GeneViT: Gene Vision Transformer with Improved DeepInsight for cancer classification.

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Abstract

Analysis of gene expression data is crucial for disease prognosis and diagnosis. Gene expression data has high redundancy and noise that brings challenges in extracting disease information. Over the past decade, several conventional machine learning and deep learning models have been developed for classification of diseases using gene expressions. In recent years, vision transformer networks have shown promising performance in many fields due to their powerful attention mechanism that provides a better insight into the data characteristics. However, these network models have not been explored for gene expression analysis. In this paper, a method for classifying cancerous gene expression is presented that uses a Vision transformer. The proposed method first performs dimensionality reduction using a stacked autoencoder followed by an Improved DeepInsight algorithm that converts the data into image format. The data is then fed to the vision transformer for building the classification model. Performance of the proposed classification model is evaluated on ten benchmark datasets having binary classes or multiple classes. Its performance is also compared with nine existing classification models. The experimental results demonstrate that the proposed model outperforms existing methods. The t-SNE plots demonstrate the distinctive feature learning property of the model.Copyright © 2023 Elsevier Ltd. All rights reserved.