Effective hybrid feature selection using different bootstrap enhances cancers classification performance
BioData Mining volume 15, Article number: 24 (2022)
Machine learning can be used to predict the different onset of human cancers. Highly dimensional data have enormous, complicated problems. One of these is an excessive number of genes plus over-fitting, fitting time, and classification accuracy. Recursive Feature Elimination (RFE) is a wrapper method for selecting the best subset of features that cause the best accuracy. Despite the high performance of RFE, time computation and over-fitting are two disadvantages of this algorithm. Random forest for selection (RFS) proves its effectiveness in selecting the effective features and improving the over-fitting problem.
This paper proposed a method, namely, positions first bootstrap step (PFBS) random forest selection recursive feature elimination (RFS-RFE) and its abbreviation is PFBS- RFS-RFE to enhance cancer classification performance. It used a bootstrap with many positions included in the outer first bootstrap step (OFBS), inner first bootstrap step (IFBS), and outer/ inner first bootstrap step (O/IFBS). In the first position, OFBS is applied as a resampling method (bootstrap) with replacement before selection step. The RFS is applied with bootstrap = false i.e., the whole datasets are used to build each tree. The importance features are hybrid with RFE to select the most relevant subset of features. In the second position, IFBS is applied as a resampling method (bootstrap) with replacement during applied RFS. The importance features are hybrid with RFE. In the third position, O/IFBS is applied as a hybrid of first and second positions. RFE used logistic regression (LR) as an estimator. The proposed methods are incorporated with four classifiers to solve the feature selection problems and modify the performance of RFE, in which five datasets with different size are used to assess the performance of the PFBS-RFS-RFE.
The results showed that the O/IFBS-RFS-RFE achieved the best performance compared with previous work and enhanced the accuracy, variance and ROC area for RNA gene and dermatology erythemato-squamous diseases datasets to become 99.994%, 0.0000004, 1.000 and 100.000%, 0.0 and 1.000, respectively.
High dimensional datasets and RFE algorithm face many troubles in cancers classification performance. PFBS-RFS-RFE is proposed to fix these troubles with different positions. The importance features which extracted from RFS are used with RFE to obtain the effective features.
Artificial intelligence (AI) is a science that plays an important role in all fields, especially in the biomedical field, and it aims to simulate reality [1, 2]. Different AI applications have been applied in this field for 20 years due to many factors, including the availability of different datasets in this field, computer devices with high capabilities and arithmetic algorithms . AI has great importance, as a survey has proven that it has great effectiveness in health, and it will outperform the performance of specialists in this field. In addition, it has proven effective in cancer research . Furthermore, AI has become providing human specialists with many information and accordingly, the decision is taken, as it has become one of the most important elements in the medical team . It also works to improve accuracy, speed up diagnosis and discover features or genes affecting cancer as recommendations for human specialists to take into consideration . AI is considered a second decision that helps the specialist make their decision . AI differs from the manual method because it provides human specialists with more information and details. Its diagnosis is more accurate and efficient and does not require more labor.
The manual method may be stressful for the patient, as it puts him under great pressure and takes more time to know the results of the sample, which makes him tense . Cancer has become very widespread in recent times, as it has become a major cause of disease and death . It can be defined as a group of more than one disease due to abnormal cell growth or changes in genes, and it can occur anywhere in the body . Many factors cause cancer including : - (1) tobacco consumption, (2) poor diet, (3) lack of physical activity, (4) alcohol, (5) radiation, (6) infection, (7) genetic factors, (8) smoking and (9) age . There are many different types of human cancer, but in this paper, we used some types that included Breast Invasive Carcinoma (BR), Bladder urothelial carcinoma (BL), Colon and rectum (CO), Glioblastoma multiform (GB), Head and neck squamous cell (HN), Kidney renal clear-cell (KI), Parkinson’s disease (PD), Prostate adenocarcinoma (PRAD) and Lung adenocarcinoma (LUAD).
There are enormous problems in big datasets involved in the features numbers, fitting time, classification accuracy, and model performance. Feature selection is a process for selecting the most relevant features and discarding insignificant ones. Feature selection plays a vital role in many directions to enhance the model performance [7,8,9]. This process aims to select the most relevant subset r features from the original R features set (r < R) in given datasets . R includes all features in a dataset. It suffers from many problems included in high dimension, noisy, repetitive and over-fitting. The ineffective features are deleted. These features diminish the classification accuracy and waste time. By deleting irrelevant features, all previous problems are solved and improved. Feature selection procedures have three major types: filter, wrapper [9, 10], and embedded . Filter procedure selects the features by evaluating their relevance of features. These features are ranked in decreased order, and low-ranking features are omitted to obtain the most relevant features . The filter approach can use many measures included in gain ratio, mutual information based feature selection (MIFS), information gain based feature selection (IGF), relaxed functional dependencies , and chi-square . This procedure does not depend on any machine learning and is faster than the wrapper procedure. Despite its simplicity, it suffers from an over-fitting problem. The best subset of features is selected depending on machine learning to estimate this subset [9, 10]. This procedure suffers from expensive computationally when applied on high dimensions. On the other hand, it guarantees to select the most relevant and effective subset of features. Feature selection is an integral part of the classification model in the embedded procedure. It is embedded in the phase of learning . This procedure has many advantages, including being less computationally expensive, reducing over-fitting problems, and selecting the most accurate features. In this direction, we adopted the integration of wrapper procedure with embedded one to select the relevant features using proposed methods to minimize the previous drawbacks and maximize the classification accuracy.
Selecting influencing features is an effective step in the classification process to obtain accurate results. Many datasets always suffer from high dimensions problems, which negatively affect the model performance’s accuracy. The feature selection step is considered one of the processes that positively impact solving many problems facing different datasets. In this direction, many authors applied different feature selection algorithms to minimize processing time, over-fitting, maximize classification accuracy and find the most relevant features, which still need more researches to improve. Therefore, there are numerous different methods for feature selection to fix the previous drawbacks included in the filter, wrapper, and embedded methods. The filter method is simple, and it selects the features based on their ranking according to a class. Still, it suffers from over-fitting problems in high dimensions datasets and disregards feature dependencies. Elsadek et al.  proposed a method using IGF to classify six human cancer types based on DNA copy number variation (CNV) dataset. The proposed method selected 16,381 features as the most relevant features. More than one learning algorithm is applied, such as logistic regression (LR), support vector machine (SVM), random forest (RF), J48, neural network, bagging and dagging. LR learning algorithm achieved the best classification accuracy of about 85% and ROC area 0.965. Rajit et al.  proposed selecting best and select percentile filter methods. The proposed method used a breast cancer dataset. There are more than one learning algorithms are used. LR classifier achieved a better result. Furthermore, many filter methods are proposed by Pinar Yildirim . Different filter methods are applied in Cfs Subset eval, principal component analysis (PCA), consistency subset eval, IGF, One-R attribute eval, and relief attribute eval. The proposed method used the Hepatitis datasets and proved that the Consistency Subset, IGF, One-R Attribute Eval, and Relief Attribute Eval filter methods achieved better results. In addition, Alirezanejad et al.  proposed a filter method for gene selection using two heuristic methods. These methods, namely, Xvariance and mutual congestion. The Xvariance gave the best results with the standard datasets, while mutual congestion enhanced the accuracy of high-dimensional datasets. Kuswanto et al.  proposed a comparison method for feature selection using different filtering methods. Three filtering methods included in MIFS, correlation based feature selection (CFS) and fast correlation based feature selection (FCBF) are applied. The results of these methods are forwarded to K-nearest neighbors (KNN) classifer. The results showed that the FCBF selected a small number of features, while other methods performed well. Furthermore, Ghasemi et al.  proposed a method using IGF and gini index to select important features. These features are used to early predict of heart disease. This proposed method aimed to minimize the dimension and maximize the performance of the diagnosis of heart disease with less medical experiments. Mahmood  proposed a method to minimize a dimension for facial expression recognition dataset. Two feature selection methods are applied to obtain minimum number of features included in Chi-Square and Relief-F. These methods selected the first highest six features. Four different classifiers are applied to evaluate the performance. In addition, Spencer et al.  proposed a method to predict heart disease dataset. Four proposed methods are used for feature selection included in ReliefF, Chi-squared, symmetrical uncertainty and PCA. Different machine learning classifiers are applied to create models for comparison. The best prediction with less subset of features is selected using Chi-Square. Mohamed et al.  proposed a method to obtain the most important subset of feature rather than the whole dataset. Chi-square, IG and Bat algorithm are applied for feature selection. Many varieties of classifiers are used to evaluate the model performance. Vikas et al.  proposed a method to minimize processing time and maximize classification accuracy using lung cancer detection. To select the most relevant features, Chi-square algorithm is applied. Two different classifiers are used to evaluate the performance included in SVM and RF.
Many authors applied wrapper methods to solve the optimization problems and to get the most important subset features using different datasets. AH et al.  proposed an algorithm using the wrapper approach. The proposed algorithm enhanced the basic salp swarm algorithm (SSA) to improve reliability, convergence speed, and classification accuracy. The algorithm was enhanced by adding inertia weight to achieve better results. Hegazy et al.  used the hybrid wrapper method by applying chaotic maps to improve the performance of the salp swarm algorithm (SSA) and overcome its drawbacks. To control the exploitation/exploration rates, they used five chaotic maps. The proposed algorithm (CSSA) was applied on twenty-seven datasets and gave the best results. Although it gave the best results using twenty-seven datasets, it did not achieve good results using high-dimensional datasets. Sanaa et al.  proposed a wrapper method included in particle swarm optimization (PSO) and genetic algorithm (GA) to classify six human cancers types using DNA CNV dataset. The hybrid proposed method was applied to minimize the features and maximize the classification accuracy. It selected 2051 features from 16,381 features. The selected features achieved 84.6% classification accuracy. However, it suffered from many problems included in over-fitting, fitting time, relevant features, and classification accuracy. RFE is considered a wrapper method for feature selection. It suffers from time-consuming, especially when using big data. Li et al.  proposed fixing the support vector machine recursive feature elimination (SVMRFE) problem. They first proposed random value-based oversampling as a resampling method. The proposed variable step size (VSSRFE) to speed up the feature selection process. Another method is proposed called linear SVM (LLSVM). The two proposed methods are used together for feature selection. Jeon et al.  proposed a hybrid RFE method using benchmark datasets. This proposed method used SVM-RFE, random forest RFE (RF-RFE), and gradient boosting machines RFE (GBM-RFE) methods which combined the feature-importance-based RFE methods. There were two types of weighting functions used in the proposed methods. The first type sums the weight of three proposed RFE methods, and the second one reflects the classification accuracies and weights of features. Rani et al.  proposed a hybrid wrapper method by integrating GA and RFE algorithms. This method is compared with other feature selection methods. The proposed method improved the classification performance after canceling irrelevant features. Zvarevashe et al.  proposed a method to select the most relevant subset features using RFE algorithm based on RF. The proposed method was compared with a deep learning algorithm. It proved its powerful for selecting features. Senan et al.  proposed a method to select the relevant features using RFE algorithm for a kidney disease dataset. Four classification algorithms are applied for the classification step. The RF algorithm gave the best results.
Many researchers used a hybrid method which combined filter and wrapper methods to select relevant features, but it had many limitations that filter method may cancel important features and wrapper methods take more time. High dimensional is another limitation when applying this hybrid . Ansari et al.  used filter and wrapper approaches as a feature selection process. They proposed two different hybrid methods. F-score feature ranker and Chi-square feature ranker are applied in the first method and took the intersection between them. The intersection between these features is applied to obtain the most important features. The results of the intersection process are applied on binary particle swarm optimization (BPSO) as a feature optimization approach. In the second one, after the intersection between features, RFE approach is applied. Zhang et al.  proposed a method to classify six human cancer types using CNV level values. Zhang selected the features using the methods of mRMR (minimum Redundancy Maximum Relevance Feature selection) and IFS (Incremental Feature Selection). The first method selected features by ranking the importance of these features. This method selected 200 features. The second method used IFS to select the optimal set of features. IFS selected 19 features with an accuracy value 0.75. However, this proposed method gave insufficient classification accuracy. Pirgazi et al.  proposed a hybrid method using filter and wrapper for feature selection in high dimensional datasets. In the first stage, they applied a filter method using the Relief method to weight the features. In the second stage, they applied a wrapper method using shuffled frog leaping algorithm (SFLA) and IWSSr algorithms. Mandal et al.  proposed a hybrid method for feature selection using the filter and wrapper method. They applied MIFS, ReliefF, Chi-Square, and Xvariance for the filter method. The union for four filter methods is applied to obtain the most important features. The wrapper method is applied using Whale Optimization Algorithm to overcome any limitation in the filter method. Venkatesh et al.  proposed a hybrid method using MIFS as a filter method and RFE as a wrapper method. The hybrid method gave better results than the individual algorithms. Gakii et al.  proposed comparison methods using three algorithms for feature selection included in the PCA, RFE and graph-based feature selection. The results proved that the graph-based feature selection enhanced the performance of sequential minimal optimization and multilayer perceptron classifiers. In addition, researchers applied a hybrid method using the advantages of both wrapper and embedded methods to obtain the most effective features to solve the drawbacks in the previous studies. Liu et al.  proposed a hybrid method using GA as a global search with an embedded regularization approach as a local search. They proposed this method to solve the over-fitting problems and select relevant features. It is compared with individual algorithms, proving its effectiveness for feature selection. Aruna et al.  proposed a hybrid method using LR and RFE algorithms for the diabetes dataset. The RFE is based on LR as an estimator. The RF is applied for a classification step. Venkatachalam et al.  proposed a hybrid method that combined the ridge regression and RFE algorithms. It solved the problem of over-fitting for feature selection. The proposed method is compared with other models. RF is applied for the classification step.
Due to the previous research gaps, this paper presents the proposed method PFBS-RFS-RFE with three positions to fix feature selection problems and improve the classification model over different datasets. It tries to enhance many issues included in time consuming using RFE algorithm, classification accuracy, over-fitting problems, fitting time and select the most effective features to know the chromosome that is considered the most developing human cancers in the datasets. Furthermore, we applied a resampling method to enhance the classification accuracy and improve the over-fitting problem . The bootstrap is a resampling method that reduces the variance and bias between features; therefore, the over-fitting problem is minimized, and classification accuracy is maximized. We utilize PFBS as a resampling step with the hybrid RFS-RFE to reduce the over-fitting problem and improve the classification accuracy. We compared the proposed methods with RFE, RFS, and with previous work over five datasets. Four efficient supervised machine learning were used to evaluate the model performance of the proposed hybrid feature selection methods. The main contributions are summarized as follows: -
We propose hybrid methods, namely, positions first bootstrap step random forest selection recursive feature elimination (PFBS-RFS-RFE) based on feature selection that combines the advantages of the wrapper and embedded methods to solve many feature selection problems, including over-fitting, time consuming, relevant features, classification accuracy and solving the problem in RFE algorithm, which suffers from time-consuming with high-dimensional datasets.
The motivation behind the proposed methods is to know the genes or features associated with cancers; therefore, we can know the chromosome that is considered the most developing human cancers by taking the average number of runs and the intersection between features.
The structure of the article is as follows. The “Introduction” section presents the feature selection troubles and how previous work tried to solve them. The “Results” section presents the results of hybrid algorithm and the comparison with other studies using the same datasets. The “Discussion” section summarizes and discusses the application of the hybrid algorithm. The “Conclusions” section presents the main idea and the importance of the proposed methods. The “Method” section presents the hybrid algorithm to enhance and solve these troubles.
The hybrid proposed methods applied two important stages included in feature selection and model performance. They are applied using proposed datasets to select the effective cancer genes and improve the drawbacks included in over-fitting and classification accuracy. The selected features are utilized to feed more than one classifier using 10 cross-validations. The proposed classifiers are LR, support vector machine (SVM), RF and bagging (Bagg). The proposed method is compared with the individual algorithm such as RFE and RF and with the previous work. The proposed methods confirmed the results.
Performance evaluation is a very important step in machine learning. Selecting the most relevant features increases the classification accuracy and decreases the classification error. We proposed a hybrid method to obtain the accurate classification value, therefore; we fixed any previous drawbacks. The proposed methods are compared with individual algorithms included in RFE and RFS using the following metrics: -
The size of feature selection: - is the number of selected features.
Processing time: - is the time of the fitting process in second.
Performance accuracy is the percentage of the samples that are correctly evaluated by a classifier.
Performance evaluation included: - Precision, F1-score, Recall, variance, Receiver operating characteristic (ROC) area, and Area under curve (AUC) [8, 12] is used to measure the classification performance by plotting the relationship between True Positive (TP) and False Positive (FP) rates.
The calculation formula is applied to evaluate the model performance using ensemble and regularization classifiers with 10 cross-validation. Table 1 presents the meanings of the symbols that used in the proposed methods. The calculation formula is as follows: -
The experiments were run in Python on a pc with windows 10, R TM CPU 1.80 GHz, and 8 GB memory. All parameter values are determined based on domain-specific knowledge or trial and error. The parameter setting for all proposed methods is given in Table 2, with a simple declaration for each parameter.
Numerical results and discussion
The fundamental goal of these proposed methods is to enhance the performance of RFE to reach the optimum subset features that show the most associated features (genes) with cancers. Another goal of the proposed methods is to solve and fix the problem of over-fitting between training and testing data. The proposed method was compared with the original algorithms included in RFE and RFS. Table 3 presents the performance of the individual algorithms such as RFE and RF using the proposed classifiers LR with 10 folds stratified cross-validation before applying the feature selection proposed methods. Stratified cross-validation splits data into folds to ensure that the ratio between label classes is the same in each fold as in the full data.
In Table 3, the RFE algorithm spent more time on feature selection with high-dimensional datasets. Therefore, it did not achieve good results for classification accuracy. The Parkinson’s disease dataset shows that the classification accuracy achieved low results before applying the proposed methods. Using the BreastEw dataset, we can notice that both RFE and RFS achieved the best results before applying the proposed methods. Still, we need to reach optimal classification accuracy with the smallest subset features. The terms Algo., over-fitting Diff., Pre, Rec, NO.F, F-Time, C-Time, and var. referred to proposed algorithms, difference percentage between training and testing dataset, Precision, Recall, Number of selected features, Fitting time of feature selection, classification fitting time and variance, respectively.
We noticed the previous results that the single algorithms suffered from many problems in the fitting time of feature selection (F-Time), classification fitting time (C-Time), number of selected features, over-fitting, and classification accuracy. Therefore, we proposed the methods to fix any previous problems in original algorithms when run as a single algorithm and obtain the most effective cancers genes. In addition, we noticed that the single algorithms did not give the best results, so we applied a hybrid method using the wrapper and embedded procedure.
In Table 4, the average results of the proposed method OFBS-RFS-RFE are presented using stratified cross-validation with proposed classifiers included in LR, SVM, RF and Bagg. The proposed methods are run 2o times to obtain the best results. The PFBS has many positions of the first bootstrap step included in OFBS, IFBS and both outer and O/IFBS. The following table presented the OFBS-RFSRFE after 20 runs.
For more illustration, in Table 4, the proposed method using OFBS-RFS-RFE enhanced the performance of RFE algorithm. The over-fitting percentage was reduced from the RNA gene dataset after applying previous classifiers, so the accuracy difference between training and testing dataset was reduced compared with the single algorithm. The LR classifier achieved the best classification accuracy result with 99.981%, while the SVM classifier gave the best variance result with 0.0000002. From DNA CNV dataset the difference between training and testing became 2.442 and 2.763% using LR and Bagg classifiers, respectively, and the accuracy results were increased with 91.020 and 92.762%, respectively using the same classifiers. In addition, the variance between features was reduced using the same classifiers to become 0.00028 and 0.00023, respectively. The OFBS-RFS-RFE enhances the over-fitting and variance and minimizes features’ fitting time and number. From the Parkinson’s disease dataset, the classification accuracy, precision, recall, f1-score, AUC and variance are enhanced to 95.000%, 0.945, 0.906, 0.922, 0.985 and 0.00062, respectively using RF classifier. It suggested that only 113.85 features were good enough for the classification step with 1.134 s as a computational time. In addition, for dermatology erythemato-squamous diseases dataset, RF classifier gave the best classification accuracy, precision, recall, f1-score, AUC and variance to become 100.000%, 1.000, 1.000, 1.000, 1.000 and 0.0. On the other hand, the OFBS-RFS-RFE using the BreastEw dataset achieved the best computational time after applying LR and SVM in contrast with the other optimizer. We can notice that the RF gave the best over-fitting percentage, precision, recall, f1-score, AUC, variance, and accuracy to become 2.00%, 0.983, .979, 0.982, 0.997, 0.000302 and 98%, respectively.
In Table 5, the average results of the proposed method PFBS-RFS-RFE using IFBS after 20 runs are presented. The different positions of bootstrap lead to different results. The IFBS used the bootstrap step inside the RFS algorithm for feature selection.
For more illustration, in Table 5, the SVM classifier achieved the best classification accuracy and variance results with 99.988% and 0.0000002, respectively. Although the inner position gave the best results using RNA gene dataset, but it did not give the best result for other datasets.
In Table 6, the average results of PFBS-RFS-RFE using O/IFBS after 20 runs are presented. In this position the FBS is placed before selecting the features and during the feature selecting algorithm.
For more illustration, in Table 6, the accuracy and variance results are increased from the RNA gene dataset to 99.994% and 0.0000004, respectively, using LR classifier. Bagg classifier gave the best accuracy and variance results using DNA CNV dataset to become 92.834% and 0.00027, respectively. In addition, RF classifier gave the best accuracy and variance using dermatology erythemato-squamous diseases dataset to become 100% and 0.0, respectively. At the same time, the O/IFBS-RFS-RFE did not give good results for other datasets.
In Fig. 1, the classification accuracy using the proposed methods is illustrated using all datasets. We can notice that RNA gene dataset achieved the best results with O/IFBS using LR classifier, while the DNA CNV dataset achieved the best results with O/IFBS using Bagg classifier. In addition, the Parkinson’s disease dataset achieved the best results with OFBS using LR classifier. The dermatology erythemato-squamous diseases and breast datasets achieved the best result using RF classifier with both OFBS and O/IFBS.
In Fig. 2, the number of selected features using the proposed methods is showed on all datasets. From this figure, we can note that the best algorithm that gave the smallest number of features was O/IFBS with RNA gene, Parkinson’s disease, dermatology erythemato-squamous diseases and breast datasets. On the other hand, the IFBS algorithm achieved the smallest number of features using DNA CNV dataset.
In Fig. 3, the variance of the proposed methods is illustrated. We can notice that the RNA gene dataset using LR and SVM classifiers gave the best variance results with all position of bootstrap. On the other hand, the DNA CNV dataset achieved the best variance result using the Bagg classifier with OFBS. In addition, the Parkinson’s disease dataset achieved the best variance result using SVM classifier with OFBS. OFBS and O/IFBS achieved the best variance result using RF and Bagg classifiers for dermatology erythemato-squamous diseases dataset. For Breast dataset, the RF classifier gave the best results with OFBS.
Comparison with other studies
The results before and after PFBS-RFS-RFE are compared. In addition, these results are compared with the previous work using the same datasets. Table 7 showed the comparison before and after applying PFBS-RFS-RFE after 20 runs. The proposed methods improved the results and solved feature selection problems in high dimensions. Table 8 presented the results of the previous studies using the same dataset.
The proposed methods were compared with filter ones methods using MIFS, IGF and mRMR. Tables 9, 10 and 11 showed the results of MIFS, IGF and mRMR for all datasets. For MIFS method, the results proved that the LR classifier gave the best accuracy for RNA gene and DNA CNV datasets, while the RF classifier gave the best accuracy for Parkinson’s disease and BreastEW datasets. In addition, SVM classifier gave the best results for dermatology erythemato-squamous diseases dataset. For IGF method, LR classifier gave the best accuracy for RNA gene dataset. SVM classifier gave the best results for DNA CNV and dermatology erythemato-squamous diseases datasets, while the RF classifier gave the best accuracy for Parkinson’s disease and BreastEW datasets. Furthermore, mRMR achieved the best results for RNA gene dataset using LR classifer, while SVM classifier gave the best results for DNA CNV dataset. In addition, RF classifer achieved the best results for dermatology erythemato-squamous diseases, Parkinson’s disease and BreastEW datasets. Although filter ones methods improved the results, they did not give better results than the PFBS-RFS-RFE.
The proposed methods were compared with many different filters methods as cited in the introduction section included in CfsSubsetEval, ReliefAttributeEval, OneRAttributeEval, ConsistencySubsetEval and PCA methods. Tables 12, 13, 14, 15 and 16 showed the results of these different filters methods. The ReliefAttributeEval method achieved the best results for RNA gene and BreastEW datasets, while ConsistencySubsetEval method gave the best results for DNA CNV dataset. In addition, CfsSubsetEval method gave the best results for Parkinson’s disease dataset, while the PCA method gave the best results for dermatology erythemato-squamous diseases dataset. Although filter methods improved the results, they did not give better results than the PFBS-RFS-RFE.
Table 17 showed the comparison between the proposed methods, MIFS, CBF and FCBF methods as cited in the introduction section. The CBF gave the best results for RNA gene dataset, while FCBF method gave the best results for DNA CNV, Parkinson’s disease and BreastEW datasets. In addition, MIFS gave the best results for dermatology erythemato-squamous diseases dataset. These methods did not give the best results when compared with the PFBS-RFS-RFE.
Table 18 showed the proposed methods compared with the Chi-square method as cited in the introduction section using SVM and RF classifiers. The SVM classifiers gave the best results for RNA gene and DNA CNV datasets, while RF classifier gave the best results for, Parkinson’s disease, BreastEW and dermatology erythemato-squamous diseases datasets. This method did not give the best results when compared with the PFBS-RFS-RFE.
Table 19 showed the proposed methods compared with the IGF, Chi-square and Bat algorithm as cited in the introduction section. The Bat algorithm gave the best results for RNA gene, DNA CNV and BreastEW datasets, while Chi-square method gave the best results for Parkinson’s disease dataset. In addition, the IGF method gave the best results for dermatology erythemato-squamous diseases dataset. These methods did not give the best results when compared with the PFBS-RFS-RFE.
Table 20 showed the comparison between the PFBS-RFS-RFE and other filter ones methods. The results showed that the PFBS-RFS-RFE gave the best results when compared with other filter ones methods.
The proposed methods were compared with some hybrid-recursive feature elimination methods as cited in the introduction section. Table 21 showed the results of the hybrid-recursive feature elimination methods for all datasets using RFE and LR. The results proved that this hybrid method gave the best results for RNA Gene, dermatology erythemato-squamous diseases and BreastEW datasets. This hybrid method did not give the best results when compared with the PFBS-RFS-RFE.
Another hybrid method is applied to show the comparison between the proposed method and hybrid method using GA and RFE. Table 22 showed the results of the hybrid method using GA and RFE. The results proved that this hybrid method gave the best results for RNA gene and BreastEW datasets. This hybrid method did not give the best result when compared with the PFBS-RFS-RFE.
In addition, the proposed method was compared with another hybrid method using ridge regression and RFE. Table 23 showed the results of the hybrid method using ridge regression and RFE. The results proved that this hybrid method gave the best results for RNA gene, dermatology erythemato-squamous diseases and BreastEW datasets. This hybrid method did not give the best result when compared with the PFBS-RFS-RFE.
Table 24 showed the comparison between the PFBS-RFS-RFE and other RFE hybrid methods. The results showed that the PFBS-RFS-RFE gave the best results when compared with other RFE hybrid methods.
After the number of runs, the selected features are intersected to know the genes (features) associated with cancers which considered the most developing human cancers. Table 25 presented the features after the intersection, which played an important role in knowing the most genes and features developing human cancers.
For DNA CNV dataset, the PHACTR4 was associated with prostate, breast and colon cancer , while RPA2 was associated with breast cancer . We can notice that the proposed method achieved the best results and reached the most effective genes that develop human cancer. For dermatology erythemato-squamous diseases dataset, the age, itching and spongiosis features were associated with psoriasis dis- ease [56, 58].
The proposed PFBS-RFS-RFE was applied to classify different human cancer using big, medium and small datasets and other medical dataset. It used five different datasets. PFBS-RFS-RFE was proposed to enhance drawbacks included in over-fitting, time-consuming, high dimension, variance and classification accuracy. The PFBS was applied in different position to obtain different results. It was applied using three positions outer, inner and outer/inner. After applying PFBS, the RFS algorithm for feature selection was applied to select the most relevant features and reduce time consumption in RFE algorithm. RFE algorithm was used to obtain the final relevant subset of features with higher classification accuracy results.
The OFBS-RFS-RFE method achieved the best results using all datasets. The RF classifier achieved the best classification accuracy with 100% using dermatology erythemato-squamous diseases dataset with 0.0 variance results. The features and time were reduced to become 16.000 and 0.500, respectively. Furthermore, LR classifier achieved the best classification accuracy result with 99.981% using RNA gene dataset, while the SVM classifier gave the best variance result with 0.0000002. The number of features and time were reduced to become 142.500 and 0.192 s, respectively. From DNA CNV dataset the difference between training and testing was reduced using LR and Bagg classifiers, and the accuracy results were increased with 91.020 and 92.762%, respectively using the same classifiers. In addition, the OFBS-RFS-RFE reduced the variance between features to become 0.00028 and 0.00023, respectively, using the previous classifiers. The number of features and time were reduced to become 675 and 2.147 s, respectively.
From Parkinson’s disease dataset the classification accuracy and variance are enhanced to become 95.000% and 0.00062, respectively using RF classifier. The features were reduced to 113.85 features which well enough for classification step with 1.134 s as a computational time. From BreastEw dataset the best computational time was after applying LR and SVM in contrast with the other optimizer. The RF gave the best variance and accuracy to become 0.000302 and 98%, respectively. The features and time were reduced to become 0.070 and 0.070 s, respectively.
The IFBS-RFS-RFE not achieves the best results in all datasets. The SVM classifier achieved the best classification accuracy and variance results from the RNA gene dataset with 99.988% and 0.0000002, respectively. The features and time were minimized to 125.25 features and 0.153 s, respectively. For other datasets it did not give good results.
The O/IFBS-RFS-RFE achieved the best results for dermatology erythemato-squamous diseases dataset. RF and Bagg classifiers gave the best results with 10 features. The classification accuracy, variance and time were improved to become 100%, 0.0 and 0.500, respectively. In addition, The O/IFBS-RFS-RFE achieved the best results in high dimension datasets using RNA gene. The LR classifier increased the accuracy and variance results to 99.994% and 0.0000004, respectively. From DNA CNV dataset, the Bagg classifier gave the best accuracy and variance results to become 92.834% and 0.00027, respectively. At the same time, the outer/inner position did not provide good results for other datasets.
For future work, our proposed method will apply the incremental feature selection (IFS) for different datasets using PFBS. The IFS will select the most relevant subset features to minimize the time when using all features and overcome the feature selection drawback.
In our study, new hybrid methods are proposed to enhance cancers classification performance using different size of datasets. The PFBS using EDF equation is enhanced the RFS and RFE performance. Many bootstrap positions are applied to improve the problem of over-fitting and to fix the feature selection problems. Furthermore, our proposed methods achieved high results using different size of datasets. It is compared with previous work and it gave high results.
We used five healthcare datasets in the experiments. The DNA CNV dataset is used in [7, 8, 12] and downloaded from the cBioPortal for Cancer Genomics [59,60,61] to classify different types of human cancers. The other four datasets are downloaded from the UCI machine learning repository  and used in [9, 23]. A brief description of each adopted dataset is presented in Table 26.
The proposed hybrid feature selection methods
The main motivation of the proposed methods is to select the most important and relevant features from all original features. This step is considered vital and plays a significant role in obtaining good classification results. Non- influencing features waste time and lead to many complex problems included in poor classification accuracy, over-fitting, and feature size. The wrapper method for feature selection selects the features based on machine learning to find optimal features, but it takes more time to obtain these features and has chances of over-fitting problems. On the other hand, the advantage of embedded methods for feature selection is that the selected features are embedded in machine learning or during the model building process. It is applied to reduce the over-fitting problem, reducing the variance between features. Based on the advantages of the two previous methods, we proposed hybrid methods for feature selection to obtain the most relevant subset feature. The proposed methods are shown in Fig. 4. Resampling method with different positions is applied to minimize the over-fitting problem and maximize the classification accuracy. After the resampling step, the most important features are selected using RFS algorithm. The hybrid between resampling and RF algorithms are applied to solve many problems such as (1) time consuming when using RFE algorithm, (2) over-fitting problem, (3) the most relevant features, and (4) classification accuracy. The wrapper method is applied to select the most important features, therefore; reduce the datasets dimensional and maximizing the classification accuracy. The RFE using LR classification as an estimator is integrated with the previous features to achieve the desired goals.
First bootstrap step as a resampling method
A lot of high-dimensional datasets suffer from over-fitting problems and low classification accuracy. We apply the FBS step as a resampling method to avoid these problems. The bootstrap samples are drawn with replacement as the same size of the original data. Given the original datasets X = X1, X2, X3, ........, XO With O observations with a distribution function called empirical distribution function (EDF). The bootstrap sample is denoted as X* = X*1, X*2, X*3, ......., X*O. The (EDF) is denoted as follows : -
Where I(·) denotes the indicator function, the bootstrap resampling method is applied in many positions to achieve the desired task. The first position of bootstrap is before selecting the essential features called OFBS, but we need to apply different positions to obtain the best results. In this position the EDF is applied as a resampling method before selecting features. The IFBS is applied during selecting the feature selection. On the other hand, the O/IFBS is applied before and during selecting features. All bootstrap positions are applied to overcome the over-fitting and classification accuracy. After these positions, the classification accuracy and over-fitting problems are improved. Therefore, the proposed positions selected the most relevant features.
Feature selection using random Forest (RFS)
A random forest algorithm is applied for feature selection to improve the performance of the classifiers, reduce the over-fitting problem and time consuming due to the disadvantage of RFE algorithm. It is considered the embedded feature selection that interacts directly with classifiers and reduces the time complexity found in the wrapper method. The RFS algorithm can identify the importance of the feature. The training samples are created using bootstrap when applying IFBS method but using all datasets to create samples when applying OFBS to improve the over-fitting and classification accuracy. The trees are constructed with a specific size. Select M trees from the dataset to build the decision trees. Decision trees are constructed from the M trees and they are repeated B times. Construct the smallest subset of features F at each node and separate the best features for F by Gini importance scores. It is sorted the features according to their scores from smallest to largest. The features below the threshold will be eliminated.
Recursive feature elimination (RFE)
Selecting the most significant features is the main goal in the classification step. In this direction, we applied RFE algorithm to select the most important features therefore; reach to the chromosome which considered the most developing human cancers. RFE is an instance of backward feature elimination. The classifier estimator is trained on the initial set of features and these features are sorted according to their weights. The features with the smallest weights are removed because these features are not important during the classification process. The previous steps are repeated until the most relevant features are reached. RFE is applied with LR as an estimator. The classification accuracy is improved after applying the proposed method. The step size is proposed in the RFE method called recursive feature elimination with cross-validation (RFECV) to achieve the best results. The features are sorted according to their importance at each step, and the smallest ranked feature is deleted. The proposed methods are presented in Tables 27, 28 and 29 as follows:
Availability of data and materials
All datasets and details are available at request from the corresponding author and as a supplement to this article.
Recursive feature elimination
Random forest for selection
Positions first bootstrap step
Positions first bootstrap step random forest selection recursive feature elimination
Outer first bootstrap step
Inner first bootstrap step
Outer/Inner first bootstrap step
Mutual information based feature
Information gain based feature selection
Copy Number Variation
Support vector machine
Principal component analysis
Correlation based feature
Fast correlation based feature selection
Salp swarm algorithm
Constant salp swarm algorithm
Particle swarm optimization
Linear support vector machine
Gradient boosting machines RFE
Binary particle swarm optimization
Minimum redundancy maximum relevance
Incremental feature selection
Shuffled frog leaping algorithm
Distribution function called empirical distribution function
Recursive feature elimination with cross-validation
Receiver operating characteristic
Positive predictive value
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Thanks to Dr. Mohamed for his help and support, thanks to Dr. Ghada for her support and guidance.
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Abdelwahed, N.M., El-Tawel, G.S. & Makhlouf, M.A. Effective hybrid feature selection using different bootstrap enhances cancers classification performance. BioData Mining 15, 24 (2022). https://doi.org/10.1186/s13040-022-00304-y
- Machine Learning
- Random Forest feature importance
- Recursive feature elimination and its disadvantages
- Learning algorithms
- High dimensional data