: Let k be the number of nearest neighbors.
2: for i = 1 to N do
3: calculate distance d(xi, x*) between x* and
every sample in D;
4: find xj, for which the distance the smallest, the set of
k closest training samples to x*;
5: y = arg max
v
I (v = y ),
( xi , yi )Dx*
i
6: end
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 Harumanis Mango Flowering Stem Prediction using Machine Learning Techniques
R.S.M. Farook, H. Ali, A. Harun, Ndzi. D. L., A. Y. M. Shakaff, Mahmad Nor Jaafar, Z. Husin, A.H.A. Aziz
The nave bayesian classifier algorithm is one of the
classification algorithms where an instance is described
with n , attributes a i (i = 1 to n) and the classified
class v from the set of possible classes V is described
as follows:
n
v = arg max P v j ( ) P(ai v j )
v i V i =1
(Equation 2)
Compute a vector of elements
n
pj = P vj ( ) P(ai v j )
i =1
(Equation 3)
which, after normalization so that the sum of p j is equal
to 1, represents class probabilities. The class probabilities
and conditional probabilities (priors) in the above
formulae are estimates from the training data: class
probability is equal to the relative class frequency, while
the conditional probability of attribute value given class is
computed by figuring out the proportion of instances with
a value of i-th attribute equal to a i among instances that
from class v j .
Relative frequency is used when computing prior
conditional probabilities. So the total number of training
examples is n and nc is the number of training example
that has the specific condition. The relative frequency
corresponding to the probability would be
nc
P=
n
(Equation 4)
SVM [17] is one of the techniques that is widely used in
classification problems. SVM separates the classes
independently with the hyperplane that maximizes the
distance from a hyperplane separating the classes to the
nearest point in the data set.
CAT is an algorithm that splits the training instances
accordingly and builds a tree that consists of root node,
internal nodes and leaf nodes as a model to be used to
classify the test examples.
Root Node
Internal Node
Leaf Node Leaf Node Leaf Node
RF builds several classification trees to a d ata set and
combines the predictions from all the trees. A
classification tree is fitted to each bootstrap samples from
the data. At each node, a small number of randomly
selected variables are made available for binary
partitioning. In random forest each variable that is
importance is measured.
The classifier models using machine learning techniques
have been built and tested using 10 fold cross validation
tests. The k-NN technique has been applied to build a
model to classify the flowering and vegetative branches.
The Euclidean metrics has been used as learning metrics.
The classification accuracy with values from 0 to 1, where
0 is the worst classification and 1 is the best classification
has been recorded. Two learner metrics in k-NN
technique performance are compared to find the better
learner technique that could be used in the classification
model. The Learner metrics are Euclidean and Hamming
metrics. The results are displayed in Figure 4. Since the
Euclidean metrics show better learning ability, this metrics
has been used through out the training and testing of the
data.
The other techniques, Nave Bayes, SVM, CAT and RF
have also been used to build the classifier models, tested
and compared to report the best technique that could
predict the flowering stems. The results are displayed and
discussed in the following section.
3. RESULT AND DISCUSSION
Figure 3 displays the result of k-NN technique
classification accuracy which varies the number of
neighbors from 1 t o 10, using 10 f old cross validation
testing. The highest classification accuracy is achieved
using Euclidean metrics for k va lue from 1 to 7 which is
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 Harumanis Mango Flowering Stem Prediction using Machine Learning Techniques
R.S.M. Farook, H. Ali, A. Harun, Ndzi. D. L., A. Y. M. Shakaff, Mahmad Nor Jaafar, Z. Husin, A.H.A. Aziz

0.6794. The accuracy decreases for k from 8 to 10, with
values from 0.6711 to 0.6589. On the other hand the
classification accuracy of Hamming learning metric is
lower than that of Euclidean metrics. The highest accuracy
is achieved at k =9 where the accuracy is 0.6534.
SVM and Classification Trees classifier models
outperform the other methods applied in this study in
predicting the flowering stems and also the vegetative
stem with accuracy levels of more than 70%.

Figure 3. The Classification Accuracy using k-NN
(k=1to10) and Different Leaning Metrics
4. CONCLUSION
The development of accurate yield prediction methods is
invaluable both to suppliers and the importers. This is
more critical in high value crops that can help in
communities and government to predict and plan
expenditure. The results presented in this paper show that
SVM and Classification trees classifier models outperform
other methods tested in this study in predicting the
flowering stems. The results also demonstrate that the
machine learning technique could be used to perform
classification on flowering and non flowering stems. This
classification algorithm can be used in Decision support
system that could predict tree yield every season using
biotic factors.

Table 2 displays the classification accuracy for the various

classification models in predicting flowering branches. 5. ACKNOWLEDGMENT
Classification Trees classifier model outperforms the Special thanks to the UniMAP Agricultural Station, for
others with 77.95% accuracy rate followed by the SVM providing the samples for data collection. This project is
classifier model. Naives Bayes classifier model also funded by UniMAP Short Grant (9001-00423), University
achieve 72.43% accuracy rate. k-NN and Random Forest Malaysia Perlis. Rohani S. Mohamed Farook
achieve less than 70% accuracy. acknowledges the sponsorship provided by UniMAP.
Table 2. Classififation Accuracy, Sensitivity and
Specificity of the Classifier Models
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