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Gene selection from large-scale gene expression data based on fuzzy interactive multi-objective binary optimization for medical diagnosis

Shahbeig S., Rahideh A., Helfroush M. S., Kazemi K.

Biocybernetics and Biomedical Engineering

2018

Vol. 38, no. 2

313--328

An efficient fuzzy interactive multi-objective optimization method is proposed to select the sub-optimal subset of genes from large-scale gene expression data. It is based on the binary particle swarm optimization (BPSO) algorithm tuned by a chaotic method. The proposed method is able to select the sub-optimal subset of genes with the least number of features that can accurately distinguish between the two classes, e.g. the normal and cancerous samples. The proposed method is evaluated on several publicly available microarray and RNA-sequencing gene expression datasets such as leukemia, colon cancer, central nervous system, lung cancer, ovarian cancer, prostate cancer and RNA-seq lung disease. The results indicate that the proposed method can identify the minimum number of genes to achieve the most accuracy, sensitivity and specificity in the classification process. Achieving 100% accuracy in six out of the seven datasets investigated in this study, demonstrates the high capacity of the proposed algorithm to find the sub-optimal subset of genes. This approach is useful in clinical applications to extract the most influential genes on a disease and to find the treatment procedure for the disease.

Hierarchical classification of normal, fatty and heterogeneous liver diseases from ultrasound images using serial and parallel feature fusion

Alivar A., Danyali H., Helfroush M. S.

Biocybernetics and Biomedical Engineering

2016

Vol. 36, no. 4

697--707

This study presents a computer-aided diagnostic system for hierarchical classification of normal, fatty, and heterogeneous liver ultrasound images using feature fusion techniques. Both spatial and transform domain based features are used in the classification, since they have positive effects on the classification accuracy. After extracting gray level co-occurrence matrix and completed local binary pattern features as spatial domain features and a number of statistical features of 2-D wavelet packet transform sub-images and 2-D Gabor filter banks transformed images as transform domain features, particle swarm optimization algorithm is used to select dominant features of the parallel and serial fused feature spaces. Classification is performed in two steps: First, focal livers are classified from the diffused ones and second, normal livers are distinguished from the fatty ones. For the used database, the maximum classification accuracy of 100% and 98.86% is achieved by serial and parallel feature fusion modes, respectively, using leave-one-out cross validation (LOOCV) method and support vector machine (SVM) classifier.