# Feature Importance Score-Based Functional Link Artificial Neural Networks for Breast Cancer Classification

Authors: Shatakshi Singh; Sunil Kumar Jangir; Manish Kumar; Madhushi Verma; Sunil Kumar; Tarandeep Singh Walia; S. M. Mostafa Kamal
Journal: BioMed Research International
 (2022)

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## Abstract

Growth of malignant tumors in the breast results in breast cancer. It is a cause of death of many women across the world. As a part of treatment, a woman might have to go through painful surgery and chemotherapy that may further lead to severe side effects. However, it is possible to cure it if it is diagnosed in the initial stage. Recently, many researchers have leveraged machine learning (ML) techniques to classify breast cancer. However, these methods are computationally expensive and prone to the overfitting problem. A simple single-layer neural network, i.e., functional link artificial neural network (FLANN), is proposed to overcome this problem. Further, the F-score is used to reduce the issue of overfitting by selecting features having a higher significance level. In this paper, FLANN is proposed to classify breast cancer using Wisconsin Breast Cancer Dataset (WBCD) (with 699 samples) and Wisconsin Diagnostic Breast Cancer (WDBC) (with 569 samples) datasets. Experimental results reveal that the proposed models can diagnose breast cancer with higher performance. The proposed model can be used in the early breast cancer diagnosis with 99.41% accuracy.


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## Body

## 1. Introduction

Cancer can spread in the whole body and accounts for the estimation of 9.6 million deaths worldwide, out of which 2.06 million deaths were caused due to breast cancer [1]. Similarly, breast cancer is caused by the growth of malignant tumors in the breast. It can be cured if it is diagnosed at an early stage. The World Health Organization (WHO) says that the survivability rate decreases from developed to developing countries due to inadequate diagnosis facilities [2].In recent years, ML has majorly been applied in health informatics to predict various diseases as they can decrease the diagnosis time and find hidden relationships between complex datasets, which is indeed a tedious task for humans [3]. Various classification techniques such as SVM, KNN, logistic regression (LR), and NB have been used along with various supportive techniques like feature selection and feature extraction to reduce the error rate and overfitting [4]. However, if one algorithm is not efficient enough, then ensemble techniques are used to improve the accuracy and make the algorithm more effective [5].Chen et al. applied the rough set-support vector machine (RS-SVM) and divided datasets in 70%-30% and 50%-50% using a 5-fold cross-validation technique during experimentation [6]. Osman, A.H., has used a two-step SVM technique in which the first step is the clustering technique which is used to find the hidden pattern and SVM is used for classification [7]. As the application of AI and ML rise for the diagnosis of diseases, it can improve the efficiency and accuracy of the breast cancer diagnosis. Such an AI powered system could help to save lives by diagnosing cancer at an early stage and prevent the deaths in women due to breast cancer [8]. AI will not only help to make the process more accurate but also help the clinicians to speed up the diagnosis with the prescreening test [9]. This paper evaluates various researchers who have worked on WBCD and WDBC datasets to classify breast cancer and compare the accuracy, precision, recall, and specificity of classification techniques applied on these datasets to classify breast-cancer.Following are the significant contributions of this research article:(1)
A novel functional link artificial neural network (FLANN)–based classifier is proposed to classify breast cancer with selected features. As per the authors’ knowledge, functional link artificial neural network for the classification of breast cancer is first introduced and applied on two datasets with different features(2)
Significant features have been selected based on the F-score for the classifier’s training to reduce the complexity(3)
The accuracy of the classifier is also examined based on selected breast cancer attributes(4)
Different algorithms, including SVM, KNN, RF, NB, and MLP, have been implemented on WBCD and WDBC datasets, and their performance is compared with the proposed FLANNThe rest of the paper is arranged as follows: Related work is discussed in Section2, highlighting some of the existing works of other researchers. In Section 3, various classification techniques implemented in this work and performance measurement techniques are discussed followed by the Results and Discussion presented in Section 4. Finally, the conclusion of this research paper is given.


## 2. Related Work

Abonyi and Szeifert have examined supervised fuzzy clustering using 5 to 6 features and a 10-fold cross-validation technique and got the classification accuracy of 95.06% [8]. Othman and Yau have compared the performance of different algorithms including Bayes network, pruned tree, single conjunctive rule learner, radial basis function, and nearest neighbors algorithm using the WEKA data mining tool and achieved the highest accuracy of 89.71% from Bayes network [9]. Rong and Yuan have developed the SVM-KNN technique in which they applied KNN near hyperplane and SVM when the point is farther, achieving 98.06% accuracy [10]. Aruna and Nandakishore had compared NB, SVM, and decision tree using WEKA Tool and found SVM as the best with an accuracy of 96.99% [11]. Salama et al. presented a comparison of multilayer perceptron (MLP), Naive Bayes (NB), sequential minimal optimization (SMO), and KNN and used principal component analysis (PCA) for feature reduction, and then they obtained an accuracy of 97.1388% [12].Gayathri and Sumanthi have presented the concept of relevance vector machine (RVM) and used the linear discriminant algorithm (LDA) [13] to reduce features to 4 and get the accuracy of 96% [14]. Shahnaz et al. compared NB, SVM, MLP, CNN, logistic regression, and KNN [15]. Li and Chen compared decision tree, SVM, random forest, LR, and NN models by dividing train and test set in 70%-30% and found that random forest is most suitable as it gave the highest accuracy 96.1%, highest area under the curve (AUC), and highest F-measure metric [16]. Adel S. Assiri et al. used a voting-based ensemble algorithm with the three best classifiers which are chosen based on their F3 score of 99.42% on the WBCD dataset [17]. T. Admassu optimized the KNN technique to optimize the Wisconsin Breast Cancer Dataset [18]. M. Zohaib et al. demonstrated that with feature selection based on chi-square, the optimal value for KNN for WBC and WBCD datasets is in the range 1-9 with the Manhattan or Canberra distance functions to measure the distance between points [19].Md. Milo Islam et al. proposed a system utilizing SVM and KNN with a K-fold cross-validation method and suggested that SVM performs better on the WBCD dataset than the KNN algorithm with an accuracy of 98.57% and specificity of 95.5% [20]. Chaurasia V. et al. applied six different ML algorithms on WDBC with all the features and then reduced the features using statistical measures before applying the stacked classifiers to minimize the probability of misclassification in results [21]. In addition, various researchers have worked on different ML techniques to classify breast cancer types. It is found that the existing models suffer from the gradient vanishing [22–24], overfitting [25, 26], and data leakage [27, 28] kind of problems. Even development of generalized model [34,35] is still defined as an ill-posed problem.Table1 presents the work of the various researchers who contributed to the same domain.Table 1
Research work available in literature for the classification of breast cancer using artificial intelligence (AI).
StudyYearAlgorithmAccuracyPene-Rayes and Sipper [1]1999Fuzzy-GA97.36%Abbass [2]2002MPANN98.1%Guo and Nandi [10]2006MLP97.89%Übeyli, E.D. [11]2007PNN (probabilistic neural network)98.15%Subashini et al. [12]2009RBFNN96.57%Fatima and Amine [6]2012Hybrid neuro-fuzzy98.25%Manning and Walsh [7]2013CGPANN96%Zeng et al. [13]2014SVM-KNN97.38%Banerjee et al. [14]2017Ensemble95.6%Amrane et al. [15]2018KNN97.51%Alwidian et al. [16]2018WCBA97.74%Bayrak et al. [17]2019ANN95.42%


## 3. Methodology

Neural networks are often preferred for solving nonlinear problems [18]. FLANN is a high-order functional link–based single layer artificial neural network. There are no hidden layers in its architecture; therefore, it provides high convergence speed compared to other networks [19]. The structure of FLANN is given in Figure 1, where input features are expanded using nonlinear mathematical functions such as exponential, trigonometric, logarithmic, power, and Chebyshev functions. In the proposed methodology, features in the breast cancer dataset are expanded using trigonometric functions, depicted in Equation (2).Figure 1
Architecture of functional link artificial neural network.The breast cancer feature input is stored in a vector containingn different features which is given as
(1)X=x1x2⋯xnT,where X can be further expanded using trigonometric functions as
(2)X=x1cosπx1sinπx1⋯cos2πx1⋯x2cosπx2sinπx2⋯cos2πx2sin2πx2⋯x1x2T.After expansion of the input feature, weights will be initialized randomly, and it is given as(3)W=w0w1w2⋯wn−1T.The weighted sum of input and bias will provide outputYj.
(4)Yj=∑k=0n−1xkjWk.Yj is then passed through a nonlinear hyperbolic logarithmic activation function as
(5)yj=12loge1+Yj1−Yj.Network error of FLANN can be computed by(6)εjn=dj−yj.The weights of the FLANN network is updated by applying the backpropagation algorithm, given as(7)wijln+1=wijln+α∆ijn,wherewijln+1 is an updated weight, similarly, wijln is the old weight, and α denotes the learning rate.∆ijn=δil+1xjl, l=L−1,L−2,⋯,0, where L denotes current layer.δip=εjng′Sip, for the output layer.=∑k=1Np+1δkp+1wkipng′Sip, for the other layers.Table2 shows the properties of SVM, MLP, DT, KNN, and NB, and these properties can be used to get better accuracy and will help in selecting an algorithm according to the need. Apart from accuracy, researchers have worked on various other metrics to evaluate the performance of the different ML algorithms. Various quality metrics such as confusion matrix, precision, specificity, accuracy, and recall are used to measure implemented ML algorithms’ performance [31]. The confusion matrix represents the data graphically, and values in the matrix are represented using colors. They include the information about the actual and classified output of the input data points. The abovementioned metrics can be mathematically represented as
(8)Accuracy=TP+TNN,Precision=TPTP+FP,Recall=TPTP+FN,Specificity=TNTN+FP,Table 2
Advantages and disadvantages of various ML algorithms [20–37].
TechniqueAdvantageDisadvantageSVMIt allows the generation of nonlinear boundariesChoice of kernelMLPAbility to learn on its ownComplexity is highDTIndependence of variables is not required. Easy to understandHigh probability of overfittingKNNTraining time is negligibleDoes not work well with large datasetNBTraining time remains constant irrespective of sizeFeatures should be independent of each otherwhere TP represents true positive results, FP is the false positives, TN is the number of true negative results, and FN denotes the false negatives in the output. Equations (8) presents the mathematical form of performance measurement criteria, and Table 3 shows the confusion matrix components which can be used to evaluate any algorithm.Table 3
Confusion matrix.
Predicted yesPredicted noActual yesTPFNActual noFPTN


## 4. Results and Discussion

The simulation work was done in the Google Colaboratory (Google Colab). It is a cloud-based Jupyter Notebook that uses Python version 3.6 platform. It provides decent computation power, 12.72 GB Random Access Memory (RAM) and 68 GB disk storage. In this study, various machine learning-based classification algorithms have been used to train the models using two different breast cancer datasets: Wisconsin Breast Cancer Dataset (WBCD) [32] and Wisconsin Diagnostic Breast Cancer Dataset (WDBC) [33]. Their performance has been compared with FLANN considering the different number of features.WBCD contains 11 columns, out of which the first column is “sample id,” which is not relevant, and the last column of the dataset contains the output, which exhibits whether the tumor is benign or malignant. In this dataset, there are 699 samples, out of which 458 (65.5%) are benign and 341 (35.5%) are malignant. In WBCD (original), 16 values are missing, which have been replaced with the mean value.The F-score of each feature is shown in Figure2 to determine the significance level of each feature, using which we found that feature numbers f5, f0, f7, and f3 play a significant role in classifying breast cancer. F-score can be computed with the help of confusion matrix for every feature. The feature importance is calculated for every decision tree by the amount that each attribute split point improves the performance measure, weighted by the number of observations the node is responsible for.Figure 2
Feature importance score of all the features in dataset.The FLANN is compared with other classification techniques such as NB, SVM, RF, KNN, and MLP. The comparison study is depicted in Table4. This table also gives the accuracy level on various features level and is selected by applying the F-score method.Table 4
Accuracy of classifiers on WBCD.
FeaturesAccuracy532TechniquesSVM97.14%97.8%95.7%Naïve Bayes96.42%97.14%97.14%Random Forest97.14%97.14%93.57%KNN95.71%95.71%97.8%MLP95.28%,96.85%94.28%.FLANN97.14%96.88%96.76%The experimental results of Table4 reveal that all the algorithms perform well, particularly with three features, i.e., Bare Nuclei, Clump Thickness and Normal Nucleoli. SVM outperformed the other ML techniques, and accuracy reached 97.8%, whereas 97.14% accuracy was obtained using FLANN. The above result demonstrates that the result mainly relies upon the significant features only, thereby eliminating redundant attributes for the training of the ML models. Furthermore, it will not only help to reduce computational complexity but also in expediting the learning process of ML techniques. Finally, the confusion matrix of classification using SVM with three features is presented in Figure 3.Figure 3
Confusion Matrix of SVM with three features.This confusion matrix provides different quality metric data such as precision (0.976), recall (0.9888) and specificity (0.964). Likewise, MLP consists of multiple perceptron in each layer and is applied to the WBCD dataset. The batch size is taken as 16, and categorical cross-entropy is used to calculate the loss. Also, Adam’s optimizer is a learning algorithm. The accuracy obtained by the MLP on only two features is 94.28%, with three features is 96.85% and with five features is 95.28%. The loss and accuracy after each epoch can be depicted using the graphs Figures4 and 5.Figure 4
Model Accuracy of MLP.Figure 5
Model-Loss after each epoch.The above graphs demonstrate the accuracy of the training and a testing dataset. Initially, the graph increases exponentially and then increases, and after a few epochs, the accuracy becomes saturated. The model’s accuracy may change with the learning rate and other ML network parameters. Similarly, the model loss is inversely proportional to the accuracy. Hence the graph decreases exponentially and is then saturated with the epoch. Since WBCD (Original) has only ten features and only one value ranging from 1-10 is considered, another dataset, i.e., WDBC having more features, was considered for the experiments.Similarly, in WDBC, there are ten features followed by the mean of values, standard error and the maximum value of the mean of the largest three values of features for each property, making it a total of 30 features. The input values of the selected features are obtained using the digitized image of the fine needle aspirant technique, and all feature values are recoded with up to four significant digits. There are no missing values in the dataset. This dataset contains 569 samples, of which 357(62.74%) are benign and 212(37.25%) malignant. This F-score of each feature is shown in Figure6.Figure 6
F-Score of all the features.Using Figure6 it is found that f21, f23, f13, f27, f1, f26, f7, f24, f4 and f15 play a major role in classifying breast cancer. Table. 5 shows the result of the experiment of different algorithms with various numbers of features.Table 5
Results of Machine Learning Techniques on WDBC.
TechniqueAccuracy when the number of features are61130SVM98.24%97.36%98.24%KNN95.61%96.49%96.49%Random forest96.49%92.98%97.14%Naive Bayes97.36%96.49%96.49%MLP96.49%96.49%97.28%FLANN95.57%97.45%99.41%SVM and Naive Bayes work better with six major features, FLANN with 11 features, and random forest with all the features.From Figure7, we can calculate the precision (97.2%), recall (100%), and specificity (95.34%). Apart from these machine learning techniques, MLP also performs well in classifying the tumor, and data are trained in the batch size of 16. The categorical cross-entropy and Adam’s optimizer were calculated to improve the accuracy level. After each forward propagation loss is calculated, the weight parameters are changed to reduce the loss and increase accuracy. The accuracy obtained when using six features is 96.49%, with 11 features 96.49%, and the highest accuracy of 97.28% was obtained when all the features were considered. Figures 8 and 9 show the accuracy and loss after each epoch when all the features are used.Figure 7
Confusion matrix of SVM with six features.Figure 8
Accuracy of a model after each epoch.Figure 9
Loss of model after each epoch.From both the above graphs, it can be concluded that loss and accuracy have an inverse relation. In the initial epochs, accuracy increases rapidly, and loss decreases, and after that rate of change of both accuracy and loss decreases, and after a few epochs, they change negligibly. Hence, the training is stopped without further delay. From Table4 and Table 5, it can be concluded that for most machine learning techniques, better results are obtained for WDBC using the same classification algorithm, but WBCD did better when FLANN was used and achieved accuracy 99.41%, which is the best among all.It can be observed that ML algorithms like NB, KNN, and SVM were able to achieve the accuracy obtained by FLANN. These algorithms have certain demerits which make it infeasible to use them for diagnosis. Naive Bayes has a strong assumption that is unrealistic for real-world data that all the input features are independent. KNN, despite of being a machine learning algorithm, cannot be used to train a model. There is no training involved when we use KNN. At the time of query, thek data points close to the query point are considered, and final output is decided. Hence, all the data need to be stored in the system and has to be accessed for each single query. SVM aso required the training data to be loaded in memory at once. This makes the algorithm computationally very expensive and unrealistic for the real-time implementation.


## 5. Conclusions

This paper presents the study based on machine learning algorithms to diagnose breast cancer using physiological measures. WBCD and WDBC datasets are used for the study. The feature selection techniques are applied to select the most significant features in the dataset. Further, the accuracy is compared based on feature selection. To avoid the overfitting issue, this paper presents a FLANN algorithm for classification on two datasets WBCD and WDBC. This algorithm is computationally effective, more accurate, and converges faster than other algorithms because it has no hidden layer. The experimental studies conclude that an accuracy of 99.41% is achieved using the proposed FLANN with all features on the WDBC dataset. WDBC dataset is better as it considers dispersion factors like the standard deviation of the features that are important in breast cancer classification. In the future, X-ray images can be used to classify cancers using deep learning. However, X-ray is more feasible than the fine needle aspirant technique and uses the regional dataset to address a specific cancer problem.



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