International Journal of Electrical and Computer Engineering (IJECE)
Vol. 12, No. 5, Oct 2022, pp. 4951∼4959
ISSN: 2088-8708, DOI: 10.11591/ijece.v12i5.pp4951-4959 ❒ 4951
Feature selection of unbalanced breast cancer data using
particle swarm optimization
Amal Elnawasany1, Mohamed Abd Allah Makhlouf1, BenBella Tawfik1, Hamed Nassar2
1Department Information Systems, Faculty of Computers and Informatics, Suez Canal University, Ismailia, Egypt
2Department of Computer Science, Faculty of Computers and Informatics, Suez Canal University, Ismailia, Egypt
Article Info
Article history:
Received Jul 27, 2021
Revised May 28, 2022
Accepted Jun 14, 2022
Keywords:
Breast cancer
Feature selection
Genetic algorithm
Particle swarm optimization
Surveillance epidemiology
and end result
Synthetic minority
oversampling technique
Unbalance data
ABSTRACT
Breast cancer is one of the significant deaths causing diseases of women around the
globe. Therefore, high accuracy in cancer prediction models is vital to improving
patients’ treatment quality and survivability rate. In this work, we presented a new
method namely improved balancing particle swarm optimization (IBPSO) algorithm
to predict the stage of breast cancer using unbalanced surveillance epidemiology and
end result (USEER) data. The work contributes in two directions. First, design and
implement an improved particle swarm optimization (IPSO) algorithm to avoid the
local minima while reducing USEER data’s dimensionality. The improvement comes
primarily through employing the cross-over ability of the genetic algorithm as a fitness
function while using the correlation-based function to guide the selection task to a min-
imal feature subset of USEER sufficiently to describe the universe. Second, develop
an improved synthetic minority over-sampling technique (ISMOTE) that avoid over-
fitting problem while efficiently balance USEER. ISMOTE generates the new objects
based on the average of the two objects with the smallest and largest distance from
the centroid object of the minority class. The experiments and analysis show that the
proposed IBPSO is feasible and effective, outperforms other state-of-the-art methods;
in minimizing the features with an accuracy of 98.45%.
This is an open access article under the CC BY-SA license.
Corresponding Author:
Amal Elnawasany
Department Information Systems, Faculty of Computers and Informatics, Suez Canal University
4.5 km the Ring Road, Ismailia, Egypt
Email: aml.elnawasany@ci.suez.edu.eg
1. INTRODUCTION
The surveillance epidemiology and end result (SEER) database [1] is an open cancer database that
provides different cancers indicators for prognosis prediction. It contains information about the occurrence,
frequency, survivability, and mortality of cancer. Cancer is typically labeled in stages from 1 to 4, with 4
being the most serious. The information collected in SEER mostly comes in high dimensionality [2]. Also,
it is unbalanced, i.e., the objects in stages 2 and 3 are too larger than those in stages 1 and 4. Therefore,
the database is referred to as an unbalance SEER (USEER) database. The two classes with the least number
of objects are referred to as minority classes, while the other two are referred to as majority classes. The
high dimensionality and unbalanced problems often hamper the breast cancer early prediction task and lead
to delayed and inaccurate results, which degrade the patient’s survival chance. Many research papers have
been recently directed to address either the high dimensionality problem or the unbalance problem and the
motivation behind this work is to propose an approach to address both.
Journal homepage: http://ijece.iaescore.com
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Data reduction is a data preprocessing technique that aims at preparing the data for prediction. Instead
of overwhelming the classifier with a huge amount of data, potentially causing many prediction errors, the
classifier will have an easier job. Although data is shrinking, the fundamental and integrity of the original data
should be retained. Data reduction decreases the processing time, storage space and computational complexity.
Data reduction techniques include feature selection and instance selection. We will employ both techniques.
SEER database contains instances for many types of cancers, while the cancer of interest is breast cancer. In
this case, only the instances of breast cancer will be selected. This is called instance selection.
Feature selection (FS) tool is an approach that enables prediction algorithms to be applied to high
dimensional data with less computations [3]. FS progresses by two steps: feature evaluation and feature set
search. Feature evaluation evaluates each feature in the dataset separately in terms of its relevance to the class
variable. On the other hand, feature set search tries various combinations of the evaluated features to arrive at a
shortlist of features that sufficiently describes the objects [4]. Among the feature evaluation tools is correlation-
based feature selection (CFS) [5]. The strength of the CFS tool comes in its ability to find a feature subset with
features that are highly correlated with the class, yet uncorrelated with each other. CFS tool measures the
goodness f(M ) of set M of features (M ⊂ A ) as (1):
f(M ) =
|M|
∑
i=1
|M|
∑
j=1
|M |ρai,aj
p
|M |+|M |(|M |−1)ρai,d
, (1)
where ρai,aj is the Pearson’s correlation coefficient between features ai and aj and is given by (2):
ρai,aj =
Cov(ai,aj)
σai σaj
, (2)
where Cov(ai,aj) is the covariance which measures of the strength of the correlation between two features ai
and aj and σak
is the standard deviation of feature ak.
The hurdle is that the size of the search space increases exponentially concerning the number of
features, whereas CFS tool needs to assess 2n feature subsets for USEER with n features. Therefore, CFS
fails miserably when it confronts the USEER. A gap filled by swarm intelligent (SI) algorithms [6] is a low
cost to search for a feature subset. Some examples of these algorithms are particle swarm optimization (PSO)
algorithm [7], genetic algorithm (GA) [8], ant colony optimization (ACO) algorithm [9], artificial bee colony
optimization (BCO) algorithm [10], bat search algorithm (BSA) [11], cuckoo optimization (CO) algorithm [12]
and elephant herding optimization (EHO) algorithm [13]. The first two are the core of the approach proposed
in the present article. Its simple operators characterize PSO algorithm and it is computationally inexpensive
in terms of both memory and cost. PSO is an algorithm that solves FS problem by iteratively improving each
particle position regarding a given measure of quality. The particle position is represented by a pivot vector
pointing at a subset of features of the balanced SEER (BSEER). PSO algorithm assumes having a swarm of
P ≥ 10 particles moving in the search-space according to simple mathematical formula, known as a velocity
function. The minimum number of particles is 10 because most of the swarms in nature have 10 particles on
average. In each iteration t ≥ 1, the particle that achieves the highest performance, being closer to the food,
is referred to as the commander and the rest are slaves. The commander is chosen afresh in each iteration
t ≥ 1. The commander guides other particles to update their position to converge towards the food. Therefore,
each particle i = 1,2,...,N in iteration t + 1 updates its position towards a better position according to the
commander’s position and the velocity function. At the end of the user defined number of iterations N, this
exercise is expected to move the swarm toward their food’s best solution. The good thing about PSO is that
it does not make assumptions about the problem under study and can search high dimensional BSEER for
minimal feature subset.
Initially, we consider that we have P ≥ 10 particles. Each particle i = 1,2,...,P at iteration t ≥ 1 has
its own pivot vector Xit = [x1,x2,...,xn], where xj ∈ {0,1}. All the particles start at iteration t = 1 by pivoting
randomly on a feature subset from the whole BSEER features. For each pivot vector Xit , we construct its
corresponding feature subset A ⊂ A by:
A = {aj| xj = 1},
which represents the set of features whose corresponding values in Xit is 1. For example, consider X12 =
[1,1,0,1,0] =⇒ A = {a1,a2,a4}.
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PSO computes the goodness f(A ) of the original set of features A in BSEER by (1). Then, at the
end of each iteration t ≥ 1, each particle is assessed through computing the goodness of their corresponding
feature subset. The pivot vector with the corresponding highest goodness f(A) is considered the commander
and is assigned to Xt. Each slave particle i = 1,2,...,P−1 updates its pivot vector Xit+1 in iteration t +1 with
respect to Xt in two steps. First, it computes its velocity Vit+1 by which the particle updates its pivot vector at
iteration t +1 and is given by:
Vit+1 = Vit +c1 f(A )Xt −c2 f(A)Xit , (3)
where c1 and c2 are two positive constants, in which c1 +c2 = 4. All the components of the velocity vector Vit
at t = 1 is of value 0. Second, the slave particles i = 1,2,...,P−1 find its updated pivot vector Xit+1 at iteration
t +1:
Xit+1 = Xt +Vit+1 . (4)
However, the PSO algorithm creates an undesirable feature subset A ⊂ A of USEER which is in-
sufficient to describe the universe [14]. This is because it employs the k-nearest neighbor (kNN) classifier
as a fitness function which is frustrated by the unbalanced nature of USEER. This issue is commonly known
as local minima feature subset; given a feature subset A ⊂ A , A is said to be local minima feature subset
if f(A) ≤ f(A ) for all values in specific interval but not the whole domain. Additionally, PSO algorithm is
considered classifier-dependent algorithm as the resultant feature subset depends heavily on the accuracy of the
kNN classifier and this fact, in turn, may result in poor accuracy with other classifiers. This calls for an im-
proved PSO algorithm to deal with USEER utilized in the present work. GA is an evolutionary algorithm that
mimics the biological behavior of genes. In contrast to the PSO algorithm, GA employs a cross-over technique
that can update the feature subset it has been found so far and avoids being trapped in the local minima.
Definition 1 (Cross-over) Given two pivot vectors Y = [1,0,0,1,1,1,0,1] and Z = [0,1,1,0,0,1,1,0]
where 1 in the ith position means that feature ai is selected and 0 otherwise. The cross-over technique randomly
chooses a position and all bits beyond that position is swapped between the two vectors to generate two new
vectors. For example, consider that position 4 is chosen then, the two new vectors are Y′ = [1,0,0,1,0,1,1,0]
and Z′ = [0,1,1,0,1,1,0,1].
Rostami and Zadeh [15] state that the unbalance format of USEER negatively impacts the early pre-
diction task of breast cancer. This is because the prediction algorithms have unpromising results on a minority
classes than on majority ones [16]. Attempts to mitigate the unbalance problem are through converting USEER
to a balanced one. This involves using object sampling (OS) technique that aims to have normally distributed
objects among classes. OS is classified into two groups: under-sampling and over-sampling. The former
progress by removing a set of objects from majority classes, while the latter progress by generating a set of
objects in the minority classes. Its low cost characterizes Under-sampling on the contrary, over-sampling do
not lose information, but it may result in an over-fitting problem, where the prediction algorithms fit to a spec-
ified set of objects and result in poor prediction accuracy with un-previously seen objects. Synthetic minority
over-sampling technique (SMOTE) [17], an example of over-sampling, has put a great effort into balancing the
USEER. It randomly chooses an object from the minority decision class and finds its k neighbor objects. Then
it generates a new object by averaging the feature values of the k objects. The process is repeated till we have
an equal number of objects in each class. This article remedies the FS and OS tasks’ limitations of USEER. The
rest of this article is organized as follows. Section 2 covers the related work. Section 3 describes the proposed
approach. In section 4, the experimental work is carried out and discussions are given. Finally, the concluding
remarks are presented in section 5.
2. RELATED WORK
Zhao et al. [18] introduce a predictive model for USEER using univariate and multivariate linear
regression (LR). They aim to predict the patient’s cancer stage using age, race, tumor size, primary site, patho-
logical grade, histologic type, and molecular subtype features. However, [19] state that social features are more
and more emphasized in breast cancer progression. Therefore, they introduce a predictive model for USEER
to assess the impact of marital status on breast cancer. Furthermore, they used a chi-square method in [20] to
analyze the associations between marital status and other features and a Kaplan Meier method to estimate sur-
vival curves. By and large, the models mentioned above result in low accuracy with the prediction algorithms.
This is because they do not consider the unbalance classes, the main characteristic of USEER. OS technique
Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)
4954 ❒ ISSN: 2088-8708
has been the topic of much research in recent years to alleviate the unbalance nature of USEER. Bertorello and
Koh [21] use a density-based synthetic minority over-sampling (DSO) method to balance USEER. They use
different weights for objects in the minority classes. Then they generate new objects regarding objects with
the highest weight. On the contrary, Luo et al. [22] state that using the objects with the least weight is better
in sampling to avoid misclassification. Tao et al. [23] propose a new over-sampling technique referred to as
self-organizing map over-sampling (SOMO) to balance USEER. The SOMO technique generates new objects
by producing a 2D representation of the input objects in the minority class, then averaging the closest objects.
Wang [24] combine the strengths of PSO algorithm and CFS tool with two synthetic over-sampling methods;
borderline-SMOTE and DSO with bayesian network (BN) algorithm and LR. Mirjalili et al. [25] examine 11
over-sampling techniques and 7 under-sampling techniques on 15 types of cancer. According to the study,
USEER degrades the performance of classifiers. They state that balancing methods enhance the classification
of USEER. Han et al. [26] introduce a distribution-sensitive over-sampling technique for balancing USEER.
They divide the objects into noise, unstable, boundary, and stable objects according to their location in the
minority class. They use a set of different methods to assess which objects are suitable to generate new objects.
They use a set of different methods to assess which objects are suitable to generate new objects. Anupama and
Jena [27] introduce increment over sampling for data streams (IOSDS) algorithm which uses a unique over-
sampling technique to almost balance USEER. The IOSDS algorithm identifies noisy and mostly misclassified
objects from the majority and minority classes by employing k-NN classifier. Then, it generates new objects
in the minority classes using artificial, replication and hybrid objects. The trouble with the above-mentioned
attempts is that they are sequential in nature, resulting in a delayed prediction. Tarkhaneh and Shen [28] intro-
duce a Mantegna Lévy flight PSO and neighborhood search (LPSONS) algorithm to reduce the dimensionality
of the USEER. They combine the strength of a velocity function, PSO algorithm with a Mantegna Lévy distri-
bution function. This formulation leads to a more diverse feature subset. Additionally, to avoid being trapped
in local minima, they combine the strengths of both a neighborhood search algorithm and a Mantegna Lévy
distribution function. Pashaei et al. [29] introduced a binary version of PSO (BPSO) algorithm to avoid being
trapped in local minima. Then, they combined the strengths of both a BPSO algorithms and a binary black
hole optimization (BBHO) algorithm to improve the exploration and exploitation steps of BPSO algorithm.
Afterward, they build a predictive model using a k-NN classifier to predict the patient’s cancer stage early. The
above attempts have one thing in common they create an undesirable feature subset of USEER because they do
not consider the unbalanced nature of USEER, a gap that is filled by the present work. Fern´andez-Delgado
et al. [30] evaluate 179 classifiers from 17 different families Bayesian, neural networks, random forests (RF),
logistic regression. The RF classifier is at the forefront of the best classifiers. Ganggayah et al. [31] build
prediction models using decision tree (DT), neural networks, support vector machine (SVM), RF and logistic
regression algorithms to detect the significant indicators of breast cancer. The results detect the cancer stage
as one of the most important indicators. The results were close; with the lowest accuracy obtained from DT
and the highest obtained from RF. A study of [32] analyzed breast cancer at an early stage by comparing the
performance of DT, RF and SVM. The results find that the RF performance is better than the other techniques
for predicting cancer at an early stage. This article circumvents these problems by introducing an improved
SMOTE to avoid the over-fitting problem and introducing an improved PSO algorithm to avoid get trapped in
local minimal while dealing with the unbalance SEER.
3. RESEARCH METHOD
As shown in Figure 1, improved balancing particle swarm optimization (IBPSO) in this work conducts
the improvement in two main directions: i) feature selection using an improved PSO algorithm (IPSO) and
ii) balancing USEER using an improved SMOTE (ISMOTE). The first direction is FS which consists of two
main steps: feature evaluation using CFS and feature set search by IPSO. First, CFS evaluates the relevance
between each feature in the database and the class variable to find the highest associated features. Second, IPSO
attempts different combinations of evaluated features to develop the best shortlist of features that adequately
describe the objects.
Accordingly, IPSO algorithm is designed as shown in algorithm 1. We try different particles to pick
the best number that fits the problem until the optimum result is saturated. IPSO algorithm tries a swarm of
10 ≤ P ≤ 50 particles. IPSO uses the goodness function, given by (1), to assess the goodness of the selected
feature subset in each iteration. When t = 1, PSO calculates the fitness value of the given BSEER and call it
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B goodness; best goodness. To this end, the algorithm aims to search for a minimal feature subset having the
same B goodness. A simple loop iterates P times to randomly initialize the P pivot vectors of the P particles,
calculate the goodness of each corresponding feature subset A. The pivot vector with the highest fitness value is
assigned to Xt. Afterward, IPSO employing the cross-over ability of GA to update the P particles pivot vectors
and iterates till a user-defined number of iterations N is reached or a minimal feature subset with B goodness
is found.
Figure 1. Process flow for the proposed IBPSO algorithm
The second direction is balancing data using ISMOTE which starts by finding the centroid for the
minority decision class. Then, it computes the distance between the objects in the class and the centroid object
using Euclidean distance. Finally, the newly generated object is the average of the two objects having the
smallest and the largest distance from the centroid. This task is repeated until we have a BSEER.
Algorithm 1 Improved particle swarm optimization (IPSO) algorithm
Input: BSEER
P, number of particles (10 ≤ P ≤ 50)
N, number of iterations (N ≥ 2)
Output: A, a minimal BSEER feature subset (A ⊂ A )
t := 1
B goodness := f(A ) as per (1)
for i = 1 to P do
Construct randomly the pivot vector Xit
A := {aj| xj = 1}, set of features whose corresponding values in Xit is 1
Calculate f(A) as per (1)
end for
Assign the pivot vector with the corresponding highest f(A) value to Xt
for k = 2 to N do
t := t +1
Cross-over the two slave pivot vectors with the corresponding highest goodness as per
Definition 1.
for i = 1 to P do
Calculate the pivot vector Xit from Xit−1 as per (3), (4)
A := {aj| xj = 1}
Calculate f(A) as per (1)
end for
Assign the pivot vector with the corresponding highest f(A) value to Xt .
if f(A) = B goodness then
break.
end if
end for
4. RESULT AND DISCUSSION
The experiments are conducted on SEER 1973-2016. SEER consists of 10,050,814 observations
for all cancer types, only 1,631,572 cases diagnosed with breast cancer. From this population, we exclude
1,383,910 whose cause of death is not breast cancer. We further exclude 93,321 who have an unknown stage.
Due to the impact of hurricane Katrina, 216 Louisiana cases diagnosed for those six-month period are excluded
Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)
4956 ❒ ISSN: 2088-8708
from the research database. We excluded 280 cases that are not active follow-up, i.e., not keeping in touch
with the patient for vital status, and exclude 2,770 cases that were not malignant cancers. The final cohort
in our study on 151,075 with 160 variables. Table 1 shows the number of instances in different stages in
BSEER before and after applying ISMOTE. The total number of balancing instances generated by ISMOTE
is 177173. The final number of features selected by IPSO is 36 features. The selected features are survival
months, first malignant primary indicator, total number of in situ/malignant tumors for a patient, radiation
recode, chemotherapy recode, radiation sequence with surgery, laterality, histology, regional nodes positive,
breast subtype, SEER cause-specific death classification, primary site, grade, tumors of adolescents and young
adults site recode, breast-adjusted N (refers to the number of nearby lymph nodes that have cancer), breast-
adjusted T (refers to the size and extent of the main tumor), scope of regional lymph node surgery (describes
the performed procedure of removal, biopsy, or aspiration of regional lymph nodes), surgery of primary site
(describes a surgical performed procedure that removes and/or destroys the tissue of the primary site), Ap-
palachia, CS schema-AJCC 6th edition, Indian health service files to identify native Americans, Louisiana,
month of diagnosis recode, hispanic identification algorithm (uses to classify cases as hispanic or not), record
number (unique sequential number for each patient identifies the number of records submitted to SEER for
that particular patient), SEER registry (used in conjunction with Patient ID to uniquely identify a patient), Site
-mal+ins (mid detail) (which is should be used in conjunction with and only with the variables site specific
(SS) sequence mal+ins (mid detail), SS sequence 1975+ mal+ins (mid detail), or SS sequence 1992+ mal+ins
(mid detail) and they are already selected with our algorithm), SS sequence 1975+ -mal (most detail), SS se-
quence 1992+ mal (most detail), SS sequence 1992+ mal+ins (most detail), and Year of birth. Table 2 shows
the performance measures of the IBPSO, the results without ISMOTE and the results without IPSO.
Table 1. Description of BSEER used in the experiments
Class before ISMOTE (Percentage) After ISMOTE (Percentage)
stage 1 9973 (6.60%) 19975( 11.3%)
stage 2 1423 (34.04%) 51423 (29.0%)
stage 3 83581 (55.32%) 83581 (47.2%)
stage 4 6098 (4.04%) 22194 (12.5%)
The best number of particles that fit our problem was 20 particles. To validate the feature subset se-
lected by IBPSO, we compare the results of IBPSO with five related SI algorithms namely, ACO, BCO, CO,
BSA and EHO, using 10-fold cross-validation as shown in Table 2 and Table 3. We can see that the perfor-
mance of the IBPSO is superior in selecting a smaller number of features while keeping its good classification
performance.
Table 2. Performance measures for the IBPSO
Evaluation measure IBPSO Without ISMOTE without IPSO
Accuracy 98.45% 64.79% 70.8%
Recall 0.985 0.648 0.708
Precision 0.985 0.652 0.714
F-Measure 0.984 0.621 0.694
MCC 0.974 0.343 0.489
ROC area 0.987 0.774 0.812
PRC area 0.986 0.706 0.724
MAE 0.0934 0.2255 0.2212
RMSE 0.1579 0.3351 0.325
To stress on the stability of the IPSO algorithm, Figure 2 shows the receiver operating characteristic
(ROC) curve for the four cancer stages. ROC curve measures the classification algorithm’s performance, the
relation between classifier specificity and sensitivity at different thresholds. Classifier sensitivity represents the
true positive rate, while specificity represents the truly negative rate. The farther the curve is from the diagonal
line, the higher the overall accuracy of the model.
There are many problems with the SEER database:
− There are many blank(s) fields or unknown data. Unfortunately, excluding all blank(s) and unknown data
leads to an empty matrix. This makes it impossible to remove all of them. So, we remove only blank and
unknown fields from target features.
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− Many features are gathered in only a specific period, which leads to inconsistency in the data. All these
features are eliminated from our study. We select only data collected after 2010.
There were some degrees of missing in our data, but SEER encode the missing data; therefore, algo-
rithms may be puzzled and deal with it as complete data. So, our further work would include other preprocess-
ing techniques for missing data rather than deletion. Also, approach for hyperparameter optimization for the
model parameter.
Table 3. Comparative experiments result of different SI algorithms
Evaluation measure BSA CO ACO BCO EHO
# selected features 33 30 43 27 37
Accuracy 69.03% 70.74% 94.05% 64.36% 64.83%
Recall 0.69 0.707 0.941 0.644 0.648
Precision 0.694 0.713 0.941 0.663 0.654
F-Measure 0.672 0.694 0.94 0.604 0.625
MCC 0.455 0.488 0.899 0.362 0.371
ROC Area 0.775 0.812 0.991 0.775 0.765
PRC Area 0.669 0.728 0.986 0.689 0.684
MAE 0.2383 0.2208 0.0965 0.2454 0.228
RMSE 0.3364 0.3248 0.1797 0.3417 0.3376
Figure 2. ROC curve for the four cancer stages
5. CONCLUSION
The proposed approach, IBPSO, is designed principally to process USEER data and predict the stage.
IBPSO conducts the improvement in two directions. First, design and implement an IPSO algorithm to avoid
being trapped in local minima while reducing USEER data’s dimensionality. The improvement comes primarily
through employing the cross-over ability of the genetic algorithm (GA) as a fitness function while using the
correlation-based function to guide the selection task in IPSO algorithm. This idea leads to a minimal feature
subset of USEER sufficiently to describe the universe. Second, develop an ISMOTE that avoid over-fitting
problem while efficiently balance USEER. ISMOTE generates the new objects based on the average of the two
objects with the smallest and largest distance from the centroid object of the minority class. The results show
that IBPSO outperforms the related algorithms to find out a minimal feature subset with an accuracy of 98.45%.
The classification accuracy of IBPSO is promising and superior to those achieved with different methods.
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BIOGRAPHIES OF AUTHORS
Amal Elnawasany is a teaching assistant at the Faculty of Computers and Informatics.
She obtained bachelor’s degree in Information Systems from Suez Canal University in 2007. She
obtained master’s degree of information systems from the Suez Canal University (Egypt) in 2015.
She can be contacted at email: aml.elnawasany@ci.suez.edu.eg.
Mohamed Abd Allah Makhlouf is currently an associate professor in Faculty of Com-
puter Science and informatics Suez Canal University. He received his first degree in Computer Sci-
ence and Operation Research, Faculty of Science, Master’s degree in Expert Systems, Faculty of
Science Cairo University. He received his Ph.D. degree in computer science, Faculty of Science,
Zagazig University. He got the Post-Doctoral studies in Computer Science from Granada Univer-
sity, Spain in 2016. His research interests: machine learning, data mining, intelligent bioinformatics,
metaheuristic optimization, decision support systems and predictive models. He can be contacted at
email: m.abdallah@ci.suez.edu.eg.
BenBella Tawfik born in September 1964, Cairo, Egypt, Graduated from Military Tech-
nical College in 1986. He got my master’s in computer engineering in 1991 from the same school
of graduation. He got his Ph.D. from Colorado State University, USA in 1998. In 2006, He vis-
ited USA-Colorado State University and earned Post Doctor Certificate in Computer Engineering.
Besides his research work, he worked as a part time professor in many schools of Computer Engi-
neering/Computers and Informatics in Egypt since 1998. He is working as an assistance professor in
Information System Department in Faculty of Computer and Informatics – Suez Canal University -
since October 2012. Three years ago, he is an associate professor working as a dean of the mentioned
department. He can be contacted at email: benbellat@gmail.com.
Hamed Nassar received the B.Sc. degree in electrical engineering from Ain Shams
University, Egypt, in May 1979 and the M.Sc. degree in electrical engineering and the Ph.D. degree
in computer engineering from the New Jersey Institute of Technology, USA, in May 1985 and May
1989, respectively. He was an Assistant Professor of computer engineering, in November 1989, an
Associate Professor of computer science, in May 1998, Professor of computer science, in March
2004 and a Professor with the Department of Computers and Informatics, Faculty of Engineering,
Beirut Arab University. Dr. Nassar is currently with the Department of Computer Science, Suez
Canal University. His most recent publication is on a functional equation arising from a network
model. His research interests include computing in mathematics, natural science, engineering and
medicine, computer graphics and computer communications (networks). He can be contacted at
email: nassar@ci.suez.edu.eg.
Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)

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Feature selection of unbalanced breast cancer data using particle swarm optimization

  • 1. International Journal of Electrical and Computer Engineering (IJECE) Vol. 12, No. 5, Oct 2022, pp. 4951∼4959 ISSN: 2088-8708, DOI: 10.11591/ijece.v12i5.pp4951-4959 ❒ 4951 Feature selection of unbalanced breast cancer data using particle swarm optimization Amal Elnawasany1, Mohamed Abd Allah Makhlouf1, BenBella Tawfik1, Hamed Nassar2 1Department Information Systems, Faculty of Computers and Informatics, Suez Canal University, Ismailia, Egypt 2Department of Computer Science, Faculty of Computers and Informatics, Suez Canal University, Ismailia, Egypt Article Info Article history: Received Jul 27, 2021 Revised May 28, 2022 Accepted Jun 14, 2022 Keywords: Breast cancer Feature selection Genetic algorithm Particle swarm optimization Surveillance epidemiology and end result Synthetic minority oversampling technique Unbalance data ABSTRACT Breast cancer is one of the significant deaths causing diseases of women around the globe. Therefore, high accuracy in cancer prediction models is vital to improving patients’ treatment quality and survivability rate. In this work, we presented a new method namely improved balancing particle swarm optimization (IBPSO) algorithm to predict the stage of breast cancer using unbalanced surveillance epidemiology and end result (USEER) data. The work contributes in two directions. First, design and implement an improved particle swarm optimization (IPSO) algorithm to avoid the local minima while reducing USEER data’s dimensionality. The improvement comes primarily through employing the cross-over ability of the genetic algorithm as a fitness function while using the correlation-based function to guide the selection task to a min- imal feature subset of USEER sufficiently to describe the universe. Second, develop an improved synthetic minority over-sampling technique (ISMOTE) that avoid over- fitting problem while efficiently balance USEER. ISMOTE generates the new objects based on the average of the two objects with the smallest and largest distance from the centroid object of the minority class. The experiments and analysis show that the proposed IBPSO is feasible and effective, outperforms other state-of-the-art methods; in minimizing the features with an accuracy of 98.45%. This is an open access article under the CC BY-SA license. Corresponding Author: Amal Elnawasany Department Information Systems, Faculty of Computers and Informatics, Suez Canal University 4.5 km the Ring Road, Ismailia, Egypt Email: aml.elnawasany@ci.suez.edu.eg 1. INTRODUCTION The surveillance epidemiology and end result (SEER) database [1] is an open cancer database that provides different cancers indicators for prognosis prediction. It contains information about the occurrence, frequency, survivability, and mortality of cancer. Cancer is typically labeled in stages from 1 to 4, with 4 being the most serious. The information collected in SEER mostly comes in high dimensionality [2]. Also, it is unbalanced, i.e., the objects in stages 2 and 3 are too larger than those in stages 1 and 4. Therefore, the database is referred to as an unbalance SEER (USEER) database. The two classes with the least number of objects are referred to as minority classes, while the other two are referred to as majority classes. The high dimensionality and unbalanced problems often hamper the breast cancer early prediction task and lead to delayed and inaccurate results, which degrade the patient’s survival chance. Many research papers have been recently directed to address either the high dimensionality problem or the unbalance problem and the motivation behind this work is to propose an approach to address both. Journal homepage: http://ijece.iaescore.com
  • 2. 4952 ❒ ISSN: 2088-8708 Data reduction is a data preprocessing technique that aims at preparing the data for prediction. Instead of overwhelming the classifier with a huge amount of data, potentially causing many prediction errors, the classifier will have an easier job. Although data is shrinking, the fundamental and integrity of the original data should be retained. Data reduction decreases the processing time, storage space and computational complexity. Data reduction techniques include feature selection and instance selection. We will employ both techniques. SEER database contains instances for many types of cancers, while the cancer of interest is breast cancer. In this case, only the instances of breast cancer will be selected. This is called instance selection. Feature selection (FS) tool is an approach that enables prediction algorithms to be applied to high dimensional data with less computations [3]. FS progresses by two steps: feature evaluation and feature set search. Feature evaluation evaluates each feature in the dataset separately in terms of its relevance to the class variable. On the other hand, feature set search tries various combinations of the evaluated features to arrive at a shortlist of features that sufficiently describes the objects [4]. Among the feature evaluation tools is correlation- based feature selection (CFS) [5]. The strength of the CFS tool comes in its ability to find a feature subset with features that are highly correlated with the class, yet uncorrelated with each other. CFS tool measures the goodness f(M ) of set M of features (M ⊂ A ) as (1): f(M ) = |M| ∑ i=1 |M| ∑ j=1 |M |ρai,aj p |M |+|M |(|M |−1)ρai,d , (1) where ρai,aj is the Pearson’s correlation coefficient between features ai and aj and is given by (2): ρai,aj = Cov(ai,aj) σai σaj , (2) where Cov(ai,aj) is the covariance which measures of the strength of the correlation between two features ai and aj and σak is the standard deviation of feature ak. The hurdle is that the size of the search space increases exponentially concerning the number of features, whereas CFS tool needs to assess 2n feature subsets for USEER with n features. Therefore, CFS fails miserably when it confronts the USEER. A gap filled by swarm intelligent (SI) algorithms [6] is a low cost to search for a feature subset. Some examples of these algorithms are particle swarm optimization (PSO) algorithm [7], genetic algorithm (GA) [8], ant colony optimization (ACO) algorithm [9], artificial bee colony optimization (BCO) algorithm [10], bat search algorithm (BSA) [11], cuckoo optimization (CO) algorithm [12] and elephant herding optimization (EHO) algorithm [13]. The first two are the core of the approach proposed in the present article. Its simple operators characterize PSO algorithm and it is computationally inexpensive in terms of both memory and cost. PSO is an algorithm that solves FS problem by iteratively improving each particle position regarding a given measure of quality. The particle position is represented by a pivot vector pointing at a subset of features of the balanced SEER (BSEER). PSO algorithm assumes having a swarm of P ≥ 10 particles moving in the search-space according to simple mathematical formula, known as a velocity function. The minimum number of particles is 10 because most of the swarms in nature have 10 particles on average. In each iteration t ≥ 1, the particle that achieves the highest performance, being closer to the food, is referred to as the commander and the rest are slaves. The commander is chosen afresh in each iteration t ≥ 1. The commander guides other particles to update their position to converge towards the food. Therefore, each particle i = 1,2,...,N in iteration t + 1 updates its position towards a better position according to the commander’s position and the velocity function. At the end of the user defined number of iterations N, this exercise is expected to move the swarm toward their food’s best solution. The good thing about PSO is that it does not make assumptions about the problem under study and can search high dimensional BSEER for minimal feature subset. Initially, we consider that we have P ≥ 10 particles. Each particle i = 1,2,...,P at iteration t ≥ 1 has its own pivot vector Xit = [x1,x2,...,xn], where xj ∈ {0,1}. All the particles start at iteration t = 1 by pivoting randomly on a feature subset from the whole BSEER features. For each pivot vector Xit , we construct its corresponding feature subset A ⊂ A by: A = {aj| xj = 1}, which represents the set of features whose corresponding values in Xit is 1. For example, consider X12 = [1,1,0,1,0] =⇒ A = {a1,a2,a4}. Int J Elec & Comp Eng, Vol. 12, No. 5, Oct 2022: 4951–4959
  • 3. Int J Elec & Comp Eng ISSN: 2088-8708 ❒ 4953 PSO computes the goodness f(A ) of the original set of features A in BSEER by (1). Then, at the end of each iteration t ≥ 1, each particle is assessed through computing the goodness of their corresponding feature subset. The pivot vector with the corresponding highest goodness f(A) is considered the commander and is assigned to Xt. Each slave particle i = 1,2,...,P−1 updates its pivot vector Xit+1 in iteration t +1 with respect to Xt in two steps. First, it computes its velocity Vit+1 by which the particle updates its pivot vector at iteration t +1 and is given by: Vit+1 = Vit +c1 f(A )Xt −c2 f(A)Xit , (3) where c1 and c2 are two positive constants, in which c1 +c2 = 4. All the components of the velocity vector Vit at t = 1 is of value 0. Second, the slave particles i = 1,2,...,P−1 find its updated pivot vector Xit+1 at iteration t +1: Xit+1 = Xt +Vit+1 . (4) However, the PSO algorithm creates an undesirable feature subset A ⊂ A of USEER which is in- sufficient to describe the universe [14]. This is because it employs the k-nearest neighbor (kNN) classifier as a fitness function which is frustrated by the unbalanced nature of USEER. This issue is commonly known as local minima feature subset; given a feature subset A ⊂ A , A is said to be local minima feature subset if f(A) ≤ f(A ) for all values in specific interval but not the whole domain. Additionally, PSO algorithm is considered classifier-dependent algorithm as the resultant feature subset depends heavily on the accuracy of the kNN classifier and this fact, in turn, may result in poor accuracy with other classifiers. This calls for an im- proved PSO algorithm to deal with USEER utilized in the present work. GA is an evolutionary algorithm that mimics the biological behavior of genes. In contrast to the PSO algorithm, GA employs a cross-over technique that can update the feature subset it has been found so far and avoids being trapped in the local minima. Definition 1 (Cross-over) Given two pivot vectors Y = [1,0,0,1,1,1,0,1] and Z = [0,1,1,0,0,1,1,0] where 1 in the ith position means that feature ai is selected and 0 otherwise. The cross-over technique randomly chooses a position and all bits beyond that position is swapped between the two vectors to generate two new vectors. For example, consider that position 4 is chosen then, the two new vectors are Y′ = [1,0,0,1,0,1,1,0] and Z′ = [0,1,1,0,1,1,0,1]. Rostami and Zadeh [15] state that the unbalance format of USEER negatively impacts the early pre- diction task of breast cancer. This is because the prediction algorithms have unpromising results on a minority classes than on majority ones [16]. Attempts to mitigate the unbalance problem are through converting USEER to a balanced one. This involves using object sampling (OS) technique that aims to have normally distributed objects among classes. OS is classified into two groups: under-sampling and over-sampling. The former progress by removing a set of objects from majority classes, while the latter progress by generating a set of objects in the minority classes. Its low cost characterizes Under-sampling on the contrary, over-sampling do not lose information, but it may result in an over-fitting problem, where the prediction algorithms fit to a spec- ified set of objects and result in poor prediction accuracy with un-previously seen objects. Synthetic minority over-sampling technique (SMOTE) [17], an example of over-sampling, has put a great effort into balancing the USEER. It randomly chooses an object from the minority decision class and finds its k neighbor objects. Then it generates a new object by averaging the feature values of the k objects. The process is repeated till we have an equal number of objects in each class. This article remedies the FS and OS tasks’ limitations of USEER. The rest of this article is organized as follows. Section 2 covers the related work. Section 3 describes the proposed approach. In section 4, the experimental work is carried out and discussions are given. Finally, the concluding remarks are presented in section 5. 2. RELATED WORK Zhao et al. [18] introduce a predictive model for USEER using univariate and multivariate linear regression (LR). They aim to predict the patient’s cancer stage using age, race, tumor size, primary site, patho- logical grade, histologic type, and molecular subtype features. However, [19] state that social features are more and more emphasized in breast cancer progression. Therefore, they introduce a predictive model for USEER to assess the impact of marital status on breast cancer. Furthermore, they used a chi-square method in [20] to analyze the associations between marital status and other features and a Kaplan Meier method to estimate sur- vival curves. By and large, the models mentioned above result in low accuracy with the prediction algorithms. This is because they do not consider the unbalance classes, the main characteristic of USEER. OS technique Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)
  • 4. 4954 ❒ ISSN: 2088-8708 has been the topic of much research in recent years to alleviate the unbalance nature of USEER. Bertorello and Koh [21] use a density-based synthetic minority over-sampling (DSO) method to balance USEER. They use different weights for objects in the minority classes. Then they generate new objects regarding objects with the highest weight. On the contrary, Luo et al. [22] state that using the objects with the least weight is better in sampling to avoid misclassification. Tao et al. [23] propose a new over-sampling technique referred to as self-organizing map over-sampling (SOMO) to balance USEER. The SOMO technique generates new objects by producing a 2D representation of the input objects in the minority class, then averaging the closest objects. Wang [24] combine the strengths of PSO algorithm and CFS tool with two synthetic over-sampling methods; borderline-SMOTE and DSO with bayesian network (BN) algorithm and LR. Mirjalili et al. [25] examine 11 over-sampling techniques and 7 under-sampling techniques on 15 types of cancer. According to the study, USEER degrades the performance of classifiers. They state that balancing methods enhance the classification of USEER. Han et al. [26] introduce a distribution-sensitive over-sampling technique for balancing USEER. They divide the objects into noise, unstable, boundary, and stable objects according to their location in the minority class. They use a set of different methods to assess which objects are suitable to generate new objects. They use a set of different methods to assess which objects are suitable to generate new objects. Anupama and Jena [27] introduce increment over sampling for data streams (IOSDS) algorithm which uses a unique over- sampling technique to almost balance USEER. The IOSDS algorithm identifies noisy and mostly misclassified objects from the majority and minority classes by employing k-NN classifier. Then, it generates new objects in the minority classes using artificial, replication and hybrid objects. The trouble with the above-mentioned attempts is that they are sequential in nature, resulting in a delayed prediction. Tarkhaneh and Shen [28] intro- duce a Mantegna Lévy flight PSO and neighborhood search (LPSONS) algorithm to reduce the dimensionality of the USEER. They combine the strength of a velocity function, PSO algorithm with a Mantegna Lévy distri- bution function. This formulation leads to a more diverse feature subset. Additionally, to avoid being trapped in local minima, they combine the strengths of both a neighborhood search algorithm and a Mantegna Lévy distribution function. Pashaei et al. [29] introduced a binary version of PSO (BPSO) algorithm to avoid being trapped in local minima. Then, they combined the strengths of both a BPSO algorithms and a binary black hole optimization (BBHO) algorithm to improve the exploration and exploitation steps of BPSO algorithm. Afterward, they build a predictive model using a k-NN classifier to predict the patient’s cancer stage early. The above attempts have one thing in common they create an undesirable feature subset of USEER because they do not consider the unbalanced nature of USEER, a gap that is filled by the present work. Fern´andez-Delgado et al. [30] evaluate 179 classifiers from 17 different families Bayesian, neural networks, random forests (RF), logistic regression. The RF classifier is at the forefront of the best classifiers. Ganggayah et al. [31] build prediction models using decision tree (DT), neural networks, support vector machine (SVM), RF and logistic regression algorithms to detect the significant indicators of breast cancer. The results detect the cancer stage as one of the most important indicators. The results were close; with the lowest accuracy obtained from DT and the highest obtained from RF. A study of [32] analyzed breast cancer at an early stage by comparing the performance of DT, RF and SVM. The results find that the RF performance is better than the other techniques for predicting cancer at an early stage. This article circumvents these problems by introducing an improved SMOTE to avoid the over-fitting problem and introducing an improved PSO algorithm to avoid get trapped in local minimal while dealing with the unbalance SEER. 3. RESEARCH METHOD As shown in Figure 1, improved balancing particle swarm optimization (IBPSO) in this work conducts the improvement in two main directions: i) feature selection using an improved PSO algorithm (IPSO) and ii) balancing USEER using an improved SMOTE (ISMOTE). The first direction is FS which consists of two main steps: feature evaluation using CFS and feature set search by IPSO. First, CFS evaluates the relevance between each feature in the database and the class variable to find the highest associated features. Second, IPSO attempts different combinations of evaluated features to develop the best shortlist of features that adequately describe the objects. Accordingly, IPSO algorithm is designed as shown in algorithm 1. We try different particles to pick the best number that fits the problem until the optimum result is saturated. IPSO algorithm tries a swarm of 10 ≤ P ≤ 50 particles. IPSO uses the goodness function, given by (1), to assess the goodness of the selected feature subset in each iteration. When t = 1, PSO calculates the fitness value of the given BSEER and call it Int J Elec & Comp Eng, Vol. 12, No. 5, Oct 2022: 4951–4959
  • 5. Int J Elec & Comp Eng ISSN: 2088-8708 ❒ 4955 B goodness; best goodness. To this end, the algorithm aims to search for a minimal feature subset having the same B goodness. A simple loop iterates P times to randomly initialize the P pivot vectors of the P particles, calculate the goodness of each corresponding feature subset A. The pivot vector with the highest fitness value is assigned to Xt. Afterward, IPSO employing the cross-over ability of GA to update the P particles pivot vectors and iterates till a user-defined number of iterations N is reached or a minimal feature subset with B goodness is found. Figure 1. Process flow for the proposed IBPSO algorithm The second direction is balancing data using ISMOTE which starts by finding the centroid for the minority decision class. Then, it computes the distance between the objects in the class and the centroid object using Euclidean distance. Finally, the newly generated object is the average of the two objects having the smallest and the largest distance from the centroid. This task is repeated until we have a BSEER. Algorithm 1 Improved particle swarm optimization (IPSO) algorithm Input: BSEER P, number of particles (10 ≤ P ≤ 50) N, number of iterations (N ≥ 2) Output: A, a minimal BSEER feature subset (A ⊂ A ) t := 1 B goodness := f(A ) as per (1) for i = 1 to P do Construct randomly the pivot vector Xit A := {aj| xj = 1}, set of features whose corresponding values in Xit is 1 Calculate f(A) as per (1) end for Assign the pivot vector with the corresponding highest f(A) value to Xt for k = 2 to N do t := t +1 Cross-over the two slave pivot vectors with the corresponding highest goodness as per Definition 1. for i = 1 to P do Calculate the pivot vector Xit from Xit−1 as per (3), (4) A := {aj| xj = 1} Calculate f(A) as per (1) end for Assign the pivot vector with the corresponding highest f(A) value to Xt . if f(A) = B goodness then break. end if end for 4. RESULT AND DISCUSSION The experiments are conducted on SEER 1973-2016. SEER consists of 10,050,814 observations for all cancer types, only 1,631,572 cases diagnosed with breast cancer. From this population, we exclude 1,383,910 whose cause of death is not breast cancer. We further exclude 93,321 who have an unknown stage. Due to the impact of hurricane Katrina, 216 Louisiana cases diagnosed for those six-month period are excluded Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)
  • 6. 4956 ❒ ISSN: 2088-8708 from the research database. We excluded 280 cases that are not active follow-up, i.e., not keeping in touch with the patient for vital status, and exclude 2,770 cases that were not malignant cancers. The final cohort in our study on 151,075 with 160 variables. Table 1 shows the number of instances in different stages in BSEER before and after applying ISMOTE. The total number of balancing instances generated by ISMOTE is 177173. The final number of features selected by IPSO is 36 features. The selected features are survival months, first malignant primary indicator, total number of in situ/malignant tumors for a patient, radiation recode, chemotherapy recode, radiation sequence with surgery, laterality, histology, regional nodes positive, breast subtype, SEER cause-specific death classification, primary site, grade, tumors of adolescents and young adults site recode, breast-adjusted N (refers to the number of nearby lymph nodes that have cancer), breast- adjusted T (refers to the size and extent of the main tumor), scope of regional lymph node surgery (describes the performed procedure of removal, biopsy, or aspiration of regional lymph nodes), surgery of primary site (describes a surgical performed procedure that removes and/or destroys the tissue of the primary site), Ap- palachia, CS schema-AJCC 6th edition, Indian health service files to identify native Americans, Louisiana, month of diagnosis recode, hispanic identification algorithm (uses to classify cases as hispanic or not), record number (unique sequential number for each patient identifies the number of records submitted to SEER for that particular patient), SEER registry (used in conjunction with Patient ID to uniquely identify a patient), Site -mal+ins (mid detail) (which is should be used in conjunction with and only with the variables site specific (SS) sequence mal+ins (mid detail), SS sequence 1975+ mal+ins (mid detail), or SS sequence 1992+ mal+ins (mid detail) and they are already selected with our algorithm), SS sequence 1975+ -mal (most detail), SS se- quence 1992+ mal (most detail), SS sequence 1992+ mal+ins (most detail), and Year of birth. Table 2 shows the performance measures of the IBPSO, the results without ISMOTE and the results without IPSO. Table 1. Description of BSEER used in the experiments Class before ISMOTE (Percentage) After ISMOTE (Percentage) stage 1 9973 (6.60%) 19975( 11.3%) stage 2 1423 (34.04%) 51423 (29.0%) stage 3 83581 (55.32%) 83581 (47.2%) stage 4 6098 (4.04%) 22194 (12.5%) The best number of particles that fit our problem was 20 particles. To validate the feature subset se- lected by IBPSO, we compare the results of IBPSO with five related SI algorithms namely, ACO, BCO, CO, BSA and EHO, using 10-fold cross-validation as shown in Table 2 and Table 3. We can see that the perfor- mance of the IBPSO is superior in selecting a smaller number of features while keeping its good classification performance. Table 2. Performance measures for the IBPSO Evaluation measure IBPSO Without ISMOTE without IPSO Accuracy 98.45% 64.79% 70.8% Recall 0.985 0.648 0.708 Precision 0.985 0.652 0.714 F-Measure 0.984 0.621 0.694 MCC 0.974 0.343 0.489 ROC area 0.987 0.774 0.812 PRC area 0.986 0.706 0.724 MAE 0.0934 0.2255 0.2212 RMSE 0.1579 0.3351 0.325 To stress on the stability of the IPSO algorithm, Figure 2 shows the receiver operating characteristic (ROC) curve for the four cancer stages. ROC curve measures the classification algorithm’s performance, the relation between classifier specificity and sensitivity at different thresholds. Classifier sensitivity represents the true positive rate, while specificity represents the truly negative rate. The farther the curve is from the diagonal line, the higher the overall accuracy of the model. There are many problems with the SEER database: − There are many blank(s) fields or unknown data. Unfortunately, excluding all blank(s) and unknown data leads to an empty matrix. This makes it impossible to remove all of them. So, we remove only blank and unknown fields from target features. Int J Elec & Comp Eng, Vol. 12, No. 5, Oct 2022: 4951–4959
  • 7. Int J Elec & Comp Eng ISSN: 2088-8708 ❒ 4957 − Many features are gathered in only a specific period, which leads to inconsistency in the data. All these features are eliminated from our study. We select only data collected after 2010. There were some degrees of missing in our data, but SEER encode the missing data; therefore, algo- rithms may be puzzled and deal with it as complete data. So, our further work would include other preprocess- ing techniques for missing data rather than deletion. Also, approach for hyperparameter optimization for the model parameter. Table 3. Comparative experiments result of different SI algorithms Evaluation measure BSA CO ACO BCO EHO # selected features 33 30 43 27 37 Accuracy 69.03% 70.74% 94.05% 64.36% 64.83% Recall 0.69 0.707 0.941 0.644 0.648 Precision 0.694 0.713 0.941 0.663 0.654 F-Measure 0.672 0.694 0.94 0.604 0.625 MCC 0.455 0.488 0.899 0.362 0.371 ROC Area 0.775 0.812 0.991 0.775 0.765 PRC Area 0.669 0.728 0.986 0.689 0.684 MAE 0.2383 0.2208 0.0965 0.2454 0.228 RMSE 0.3364 0.3248 0.1797 0.3417 0.3376 Figure 2. ROC curve for the four cancer stages 5. CONCLUSION The proposed approach, IBPSO, is designed principally to process USEER data and predict the stage. IBPSO conducts the improvement in two directions. First, design and implement an IPSO algorithm to avoid being trapped in local minima while reducing USEER data’s dimensionality. The improvement comes primarily through employing the cross-over ability of the genetic algorithm (GA) as a fitness function while using the correlation-based function to guide the selection task in IPSO algorithm. This idea leads to a minimal feature subset of USEER sufficiently to describe the universe. Second, develop an ISMOTE that avoid over-fitting problem while efficiently balance USEER. ISMOTE generates the new objects based on the average of the two objects with the smallest and largest distance from the centroid object of the minority class. The results show that IBPSO outperforms the related algorithms to find out a minimal feature subset with an accuracy of 98.45%. The classification accuracy of IBPSO is promising and superior to those achieved with different methods. REFERENCES [1] SEER, “SEER*stat software.” National Cancer Institute. https://seer.cancer.gov/seerstat/ (accessed Jan. 2, 2020). [2] B. Ghaddar and J. Naoum-Sawaya, “High dimensional data classification and feature selection using sup- port vector machines,” European Journal of Operational Research, vol. 265, no. 3, pp. 993–1004, 2018, doi: 10.1016/j.ejor.2017.08.040. [3] V. Bolón-Canedo and A. Alonso-Betanzos, “Ensembles for feature selection: a review and future trends,” Information Fusion, vol. 52, pp. 1–12, Dec. 2019, doi: 10.1016/j.inffus.2018.11.008. Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)
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  • 9. Int J Elec & Comp Eng ISSN: 2088-8708 ❒ 4959 10.1016/j.heliyon.2019.e01275. [29] E. Pashaei, E. Pashaei, and N. Aydin, “Gene selection using hybrid binary black hole algorithm and modified binary particle swarm optimization,” Genomics, vol. 111, no. 4, pp. 669–686, Jul. 2019, doi: 10.1016/j.ygeno.2018.04.004. [30] M. Fernández-Delgado, E. Cernadas, S. Barro, and D. Amorim, “Do we need hundreds of classifiers to solve real world classification problems?,” Journal of Machine Learning Research, vol. 15, pp. 3133–3181, 2014 [31] M. D. Ganggayah, N. A. Taib, Y. C. Har, P. Lio, and S. K. Dhillon, “Predicting factors for survival of breast cancer patients using machine learning techniques,” BMC Medical Informatics and Decision Making, vol. 19, no. 1, Dec. 2019, doi: 10.1186/s12911-019-0801-4. [32] N. A. Farooqui, “A study on early prevention and detection of breast cancer using three-machine learning techniques,” International Journal of Advanced Research in Computer Science, vol. 9, no. 2, pp. 37–42, 2017. BIOGRAPHIES OF AUTHORS Amal Elnawasany is a teaching assistant at the Faculty of Computers and Informatics. She obtained bachelor’s degree in Information Systems from Suez Canal University in 2007. She obtained master’s degree of information systems from the Suez Canal University (Egypt) in 2015. She can be contacted at email: aml.elnawasany@ci.suez.edu.eg. Mohamed Abd Allah Makhlouf is currently an associate professor in Faculty of Com- puter Science and informatics Suez Canal University. He received his first degree in Computer Sci- ence and Operation Research, Faculty of Science, Master’s degree in Expert Systems, Faculty of Science Cairo University. He received his Ph.D. degree in computer science, Faculty of Science, Zagazig University. He got the Post-Doctoral studies in Computer Science from Granada Univer- sity, Spain in 2016. His research interests: machine learning, data mining, intelligent bioinformatics, metaheuristic optimization, decision support systems and predictive models. He can be contacted at email: m.abdallah@ci.suez.edu.eg. BenBella Tawfik born in September 1964, Cairo, Egypt, Graduated from Military Tech- nical College in 1986. He got my master’s in computer engineering in 1991 from the same school of graduation. He got his Ph.D. from Colorado State University, USA in 1998. In 2006, He vis- ited USA-Colorado State University and earned Post Doctor Certificate in Computer Engineering. Besides his research work, he worked as a part time professor in many schools of Computer Engi- neering/Computers and Informatics in Egypt since 1998. He is working as an assistance professor in Information System Department in Faculty of Computer and Informatics – Suez Canal University - since October 2012. Three years ago, he is an associate professor working as a dean of the mentioned department. He can be contacted at email: benbellat@gmail.com. Hamed Nassar received the B.Sc. degree in electrical engineering from Ain Shams University, Egypt, in May 1979 and the M.Sc. degree in electrical engineering and the Ph.D. degree in computer engineering from the New Jersey Institute of Technology, USA, in May 1985 and May 1989, respectively. He was an Assistant Professor of computer engineering, in November 1989, an Associate Professor of computer science, in May 1998, Professor of computer science, in March 2004 and a Professor with the Department of Computers and Informatics, Faculty of Engineering, Beirut Arab University. Dr. Nassar is currently with the Department of Computer Science, Suez Canal University. His most recent publication is on a functional equation arising from a network model. His research interests include computing in mathematics, natural science, engineering and medicine, computer graphics and computer communications (networks). He can be contacted at email: nassar@ci.suez.edu.eg. Feature selection of unbalanced breast cancer data using particle swarm optimization (Amal Elnawasany)