Paper ID: 2410.07260

Precision Cancer Classification and Biomarker Identification from mRNA Gene Expression via Dimensionality Reduction and Explainable AI

Farzana Tabassum, Sabrina Islam, Siana Rizwan, Masrur Sobhan, Tasnim Ahmed, Sabbir Ahmed, Tareque Mohmud Chowdhury

Gene expression analysis is a critical method for cancer classification, enabling precise diagnoses through the identification of unique molecular signatures associated with various tumors. Identifying cancer-specific genes from gene expression values enables a more tailored and personalized treatment approach. However, the high dimensionality of mRNA gene expression data poses challenges for analysis and data extraction. This research presents a comprehensive pipeline designed to accurately identify 33 distinct cancer types and their corresponding gene sets. It incorporates a combination of normalization and feature selection techniques to reduce dataset dimensionality effectively while ensuring high performance. Notably, our pipeline successfully identifies a substantial number of cancer-specific genes using a reduced feature set of just 500, in contrast to using the full dataset comprising 19,238 features. By employing an ensemble approach that combines three top-performing classifiers, a classification accuracy of 96.61% was achieved. Furthermore, we leverage Explainable AI to elucidate the biological significance of the identified cancer-specific genes, employing Differential Gene Expression (DGE) analysis.

Submitted: Oct 8, 2024