Lung cancer subtyping from gene expression data using general and enhanced Fuzzy min–max neural networks

Abstract

Abstract In this article, we address the problem of lung cancer diagnosis from gene expression data, which is now recognized as an effective means for early treatment and prevention of cancer. Specifically, we employ Fuzzy min–max (FMM) classifier for the task which is a well‐known neuro‐fuzzy neural network. The idea is to take advantage of the fuzzy class definitions whose boundaries are set using the min–max hyperbox constructed for each class. We implement two advanced FMM neural network architectures: general Fuzzy min–max (GFMM) and enhanced Fuzzy min–max (EFMM) for the classification of lung cancer subtypes from gene expression data. The advantage of GFMM is that it involves very simple operations for hyperbox manipulation, and can handle both labeled and unlabeled data. On the other hand, EFMM proposes three heuristic rules related to hyperbox expansion, contraction and the overlap test, which enhances the learning algorithm. We perform the classification of gene expression data using these two models, and then we analyze the performance by visualizing the hyperboxes obtained after training, and compare the accuracies of these classifiers with the state of the art. Least absolute shrinkage and selection operator (LASSO) is used for selecting the informative genes from the high‐dimensional gene expression data. From the empirical results, we observe that GFMM with LASSO gives the best performance of all, with validation accuracy of 98.04% and cross‐validation accuracy of 94.06%.

Keywords

• feature selection
• fuzzy min–max neural network
• gene expression
• least absolute shrinkage and selection operator
• lung cancer