IDENTIFICATION OF CITRUS GREENING (HLB)

USING A VIS-NIR SPECTROSCOPY TECHNIQUE

A. R. Mishra, D. Karimi, R. Ehsani, W. S. Lee

ABSTRACT. Citrus greening, also known as Huanglongbing or HLB, is a major threat to the U.S. citrus industry. Current-
ly, scouting and visual inspection are used for screening infected trees. However, this is a time-consuming and expensive
method for HLB disease detection. Moreover, as it is subjective, the current method exhibits high detection error rates.
The objective of this study was to investigate the potential of visible and near-infrared (VIS-NIR) spectroscopy for identify-
ing HLB-infected citrus trees. The spectral data from infected and healthy orange trees of the Valencia variety were col-
lected from four different orchards in Florida. Two different spectroradiometers with a spectral range of 350 to 2500 nm
were used to collect the canopy reflectance spectral data. Three classification techniques were used to classify the data: k-
nearest neighbors (KNN), logistic regression (LR), and support vector machines (SVM). Analysis showed that using only
one canopy reflectance observation per tree was inadequate. None of the classification methods was successful in discrim-
inating healthy trees from HLB-infected trees because of the large variability in the canopy reflectance spectral data.
When five spectra from the same tree were used for classification, the SVM and weighted KNN methods classified spectra
with 3.0% and 6.5% error rates, respectively. The results from this study indicate that canopy VIS-NIR spectral reflectance
data can be used to detect HLB-infected citrus trees; however, high classification accuracy (>90%) requires multiple
measurements from a single tree.
Keywords. Support vector machines, k-Nearest neighbors, Logistic regression, Citrus greening.

C
itrus greening, also known as Huanglongbing
(HLB) (Candidatus Liberibacter asiaticus), is a
systemic bacterial disease transmitted by Asian
citrus psyllids (Diaphorina citri Kuwayama). The
disease is causing substantial economic losses to the citrus
industry by shortening the life span of infected trees. In the
infected citrus orchards, trees decline and the productive
duration of fruit bearing is reduced. As no cure has been re-
ported for citrus greening so far, removing the infected
trees can reduce the spread of HLB. The elimination and
removal of infected trees due to citrus canker (Xanthomo-
nas citri subsp. citri) and HLB contributed to a gross loss
of 8,061 ha (19,918 acres) in Florida (NASS, 2009). Mura-
ro (2007) reported that the total costs of growing citrus fruit
increased from $4,096 to $5,643 per ha due to HLB.
The first visible sign of citrus greening may either be
leaf yellowing or mottling, which is not uniform and can
affect one branch without having any effect on another
(Schneider, 1968). Figure 1 shows HLB-infected and
Submitted for review in March 2011 as manuscript number IET 8453;
approved for publication by the Information & Electrical Technologies
Division of ASABE in February 2012.
The authors are Ashish R. Mishra, ASABE Student Member, Grad-
uate Research Assistant, Davood Karimi, ASABE Member, Postdoctoral
Researcher, Reza Ehsani, ASABE Member, Associate Professor, Citrus
Research and Education Center (CREC), University of Florida, Lake Al-
fred, Florida; and Won Suk Lee, ASABE Member, Associate Professor,
Department of Agricultural and Biological Engineering, University of
Florida, Gainesville, Florida. Corresponding author: Reza Ehsani, Citrus
Research and Education Center (CREC), 700 Experiment Station Rd.,
Lake Alfred, FL 33850; phone: 863-956-1151, ext. 1228; e-mail: ehsani@
ufl.edu.
healthy leaves. Yellow, angular blotching has been consid-
ered a symptom specific to HLB disease and consists of
blotches of yellow on dark greenish-gray leaves. HLB
symptoms appear on leafy shoots as they grow from
branches and after leaves have matured normally. By the
time these symptoms are apparent, a tree can already be se-
verely affected. Takushi et al. (2007) reported that the
starch content of HLB-infected leaves can be 20 times
higher than that of healthy leaves. Etxeberria et al. (2009)
studied the anatomical distribution of abnormally high lev-
els of starch in HLB-infected Valencia orange trees. They
reported phloem collapse in HLB-infected leaves in addi-
tion to starch accumulation. They found multiple starch
grains per chloroplast in HLB-infected leaf palisade cells,
whereas healthy leaf chloroplasts had a small number of li-
pid inclusions and occasional smaller starch grains. They
further reported that HLB-infected leaves have a corky tex-
ture due to the thicker photosynthetic cell walls.
Accurate diagnosis of HLB is essential before applying
control strategies like tree removal. HLB diagnosis is diffi-
cult to make based on field observations, as the symptoms
resemble nutrient deficiencies such as iron or zinc deficien-
cy (Etxeberria et al., 2007). Electron microscopy and bioas-
say can be used to diagnose HLB, but these methods are
time-consuming and impractical (Chung and Brlansky,
2005). Molecular methods such as real-time polymerase
chain reaction (PCR) based assays are used to detect the
presence of HLB. However, identification of suspected
plants by foliar and fruit symptoms is required by a trained
scouting crew prior to real-time PCR assays. Because the
current HLB detection methods are expensive, time-

Transactions of the ASABE

Vol. 55(2): 711-720 © 2012 American Society of Agricultural and Biological Engineers ISSN 2151-0032 711

(a)
(b)
Figure 1. (a) HLB-infected leaves and (b) healthy leaves.
consuming, and tedious, a rapid and reliable method to dis-
tinguish HLB-infected trees from healthy trees is necessary.
Sankaran et al. (2010) reviewed various visible (VIS)
and near-infrared (NIR) spectroscopy studies that were
used in plant disease detection. Previous studies have
shown that VIS-NIR spectroscopy has the potential to iden-
tify plant anomalies due to disease or malnutrition (Mu-
hammed, 2005; Yang et al., 2007; Naidu et al., 2009;
Huang and Apan, 2006; Liu et al., 2007; Poole et al., 2008;
Delalieux et al., 2007). The VIS-NIR spectrum of a leaf
contains information on plant pigment concentration, leaf
cellular structure, and leaf moisture content (Borengasser et
al., 2001). Muhammed (2005) investigated fungal disease
severity in wheat using canopy reflectance. He used 120
hyperspectral crop reflectance data vectors of 164 spectral
bands corresponding to fungal disease infected trees and
healthy trees. The author used a nearest neighbor classifier
and characterized the disease severity successfully. VIS-
NIR spectroscopy was utilized in characterizing insect in-
festation in a rice canopy caused by brown planthoppers
(Nilaparvata lugens Stål) and leaffolders (Cnaphalocrosis
medinalis Guenee (Lep., Pyralidae)) by Yang et al. (2007).
The authors used linear correlation intensity analysis and
correlation coefficients to characterize infestation severity
over the range of 350 to 2,400 nm. They found that the cor-
relation coefficient (r) at 426 nm was the highest (r =
0.878), and the coefficient of determination (R2) of a ratio
index (RNIR/RRed) was the highest (R2 = 0.922, p < 0.001)
with brown planthopper insect infestation. Naidu et al.
(2009) investigated viral infection in grapevines (Vitis vi-
712
nifera L.) that causes leaf roll disease. They used vegeta-
tion indices to discriminate this disease and reported an ac-
curacy of 75% with discriminant analysis. In another study,
Sclerotinia rot disease caused by the fungus Sclerotinia
sclerotinia was investigated on celery (Apium graveolens)
by Huang and Apan (2006) under field conditions using
hyperspectral data. The authors concluded that the VIS-
NIR range from 400 to 1300 nm was as good as the full
spectrum (400 to 2500 nm) to detect this disease. Smith et
al. (2005) studied plant stress caused by elevated levels of
natural gas in the soil, dilute herbicide solution, and ex-
treme shade. They found that the red edge position in the
spectral data was strongly correlated with chlorophyll con-
tent across all treatments. The ratio of reflectance centered
on the wavelengths at 670 and 560 nm was used to detect
increases in red pigmentation in gas and herbicide stressed
leaves. Stress due to extreme shade could be distinguished
from the stress caused by natural gas and herbicide from
the change in the spectrum. Liu et al. (2007) characterized
and estimated rice brown spot disease severity using step-
wise regression, principal component regression, and par-
tial least squares regression. They concluded that it was
feasible to estimate the disease severity using hyperspectral
reflectance from the leaves. Poole et al. (2008) investigated
HLB discrimination with VIS/NIR spectroscopy in the lab.
They found that reflectance associated with chlorophyll ab-
sorption decreased in HLB-infected leaves. Their partial
least squares (PLS) analysis showed a larger absorption
band at 612 nm, which was affected by chlorosis in HLB-
infected leaves. Lee et al. (2008) used aerial hyperspectral
imaging to detect HLB by applying spectral angle mapping
(SAM) and spectral feature fitting (SFF) methods. They re-
ported that it was difficult to obtain good results with SAM
and SFF because of the positioning errors in GPS ground
truthing and aerial imaging, and the spectral similarity be-
tween non-symptomatic HLB-infected trees and healthy
trees. Delalieux et al. (2007) used hyperspectral imaging
and parametric approaches such as logistic regression, par-
tial least squares, discriminant analysis, and tree-based
modeling to detect biotic stress (apple scab; Venturia in-
qequalis (Cooke) G. Winter) in apple trees.
A method for timely detection of HLB in the field can
assist growers to better manage and control the disease, re-
sulting in significant production and economic benefits.
The long-term goal of this study is to develop a ground-
based method to detect HLB at the early stages of devel-
opment in citrus orchards. The specific objective of this
study was to investigate the possibility of identifying HLB-
infected trees using VIS-NIR spectroscopy and to compare
three classification techniques to analyze the spectral data.
MATERIALS AND METHODS
FIELD EXPERIMENTS
A total of 1,239 spectra were collected from 135 (80
HLB, 55 healthy) Valencia orange trees. Table 1 shows de-
tailed information on the data used in this study. All the
healthy and HLB-infected trees in this study were 15 to 20
years old. Spectral data were collected using two portable
TRANSACTIONS OF THE ASABE
 Table 1. Spectral data used in this study.
Location Data Collection No. of Trees
in Florida Date HLB
Lake Alfred 13 June 2007 2 2
Lake Alfred 25 June 2007 4 4
Lake Placid 22 February 2007 4 4
Immokalee 16 January 2009 10
Immokalee 5 February 2009 10
Immokalee 27 February 2009 10
Southern Garden 24 March 2009 40
spectroradiometers. The first series of data were collected
with a FieldSpec 3 spectroradiometer (Analytical Spectral
Devices - ASD, Boulder, Colo.). Reflectance data from 350
to 2,500 nm were collected using the spectroradiometer and
transmitted wirelessly to a laptop computer. The equipment
was set up to use an average of ten scans to represent a sin-
gle observation. Bare fiber optic cable with 25° field of
view (FOV) was used for data collection. The ASD Field-
Spec spectroradiometer has a circular field of view. The in-
tegration time was optimized using the optimization option
within the software. Optimization values depend on the re-
sponse to light in a particular spectral region. The bare fiber
optic cable was placed at a distance of approximately 50 to
80 cm from the tree canopy, where the canopy was in the
range of FOV of the sensor. During data collection, the area
scanned by the spectroradiometer was approximately 385
to 988 cm2.
The second series of data were collected using a SVC
HR-1024 portable spectroradiometer (Spectra Vista Corp.,
Poughkeepsie, N.Y.). The spectral range of the SVC is 350
to 2,500 nm with spectral resolutions of 3.5 nm (at 350 to
1,000 nm), 9.5 nm (at 1,000-1,850 nm), and 6.5 nm (at
1,850 to 2,500 nm), which was similar to the ASD Field-
Spec spectroradiometer. The SVC HR-1024 spectroradiom-
eter communicated with a handheld PDA through a wire-
less connection. All the data were collected with 4° FOV.
The FOV of the SVC spectroradiometer was rectangular,
which covered an area of 4.8 × 9.4 cm from a distance of 1
m; the area was approximately 45 cm2. The SVC spectrora-
diometer had a minimum integration time of 1 ms. Under
field conditions, the scan time was set at 4 s. Laboratory
tests were conducted with various objects to compare the
spectral signatures of the ASD FieldSpec and SVC HR-
1024 spectroradiometers. Similar results were obtained
from both spectroradiometers.
Dark current measurements were automatically taken
immediately prior to the reference or target scans by both
the ASD FieldSpec and SVC spectroradiometers. The FOV
for both sensors would only cover a small section of a
branch. The spectral data were collected from sunlit cano-
pies between 11:00 a.m. to 2:00 p.m. with no additional ar-
tificial light. Spectral reflectance was collected from tree
canopies from sunlit sides of the tree canopy to maximize
the incident light intensity. In the case of HLB-infected
trees, the reflectance spectral data were collected only from
branches with symptomatic leaves. These symptomatic
leaves were marked by trained scouts and confirmed by
PCR test before data collection. Reference readings of a
white panel were collected every 10 min to reduce errors in
reflectance caused by changes in atmospheric conditions.
55(2): 711-720
No. of Spectra Spectroradiometer
Healthy HLB Healthy Type
119 122 ASD
90 60 ASD
24 24 ASD
5 100 50 SpectraVista
5 100 50 SpectraVista
5 100 50 SpectraVista
30 200 150 SpectraVista
Both spectroradiometers provided relative reflectance val-
ues of the tree canopy based on the reference value. The da-
ta analysis described in this article was performed in
Matlab (Mathworks, Inc., Natick, Mass.).
SPECTRAL PRETREATMENT AND FEATURE SELECTION
Multiplicative scatter correction (MSC) was performed
on the NIR portion of the spectra (Martens and Naes,
2001). Then the local mean and the first and second deriva-
tives were calculated at 25 nm intervals from 375 to 1,325
nm, from 1,500 to 1,750 nm, and from 2,050 to 2,300 nm
(removing the noisy regions). At each of these 61 points,
the local mean was computed by averaging the spectral re-
flectance values for that wavelength and its four neighbors.
For example, the local mean at 375 nm was computed by
averaging from 373 to 377 nm. In order to avoid noise am-
plification, which results from differentiation, the Savitzky-
Golay method (Orfanidis, 1996) was used to compute the
first and second derivatives. A quadratic polynomial and a
window size of 21 were used. Since three values were
computed for each of the 61 points mentioned above (i.e.,
the mean and the first and second derivatives), each spec-
trum was represented by a feature vector of 183 elements.
Because the number of features was significantly high and
many of these features could be correlated, principal com-
ponent analysis (PCA) was performed to reduce the number
of features (fig. 2). The 183 spectral elements were reduced
to 25 principal components (PCs) that accounted for more
than 90% of the variance within the data. From figure 2, it
can be seen that the first 25 PCs contribute about 90% of
the variance. A preliminary analysis was performed to see
whether increasing the number of PCs would improve the
classification results. No significant improvements were
obtained by increasing the number of PCs beyond 25. Fig-
ure 3 shows a plot of PCA loadings for the first two princi-
pal components.
Figure 2. Variance of data explained by principal component analysis.
713
 (a)

(b)

(c)
Figure 3. (a) Sample spectrum, (b) loading coefficients for the first PC, and (c) loading coefficients for the second PC.

are then used to find the k training samples that are closest
CLASSIFICATION METHODS to the unknown sample, and a prediction is made based on
The vectors of the principal components were used as these nearest neighbors. For a classification problem, this
the input to the classification algorithms. The output classes can be done simply by a majority vote. A more sophisticat-
obtained from the classification models were the “diseased” ed approach, used in this study, was to give a different
and “healthy” trees. For each classification method, 75% of weight to the contribution of each of the k-nearest neigh-
the data were used for training, while 25% of the data were bors in the prediction. Commonly, a weight that is inversely
used for testing the accuracy of the classifier. proportional to the square of the Euclidian distance is used
(Mitchell, 1997):
Weighted k-Nearest Neighbors (KNN)
Weighted k-nearest neighbors (KNN) is an instance- K
based classification algorithm. This type of algorithm does f̂ ( xunknown ) = argmax
v∈V
 wi δ ( v, f ( xi ) )
not develop an explicit function or model for predicting the i =1 (1)
target classes. Instead, all the training samples are stored, where
and computation is delayed until a new unknown sample 1
must be classified. For a new sample, the Euclidian dis- wi =
n
 ( xunknown − xij )
j 2
tance between its feature vector and the feature vectors of
the training samples is computed. The computed distances j =1
(2)

714 TRANSACTIONS OF THE ASABE

 In equations 1 and 2, f̂ indicates the predicted class for
the new unknown feature vector xunknown, x ij denotes the jth
element of the ith feature vector, wi are the weights, and the
function δ is defined as follows:
1 if a = b
δ ( a,b ) = 
0 otherwise
A k of 12 was used in this study based on preliminary anal-
ysis of the data.
Logistic Regression (LR)
Logistic regression provides a model for the probability
of occurrence of an event by fitting the data to a logistic
curve. As shown in figure 4, this curve maps the entire real
axis onto the interval [0,1], making it ideal for modeling the
probability of an event. When used in classification, the
variable z is usually defined as a linear combination of the
features (Witten and Frank, 2005):
( )
g θ ( x ) = f θT x =
1
1 + e −θ
T
x rating hyperplane can be calculated using the following
where θ is the parameter vector, x is the feature vector, and
f(t) = 1 if t ≥ 0 and f(t) = 0 if t < 0. A batch gradient descent
approach was used for training the model, as shown in the
following pseudo code:
only two target classes. However, it can be generalized to
solve problems that involve more than two classes. For lin-
early separable data, such as the data that are shown in fig-
ure 5a, one can draw many different hyperplanes that can
separate the data. The goal in SVM is to find a hyperplane
that separates the data with the largest possible margin, as
shown in figure 5b. SVM uses numeric labels 1 and -1 to
(3)
identify the two classes. In this article, the following nota-
tion is used to show the SVM classifier (Webb, 2002):
(
y = gw ( x ) = f wT x + w0 ) (5)
The parameters w and w0 define the decision boundary
(i.e., the separating hyperplane). The intercept w0 is a sca-
lar, while w and the feature vector x are n-dimensional vec-
tors. In equation 5, f(t) = 1 if t ≥ 0 and f(t) = -1 if t < 0. The
equation defining the separating hyperplane is as follows:
wT x + w0 = 0 (6)
The geometric margin of the ith example from the sepa-
(4) equation:
 wT x i + w0 
Di = y i  
 w 
  (7)
i i t
Here, a positive D would mean that y and w x + b are of

Do until convergence {
for all j
N
θj = θj +ε  xij ( yi − gθ ( xi ) )
i =1
end
}
where N is the number of features, ε is the learning rate,
and y is the true label (either 1 or 0). A sufficiently small ε
will ensure that the global optimum will be achieved, alt-
hough the computation time will increase by decreasing the
value of ε. In this study, a value of ε = 0.001 was used.
Support Vector Machines (SVM) (a)
Support vector machines (SVM) is one of the most suc-
cessful machine learning algorithms that is widely used in
various fields (Byvatov and Schneider, 2003; Rumpf et al.,
2010). The basic SVM solves a classification problem with

(b)
Figure 5. (a) Example of a linearly separable set of data, and (b) the
Figure 4. Logistic curve describing the logistic regression model. maximum margin classifier for this data set.

55(2): 711-720 715

the same sign, or equivalently, the ith example is correctly N
1 N
classified. The geometric margin of the classifier with re- max α  αi − 2  yi y j αi α j ( xi ,x j )
spect to the set of all training samples, {(x1,y1), ..., (xN,yN)}, i =1 i, j =1
is defined as the minimum of the geometric margins for αi ≥ 0, i = 1, ,N
each sample: 
D = min Di such that:  N
i =1:N (8) 
i
 αi y = 0
 i =1 (12)
Therefore, the goal of SVM is to find a separating hy-
perplane that maximizes D. In mathematical terms, SVM In equation 12, αi are the Lagrange multipliers, and
will pose the following optimization problem: (xi,xj) indicates the inner product between the ith and jth
feature vectors. The interesting point is that all of the La-
max w,w0 D
grange multipliers are zero except for the ones that corre-

such that: 
( 0 )
 y i wT x i + w ≥ D, i = 1, , N spond to the support vectors. Once the above optimization
problem is solved, w and w0 can be found using the follow-
 w = 1 ing equations:
(9)
 N
The second constraint, w = 1 , is a non-convex con-
straint, and this optimization problem cannot be directly
 w=

 αi y i xi
i =1
solved. It can be shown (Gunn, 1998) that this optimization 
problem can be replaced by the following equivalent prob-  max i,yi =−1wT xi + min i,y i =1wT xi
 w0 = −
lem:  2 (13)
1 2
min w,w0 w It is important to note that the new optimization problem
2
in equation 12 is only in terms of the inner products of the
( )
such that: y i wT xi + w0 ≥ 1, i = 1, ,N
(10)
feature vectors. Moreover, with the new definition of w in
terms of Lagrange multipliers (eq. 13), for a new example
In equation 10, yi(wTxi + w0) is called the functional x, the prediction of the SVM classifier can be written as fol-
margin and is shown by di. The difference between the lows:
functional margin and the geometric margin is that multi- N 
plying w and w0 by a constant will not change the geomet-
 
y = gw ( x ) = f  αi yi x,xi + w0 ( )

ric margin but will change the functional margin. The func-  i =1  (14)
tional and geometric margins are related as follows:
In other words, the entire algorithm can be written in terms
di of the inner products of the feature vectors.
Di =
w (11) In many practical applications, the data are not linearly
separable, or even if they are, the optimal margin classifier
Equation 10 means that the optimal margin classifier described so far may not be the best choice because it can
sought by SVM can be found by minimizing the norm of w, be very sensitive to outliers. Therefore, a modified version
under the constraint that the functional margin for all ex- of the SVM problem is defined as follows (Webb, 2002):
amples is at least equal to 1. It is easy to see that the mini-
N
mum margin always belongs to the points that are on the 1 2
edge of the widest strip that separates the data, as shown in min w,w0 w + C  ξi
2 i =1
figure 5b. Only for these points yi(wTxi + w0) = 1; for the
remaining points, yi(wTxi + w0) > 1. These points are called
the “support vectors” and usually comprise a very small such that: 
( 0 i )
 yi wT xi + w ≥ 1 − ξ , i = 1, ,N

fraction of the total number of points, resulting in a huge ξ

reduction in the computational cost.
Although the optimization problem in equation 10 can
be solved by commercially available quadratic program-
ming code, an easier equivalent problem can be found by
using the method of Lagrange multipliers (Strang, 1991).
Using this method, the following dual optimization prob-
lem will be obtained:
 i ≥ 0, i = 1, ,N (15)
With this definition, some of the examples are allowed
to fall on the wrong side of the separating hyperplane.
However, for each such example, a cost (ξi) will be consid-
ered. The parameter C determines the importance that we
attach to these errors. Once again, the method of Lagrange
multipliers can convert this problem into an easier one. The
resulting problem is as follows:

716 TRANSACTIONS OF THE ASABE

 N
1 N The parameters C and γ in the problem are unknown.
max α  αi − 2  yi y j αi α j ( xi ,x j ) Therefore, the first step in solving the problem is to find the
i =1 i, j =1 optimum values for these parameters. The grid search pro-
C ≥ αi ≥ 0, i = 1, ,N cedure suggested by Hsu et al. (2008) was used for this
 purpose. First, the approximate values of the optimum C
such that:  N and γ were found on a coarse grid with C = 2-8, 2-4, ..., 230
i
 αi y = 0 and γ = 2-14, 2-10, ..., 224. After finding the approximate val-
 i =1 (16) ues for the best C and γ, a finer grid was defined to search
This is the same as the previous optimization problem in for more accurate values of the optimum C and γ.
equation 12, except that the first constraint has changed Reducing the Classification Error by
from αi ≥ 0 to C ≥ αi ≥ 0. Using Multiple Measurements
Although the SVM algorithm described so far is already The goal of the present study was to evaluate classifica-
a very powerful method, significant improvements would tion algorithms that can be used for automatic detection of
result by introducing kernels. The idea is to map the feature HLB-infected citrus trees in the field. The preliminary re-
vector xi into a higher-dimensional space using a mapping sults indicated that the classification accuracy from the sta-
function Φ(xi). As mentioned before, the entire SVM algo- tistical methods used to classify HLB-infected trees were
rithm can be written in terms of the inner products of the low when data with single measurements were considered
feature vectors. After mapping feature vectors using Φ, all for analysis (data not shown). This could be due to variabil-
instances of the inner products of the feature vectors, (xi,xj), ity in the experimental conditions, such as the amount of
will be replaced by the inner product of the corresponding sunlight, orientation of the leaves with respect to the sensor,
mapped feature vectors, (Φ(xi),Φ(xj)). This inner product is and sensor measuring angle. Therefore, it was hypothesized
called a kernel: that high detection accuracy can be achieved through mul-

( ) ( ( ) ( ))
K xi ,x j = Φ xi ,Φ x j
(17)
tiple measurements on a single tree. In this study, we inves-
tigated the accuracy of the three classification methods
(KNN, LR, and SVM) using spectral data from one, three,
The idea of kernels significantly improves the SVM or five measurements from different canopy areas of the
technique in terms of both its accuracy and the scope of same tree.
problems that it can solve. Various different kernels have When more than one measurement was presented to the
been introduced and used in practice (Cherkassky and Mu- classifier, a simple method based on majority voting can be
lier, 2007). Following the suggestion of Hsu et al. (2008), a used to determine the classification group. The tree is la-
Gaussian kernel was used in this study: beled an HLB-infected tree when more than half of the
measurements from that tree are classified as HLB infected.
( )
 2
K xi ,x j = exp  γ xi − x j  An improved approach is to consider the confidence of the
  (18) classifier for its prediction on each of the measurements.
For example, if a classifier predicts “infected” on two out
Therefore, the SVM problem that was solved in this
of five measurements with very high confidence and
study was of the following form:
“healthy” on the three remaining measurements with very
N N low confidence, it would be more reasonable to classify the
 αi − 2  yi y j αi α j K ( xi ,x j )
1
max α tree as “infected.” Our analysis was based on the majority
i =1 i, j =1 with confidence of the classifier.
C ≥ αi ≥ 0, i = 1, ,N For the KNN algorithm, the following equation was
 used to estimate the confidence of each prediction:
such that:  N i
 αi y = 0 KNN confidence=
 i =1
 wi ( for those among the k nearest neighbors that
( 
)
2
have the same class as the predicted class )
where: K xi ,x j = exp  γ xi − x j 
  (19)
÷  wi ( for all of the k nearest neighbors )
(20)
To solve this problem, the sequential minimal optimiza-
tion (SMO) algorithm was used. This algorithm solves the where wi is as defined in equation 2. For the LR method,
above optimization problem by a coordinate ascent ap- the value of the function gθ(x) in equation 4 can be used to
proach. Because of the second constraint in the problem, calculate a measure of confidence in prediction. The closer
N gθ(x) is to either 0 or 1, the more confident is the prediction.
i.e.,  αi yi = 0 , it is not possible to change only one of the Therefore, the value gθ ( x ) − 0.5 was used to evaluate the
i =1
Lagrange multipliers. The SMO algorithm optimizes the confidence of the predictions by the LR method:
function with respect to two Lagrange multipliers simulta- LR confidence = gθ ( x ) − 0.5
neously. The advantage of this approach is that the inner- (21)
most loop is very fast compared to other algorithms (Platt, For the SVM classifier, the value of the function gw(x) in
1998). equation 14 can be used as a measure of confidence in pre-

55(2): 711-720 717

diction. The larger the absolute value of this function, the
more confident is the prediction. Therefore, g w ( x ) was
used to evaluate the confidence of predictions by the SVM
method:
SVM confidence = g w ( x ) (22)

RESULTS AND DISCUSSION

Figure 6 shows an example of the collected spectra for
both healthy and HLB-infected leaves. Each observation is
an average of ten measurements. In general, the reflectance
in the visible region (400 to 700 nm) of HLB-infected (a)
leaves was higher than that of healthy leaves. This finding
is accordance with Poole et al. (2008) and supports our hy-
pothesis that due to the chlorosis in HLB-infected trees,
they absorb less visible light, resulting higher reflectance in
the visible region. In the NIR region, the canopy reflec-
tance of HLB-infected leaves in most cases was lower than
that of healthy leaves.
For the SVM method, the first step was to find the opti-
mum values for C and γ. As mentioned before, this was
performed by a gird search. Figure 7 shows typical contour
graphs that were used to find the optimum parameter val-
ues. First, the classification error was evaluated on a coarse
grid (fig. 7a) to find approximate estimates for C and γ. (b)
Then a finer grid was defined (fig. 7b) and used to deter-
mine accurate values of C and γ that minimized the classi- Figure 7. Contour plots of classification error for finding the
optimum values for the parameters C and γ.
fication error. In the specific case shown in figure 7, the
lowest classification error was approximately 18%, which
trees that were classified as HLB infected) and the false
was obtained for C = 28 and γ = 34.
negative rate (i.e., the percentage of HLB-infected trees
Analysis showed that MSC correction of the spectra did
that were classified as healthy).
not improve the classification accuracy. In other words,
It can be seen from table 2 that the classification error
when MSC, as described earlier in the Spectral Pretreat-
with a single spectrum was relatively large. However, when
ment and Feature Selection section, was removed as a pre-
three or five spectra from the same tree were used, the clas-
treatment procedure, the classification error did not im-
sification error decreased. The SVM method demonstrated
prove for any of the three classification techniques. Table 2
lower classification errors than the other two methods, es-
shows the classification error for each of the three classifi-
pecially with five spectra. For the SVM and KNN methods,
cation techniques without MSC correction. The table shows
the false negative error rate was slightly higher than the
the percentage of misclassified citrus trees when one, three,
false positive error rate, whereas for the LR technique, the
or five spectral measurements from each tree were used for
reverse was true. Because the amount of data was limited, it
classification. In addition to the overall error, the table also
was decided to build the classifiers using the pooled data
shows false positive rate (i.e., the percentage of healthy
from all seven field experiments. As previously mentioned,
75% of the entire dataset was used to build each classifier,
and the rest of the data were used to evaluate the classifiers.
The errors mentioned in table 2 are the average classifica-
Table 2. Average classification error for the three
classification techniques.
Logistic k-Nearest Support Vector
Type of Error Regression Neighbors Machines
One measurement
False positive (%) 37 20 13
False negative (%) 33 25 23
Overall error (%) 35 23 18
Three measurements
False positive (%) 25 8.8 4.5
False negative (%) 21 13 7.5
Overall error (%) 23 11 6.2
Five measurements
False positive (%) 20 5.8 2.9
Figure 6. Representative spectra from leaves of two healthy and two False negative (%) 17 7.1 3.0
HLB-infected trees. Overall error (%) 19 6.5 3.0

718 TRANSACTIONS OF THE ASABE

tion errors for the testing data from all seven field experi-
ments. The classification error can also be computed for the
testing data from each field experiment separately. Our
analysis showed that the classification error was very close
for different field experiments. For field experiments that
provided more data (i.e., 13 June 2007 and 24 March
2009), the classification error was slightly less than that of
the field experiments that provided less data. We assume
that this was because more spectra from the field experi-
ments with a larger amount of data were used in building
the classifier, thus biasing the classifier toward the pattern
in the data from those field experiments.
The classifiers obtained by the weighted KNN, logistic
regression, and SVM algorithms can be programmed on a
microcontroller. The three algorithms were also very differ-
ent in terms of computation time. For SVM-based classifi-
cation, the most time-consuming step was to find the opti-
mum values for C and γ. The grid search method for
optimal value selection used in this study took several
hours (about 8 h) on a PC. Although there are faster meth-
ods for finding C and γ (Hsu et al., 2008), this step is inher-
ently time consuming. The batch gradient descent algo-
rithm described previously for the logistic regression
method took approximately 12 s to complete on a PC with
a 4.8 GHz processor and 512 MB of RAM. As mentioned
before, the KNN method does not produce any model from
the data. Therefore, for the KNN algorithm, there is no
computation until a new spectrum is to be classified. Once
the model (i.e., the classifier) is obtained, the computation
time for classification of a new spectrum is very fast for
SVM and logistic regression. On the same PC as mentioned
above, the time to make a prediction based on three spectra
from the same tree was only 0.06 ms for the logistic regres-
sion classifier, whereas for the weighted KNN and SVM
methods, this time was 5.5 and 5.0 ms, respectively. There-
fore, the logistic regression method was computationally
much faster. However, because the KNN and SVM algo-
rithms yielded better classification accuracy than logistic
regression, they are preferable algorithms for HLB detec-
tion in citrus groves.
CONCLUSION
The goal of this study was to evaluate machine learning
techniques for rapid detection of HLB-infected citrus trees.
Canopy reflectance spectra were measured on infected and
healthy trees using a spectroradiometer, and three common
classification algorithms (logistic regression, k-nearest
neighbor, support vector machines) were used to distin-
guish the infected trees from the healthy trees. The results
indicated that a single measurement was insufficient for ac-
curate detection of the infected trees with the three ap-
proaches used in this study. The classification error was be-
tween 18% and 35% using a single spectrum. However,
using multiple spectral measurements from the tree canopy
of a single tree, the classification accuracy increased. The
SVM method showed an accuracy greater than 97% when
it was provided with five spectra from different leaves on
the same tree. Under real field conditions, variation of sun-
55(2): 711-720
light and other environmental factors can produce noise
that might reduce the classification accuracy. Under these
conditions, multiple measurements will be necessary to en-
sure acceptable classification accuracy.
ACKNOWLEDGEMENTS
This research was supported under Project No. 81086 of
the Florida Citrus Production Research Advisory Council,
Peter McClure, Chairman. The authors would like to thank
Dr. Sindhuja Sankaran and Sherrie Buchanon for their as-
sistance in this study.
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