Whale optimization algorithm is a newly proposed bio-inspired optimization technique introduced in 2016 which imitates the hunting demeanor of humpback whales. In this paper, to enhance solution accuracy, reliability and convergence speed, we have introduced some modifications on the basic WOA structure. First, a new control parameter, inertia weight, is proposed to tune the impact on the present best solution, and an improved whale optimization algorithm (IWOA) is obtained. Second, we assess IWOA with various transfer functions to convert continuous solutions to binary ones. The proposed algorithm incorporated with the K-nearest neighbor classifier as a feature selection method for identifying feature subset that enhancing the classification accuracy and limiting the size of selected features. The proposed algorithm was compared with binary versions of the basic whale optimization algorithm, particle swarm optimization, genetic algorithm, antlion optimizer and grey wolf optimizer on 27 common UCI datasets. Optimization results demonstrate that the proposed IWOA not only significantly enhances the basic whale optimization algorithm but also performs much superior to the other algorithms.
Background
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.
Method
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.
Results
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.
Conclusion
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.
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