Explainable AI based feature selection in cancer RNA-seq

Abstract

Identifying informative features in bioinformatics is challenging due to their small proportion within large datasets. We propose a scalable and interpretable feature selection framework for cancer RNA-seq by transforming non-image bio-data into 2D formats and applying convolutional neural networks (CNNs) with transfer learning for efficient classification. Explainable artificial intelligence (XAI) techniques identify and prioritize important features, while principal component analysis (PCA) determines the optimal number of selected features, ensuring transparency and reliability. Comparative analysis of CNN and XAI highlights the effectiveness of our approach, providing a robust framework for high-dimensional genomic data analysis with applications in cancer diagnosis and prognosis. © 2025